Coronaviridae: - May 2022 - Volume 20

Reviews
SARS-CoV-2 pathogenesis
Mart M. Lamers and Bart L. Haagmans ✉
Abstract | The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

has caused a devastating pandemic. Although most people infected with SARS-CoV-2 develop
a mild to moderate disease with virus replication restricted mainly to the upper airways, some
progress to having a life-threatening pneumonia. In this Review, we explore recent clinical
and experimental advances regarding SARS-CoV-2 pathophysiology and discuss potential
mechanisms behind SARS-CoV-2-associated acute respiratory distress syndrome (ARDS),
specifically focusing on new insights obtained using novel technologies such as single-cell omics,
organoid infection models and CRISPR screens. We describe how SARS-CoV-2 may infect the
lower respiratory tract and cause alveolar damage as a result of dysfunctional immune responses.
We discuss how this may lead to the induction of a ‘leaky state’ of both the epithelium and the
endothelium, promoting inflammation and coagulation, while an influx of immune cells leads to
overexuberant inflammatory responses and immunopathology. Finally, we highlight how these
findings may aid the development of new therapeutic interventions against COVID-19.
Acute respiratory distress Coronaviruses (family Coronaviridae) are common which forms trimers on the surface of virions10. The spike
syndrome pathogens of humans and animals. Four coronavi- protein consists of two subunits: the S1 subunit, which
(ARDS). Life-threatening lung ruses are endemic in humans (human coronavirus binds to the host entry receptor angiotensin-converting
condition in which the lungs NL63 (HCoV-NL63), HCoV-229E, HCoV-OC43 and enzyme 2 (ACE2)11, and the S2 subunit, which mediates
cannot provide enough
oxygen to the body after
HCoV-HKU1) and typically infect the upper respira- membrane fusion (Fig. 1b). These two subunits are sep-
acute lung injury. tory tract, causing common-cold symptoms. In the past arated by the S1–S2 site, which contains a furin cleav-
two decades, three zoonotic coronaviruses (severe acute age motif and is cleaved in the virus-producing cell.
respiratory syndrome coronavirus (SARS-CoV), Middle After binding to ACE2 on the target cell, the spike pro-
East respiratory syndrome coronavirus (MERS-CoV) tein is cleaved by the transmembrane serine protease
and SARS-CoV-2) have infected humans, after spill- TMPRSS2 at the S2′ site12–14. This cleavage activates the
ing over from animal reservoirs1–4. SARS-C oV orig- S2 subunit trimers to fuse viral and host lipid bilayers,
inated in China and caused an epidemic in 2003, releasing the viral ribonucleoprotein complex into the
whereas MERS-C oV is currently causing intermit- cell. Another entry route that may be used by the virus is
tent outbreaks in the Middle East. SARS-CoV-2, the the endosome, in which cathepsins can cleave the spike
causative agent of COVID-19, was first detected in protein, but this route is not efficiently used in primary
Wuhan, China, in late 2019 in a cluster of patients with epithelial cells14–17. Other co-receptors (for example,
pneumonia5. These three viruses can replicate in the neuropilin 1) and proteases (for example, cathepsin L,
lower respiratory tract and may cause a potentially fatal TMPRSS11D and TMPRSS13) have been proposed to
acute respiratory distress syndrome (ARDS) (Box 1). be involved in SARS-CoV-2 entry as well18–21, but their
SARS-CoV-2, which shares 79% sequence similar- respective contribution to SARS-CoV-2 pathogenesis
ity with SARS-CoV, belongs to the genus Sarbecovirus6. remains unclear14.
This virus encodes a set of structural proteins (mem- The first cells targeted by SARS-CoV-2 during nat-
brane protein, nucleocapsid protein, envelope protein ural infection in humans are likely to be multiciliated
and spike glycoprotein), non-structural proteins (of cells in the nasopharynx or trachea, or sustentacular cells
which most compose the viral replication and transcrip- in the nasal olfactory mucosa22–24. After entry, the
tion complex) and accessory proteins. The structural positive-sense SARS-CoV-2 genome directly initiates
Viroscience Department, proteins — together with a lipid bilayer derived from the the production of viral proteins, including the replicase
Erasmus Medical Center,
Rotterdam, Netherlands.
host — form an enveloped virion (or virus particle) that proteins that form replication factories from endo-
✉e-mail: b.haagmans@ delivers viral genomic RNA into the cell (Fig. 1a). The plasmic reticulum membranes25,26. These replication
erasmusmc.nl accessory proteins are dispensable for replication but factories contain double-membrane vesicles in which
https://doi.org/10.1038/ often have immunoevasive activities7–9. The main deter- transcription occurs, shielding the double-stranded
s41579-022-00713-0 minant of coronavirus tropism is the spike glycoprotein, RNA (dsRNA) transcription intermediates from
270 | May 2022 | volume 20 www.nature.com/nrmicro
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Box 1 | Pathogenesis of other human coronavirus diseases responses that help clear the virus. If the virus is not
cleared by innate or adaptive responses, it can spread to
The coronavirus family contains a high diversity of viruses, many of which originate the lower respiratory tract by inhalation of virus particles
in bats. Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 from the upper respiratory tract or by gradual dissemi-
share 79% sequence similarity across the entire genome. Severe COVID-19 is highly
nation along the tracheobronchial tree. Alternatively, the
similar to SARS, the term used to describe severe SARS-CoV disease. Both viruses
initial site of infection can be the lower respiratory tract.
cause similar symptoms and can lead to ARDS with diffuse alveolar damage as a typical
histological pattern, infect ciliated and alveolar type 2 cells, and use angiotensin- This can ultimately lead to the infection of the alveoli,
converting enzyme 2 (ACE2) as their entry receptor13,14,193. SARS-CoV causes causing inflammation and limiting gas exchange. In the
immunopathology similar to that caused by SARS-CoV-2, with typical inflammatory alveoli, SARS-CoV-2 has been shown to primarily infect
macrophage infiltration and frequent pulmonary embolisms194,195. However, as SARS-CoV alveolar type 2 (AT2) cells both in vivo and in vitro23,32–37.
caused only ~8,000 cases, there are relatively limited clinical data. From the available Whereas alveolar type 1 (AT1) cells cover most of the
data it seems that SARS-CoV may have been more virulent (case fatality rate of ~10% alveolar surface and mediate gas exchange, AT2 cells
for SARS-CoV versus ~1% for SARS-CoV-2 (ref.196)) and may have more frequently secrete pulmonary surfactants necessary for lubricating
caused diarrhoea than SARS-CoV-2 (16–73% for SARS-CoV196 versus 7.4% for SARS-CoV-2 the lung, which reduces surface tension in the alveoli
(ref.197)). In contrast to those infected with SARS-CoV-2, people infected with SARS-CoV
during respiration. In addition, AT2 cells are the
were not infectious before the onset of symptoms196, which may indicate that SARS-CoV-2
progenitor cells of AT1 cells in the adult human lung38.
replicates more quickly initially and may explain why SARS-CoV transmission could be
effectively halted by public health interventions. Increasing age and male sex were risk The COVID-19 pandemic continues to cause an
factors for severe SARS196. immense global health crisis, with more than 3.5 mil-
Little is known on the pathology of Middle East respiratory syndrome coronavirus lion deaths. The overall case fatality rate of COVID-19 is
(MERS-CoV) infection owing to the scarcity of autopsies performed in the Middle ~1%, and around 3–20% of people with COVID-19
East, but the case fatality rate associated with MERS-CoV is around 35%. Clinical and require hospitalization39,40, of which a considerable sub-
radiological observations indicate that the disease caused by MERS-CoV is similar to set (~10–30%) require intensive care41–43, putting great
COVID-19 and SARS198. Compared with SARS-CoV and SARS-CoV-2, MERS-CoV uses a strain on health systems. Currently, no specific therapies
different entry receptor, DPP4 (ref.199), which in humans is expressed on alveolar type 1 for COVID-19 have been developed, highlighting our
cells, alveolar type 2 cells and macrophages in the alveoli200. Epithelial cells in the human limited understanding of the pathogenesis of COVID-19.
upper respiratory tract in health do not seem to express DPP4 (with the exception of
In this Review, we explore recent clinical and experimen-
submucosal glands)200, which may be why there has not yet been sustained transmission
of MERS-CoV in the human population. Secondary cases do occur, but they generally tal advances in understanding SARS-CoV-2 pathogen-
have a lower chance of death, indicating that MERS-CoV is severest in individuals with esis, interactions with host cells and the involvement of
specific co-morbidities198,201. As with SARS and COVID-19, the main risk factors for the immune system in the development of severe dis-
severe MERS are increasing age and male sex198. When compared with SARS and ease. Specifically, we focus on mechanisms underlying
COVID-19, predominantly type 2 diabetes and chronic kidney disease are important the development of COVID-19-associated ARDS.
co-morbidities for MERS. The disease severity of MERS, SARS and COVID-19 increases
with age. COVID-19 clinical findings
The seasonal alphacoronavirus human coronavirus NL-63 (HCoV-NL63) is currently SARS-CoV-2 is transmitted through respiratory drop-
distributed globally202, but likely jumped from bats to humans several hundred years lets and aerosols, and the median incubation period is
ago203,204. Although HCoV-NL63 is distantly related to SARS-CoV-2 and SARS-CoV, it
4–5 days before symptom onset44–46. Although in some
uses ACE2 for cellular entry, but is not associated with severe lower respiratory tract
infection. One potential reason for this difference may be that HCoV-NL63 uses a cases the infection is asymptomatic, most patients pres-
different protease for entry. Although there is some evidence supporting and contradicting ent with mild to moderate respiratory disease, experienc-
the view that laboratory strains of HCoV-NL63 can use TMPRSS2 (refs205,206), it is currently ing cough, fever, headache, myalgia and diarrhoea46–50.
unclear which protease is used by this virus in relevant cells. Recent findings showing that Severe illness usually begins approximately 1 week after
the SARS-CoV-2 Omicron variant does not efficiently use TMPRSS2, or infect alveolar symptom onset. The most common symptom of severe
type 2 cells37, suggests that TMPRSS2 use may be an indicator for causing severe disease is dyspnoea (shortness of breath), which is a
pulmonary disease. Further work is needed to address the mechanism behind this result of hypoxaemia50,51. Soon after the onset of dysp-
difference. noea and hypoxaemia, progressive respiratory failure
develops in patients with severe COVID-19. These
detection by cytoplasmic pattern recognition receptors patients generally meet the criteria for ARDS47,52, which
(PRRs) (Fig. 1c). The main cytoplasmic PRR capable of is defined as severe hypoxaemia and bilateral radio-
detecting SARS-CoV-2 is thought to be MDA5 (refs27,28), graphic opacities occurring within 7 days of exposure
which recognizes long dsRNAs and initiates a signal- to known predisposing factors that is not fully explained
ling cascade to promote the transcription of type I and by heart failure or fluid overload53. ARDS is a form of
type III interferons. Interferons and chemokines are lung injury that is characterized by inflammation, pul-
also produced by bystander epithelial cells and local monary vascular leakage and consequently a loss of aer-
immune cells (for example, neutrophils and macro ated lung tissue. Patients with COVID-19 with hypoxic
phages) in response to the detection of SARS-CoV-2 respiratory failure have evidence of systemic hyperin-
using endosomal Toll-like receptors (TLRs) or paracrine flammation, including release of pro-inflammatory
Alveoli effects of locally produced interferons29–31. Interferons cytokines, such as interleukin-1 (IL-1), IL-6, IL-8 and
Tiny air sacs in the lungs where signal in an autocrine and paracrine fashion to induce TNF, and elevated concentrations of inflammatory
oxygen and carbon dioxide are an antiviral cellular state through the production of markers, including D-dimer, ferritin and C-reactive
exchanged. interferon-stimulated genes, which may have direct or protein (CRP)49,54. Serum levels of IL-6, IL-8 and TNF
Hypoxaemia
indirect (attraction of immune cells) antiviral functions. at the time of hospitalization are strong and indepen
A below-normal level of oxygen At the same time, the production of cytokines also pro- dent predictors of patient survival54. Severe COVID-19
in the blood. motes the development of adaptive B cell and T cell may also lead to extrapulmonary disease, including
NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 271
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Spike protein (S)
Nucleocapsid protein (N)
RNA genome
Membrane protein (M)

Envelope protein (E)
b 2 Cleavage of
S protein
1 SARS-CoV-2
3 Activation of
S2 domain
4 Fusion of viral and
host membranes
S2
S2′ site
S1
Activated S2
Target cell Protease

ACE2
TMPRSS2
Type I/III IFN signal Type I IFN

receptor Type III IFN
c in an autocrine and receptor
paracrine fashion
Type I/III IFN
JAK1 JAK1
DMV with
viral dsRNA TYK2 TYK2
RIG-I MDA5
STAT1 P
IRF9
STAT2 P
MAVS
P IRF3 P IRF7
STAT1 P
IRF9
P IRF3 P IRF7 Type I/III IFN STAT2 P ISGs
ISRE
Fig. 1 | Molecular and cellular pathogenesis of SARS-CoV-2. a | The severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) virion consists of the following structural proteins: spike protein (S), nucleocapsid protein (N), membrane
protein (M) and envelope protein (E). b | The S protein attaches to the receptor angiotensin-converting enzyme 2 (ACE2)
on the host cell using the S1 domain (stage 1). This allows TMPRSS2 to cleave the S protein (stage 2), leading to activation
of the S2 domain for fusion (stage 3). Activated S2 fuses viral and host lipid bilayers, leading to deposition of the viral
positive-sense, single-stranded RNA genome into the host cell (stage 4). c | Viral replication creates double-stranded
RNA (dsRNA) replication intermediates that can activate cytoplasmic innate immune sensing pathways through
activation of MDA5 or RIG-I, initiating a signalling cascade though MAVS that eventually leads to the production
of type I and type III interferons (IFNs). These interferons act in a paracrine and autocrine fashion via the plasma
membrane receptors and a JAK–STAT1/2 signalling cascade and lead to the production of interferon-stimulated genes
(ISGs) that have direct and indirect antiviral functions. DMV, double-membrane vesicle; ISRE, interferon-sensitive
response element.
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Rhabdomyolysis
gastrointestinal symptoms and acute cardiac, kidney a type of lung injury characterized by “endothelial and
A potentially life-threatening and liver injury, in addition to cardiac arrhythmias, alveolar lining cell injury which leads to fluid and cellu-
condition resulting from the rhabdomyolysis , coagulopathy and shock55. Although lar exudation and in some cases progresses to extensive
breakdown of muscles with SARS-CoV-2 RNA has been detected in several organs at interstitial fibrosis”77. DAD is typically characterized
leakage of muscle contents
low levels56–59, it is largely unknown to what extent these by an initial exudative phase with oedema, dying cells,
into the circulation.
manifestations are the result of direct infection. Clearly, hyaline membranes and inflammation. This is followed
Coagulopathy the intestine can also be infected by SARS-C oV-2, by a proliferative (or organizing) phase with AT2 cell
An imbalance in coagulation and gastrointestinal symptoms are relatively frequent, hyperplasia in an attempt to regenerate the alveoli.
resulting in either excessive
yet it is unknown how intestinal infection contributes In some cases, there can be a fibrotic phase with fibrosis
bleeding or clotting.
to severe COVID-19. There is also evidence of the shed- mostly within the alveolar septa. The clinical syndrome
Anosmia ding of viral RNA in faeces60,61 and productive infection ARDS can be caused by a wide range of predisposing
The inability to smell. of gut enterocytes62, which express higher levels of ACE2 factors, including viral infection.
than respiratory cells. In addition, sustentacular cells Histological examination of lung tissues of deceased
Pulmonary fibrosis
A condition in which the
are the main target of SARS-CoV-2 in the nasal olfac- individuals with COVID-19 on autopsy show that DAD is
lungs are scarred, impairing tory mucosa, which may be the cause of COVID-19- the predominant pattern of lung injury78. The DAD in
the exchange of oxygen for related anosmia 24,63. Although increasing evidence lungs of deceased individuals with COVID-19 shows
carbon dioxide. suggests that severe COVID-19 is an inflammatory features of the exudative and proliferative phases with
disease affecting many organs, the primary cause of interstitial and intra-alveolar oedema, dying pneumo-
Hyaline membranes
Fibrin-rich exudates that
COVID-19 is pulmonary viral replication, and therefore cytes, hyaline membranes, microvascular thrombosis,
seal the alveoli from fluid this Review focuses mainly on the pathophysiology of capillary congestion and AT2 cell hyperplasia78,79. The
accumulation but also COVID-19-associated ARDS. death of pneumocytes was confirmed by single-cell
limit oxygen exchange. Increased age, obesity and male sex are well-established sequencing and immunostaining of COVID-19 lungs,
Coagulation
risk factors for the development of severe COVID-19 which indeed showed a reduction of AT2 and AT1 cells
Blood clotting. (refs64–66). Common co-morbidities include hyperten- compared with control lungs80–82.
sion, heart failure, cardiac arrhythmia, diabetes, kidney
Fibrinolysis failure and chronic pulmonary disease42. In addition, Alveolar epithelial damage and an imbalance in coagu
The process of the breakdown
there are genetic predispositions to developing severe lation and fibrinolysis. Alveolar cell death or damage
of blood clots.
COVID-19, which can be highly informative in under- leads to a disruption of the alveolar epithelium, which
standing SARS-CoV-2 pathophysiology. Genome-wide sets off another key feature of the exudative phase of
association studies have linked loci containing variants DAD seen in COVID-19: an imbalance between the acti-
at DPP9 and FOXP4 (refs67,68), which have been linked vation of coagulation and the inhibition of fibrinolysis83.
to pulmonary fibrosis69, as well as variants at the chemok- This process results in the formation of hyaline mem-
ine receptor genes CXCR6 and CCR9 (for which CCR1 branes, which are fibrin-rich exudates that seal the
and CCR2 are flanking genes) to severe COVID-19 alveoli from fluid accumulation, but also limit oxygen
(refs67,68,70). In addition, genetic predispositions for severe exchange84. The same process is responsible for the for-
COVID-19 concern genes involved in TLR3-dependent mation of fibrin thrombi, which are found in the small
and TLR7-dependent type I interferon induction and arterial vessels (less than 1 mm in diameter) in most
amplification71,72 and in type I interferon detection68. severe COVID-19 cases85–88. Patients with fibrin thrombi
These findings point towards an important role for present with elevated levels of D-dimers, fibrin degra-
interferon signalling in combatting SARS-CoV-2. This dation products that accumulate upon fibrinolysis89,
is underlined by studies that have found that neutraliz- and high D-dimer levels are associated with fatal out-
ing autoantibodies to interferon-α (IFNα) are associated comes in COVID-19 (refs51,89,90). Low platelet count
with severe COVID-19 (refs73,74). These antibodies are is associated with severe COVID-19, likely because
present in ~4% of uninfected individuals older than platelets are used up for clotting91. Early initiation of
70 years and have been estimated to contribute to ~20% prophylactic anticoagulation was shown to prevent
of COVID-19-related deaths75. severe disease and death of hospitalized patients with
COVID-19, suggesting that coagulation plays a major role
Pathological findings in SARS-CoV-2 pathophysiology92. The prothrombotic
Diffuse alveolar damage and COVID-19-associated state seen in patients with COVID-19 is reminiscent of
ARDS. Traditionally, pathologists have investigated a process known as immunothrombosis, in which the
the mechanisms behind diseases using histological and immune and coagulation systems cooperate to block
immunohistochemical methods. However, in recent pathogens and limit their spread93,94.
years the development of single-cell omics has enabled What triggers the imbalance in the coagulation sys-
us to combine what we see through the microscope with tem in COVID-19 is currently poorly understood, but it
quantitative data on cell types and cell type-specific RNA may start with the disruption of the alveolar epithelium.
expression patterns. In this section, we aim to integrate A wide variety of stimuli, such as hypoxia, cytokines,
histological data on classical and COVID-19-associated chemokines and damage-associated molecular patterns,
ARDS with new insights from single-cell omics. can induce a leaky state in both the endothelium and
Histological examination of ARDS cases revealed a the epithelium in which the bonds between cells can be
common histological lung injury pattern, known as dif- disrupted95,96. These stimuli trigger endothelial activa-
fuse alveolar damage (DAD)76. The term ‘diffuse alveolar tion and may lead to endothelial cell death, which has
damage’ was coined by Katzenstein in 1976 to describe been observed in COVID-19 cases97. Virus particles
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Tissue factor
were observed inside endothelial cells, but it is currently expression of tissue factor by neutrophils106. Recently,
A protein present inside unclear whether these cells support viral replication a population of CD16-expressing T cells was identi-
endothelial cells or on the in vivo and whether infection of these cells contributes fied in patients with severe COVID-19 (ref.107). CD16,
surface of many non-vascular to disease severity. In normal physiological conditions, which was induced by complement activation, enabled
cells, normally separated
tissue factor resides inside endothelial cells and in tis- immune complex-mediated degranulation and cytotoxi
from the blood by the vascular
endothelium, but which sues, but when the endothelium is disrupted, vascular city. These cells promoted microvascular endothelial cell
interacts with blood coagulation coagulation factors can interact with tissue factor, damage and release of the chemokines IL-8 and CCL2.
factors when the endothelium triggering the extrinsic coagulation pathway and ulti- Another factor that will likely promote clotting in the
is disrupted, triggering the
mately leading to the cleavage of fibrinogen into fibrin, lungs of individuals with COVID-19 is the epithelial
extrinsic coagulation pathway.
a major component of clots and hyaline membranes98 production of IL-6, which induces the transcription
Neutrophil extracellular (Fig. 2) . Tissue damage can also trigger the intrinsic of clotting factors in the liver and tissue factor in the
traps coagulation pathway through activation of factor XII by endothelium. Elevated levels of circulating IL-6 are
(NETs). Large, extracellular, stimuli such as extracellular RNA, DNA and exposed predictive of severe COVID-19 (refs54,108,109). A recent
web-like structures composed
collagen99. At the same time, platelets seal the exposed study tested the effect of the IL-6 monoclonal antibody
of cytosolic and granule
proteins that are assembled subendothelial extracellular matrix to stop leakage and tocilizumab against severe COVID-19 and found that
on a scaffold of decondensed provide factors to sustain coagulation100. Immune cells, this therapy increased survival and the chance of dis-
chromatin and secreted attracted by cytokines and chemokines, also contrib- charge from hospital by 28 days in patients receiving
by neutrophils.
ute to clotting93. Monocytes and monocyte-derived corticosteroids110.
microvesicles can present tissue factor on their sur- The formation of fibrin thrombi is counteracted
faces, following the activation of PRRs93,101. Neutrophils by the fibrinolysis pathway. This pathway is inhibited by
release neutrophil extracellular traps (NETs)102,103, which plasminogen activator inhibitor 1 (PAI1; also known as
can directly activate factor XII. In patients with severe SERPINE1). PAI1 inhibits tissue plasminogen activator
COVID-19, neutrophils express high levels of tissue and urokinase, which both activate fibrinolysis by turning
factor and release NETs coated with tissue factor, which plasminogen into its active fibrin-degrading form, plas-
may further promote clotting103. NETs drive coagula- min. PAI1 expression is highly increased in COVID-19,
tion by recruiting platelets, which in turn can release and high levels of PAI1 are associated with worse res-
pro-inflammatory cytokines in platelet-derived extra- piratory status111,112, suggesting that this factor may
cellular vesicles upon activation104. In turn, activated contribute to the clotting imbalance observed in severe
platelets interact with neutrophils to stimulate NETosis COVID-19. Increased PAI1 expression was also observed
(the formation of NETs)105. Emerging evidence suggests in mice infected with SARS-C oV113. Interestingly, in
that SARS-CoV-2 can trigger complement activation, this mouse model, PAI1 protected mice from exten-
in particular, the lectin pathway, leading to the gener- sive lung haemorrhage, which may be a consequence
ation of the cleavage fragment C5a, which increases of uncontrolled fibrinolysis in the absence of PAI1.
Platelets ↓ PAI1 ↑ Fibrinolysis ↓ Fibrin
Active TF
Inactive TF NETosis
Extrinsic Thrombus
coagulation
CD16+
cytotoxic
Monocyte T cell
Neutrophil IL-1β, IL-8, TNF,
Activated platelets CCL2/3/7/8 IL-8, CCL2
Type I/III IFN, IL-6, PAI1 Endothelial activation Exposed collagen Intrinsic coagulation
Replication Cell death
Fig. 2 | Immunothrombosis in severe COVID-19. Severe COVID-19 is extracellular matrix can trigger both extrinsic coagulation (via activated
characterized by an imbalance in coagulation and fibrinolysis, which may tissue factor (TF)) and intrinsic coagulation (for example, via collagen, RNA
begin with the disruption of the alveolar epithelium. A wide variety of stimuli, or DNA), leading to fibrin deposition. Activated platelets bind to the exposed
such as hypoxia, cytokines, chemokines and damage-associated molecular extracellular matrix to seal the injury and stimulate neutrophils together with
patterns, can induce a leaky state in both the endothelium and the monocytes to release neutrophil extracellular traps (NETs). NETs contain TF
epithelium in which the bonds between cells can be disrupted. These stimuli and DNA, stimulating intrinsic and extrinsic coagulation. Ultimately, this
can trigger endothelial activation, may lead to endothelial cell death and immune system-driven process leads to the formation of fibrin thrombi and
recruit immune cells (neutrophils and monocytes). CD16+ T cells can promote depletion of platelets. In the meantime, fibrinolysis may be reduced owing
microvascular endothelial cell injury and release of chemokines. The exposed to high plasminogen activator inhibitor 1 (PAI1) levels. IFN, interferon.
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PAI1 expression is induced by interferon and inhi the difference in cell composition in bronchoalveolar
bits entry of influenza A virus by counteracting pro- lavage fluid between mild or moderate cases and severe
teolytic activation of the haemagglutinin protein by cases and noted that in severe cases there were higher
TMPRSS2 (ref.114). As SARS-CoV-2 relies on TMPRSS2 levels of pro-inflammatory macrophages but lower levels
as well for proteolytic activation12,14, PAI1 may also of myeloid DCs, plasmacytoid DCs and T cells 121.
exert antiviral effects against SARS-CoV-2. Altogether, Impaired B cell function in individuals with cancer
the findings indicate that SARS-C oV-2 replication who contracted COVID-19 was not associated with
in the lower part of the lungs causes injury to the alveolar increased mortality, whereas a lack of adequate CD8+
epithelium and endothelium, triggering an imbalance in T cell responses correlated with higher viral load and
coagulation and fibrinolysis involving fibrin, cytokines, increased mortality122. Alveolar macrophages isolated
chemokines, platelets, monocytes, neutrophils, NETs, from bronchoalveolar lavage fluid samples expressed the
complement activation and PAI1 (Fig. 2). chemokines CCL7, CCL8 and CCL13, which can drive
recruitment of T cells as well as monocytes via CCR2
The roles and phenotypes of immune cells in COVID-19- (ref.120). SARS-C oV-2 RNA, including the negative-
associated ARDS. Epithelial damage and inflammation strand replicative intermediate, was also found within
attract immune cells. Histology sections of COVID-19 inflammatory monocytes and macrophages, suggest-
lung show immune cell infiltrates that are largely com- ing that they may become infected81,120. Although this
posed of macrophages in the alveolar lumina and infection is likely abortive123,124, it could further amplify
lymphocytes in the interstitium78. Single-cell sequenc- the production of pro-inflammatory cytokines by trig-
ing of post-mortem COVID-19 lung tissue indicates gering pyroptosis125,126. The triggering of pyroptosis may
increased infiltration of monocytes and macrophages be induced by the inflammasome activator NRLP1,
in comparison with control lungs, and it was noted which was recently shown to be directly triggered by
that monocyte-d erived macrophages and alveolar dsRNA127. Notably, NLRP1-mediated inflammasome
macrophages were aberrantly activated80. In the blood, activation is inhibited by DPP9, and an intronic variant
patients with mild COVID-19 had increased levels of in the gene encoding DPP9 was recently found to be
inflammatory monocytes expressing high levels associated with severe COVID-19 (ref.68), and previously
of HLA-DR, whereas patients with severe COVID-19 had this gene was linked to pulmonary fibrosis69. In addi-
monocytes expressing low levels of HLA-DR115, which tion, macrophages that have internalized virus particles
are indicative of monocyte dysfunction116. Monocyte- may facilitate spreading of SARS-CoV-2 in the lungs120.
derived macrophages differentially expressed two long Alternatively, the SARS-CoV-2 RNA within these cells
non-coding RNAs (NEAT1 and MALAT1) involved in can be derived from phagocytosis of dead epithelial
aberrant macrophage activation and impaired T cell cells. Another single-cell sequencing study investigated
immunity117. Alveolar macrophages showed strongly nasopharyngeal responses and noted that inflammatory
decreased mRNA and protein expression of the recep- macrophages were enriched in patients with COVID-19
tor tyrosine kinase AXL, which is important for the with critical disease and expressed CCL2, CCL3, CCL20,
clearance of apoptotic cells to reduce inflammation CXCL1, CXCL3, CXCL10, IL8 (also known as CXCL8),
during tissue regeneration118. Monocyte-derived or IL1B and TNF128. The induction of CCL2 and CCL3 cor-
macrophage-derived IL-1β and epithelial cell-derived responded to an induction of CCR1 — the gene encod-
IL-6 have emerged as unique features of SARS-CoV-2 ing the CCL3 receptor — in neutrophils, cytotoxic T cells
infection compared with other types of viral and bac- and macrophages, indicating that inflammatory macro
terial pneumonia80. Single-cell sequencing of the lungs phages may drive respiratory inflammation in response
from another cohort of individuals with fatal COVID-19 to SARS-C oV-2. Patients with critical COVID-19
showed increased levels of dendritic cells (DCs), macro also displayed a strong enrichment of neutrophils in the
phages and natural killer (NK) cells81. Interestingly, no nasopharynx compared with patients with moderate
significant increases in the levels of T cells were detected COVID-19 and controls.
in single-cell sequencing analyses of post-mortem lung Neutrophils are the first responders in many viral
tissues compared with controls, indicating that the lym- infections and play crucial roles in antiviral immunity in
phocytes seen in histology sections on autopsy may be the airways129, but as mentioned earlier herein, excessive
predominantly NK cells. Elevated levels of circulating NET formation can be detrimental. Whereas neutrophils
adaptive NK cells and an increase in the levels of ‘armed’ are generally abundantly observed in ARDS caused by
NK cells containing high levels of cytotoxic proteins have various agents (including infectious agents), only ~30%
also been associated with severe disease119. Low levels of patients with severe COVID-19 exhibited neutro-
of T cell infiltration could suggest that impaired T cell philia in bronchoalveolar lavage fluid120,130, and neutro-
responses contribute to lethal outcomes in COVID-19. phils are not the dominant immune cell in COVID-19
In a study that performed single-cell sequencing on lung histology sections78,131,132. In peripheral blood, how-
Intubation
The placement of a flexible bronchoalveolar lavage fluid obtained from patients ever, neutrophilia is commonly observed in patients with
plastic tube through the throat with severe COVID-19 (within 48 h of intubation), an severe COVID-19 (refs47,49,133–135). One study suggested
into the trachea (windpipe) to enrichment of monocytes and also CD8+ T cells was that neutrophils are massively enriched in asympto-
facilitate breathing. observed compared with non-pneumonia controls120; matic individuals, and are mildly increased in critically
Pyroptosis
however, of these patients, 75% survived the infection, ill patients, but that the phenotypes of these neutrophils
An inflammatory form of lytic perhaps pointing to a beneficial role for T cells in pre- are heterogeneous136. In contrast to the neutrophils of
programmed cell death. venting fatal outcomes. In agreement, a study investigated asymptomatic individuals, the neutrophils of critically
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ill patients expressed proteins involved in inflamma- Notably, compared with controls, Pou2f3 −/− mice,
tory pathways, neutrophil degranulation and NETs. which lack tuft cells, showed decreased infiltration of
Interestingly, a study detected a progenitor-like neu- macrophages and decreased expression of chemokine
trophil population that expressed genes involved in genes (for example, Ccl3 and Ccl8) in response to influ-
degranulation specifically in patients with COVID-19 enza A virus infection, indicating that these cells may
with ARDS137. Another study also described neutrophil contribute to the pathophysiology of COVID-19 (ref.80).
precursors, as well as dysfunctional neutrophils express-
ing programmed cell death 1 ligand 1 (PDL1)115 in the The fibrotic phase of COVID-19-associated ARDS.
peripheral blood of patients with severe COVID-19. Patients with severe COVID-19-a ssociated ARDS
Altogether, these data indicate that the phenotypes display clinical, radiographic, histopathological and
of neutrophils in COVID-19 are heterogeneous and that ultrastructural hallmarks of pulmonary fibrosis 148.
neutrophils could be protective early and pathological Studies have also noted the expansion of fibroblasts in
later in the infection. COVID-19 lungs80,81, and the degree of fibrosis corre-
lated with the duration of the disease, indicating that
The proliferative phase of COVID-19-associated ARDS. fibrosis increases over time in COVID-19. A subset of
The proliferative phase of DAD is characterized by AT2 fibroblasts expressed CTHRC1, a marker for pathologi
cell hyperplasia, which may reflect the proliferation cal fibroblasts, which may contribute to the formation
of AT2 cells in an attempt to regenerate the damaged of pathological extracellular matrix and may drive lung
lung78,79. AT2 cell hyperplasia is observed in COVID-19- scarring149. A recent single-cell transcriptomic study
associated ARDS. Single-c ell sequencing revealed revealed a population of CD163+ monocyte-derived
that AT2 and AT1 cells from patients with COVID-19 macrophages that expressed a profibrotic gene set and
expressed lower levels of defining markers compared displayed similarity to idiopathic pulmonary fibrosis-
with controls. AT2 cells from patients with COVID-19 associated macrophages148. Notably, human monocytes
displayed decreased expression of ETV5, which encodes stimulated in vitro with SARS-CoV-2, but not influenza
a transcription factor required for maintaining AT2 cell A virus or viral RNA analogues, displayed a similar
identity. Expression of this gene is also associated transcriptional profile, indicating that SARS-C oV-2
with differentiation towards AT1 cells 138. However, directly triggers this response. These data indicate that
COVID-19 AT1 cells expressed lower levels of CAV1, a fibrotic phase occurs in COVID-19-associated DAD,
a marker of late AT1 cell maturation139. These data may which may impair regeneration, leading to chronic
suggest that the AT2 cells in COVID-19 lungs cannot respiratory failure.
effectively differentiate to AT1 cells80,81. Recent studies
have identified an AT2 cell state associated with lung Mechanisms from in vitro and in vivo findings
injury (for example, idiopathic pulmonary fibrosis) and In the previous sections, we saw how a tremendous
that is characterized by failure to fully differentiate into number of descriptive studies have contributed to our
AT1 cells140–142. This cell state has been termed ‘damage- understanding of severe COVID-19. However, the
associated transient progenitors’ (DATPs), ‘alveolar dif- mechanisms underlying severe COVID-19 are still
ferentiation intermediate’ or ‘pre-AT1 transitional cell largely unknown and need to be assessed experimen-
state’ (PATS). The relative amount of cells in this state tally. Arguably, the main questions in understanding
is increased in COVID-19 lungs and they express genes SARS-CoV-2 pathogenesis are as follows: what triggers
associated with p53, TNF signalling and the hypoxia the inflammatory cascade that leads to ARDS and at
response via HIF1α80. This state may be associated what stages does this cascade become a self-perpetuating
with prolonged interferon signalling as a study recently positive feedback loop? COVID-19 animal (Box 2) and
demonstrated that type I and type III interferons inter- in vitro (Box 3) experimental model systems are pivotal
fere with lung repair after influenza virus infection in to study this, and for assessing therapeutic interventions.
mice, and that interferon-induced p53 directly reduces
epithelial cell proliferation and differentiation143. A sub- Mechanisms behind early upper respiratory tract infec-
set of cells, distinct from KRT5+TP63+ airway basal cells, tion and dissemination to the lungs. Early events in
expressing genes associated with the PATS programme infection may have a great influence on the development
(KRT8, CLDN4, CDKN1A and TP63) were identified of severe disease. The first cells targeted by SARS-CoV-2
in COVID-19 lungs81,82. These cells may resemble a during natural infection in humans are likely to be the
cell type, termed ‘TP63+ intrapulmonary basal-like ACE2+TMPRSS2+ multiciliated airway cells in the naso-
progenitor cells’, identified in mice in response to lung pharynx or trachea22–24. Nasal ciliated cells express high
injury caused by H1N1 influenza A virus144–146. It is cur- levels of ACE2 and TMPRSS2 on the apical membrane
rently unclear how these transitional cells contribute to (despite low mRNA levels)22,23,150. This had already been
the regeneration response, but typically they differen- predicted on the basis of findings from studies of SARS-
tiate into tuft cells (also called ‘brush cells’ or ‘chem- CoV151,152 and how readily these cells can be infected
osensory cells’) and secretory cells (club cells and goblet by SARS-CoV-2 in air–liquid interface differentiated
cells) and rarely give rise to AT2 cells or AT1 cells144,145,147. 2D human airway cultures23,62. In most COVID-19
In agreement, a study noted an increase in the levels cases, the infection is likely cleared at this stage through
of ectopic tuft-like cells in COVID-19 lungs. The the induction of type I or type III interferon, and the
numbers of tuft cells were also increased threefold in induction of B and T cell responses; however, in some
the upper airways of patients with COVID-19 (ref.80). cases the virus can spread to the lower respiratory tract.
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Box 2 | COVID-19 animal models upward flow of mucus in the branching airways154, pos-
sibly facilitating dissemination of virus into the alveoli.
Animal models are important tools for investigating viral pathogenesis and testing Once the virus reaches the alveoli, it seems that the AT2
intervention strategies (reviewed extensively in ref.207). For severe acute respiratory cells there are susceptible to infection as they express
syndrome coronavirus 2 (SARS-CoV-2), several animal models have been established, ACE2 and TMPRSS2; they have been found to contain
but most develop a relatively mild disease compared with severe COVID-19 cases.
viral RNA on autopsy23. However, the lack of available
In ferrets, SARS-CoV-2 replicates mainly in the upper respiratory tract, with hardly
any lung pathology208,209. Cynomolgus macaques show some signs of lung pathology material from the early stages of the disease limits our
with diffuse alveolar damage, with focal exudation, fibrin deposition, inflammatory understanding of the early stages of alveolar infection.
macrophages and fewer neutrophils and lymphocytes210. Similar results were obtained Studies on AT2 cell organoids allow modelling of this
in rhesus macaques, and a slightly more severe disease with coagulation abnormalities phase32–34. These studies showed that AT2 cells grown
reminiscent of the coagulopathy observed in patients with COVID-19 (for example, in vitro as organoids express ACE2 and TMPRSS2 on
thrombocytopenia and pulmonary microthrombi) is observed in African green their apical membranes, but express little mRNA of
monkeys211–213. Syrian hamsters are very sensitive to wild-type SARS-CoV-2, shed high the encoding genes, without requiring differentiation.
levels of infectious virus and develop upper and lower respiratory tract infection, but SARS-CoV-2 infection in these cells led to the induc-
the disease is mild to moderate214. Notably, aged and male hamsters seem to develop tion of a type I and type III interferon response. One
a more severe disease than young and female hamsters, respectively215,216. Roborovski
study also noted that AT2 cells can lose their AT2 marker
hamsters compared with Syrian hamsters develop a more severe disease with
pulmonary microthombi217. gene expression in response to the infection and may
As wild-type SARS-CoV-2 does not efficiently infect mice owing to ineffective gain expression of basal cell marker genes, reminiscent
angiotensin-converting enzyme 2 (ACE2) binding218, lethal mouse-adapted SARS-CoV-2 of the transitional AT2 cell described in vivo80,81. Besides
models have been set up that capture multiple aspects of severe COVID-19 (refs219–221). interferon responses, apoptosis of infected AT2 cells and
Mice infected with mouse-adapted strains develop diffuse alveolar damage, with focal the induction of inflammatory responses were modelled
exudation, sloughed epithelial cells, cellular debris, fibrin deposition and accumulation as well32. Similar findings were obtained with use of a
of inflammatory cells (neutrophils, macrophages and lymphocytes). More severe disease primary alveolosphere model155. Another important
was observed in aged mice219–221, which is in line with results obtained with SARS-CoV aspect that is modelled in these systems is the decrease
in aged cynomolgus macaques222. A study also noted vessel and basement membrane in surfactant gene expression in AT2 cells, which is also
damage with adherent inflammatory cells in aged mice, but coagulopathies are not
observed in vivo in late stages of the disease81. These data
typical for SARS-CoV-2 infection in mice. Transgenic mouse models expressing human
ACE2 (for example, under the K18 or endogenous mouse Ace2 promoter) have also indicate that interferon induction, apoptosis, inflamma-
been developed (reviewed extensively in ref.207). tion and loss of surfactant production and AT2 identity
Several studies have used the hamster model to assess differences in pathogenicity are direct effects of virus replication. Recent findings
between SARS-CoV-2 variants. Some variants appear to be more or less pathogenic regarding the newly emerged Omicron variant support
in this model223,224, but these results must be interpreted with caution as they may be a central role for AT2 infection in SARS-CoV-2 patho-
species specific. Some mutations may by chance increase hamster infectivity, such as genesis. The Omicron variant appears to cause fewer
N501Y, which increases binding to ACE2 (ref.225). In addition, it is difficult to standardize hospitalizations and has lost the ability to efficiently
the infectious inoculum as some variants are attenuated on Vero cells, which are replicate in AT2 cell organoids, whereas it efficiently rep
commonly used to grow and titrate virus stocks. In addition, SARS-CoV-2 rapidly adapts
licates in airway organoids37. Soon, alveolar models
to Vero cells upon passaging16,26,226,227 (Box 3), and different isolates may be more or
may be improved by mimicking the ratio of AT2 cells to
less prone to culture adaptation. Cells containing an active TMPRSS2-mediated entry
pathway (for example, TMPRSS2-expressing Vero E6 cells, Calu-3 cells or human airway AT1 cells found in human alveoli and growing the cells
organoids) can be used to prevent culture adaptation16. Before such comparative studies at air–liquid interfaces to allow modelling of leakage.
are performed, stocks should be grown on cells containing an active TMPRSS2-mediated Such systems may also include endothelial cells or speci
entry pathway, characterized by deep sequencing, and care must be taken that different fic immune cell subsets to investigate cell type-specific
variants are similarly infectious on the cell line used for titrations. contributions to SARS-C oV-2 pathogenesis. Human
organoids can also be used to investigate the roles of spe-
SARS-CoV-2 may move deep into the lungs by inhala- cific genes in SARS-CoV-2 pathogenesis using CRISPR
tion of virus particles from the upper respiratory tract, systems (Box 3).
gradually spread by infecting airway cells distally along
the tracheobronchial tree or initially directly infect cells The role of interferons in dissemination and their appli-
in the lower respiratory tract. From in vitro studies using cation in treatment. Dissemination of SARS-CoV-2 to
2D differentiated air–liquid interface organoids, it was the lower lung can be the result of poor or efficiently
concluded that ciliated cells in the lower airways are inhibited type I or type III interferon responses. Besides
the main SARS-CoV-2 target, while club cells may be autoantibodies to interferon73–75 and inborn defects in
infected occasionally as well36. In 3D distal airway orga- interferon signalling71,72, low induction of local and sys-
noids, club cells were identified as the main viral target temic interferon responses has indeed been observed
cell, but these organoids are relatively poorly permis- in patients with severe COVID-19 (refs156,157), and this
sive to infection and consist mainly of progenitor cells, appears to be a general phenomenon associated with
with few mature ciliated cells present34. The infection ageing158, including a decrease in the amount of func-
of secretory airway cells appears to be rare in vivo22, tional plasmacytoid DCs158,159. One study additionally
at least in the upper respiratory tract. In general, the noted that expression of mTOR signalling proteins was
interferon response triggered in infected airway epi- decreased in plasmacytoid DCs, suggesting that they
thelial cells is relatively dampened compared with that may have impaired type I interferon signalling160,161.
triggered by infection with influenza A virus153. Ciliated Although children can become infected with SARS-
cell infection leads to the loss of ciliation in reconstituted CoV-2 and shed levels of virus comparable to those
human bronchial epithelial cells, which can disturb the shed by adults162, they rarely develop lethal disease66.
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Recently, a study characterized the single-cell transcrip- goblet cells and neutrophils. Single-cell sequencing of
tional landscape in the upper airways of children and nasal epithelial cells from patients with COVID-19
adults, and discovered that children display higher basal showed extensive induction of type I and type III inter-
levels of relevant PRRs, RIG-I and MDA5, in upper air- feron responses in patients with mild disease, whereas
way epithelial cells, macrophages and DCs. In addition, cells from patients with severe disease were essentially
children displayed stronger innate antiviral responses muted in their antiviral capacity despite higher local
upon SARS-CoV-2 infection than adults. Notably, at the inflammatory myeloid cell populations and equivalent
baseline, children had fewer nasal ciliated cells but more viral loads156. In vitro studies have shown that SARS-
CoV-2 is a poor inducer of interferon153 owing to the way
SARS-CoV-2 shields its RNA from detection by the host
Box 3 | Experimental systems to study SARS-CoV-2 using membrane-enclosed replication factories and the
expression of viral proteins that actively block key com-
Traditionally, in vitro model systems in virology are transformed or cancerous cell lines,
which have drifted extensively from their natural in vivo counterparts and often have
ponents of RIG-I-like receptor signalling163–165. On the
defects in cellular innate immunity, allowing unbridled viral replication. Therefore, other hand, SARS-CoV-2 is more attenuated by type I
findings from traditional in vitro systems should be interpreted with caution. Animal interferon pretreatment than SARS-CoV166. Compared
models are important for studying viral pathogenesis and the effect of interventions. with influenza A virus, SARS-CoV-2 appears to induce
However, animal models are labour-intensive and expensive, and often recapitulate less type I interferon, but fails to counteract STAT1 phos-
only specific aspects of a particular human disease. This is also the case for severe phorylation upon type I interferon pretreatment, result-
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) animal models207. An issue with ing in ablation of SARS-CoV-2 replication. Similarly,
both cell lines and animal models is that the viral target cells in these systems are not in a bronchoalveolar SARS-C oV-2 infection model,
representative of the target cells in humans in vivo. This is best exemplified by the rapid pretreatment with low concentrations of type III inter-
adaptation of SARS-CoV-2 to specific cell lines16,26,226 and animals209,220,221, and indicates
feron significantly reduced SARS-CoV-2 replication36.
mismatches in virus–host interactions, which could result in the incorrect modelling of
defining features of COVID-19 pathophysiology in humans.
In this model, type III interferons were effective
Human primary cell models offer an attractive alternative to cell lines and animal against SARS-CoV-2 replication even when added 24 h
models. Primary bronchial or tracheal airway epithelial cultures have been used after infection.
extensively in virology and accurately model the human airway, but not all cells can be From SARS-C oV studies in mice, we know that
cultured in vitro while maintaining their in vivo phenotypes. For example, human primary robust viral replication accompanied by delayed type I
alveolar type 2 cells rapidly differentiate to an alveolar type 1-like cell in 2D culture228. interferon responses leads to the induction of overex-
Such primary alveolar cultures are poorly susceptible to SARS-CoV-2 (ref.23). In addition, uberant inflammatory responses and consequent lung
traditional primary cell cultures are generally not amenable to genetic engineering. immunopathology167. Work done on mouse coronavi-
In the past few years, human organoids have emerged as important tools for studying ruses showed that plasmacytoid DCs and plasmacytoid
viruses62,229–233. Although human airway organoids had been established several years
DC-derived type I interferon are crucial for controlling
before the onset of the COVID-19 pandemic234, methods to grow human adult-derived
alveolar organoids were not published until the autumn of 2020, when three groups
coronavirus infection168. Plasmacytoid DCs are special-
published their alveolar type 2 cell organoid models and data on SARS-CoV-2 infection ized for the rapid production of large amounts of type I
modelling32–34. The intestinal epithelium was also shown to support productive viral interferon in response to viruses and are believed to be
infection with use of intestinal organoids62,233. A major advantage of intestinal organoids particularly important to control viral infections of the
is that they can be efficiently genetically modified using CRISPR tools. lungs169. A recent in vitro study of SARS-CoV-2 showed
Recent studies have used CRISPR–Cas9 knockout screens to identify factors that these cells are the predominant source of IFNα, which
essential for SARS-CoV-2 replication in cell lines21,235,236. However, these results should is released in response to cell–cell contact with infected
be validated in more physiologically relevant infection models237, such as organoids, epithelial cells (via the αLβ2 integrin–ICAM1 complex)
to identify which genes or pathways are important enough for the virus to be realistic in a TLR7-dependent manner170. This study also demon-
druggable targets. A recent study generated a validated clonal biobank of organoids
strated that plasmacytoid DC responsiveness correlated
containing deletions of genes involved in coronavirus replication, including (putative)
(co-)receptors, spike-activating proteases, attachment factors and several genes
with disease severity, and is particularly impaired in
involved in coronavirus replication14. This study validated that angiotensin-converting patients with severe COVID-19. Moreover, patients with
enzyme 2 (ACE2) is indispensable for SARS-CoV-2 replication in gut organoids. mild COVID-19 had high IFNα and IFNλ blood levels at
Deletion of the proposed co-receptor NRP1 did not impact virus replication18,19. early time points, whereas IL-6 levels were increased in
This study also showed that cathepsin L and cathepsin B are not essential for individuals with severe infections. In SARS-CoV-infected
SARS-CoV-2 replication, whereas TMPRSS2 is. Although in vitro several other mice, early administration of type I interferon ameliorated
transmembrane serine proteases (for example, TMPRSS4, TMPRSS11D and TMPRSS13) immunopathology167, similar to results obtained with
can prime SARS-CoV-2 (ref.20), deletion of the encoding genes in gut organoids did pegylated IFNα in SARS-CoV-infected macaques171 and
not impact SARS-CoV-2 replication, demonstrating the relevance of genetic knockout in MERS-CoV-infected mice172. In SARS-CoV-infected
experiments in physiologically relevant models. Another study used inhibitors to show
mice, the delayed type I interferon response was asso-
that SARS-CoV-2 uses serine proteases (likely TMPRSS2), but not cathepsins, for entry
into human airway organoids, suggesting that intestinal and pulmonary epithelial
ciated with increased accumulation of inflammatory
cells possess a similar SARS-CoV-2 entry route15. These findings may also explain monocyte–macrophages, resulting in elevated inflam-
why hydroxychloroquine was not effective against COVID-19 as the virus enters matory cytokine levels, vascular leakage and impaired
physiologically relevant cells using TMPRSS2 before reaching an acidified endosome virus-specific T cell responses167, reminiscent of single-
with active cathepsins. Drugs targeting TMPRSS2 specifically may be efficient in cell sequencing data from patients with COVID-19
blocking SARS-CoV-2 entry and dissemination. (refs 80,81,120) . Depletion of inflammatory monocyte–
A big advantage of 3D organoid technology is that co-cultures with all kinds of cell macrophages using monoclonal antibody treatment
types (for example, immune cells and endothelial cells) are possible. Organoid studies can reduced the levels of inflammatory cytokines (CCL2,
greatly advance our mechanistic understanding of severe COVID-19, especially when TNF and IL-6) in the lung and resulted in protection
combined with novel techniques, such as CRISPR gene editing and single-cell omics.
from lethal disease167, showing that these cells play a
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major role in coronavirus-induced pathogenesis. In con- Mild or symptomatic case

trast, a recent study of SARS-C oV-2-infected mice • Rapid IFN response
• Few or no symptoms
showed that mice lacking the receptor CCR2, which • Controlled viral replication
Magnitude
mediates monocyte chemotaxis, had higher viral loads in
the lungs, increased lung viral dissemination and elevated
inflammatory cytokine responses173. This indicates that Virus replication
monocytes could be protective early and pathological Type I/III IFN response
Disease
later during infection resolution in COVID-19, similarly Time
to neutrophils. These data are consistent with findings in
• Delayed or poor IFN
SARS-CoV-2-infected mice, which were protected from Severe COVID-19 response
death and cytokine shock after TNF and IFNγ had been • Increased viral replication
• Potentially fatal disease
neutralized174. This study also found that the combination
Magnitude
• Auto-IFN antibodies
of these two cytokines induced inflammatory cell death • Mutations in IFN or TLR
in immune cells, known as PANoptosis. signalling genes
• Poor plasmacytoid
Overall, it seems that type I and type III interferons DC responses
protect against severe coronavirus-induced pneumonia • Inflammatory monocytes
when their expression or administration is timed cor- Time and neurophils
• Immunothrombosis
rectly (Fig. 3). Given that SARS-CoV-2 effectively inhibits
early type I and type III interferon responses, inflam- Fig. 3 | Delayed or poor type I and type III interferon
matory responses induced in certain cell types could responses increase COVID-19 severity. A rapid interferon
underlie severe disease. Cross-regulation between type I (IFN) response is associated with controlled viral replication
or type III interferon and IL-1β signalling systems could and mild disease (top graph), whereas a poor or delayed
potentially further unleash inflammatory responses in interferon response is associated with increased viral
the absence of appropriate interferon responses175. IL-1β replication and severe disease (bottom graph). DC, dendritic
cell; TLR, Toll-like receptor.
secretion is triggered by inflammasome activation in
myeloid cells, and inflammasomes may be triggered
by SARS-CoV-2. dsRNA can activate NLRP1 (ref.127), ventilation. Clinical management of COVID-19, how-
whereas several viral proteins, complement activation, ever, has improved during the pandemic. In the first
reactive oxygen species and cell debris containing double- wave in Germany, ~30% of hospitalized patients required
stranded DNA can activate NLRP3 (ref.175). IL-1β is a intensive care, whereas this dropped to ~14% in the
pleiotropic pro-inflammatory cytokine stimulating second wave42,43. This drop was associated with several
inflammatory responses. In support of this, IL-6 and changes in the management of patients with COVID-19,
TNF secretion is completely abolished in vitro in including fine-tuning of ventilation procedures, measures
SARS- CoV-2-infected primary monocytes treated with to prevent thromboembolisms43,176 and administration of
exogenous IL-1 receptor antagonist (IL-1RA)125. Thus, the corticosteroid dexamethasone177,178. Corticosteroids
simultaneous inhibition of type I or type III interferon are frequently used general inhibitors of inflammation.
signalling and inflammasome activation could trig- Administration of dexamethasone was shown to reduce
ger hyperinflammation, resulting in lung damage and mortality associated with patients with severe COVID-19
reduced lung regeneration143. by 50%177,178. Additionally, the inhaled corticosteroid
budesonide reduced the likelihood of needing urgent
Conclusions and perspectives medical care179. A neutralizing monoclonal antibody to
Most people infected with SARS-CoV-2 do not develop IL-6 (tocilizumab) and a JAK1/2 inhibitor (baricitinib)
severe disease, and the infection is likely limited to were also shown to increase survival in hospitalized
ciliated and sustentacular cells in the upper conduct- patients110,180. Tocilizumab treatment restored decreased
ing airways. However, in some people, infection with HLA-DR expression on monocytes in vitro134, indicating
the virus leads to a severe pneumonia dominated by that the downregulation of HLA-DR on monocytes may
immunopathology likely set off by infection of the lower be driven by IL-6.
respiratory tract. Individuals with severe COVID-19 Direct antiviral strategies are therefore expected to
often have predispositions that lead to poor or mistimed be effective only when they are administered very early.
immune responses, in particular type I or type III inter- Indeed, the antiviral ribonucleoside analogue molnu
feron responses. Alveolar damage may be a direct effect piravir was shown be effective against hospitalization
of the infection of AT2 cells or an indirect effect caused by and death in outpatients181 but ineffective in patients
local inflammatory responses. A ‘leaky state’ of both the hospitalized with COVID-19 (ref. 182) . Similarly, an
epithelium and the endothelium is induced, promoting interim analysis of a clinical trial testing a combina-
inflammation and coagulation, with key roles for mono- tion of the viral protease inhibitors PF-07321332 and
cytes or macrophages and neutrophils, which further ritonavir suggests that this therapy is effective when
amplify pro-inflammatory and/or profibrotic responses. administered early in non-hospitalized adults with
Thromboembolism Uncontrolled inflammation ultimately leads to severe COVID-19 (ref.183). The use of the broadly acting nucle-
Obstruction of a blood immunopathology characteristic of COVID-19 (Fig. 4). oside analogue remdesivir showed no clinical benefit in
vessel by a blood clot that
has become dislodged from
The initial treatment strategy for patients with severe patients with severe COVID-19 (ref.184). An inhibitor
another location in the COVID-19 was oxygen therapy using a high-flow oxygen of virus entry through the endosomal route, hydroxy-
circulation. nasal cannula or orotracheal intubation and mechanical chloroquine, was also not effective185, perhaps partially
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because SARS-CoV-2 does not use this entry route in as the virus has already disseminated deep into the lungs
physiologically relevant cells14,15 (Box 3). Another way and triggered immunopathology.
to directly block virus replication by using monoclonal Intervention strategies to effectively treat coronavirus-
antibodies or convalescent plasma did not increase sur- associated ARDS are needed. Clinical observations
vival in patients hospitalized with COVID-19 (refs186–188) confirm that the critical stage of severe COVID-19 is
but did reduce the chance of COVID-19-related hospi- dominated by immunopathology, with virus replica-
talization and death in outpatients189. These studies con- tion playing a secondary role. The beneficial effects
firm that direct antiviral approaches are unlikely to have of corticosteroids and tocilizumab in patients with
large effects on mortality when patients are hospitalized, severe COVID-19 suggests that better, and perhaps
Healthy alveolus COVID-19-associated ARDS
Deciliation
Endothelial
Macrophage
activation
hyperinflammation,
pyroptosis and
stimulation of Fibrin deposition
profibrotic responses
Thrombus formation
Surfactant IL-1β, IL-8, TNF,

production TGFβ, CCL2/3/7/8
AT2 cell death
NETosis
Replication
AT2 cell
O O → DATP
O O Fluid
Type I/III CD16+ cytotoxic T cell
IFN, IL-6,
PAI1
Fibrosis
Infiltration
O C O O C O
Chemoattractant production
Neutrophilia
Fig. 4 | A model for COVID-19-associated acute respiratory distress phenotypes and can further promote inflammation and coagulation.
syndrome development. Severe acute respiratory syndrome coronavirus 2 Immature neutrophil populations are increased in severe COVID-19.
(SARS-CoV-2) infection starts with the infection of ciliated cells in the Neutrophils, activated by platelets, release neutrophil extracellular traps
upper conducting airways, from where the virus can spread down the bron- (NETs) containing tissue factor, promoting the formation of microthrombi.
chiotracheal tree to the alveoli, likely as a result of poor or mistimed immune The upregulation of plasminogen activator inhibitor 1 (PAI1) may further
responses, in particular type I and type III interferon (IFN) responses. promote microthrombus formation by inhibiting fibrinolysis. Eventually,
Alveolar damage may be a direct effect of the infection of alveolar type 2 platelets may be used up, leading to thrombocytopenia. Macrophages in
(AT2) cells or an indirect effect caused by local inflammatory responses, the alveoli may adopt a pro-inflammatory profibrotic phenotype and when
which can result in endothelial activation. AT2 cells adopt a infected may go into pyroptosis, while hyperinflammation may promote
damage-associated transient progenitor (DATP) phenotype, an AT2 cell PANoptosis of T cells. CD16+ T cells are induced by complement activation
state associated with lung injury and that is characterized by failure to fully and promote microvascular endothelial cell injury and the release of
differentiate into AT2 cells. The disrupted epithelium and endothelium chemokines. ‘Armed’ natural killer cells expressing high levels of cytotoxic
allow fluid to leak into the alveoli. The exposed subendothelial extracellular proteins are also associated with severe disease. The end result is a focal
matrix attracts and activates platelets and initiates the coagulation cas- pattern of highly inflamed and flooded lung tissue, impairing oxygen
cade, leading to fibrin deposition. At the same time, immune cells, such as exchange and leading to hypoxaemia. ARDS, acute respiratory distress
monocytes and neutrophils, are attracted, and these have dysfunctional syndrome.
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more specific, immunomodulatory agents may further susceptibility or disease severity may be preactivation
improve clinical outcomes. Recent studies suggest that of the innate immune system to a state reminiscent of the
reducing inflammation by counteracting immune cell airways of children191, a concept referred to as ‘trained
infiltration (for example, by blocking chemokine recep- immunity’192.
tor CCR1, CCR2 or CCR5 (ref.128)), inflammasome Tragically, the planet’s current changes in climate,
activation, NETosis or complement activation may be wildlife trade, ecosystem health, land use, urbaniza-
a worthwhile strategy. Ideally these interventions are tion and global connectivity guarantee that humans
combined with effective antivirals that are adminis- will face new zoonotic coronaviruses, or other zoonotic
tered early to non-hospitalized patients at risk of severe viruses capable of causing severe pneumonia, in the
disease. next few decades. An enormous amount of work has
The roll-out of highly efficacious vaccines has tre- been done to try to understand how SARS-C oV-2
mendously decreased the incidence of COVID-19 in causes COVID-19, but the lack of an effective treatment
developed countries, and a global effort to distribute for COVID-19-associated ARDS shows that there
these vaccines equally is the only way out of this pan- is still a lot to be learned before we are prepared for
demic at the moment 190. Although vaccination has future zoonotic coronavirus pandemics.
been shown to be the best way to prevent infection and
severe disease, another interesting way of decreasing Published online 30 March 2022
1. Drosten, C. et al. Identification of a novel coronavirus 20. Hoffmann, M. et al. Camostat mesylate inhibits 39. Mahajan, S. et al. SARS-CoV-2 infection
in patients with severe acute respiratory syndrome. SARS-CoV-2 activation by TMPRSS2-related proteases hospitalization rate and infection fatality rate
N. Engl. J. Med. 348, 1967–1976 (2003). and its metabolite GBPA exerts antiviral activity. among the non-congregate population in Connecticut.
2. Peiris, J. S. et al. Coronavirus as a possible cause EBioMedicine 65, 103255 (2021). Am. J. Med. 134, 812–816 e812 (2021).
of severe acute respiratory syndrome. Lancet 361, 21. Wei, J. et al. Genome-wide CRISPR screens reveal 40. Petersen, E. et al. Comparing SARS-CoV-2 with
1319–1325 (2003). host factors critical for SARS-CoV-2 infection. Cell SARS-CoV and influenza pandemics. Lancet Infect. Dis.
3. Kuiken, T. et al. Newly discovered coronavirus as the 184, 76–91 e13 (2021). 20, e238–e244 (2020).
primary cause of severe acute respiratory syndrome. 22. Ahn, J. H. et al. Nasal ciliated cells are primary 41. Wiersinga, W. J., Rhodes, A., Cheng, A. C.,
Lancet 362, 263–270 (2003). targets for SARS-CoV-2 replication in the early stage Peacock, S. J. & Prescott, H. C. Pathophysiology,
4. Zaki, A. M., van Boheemen, S., Bestebroer, T. M., of COVID-19. J. Clin. Invest. 131, e148517 (2021). transmission, diagnosis, and treatment of coronavirus
Osterhaus, A. D. & Fouchier, R. A. Isolation of a novel 23. Hou, Y. J. et al. SARS-CoV-2 reverse genetics reveals disease 2019 (COVID-19): a review. JAMA 324,
coronavirus from a man with pneumonia in Saudi a variable infection gradient in the respiratory tract. 782–793 (2020).
Arabia. N. Engl. J. Med. 367, 1814–1820 (2012). Cell 182, 429–446.e414 (2020). 42. Karagiannidis, C. et al. Case characteristics, resource
5. Zhu, N. et al. A novel coronavirus from patients with 24. Khan, M. et al. Visualizing in deceased COVID-19 use, and outcomes of 10 021 patients with COVID-19
pneumonia in China, 2019. N. Engl. J. Med. 382, patients how SARS-CoV-2 attacks the respiratory admitted to 920 German hospitals: an observational
727–733 (2020). and olfactory mucosae but spares the olfactory bulb. study. Lancet Resp. Med. 8, 853–862 (2020).
6. Coronaviridae Study Group of the International Cell 184, 5932–5949.e15 (2021). 43. Karagiannidis, C., Windisch, W., McAuley, D. F.,
Committee on Taxonomy of Viruses. The species 25. Knoops, K. et al. SARS-coronavirus replication is Welte, T. & Busse, R. Major differences in ICU
Severe acute respiratory syndrome-related supported by a reticulovesicular network of modified admissions during the first and second COVID-19
coronavirus: classifying 2019-nCoV and naming it endoplasmic reticulum. PLoS Biol. 6, e226 (2008). wave in Germany. Lancet Respir. Med. 9, e47–e48
SARS-CoV-2. Nat. Microbiol. 5, 536–544 (2020). 26. Ogando, N. S. et al. SARS-coronavirus-2 replication (2021).
7. V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. in Vero E6 cells: replication kinetics, rapid adaptation 44. Lauer, S. A. et al. The incubation period of coronavirus
& Thiel, V. Coronavirus biology and replication: and cytopathology. J. Gen. Virol. 101, 925–940 disease 2019 (COVID-19) from publicly reported
implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, (2020). confirmed cases: estimation and application.
155–170 (2021). 27. Yin, X. et al. MDA5 governs the innate immune Ann. Intern. Med. 172, 577–582 (2020).
8. Wong, L. R. & Perlman, S. Immune dysregulation response to SARS-CoV-2 in lung epithelial cells. 45. Li, Q. et al. Early transmission dynamics in Wuhan,
and immunopathology induced by SARS-CoV-2 and Cell Rep. 34, 108628 (2021). China, of novel coronavirus-infected pneumonia.
related coronaviruses - are we our own worst enemy? 28. Sampaio, N. G. et al. The RNA sensor MDA5 detects N. Engl. J. Med. 382, 1199–1207 (2020).
Nat. Rev. Immunol. 22, 47–56 (2022). SARS-CoV-2 infection. Sci. Rep. 11, 13638 (2021). 46. Guan, W. J. et al. Clinical characteristics of coronavirus
9. Redondo, N., Zaldivar-Lopez, S., Garrido, J. J. 29. Khanmohammadi, S. & Rezaei, N. Role of Toll-like disease 2019 in China. N. Engl. J. Med. 382,
& Montoya, M. SARS-CoV-2 accessory proteins receptors in the pathogenesis of COVID-19. J. Med. 1708–1720 (2020).
in viral pathogenesis: knowns and unknowns. Virol. 93, 2735–2739 (2021). 47. Huang, C. et al. Clinical features of patients infected
Front. Immunol. 12, 708264 (2021). 30. Sariol, A. & Perlman, S. SARS-CoV-2 takes its Toll. with 2019 novel coronavirus in Wuhan, China. Lancet
10. Hulswit, R. J., de Haan, C. A. & Bosch, B. J. Nat. Immunol. 22, 801–802 (2021). 395, 497–506 (2020).
Coronavirus spike protein and tropism changes. 31. Kayesh, M. E. H., Kohara, M. & Tsukiyama-Kohara, K. 48. Chandra, A., Chakraborty, U., Pal, J. & Karmakar, P.
Adv. Virus Res. 96, 29–57 (2016). An overview of recent insights into the response of Silent hypoxia: a frequently overlooked clinical
11. Zhou, P. et al. A pneumonia outbreak associated with TLR to SARS-CoV-2 infection and the potential of TLR entity in patients with COVID-19. BMJ Case Rep. 13,
a new coronavirus of probable bat origin. Nature 579, agonists as SARS-CoV-2 vaccine adjuvants. Viruses e237207 (2020).
270–273 (2020). 13, 2302 (2021). 49. Chen, N. et al. Epidemiological and clinical
12. Hoffmann, M. et al. SARS-CoV-2 cell entry depends 32. Katsura, H. et al. Human lung stem cell-based characteristics of 99 cases of 2019 novel coronavirus
on ACE2 and TMPRSS2 and is blocked by a clinically alveolospheres provide insights into SARS-CoV-2- pneumonia in Wuhan, China: a descriptive study.
proven protease inhibitor. Cell 181, 271–280 e278 mediated interferon responses and pneumocyte Lancet 395, 507–513 (2020).
(2020). dysfunction. Cell Stem Cell 27, 890–904.e8 50. Wang, D. et al. Clinical characteristics of 138
13. Li, W. et al. Angiotensin-converting enzyme 2 (2020). hospitalized patients with 2019 novel coronavirus-
is a functional receptor for the SARS coronavirus. 33. Youk, J. et al. Three-dimensional human alveolar infected pneumonia in Wuhan, China. JAMA 323,
Nature 426, 450–454 (2003). stem cell culture models reveal infection response to 1061–1069 (2020).
14. Beumer, J. et al. A CRISPR/Cas9 genetically SARS-CoV-2. Cell Stem Cell 27, 905–919.e10 (2020). 51. Zhou, F. et al. Clinical course and risk factors for
engineered organoid biobank reveals essential host 34. Salahudeen, A. A. et al. Progenitor identification and mortality of adult inpatients with COVID-19 in Wuhan,
factors for coronaviruses. Nat. Commun. 12, 5498 SARS-CoV-2 infection in human distal lung organoids. China: a retrospective cohort study. Lancet 395,
(2021). Nature 588, 670–675 (2020). 1054–1062 (2020).
15. Mykytyn, A. Z. et al. SARS-CoV-2 entry into human 35. Huang, J. et al. SARS-CoV-2 infection of pluripotent 52. Goh, K. J. et al. Rapid progression to acute respiratory
airway organoids is serine protease-mediated and stem cell-derived human lung alveolar type 2 cells distress syndrome: review of current understanding
facilitated by the multibasic cleavage site. eLife 10, elicits a rapid epithelial-intrinsic inflammatory of critical illness from coronavirus disease 2019
e64508 (2021). response. Cell Stem Cell 27, 962–973.e7 (2020). (COVID-19) Infection. Ann. Acad. Med. Singap. 49,
16. Lamers, M. M. et al. Human airway cells prevent 36. Lamers, M. M. et al. An organoid-derived 108–118 (2020).
SARS-CoV-2 multibasic cleavage site cell culture bronchioalveolar model for SARS-CoV-2 infection 53. Ranieri, V. M. et al. Acute respiratory distress
adaptation. eLife 10, e66815 (2021). of human alveolar type II-like cells. EMBO J. 40, syndrome the berlin definition. J. Am. Med. Assoc.
17. Hoffmann, M. et al. Chloroquine does not inhibit e105912 (2021). 307, 2526–2533 (2012).
infection of human lung cells with SARS-CoV-2. Nature 37. Lamers, M. M. et al. SARS-CoV-2 Omicron efficiently 54. Del Valle, D. M. et al. An inflammatory cytokine
585, 588–590 (2020). infects human airway, but not alveolar epithelium. signature predicts COVID-19 severity and survival.
18. Cantuti-Castelvetri, L. et al. Neuropilin-1 facilitates bioRxiv https://doi.org/10.1101/2022.01.19.476898 Nat. Med. 26, 1636–1643 (2020).
SARS-CoV-2 cell entry and infectivity. Science 370, (2022). 55. Berlin, D. A., Gulick, R. M. & Martinez, F. J. Severe
856–860 (2020). 38. Barkauskas, C. E. et al. Type 2 alveolar cells are stem Covid-19. N. Engl. J. Med. 383, 2451–2460 (2020).
19. Daly, J. L. et al. Neuropilin-1 is a host factor for cells in adult lung. J. Clin. Invest. 123, 3025–3036 56. Puelles, V. G. et al. Multiorgan and renal tropism of
SARS-CoV-2 infection. Science 370, 861–865 (2020). (2013). SARS-CoV-2. N. Engl. J. Med. 383, 590–592 (2020).
0123456789();:
Reviews
57. Bhatnagar, J. et al. Evidence of severe acute 84. Iba, T., Levy, J. H., Levi, M. & Thachil, J. Coagulopathy 108. Herold, T. et al. Elevated levels of IL-6 and CRP
respiratory syndrome coronavirus 2 replication in COVID-19. J. Thromb. Haemost. 18, 2103–2109 predict the need for mechanical ventilation in COVID-19.
and tropism in the lungs, airways, and vascular (2020). J. Allergy Clin. Immunol. 146, 128–136 e124 (2020).
endothelium of patients with fatal coronavirus disease 85. Klok, F. A. et al. Confirmation of the high cumulative 109. Galvan-Roman, J. M. et al. IL-6 serum levels predict
2019: an autopsy case series. J. Infect. Dis. 223, incidence of thrombotic complications in critically ill severity and response to tocilizumab in COVID-19:
752–764 (2021). ICU patients with COVID-19: an updated analysis. An observational study. J. Allergy Clin. Immunol. 147,
58. Bradley, B. T. et al. Histopathology and ultrastructural Thromb. Res. 191, 148–150 (2020). 72–80 e78 (2021).
findings of fatal COVID-19 infections in Washington 86. Klok, F. A. et al. Incidence of thrombotic complications 110. Group, R. C. Tocilizumab in patients admitted to
State: a case series. Lancet 396, 320–332 (2020). in critically ill ICU patients with COVID-19. Thromb. hospital with COVID-19 (RECOVERY): a randomised,
59. Lindner, D. et al. Association of cardiac infection with Res. 191, 145–147 (2020). controlled, open-label, platform trial. Lancet 397,
SARS-CoV-2 in confirmed COVID-19 autopsy cases. 87. Camprubi-Rimblas, M., Tantinya, N., Bringue, J., 1637–1645 (2021).
JAMA Cardiol. 5, 1281–1285 (2020). Guillamat-Prats, R. & Artigas, A. Anticoagulant 111. Zuo, Y. et al. Plasma tissue plasminogen activator
60. Chen, Y. et al. The presence of SARS-CoV-2 RNA therapy in acute respiratory distress syndrome. and plasminogen activator inhibitor-1 in hospitalized
in the feces of COVID-19 patients. J. Med. Virol. 92, Ann. Transl. Med. 6, 36 (2018). COVID-19 patients. Sci. Rep. 11, 1580 (2021).
833–840 (2020). 88. Tang, N., Li, D., Wang, X. & Sun, Z. Abnormal 112. Mackman, N., Antoniak, S., Wolberg, A. S., Kasthuri, R.
61. Wang, W. et al. Detection of SARS-CoV-2 in different coagulation parameters are associated with & Key, N. S. Coagulation abnormalities and
types of clinical specimens. JAMA 323, 1843–1844 poor prognosis in patients with novel coronavirus thrombosis in patients infected with SARS-CoV-2
(2020). pneumonia. J. Thromb. Haemost. 18, 844–847 and other pandemic viruses. Arterioscler. Thromb.
62. Lamers, M. M. et al. SARS-CoV-2 productively infects (2020). Vasc. Biol. 40, 2033–2044 (2020).
human gut enterocytes. Science 369, 50–54 (2020). 89. Grasselli, G. et al. Pathophysiology of COVID-19- 113. Gralinski, L. E. et al. Mechanisms of severe
63. Meinhardt, J. et al. Olfactory transmucosal associated acute respiratory distress syndrome: acute respiratory syndrome coronavirus-induced
SARS-CoV-2 invasion as a port of central nervous a multicentre prospective observational study. acute lung injury. mBio 4, e00271-13 (2013).
system entry in individuals with COVID-19. Lancet Respir. Med. 8, 1201–1208 (2020). 114. Dittmann, M. et al. A serpin shapes the extracellular
Nat. Neurosci. 24, 168–175 (2021). 90. Al-Samkari, H. et al. COVID-19 and coagulation: environment to prevent influenza A virus maturation.
64. Williamson, E. J. et al. Factors associated with bleeding and thrombotic manifestations of SARS-CoV-2 Cell 160, 631–643 (2015).
COVID-19-related death using OpenSAFELY. infection. Blood 136, 489–500 (2020). 115. Schulte-Schrepping, J. et al. Severe COVID-19 is
Nature 584, 430–436 (2020). 91. Lippi, G., Plebani, M. & Henry, B. M. Thrombocytopenia marked by a dysregulated myeloid cell compartment.
65. Grasselli, G. et al. Baseline characteristics and is associated with severe coronavirus disease 2019 Cell 182, 1419–1440 e1423 (2020).
outcomes of 1591 patients infected with SARS-CoV-2 (COVID-19) infections: a meta-analysis. Clin. Chim. Acta 116. Venet, F., Demaret, J., Gossez, M. & Monneret, G.
admitted to ICUs of the Lombardy region, Italy. JAMA 506, 145–148 (2020). Myeloid cells in sepsis-acquired immunodeficiency.
323, 1574–1581 (2020). 92. Rentsch, C. T. et al. Early initiation of prophylactic Ann. N. Y. Acad. Sci. 1499, 3–17 (2021).
66. O’Driscoll, M. et al. Age-specific mortality and immunity anticoagulation for prevention of coronavirus disease 117. Hewitson, J. P. et al. Malat1 suppresses immunity to
patterns of SARS-CoV-2. Nature 590, 140–145 (2021). 2019 mortality in patients admitted to hospital in infection through promoting expression of Maf and
67. Initiative, C.-H. G. Mapping the human genetic the United States: cohort study. BMJ 372, n311 IL-10 in Th cells. J. Immunol. 204, 2949–2960
architecture of COVID-19. Nature 600, 472–477 (2021). (2020).
(2021). 93. Bonaventura, A. et al. Endothelial dysfunction and 118. Doran, A. C., Yurdagul, A. & Tabas, I. Efferocytosis in
68. Pairo-Castineira, E. et al. Genetic mechanisms of critical immunothrombosis as key pathogenic mechanisms health and disease. Nat. Rev. Immunol. 20, 254–267
illness in COVID-19. Nature 591, 92–98 (2021). in COVID-19. Nat. Rev. Immunol. 21, 319–329 (2020).
69. Fingerlin, T. E. et al. Genome-wide association study (2021). 119. Maucourant, C. et al. Natural killer cell immunotypes
identifies multiple susceptibility loci for pulmonary 94. Engelmann, B. & Massberg, S. Thrombosis as an related to COVID-19 disease severity. Sci. Immunol. 5,
fibrosis. Nat. Genet. 45, 613–620 (2013). intravascular effector of innate immunity. Nat. Rev. eabd68732 (2020).
70. Severe Covid-19 GWAS Group. Genomewide Immunol. 13, 34–45 (2013). 120. Grant, R. A. et al. Circuits between infected
association study of severe Covid-19 with respiratory 95. Meyer, N. J., Gattinoni, L. & Calfee, C. S. Acute macrophages and T cells in SARS-CoV-2 pneumonia.
failure. N. Engl. J. Med. 383, 1522–1534 (2020). respiratory distress syndrome. Lancet 398, 622–637 Nature 590, 635–641 (2021).
71. Asano, T. et al. X-linked recessive TLR7 deficiency in (2021). 121. Liao, M. et al. Single-cell landscape of bronchoalveolar
~1% of men under 60 years old with life-threatening 96. Millar, F. R., Summers, C., Griffiths, M. J., immune cells in patients with COVID-19. Nat. Med.
COVID-19. Sci. Immunol. 6, eabl4348 (2021). Toshner, M. R. & Proudfoot, A. G. The pulmonary 26, 842–844 (2020).
72. Zhang, Q. et al. Inborn errors of type I IFN immunity in endothelium in acute respiratory distress syndrome: 122. Huang, A. et al. CD8 T cells compensate for impaired
patients with life-threatening COVID-19. Science 370, insights and therapeutic opportunities. Thorax 71, humoral immunity in COVID-19 patients with
eabd4570 (2020). 462–473 (2016). hematologic cancer. Res. Sq. https://doi.org/
73. Bastard, P. et al. Autoantibodies against type I IFNs in 97. Varga, Z. et al. Endothelial cell infection and 10.21203/rs.3.rs-162289/v1 (2021).
patients with life-threatening COVID-19. Science 370, endotheliitis in COVID-19. Lancet 395, 1417–1418 123. Zheng, J. et al. Severe acute respiratory syndrome
eabd4585 (2020). (2020). coronavirus 2-induced immune activation and death
74. Koning, R. et al. Autoantibodies against type I 98. Owens, A. P. III & Mackman, N. Tissue factor and of monocyte-derived human macrophages and
interferons are associated with multi-organ failure in thrombosis: the clot starts here. Thromb. Haemost. dendritic cells. J. Infect. Dis. 223, 785–795 (2021).
COVID-19 patients. Intens. Care Med. 47, 704–706 104, 432–439 (2010). 124. Hui, K. P. Y. et al. Tropism, replication competence,
(2021). 99. Kenawy, H. I., Boral, I. & Bevington, A. Complement- and innate immune responses of the coronavirus
75. Bastard, P. et al. Autoantibodies neutralizing type I coagulation cross-talk: a potential mediator of the SARS-CoV-2 in human respiratory tract and
IFNs are present in ~4% of uninfected individuals physiological activation of complement by low pH. conjunctiva: an analysis in ex-vivo and in-vitro
over 70 years old and account for ~20% of COVID-19 Front. Immunol. 6, 215 (2015). cultures. Lancet Respir. Med. 8, 687–695 (2020).
deaths. Sci. Immunol. 6, eabl4340 (2021). 100. Swieringa, F., Spronk, H. M. H., Heemskerk, J. W. M. 125. Ferreira, A. C. et al. SARS-CoV-2 engages
76. Cardinal-Fernandez, P., Lorente, J. A., Ballen- & van der Meijden, P. E. J. Integrating platelet inflammasome and pyroptosis in human primary
Barragan, A. & Matute-Bello, G. Acute respiratory and coagulation activation in fibrin clot formation. monocytes. Cell Death Discov. 7, 43 (2021).
distress syndrome and diffuse alveolar damage. new Res. Pract. Thromb. Haemost. 2, 450–460 (2018). 126. Zhang, J. et al. Pyroptotic macrophages stimulate
insights on a complex relationship. Ann. Am. Thorac. 101. Del Conde, I., Shrimpton, C. N., Thiagarajan, P. the SARS-CoV-2-associated cytokine storm. Cell Mol.
Soc. 14, 844–850 (2017). & Lopez, J. A. Tissue-factor-bearing microvesicles Immunol. 18, 1305–1307 (2021).
77. Katzenstein, A. L., Bloor, C. M. & Leibow, A. A. arise from lipid rafts and fuse with activated platelets 127. Bauernfried, S., Scherr, M. J., Pichlmair, A.,
Diffuse alveolar damage–the role of oxygen, shock, to initiate coagulation. Blood 106, 1604–1611 Duderstadt, K. E. & Hornung, V. Human NLRP1 is a
and related factors. A review. Am. J. Pathol. 85, (2005). sensor for double-stranded RNA. Science 371, 482
209–228 (1976). 102. Ouwendijk, W. J. D. et al. High levels of neutrophil (2021).
78. Carsana, L. et al. Pulmonary post-mortem findings extracellular traps persist in the lower respiratory 128. Chua, R. L. et al. COVID-19 severity correlates with
in a series of COVID-19 cases from northern Italy: tract of critically ill patients with coronavirus disease airway epithelium-immune cell interactions identified
a two-centre descriptive study. Lancet Infect. Dis. 20, 2019. J. Infect. Dis. 223, 1512–1521 (2021). by single-cell analysis. Nat. Biotechnol. 38, 970–979
1135–1140 (2020). 103. Skendros, P. et al. Complement and tissue factor- (2020).
79. Menter, T. et al. Postmortem examination of enriched neutrophil extracellular traps are key drivers 129. Galani, I. E. & Andreakos, E. Neutrophils in viral
COVID-19 patients reveals diffuse alveolar damage in COVID-19 immunothrombosis. J. Clin. Invest. 130, infections: current concepts and caveats. J. Leukoc.
with severe capillary congestion and variegated 6151–6157 (2020). Biol. 98, 557–564 (2015).
findings in lungs and other organs suggesting vascular 104. Sang, Y., Roest, M., de Laat, B., de Groot, P. G. 130. Rendeiro, A. F. et al. The spatial landscape of lung
dysfunction. Histopathology 77, 198–209 (2020). & Huskens, D. Interplay between platelets and pathology during COVID-19 progression. Nature 593,
80. Melms, J. C. et al. A molecular single-cell lung atlas coagulation. Blood Rev. 46, 100733 (2021). 564–569 (2021).
of lethal COVID-19. Nature 595, 114–119 (2021). 105. Page, C. & Pitchford, S. Neutrophil and platelet 131. Menter, T. et al. Post-mortem examination of
81. Delorey, T. M. et al. COVID-19 tissue atlases reveal complexes and their relevance to neutrophil COVID19 patients reveals diffuse alveolar damage
SARS-CoV-2 pathology and cellular targets. Nature recruitment and activation. Int. Immunopharmacol. with severe capillary congestion and variegated
595, 107–113 (2021). 17, 1176–1184 (2013). findings of lungs and other organs suggesting
82. Chen, J., Wu, H., Yu, Y. & Tang, N. Pulmonary alveolar 106. Kambas, K. et al. C5a and TNF-alpha up-regulate vascular dysfunction. Histopathology 77, 198–209
regeneration in adult COVID-19 patients. Cell Res. 30, the expression of tissue factor in intra-alveolar (2020).
708–710 (2020). neutrophils of patients with the acute respiratory 132. De Michele, S. et al. Forty postmortem examinations
83. Sebag, S. C., Bastarache, J. A. & Ware, L. B. distress syndrome. J. Immunol. 180, 7368–7375 in COVID-19 Patients. Am. J. Clin. Pathol. 154,
Therapeutic modulation of coagulation and fibrinolysis (2008). 748–760 (2020).
in acute lung injury and the acute respiratory distress 107. Georg, P. et al. Complement activation induces 133. Lucas, C. et al. Longitudinal analyses reveal
syndrome. Curr. Pharm. Biotechno 12, 1481–1496 excessive T cell cytotoxicity in severe COVID-19. immunological misfiring in severe COVID-19.
(2011). Cell 185, 493–512.e25 (2022). Nature 584, 463–469 (2020).
0123456789();:
Reviews
134. Giamarellos-Bourboulis, E. J. et al. Complex 161. Cao, W. et al. Toll-like receptor-mediated induction admitted to hospital with COVID-19 (DisCoVeRy):
immune dysregulation in COVID-19 patients with of type I interferon in plasmacytoid dendritic cells a phase 3, randomised, controlled, open-label trial.
severe respiratory failure. Cell Host Microbe 27, requires the rapamycin-sensitive PI(3)K-mTOR- Lancet Infect. Dis. 22, 209–221 (2022).
992–1000 e1003 (2020). p70S6K pathway. Nat. Immunol. 9, 1157–1164 185. Group, R. C. et al. Effect of hydroxychloroquine in
135. Qin, C. et al. Dysregulation of immune response in (2008). hospitalized patients with Covid-19. N. Engl. J. Med.
patients with coronavirus 2019 (COVID-19) in Wuhan, 162. Jones, T. C. et al. Estimating infectiousness throughout 383, 2030–2040 (2020).
China. Clin. Infect. Dis. 71, 762–768 (2020). SARS-CoV-2 infection course. Science 373, eabi5273 186. Group, R. C. Convalescent plasma in patients admitted
136. Wu, P. et al. The trans-omics landscape of COVID-19. (2021). to hospital with COVID-19 (RECOVERY): a randomised
Nat. Commun. 12, 4543 (2021). 163. Han, L. et al. SARS-CoV-2 ORF9b antagonizes type I controlled, open-label, platform trial. Lancet 397,
137. Wilk, A. J. et al. A single-cell atlas of the peripheral and III interferons by targeting multiple components of 2049–2059 (2021).
immune response in patients with severe COVID-19. the RIG-I/MDA-5-MAVS, TLR3-TRIF, and cGAS-STING 187. National Institutes of Allergy and Infectious Diseases
Nat. Med. 26, 1070–1076 (2020). signaling pathways. J. Med. Virol. 93, 5376–5389 Statement — NIH-sponsored ACTIV-3 trial closes
138. Zhang, Z. et al. Transcription factor Etv5 is essential (2021). LY-CoV555 sub-study. https://www.niaid.nih.gov/
for the maintenance of alveolar type II cells. Proc. Natl 164. Li, J. Y. et al. The ORF6, ORF8 and nucleocapsid news-events/statement-nih-sponsored-activ-3-trial-
Acad. Sci. USA 114, 3903–3908 (2017). proteins of SARS-CoV-2 inhibit type I interferon closes-ly-cov555-sub-study (2020).
139. Little, D. R. et al. Transcriptional control of lung signaling pathway. Virus Res. 286, 198074 (2020). 188. ACTIV-3/TICO LY-CoV555 Study Group. A neutralizing
alveolar type 1 cell development and maintenance 165. Wu, J. et al. SARS-CoV-2 ORF9b inhibits RIG-I-MAVS monoclonal antibody for hospitalized patients with
by NK homeobox 2-1. Proc. Natl Acad. Sci. USA 116, antiviral signaling by interrupting K63-linked Covid-19. N. Engl. J. Med. 384, 905–914 (2021).
20545–20555 (2019). ubiquitination of NEMO. Cell Rep. 34, 108761 189. Weinreich, D. M. et al. REGN-COV2, a neutralizing
140. Choi, J. et al. Inflammatory signals induce AT2 (2021). antibody cocktail, in outpatients with Covid-19.
cell-derived damage-associated transient progenitors 166. Lokugamage, K. G. et al. Type I interferon N. Engl. J. Med. 384, 238–251 (2021).
that mediate alveolar regeneration. Cell Stem Cell 27, susceptibility distinguishes SARS-CoV-2 from 190. Creech, C. B., Walker, S. C. & Samuels, R. J.
366 (2020). SARS-CoV. J. Virol. 94, e01410 (2020). SARS-CoV-2 vaccines. JAMA 325, 1318–1320
141. Kobayashi, Y. et al. Persistence of a regeneration- 167. Channappanavar, R. et al. Dysregulated type I (2021).
associated, transitional alveolar epithelial cell state interferon and inflammatory monocyte-macrophage 191. Loske, J. et al. Pre-activated antiviral innate immunity
in pulmonary fibrosis. Nat. Cell Biol. 22, 934 (2020). responses cause lethal pneumonia in SARS-CoV- in the upper airways controls early SARS-CoV-2
142. Strunz, M. et al. Alveolar regeneration through a Krt8+ infected mice. Cell Host Microbe 19, 181–193 infection in children. Nat. Biotechnol. 40, 319–324
transitional stem cell state that persists in human lung (2016). (2022).
fibrosis. Nat. Commun. 11, 3559 (2020). 168. Cervantes-Barragan, L. et al. Control of coronavirus 192. Netea, M. G. et al. Trained immunity: a tool
143. Major, J. et al. Type I and III interferons disrupt lung infection through plasmacytoid dendritic-cell-derived for reducing susceptibility to and the severity of
epithelial repair during recovery from viral infection. type I interferon. Blood 109, 1131–1137 (2007). SARS-CoV-2 infection. Cell 181, 969–977 (2020).
Science 369, 712–717 (2020). 169. Swiecki, M. & Colonna, M. Unraveling the functions 193. Totura, A. L. & Baric, R. S. SARS coronavirus
144. Vaughan, A. E. et al. Lineage-negative progenitors of plasmacytoid dendritic cells during viral infections, pathogenesis: host innate immune responses and
mobilize to regenerate lung epithelium after major autoimmunity, and tolerance. Immunol. Rev. 234, viral antagonism of interferon. Curr. Opin. Virol. 2,
injury. Nature 517, 621–U211 (2015). 142–162 (2010). 264–275 (2012).
145. Costa, M. F. D., Weiner, A. I. & Vaughan, A. E. 170. Venet, M. et al. SARS-CoV-2 infected cells trigger an 194. Gu, J. & Korteweg, C. Pathology and pathogenesis
Basal-like progenitor cells: a review of dysplastic acute antiviral response mediated by plasmacytoid of severe acute respiratory syndrome. Am. J. Pathol.
alveolar regeneration and remodeling in lung repair. dendritic cells in mild but not severe COVID-19 170, 1136–1147 (2007).
Stem Cell Rep. 15, 1015–1025 (2020). patients. medRxiv https://doi.org/10.1101/ 195. Giannis, D., Ziogas, I. A. & Gianni, P. Coagulation
146. Kanegai, C. M. et al. Persistent pathology in influenza- 2021.09.01.21262969 (2021). disorders in coronavirus infected patients: COVID-19,
infected mouse lungs. Am. J. Respir. Cell Mol. Biol. 55, 171. Haagmans, B. L. et al. Pegylated interferon-alpha SARS-CoV-1, MERS-CoV and lessons from the past.
613–615 (2016). protects type 1 pneumocytes against SARS J. Clin. Virol. 127, 104362 (2020).
147. Rane, C. K. et al. Development of solitary coronavirus infection in macaques. Nat. Med. 10, 196. WHO. Consensus Document on the Epidemiology of
chemosensory cells in the distal lung after severe 290–293 (2004). Severe Acute Respiratory Syndrome (WHO, 2003).
influenza injury. Am. J. Physiol. Lung Cell Mol. Physiol. 172. Channappanavar, R. et al. IFN-I response timing 197. Parasa, S. et al. Prevalence of gastrointestinal
316, L1141–L1149 (2019). relative to virus replication determines MERS symptoms and fecal viral shedding in patients
148. Wendisch, D. et al. SARS-CoV-2 infection triggers coronavirus infection outcomes. J. Clin. Invest. 129, with coronavirus disease 2019: a systematic review
profibrotic macrophage responses and lung fibrosis. 3625–3639 (2019). and meta-analysis. JAMA Netw. Open 3, e2011335
Cell 184, 6243–6261 e6227 (2021). 173. Vanderheiden, A. et al. CCR2 signaling restricts (2020).
149. Tsukui, T. et al. Collagen-producing lung cell atlas SARS-CoV-2 infection. mBio 12, e0274921 (2021). 198. van den Brand, J. M., Smits, S. L. & Haagmans, B. L.
identifies multiple subsets with distinct localization 174. Karki, R. et al. Synergism of TNF-alpha and IFN- Pathogenesis of Middle East respiratory syndrome
and relevance to fibrosis. Nat. Commun. 11, 1920 gamma triggers inflammatory cell death, tissue coronavirus. J. Pathol. 235, 175–184 (2015).
(2020). damage, and mortality in SARS-CoV-2 infection and 199. Raj, V. S. et al. Dipeptidyl peptidase 4 is a functional
150. Muus, C. et al. Single-cell meta-analysis of SARS-CoV-2 cytokine shock syndromes. Cell 184, 149–168 e117 receptor for the emerging human coronavirus-EMC.
entry genes across tissues and demographics. (2021). Nature 495, 251–254 (2013).
Nat. Med. 27, 546–559 (2021). 175. Vora, S. M., Lieberman, J. & Wu, H. Inflammasome 200. Meyerholz, D. K., Lambertz, A. M. & McCray, P. B. Jr.
151. Sims, A. C. et al. Severe acute respiratory syndrome activation at the crux of severe COVID-19. Nat. Rev. Dipeptidyl peptidase 4 distribution in the human
coronavirus infection of human ciliated airway Immunol. 21, 694–703 (2021). respiratory tract: implications for the Middle East
epithelia: role of ciliated cells in viral spread in 176. Kluge, S. et al. Recommendations on inpatient respiratory syndrome. Am. J. Pathol. 186, 78–86
the conducting airways of the lungs. J. Virol. 79, treatment of patients with COVID-19. Dtsch. Arztebl. (2016).
15511–15524 (2005). Int. 118, 1 (2021). 201. Tsang, T. K., Wang, C., Yang, B. Y., Cauchemez, S. &
152. Jia, H. P. et al. ACE2 receptor expression and severe 177. Group, R. C. et al. Dexamethasone in hospitalized Cowling, B. J. Using secondary cases to characterize
acute respiratory syndrome coronavirus infection patients with Covid-19. N. Engl. J. Med. 384, the severity of an emerging or re-emerging infection.
depend on differentiation of human airway epithelia. 693–704 (2021). Nat. Commun. 12, 6372 (2021).
J. Virol. 79, 14614–14621 (2005). 178. Sterne, J. A. C. et al. Association between 202. Fielding, B. C. Human coronavirus NL63: a clinically
153. Blanco-Melo, D. et al. Imbalanced host response administration of systemic corticosteroids and important virus? Future Microbiol. 6, 153–159 (2011).
to SARS-CoV-2 drives development of COVID-19. mortality among critically ill patients with COVID-19. 203. Donaldson, E. F. et al. Metagenomic analysis of the
Cell 181, 1036–1045 (2020). A meta-analysis. JAMA 324, 1330–1341 (2020). viromes of three North American bat species: viral
154. Robinot, R. et al. SARS-CoV-2 infection induces the 179. Ramakrishnan, S. et al. Inhaled budesonide in the diversity among different bat species that share a
dedifferentiation of multiciliated cells and impairs treatment of early COVID-19 (STOIC): a phase 2, common habitat. J. Virol. 84, 13004–13018 (2010).
mucociliary clearance. Nat. Commun. 12, 4354 (2021). open-label, randomised controlled trial. Lancet Respir. 204. Huynh, J. et al. Evidence supporting a zoonotic origin
155. Mulay, A. et al. SARS-CoV-2 infection of primary Med. 9, 763–772 (2021). of human coronavirus strain NL63. J. Virol. 86,
human lung epithelium for COVID-19 modeling 180. Marconi, V. C. et al. Efficacy and safety of baricitinib 12816–12825 (2012).
and drug discovery. Cell Rep. 35, 109055 (2021). for the treatment of hospitalised adults with COVID-19 205. Rebendenne, A. et al. Bidirectional genome-wide
156. Ziegler, C. G. K. et al. Impaired local intrinsic immunity (COV-BARRIER): a randomised, double-blind, parallel- CRISPR screens reveal host factors regulating
to SARS-CoV-2 infection in severe COVID-19. Cell 184, group, placebo-controlled phase 3 trial. Lancet Respir. SARS-CoV-2, MERS-CoV and seasonal coronaviruses.
4713–4733 e4722 (2021). Med. 9, 1407–1418 (2021). bioRxiv https://doi.org/10.1101/2021.05.19.444823
157. Hadjadj, J. et al. Impaired type I interferon activity 181. Jayk Bernal, A. et al. Molnupiravir for oral treatment (2021).
and inflammatory responses in severe COVID-19 of Covid-19 in nonhospitalized patients. N. Engl. J. 206. Kawase, M., Shirato, K., van der Hoek, L., Taguchi, F.
patients. Science 369, 718–724 (2020). Med. 386, 509–520 (2022). & Matsuyama, S. Simultaneous treatment of human
158. Feng, E., Balint, E., Poznanski, S. M., Ashkar, A. A. 182. Arribas, J. R. et al. Randomized trial of molnupiravir bronchial epithelial cells with serine and cysteine
& Loeb, M. Aging and interferons: impacts on or placebo in patients hospitalized with Covid-19. protease inhibitors prevents severe acute respiratory
inflammation and viral disease outcomes. Cells 10, NEJM Evid. https://doi.org/10.1056/EVIDoa2100044 syndrome coronavirus entry. J. Virol. 86, 6537–6545
708 (2021). (2021). (2012).
159. Agrawal, A. Mechanisms and implications of 183. Pfizer. Pfizer’s novel COVID-19 oral antiviral treatment 207. Munoz-Fontela, C. et al. Animal models for COVID-19.
age-associated impaired innate interferon secretion candidate reduced risk of hospitalization or death by Nature 586, 509–515 (2020).
by dendritic cells: a mini-review. Gerontology 59, 89% in interim analysis of phase 2/3 EPIC-HR study. 208. Kim, Y. I. et al. Infection and rapid transmission
421–426 (2013). https://www.pfizer.com/news/press-release/press- of SARS-CoV-2 in ferrets. Cell Host Microbe 27,
160. Arunachalam, P. S. et al. Systems biological release-detail/pfizers-novel-covid-19-oral-antiviral- 704–709 e702 (2020).
assessment of immunity to mild versus severe treatment-candidate (2021). 209. Richard, M. et al. SARS-CoV-2 is transmitted via
COVID-19 infection in humans. Science 369, 184. Ader, F. et al. Remdesivir plus standard of care versus contact and via the air between ferrets. Nat. Commun.
1210–1220 (2020). standard of care alone for the treatment of patients 11, 3496 (2020).
0123456789();:
Reviews
210. Rockx, B. et al. Comparative pathogenesis of COVID-19, 220. Leist, S. R. et al. A mouse-adapted SARS-CoV-2 231. Ettayebi, K. et al. Replication of human noroviruses
MERS, and SARS in a nonhuman primate model. induces acute lung injury and mortality in standard in stem cell-derived human enteroids. Science 353,
Science 368, 1012–1015 (2020). laboratory mice. Cell 183, 1070–1085.e1012 1387–1393 (2016).
211. Blair, R. V. et al. Acute respiratory distress in aged, (2020). 232. Qian, X., Nguyen, H. N., Jacob, F., Song, H.
SARS-CoV-2-infected African green monkeys but 221. Gu, H. et al. Adaptation of SARS-CoV-2 in BALB/c mice & Ming, G. L. Using brain organoids to understand
not rhesus macaques. Am. J. Pathol. 191, 274–282 for testing vaccine efficacy. Science 369, 1603–1607 Zika virus-induced microcephaly. Development 144,
(2021). (2020). 952–957 (2017).
212. Munster, V. J. et al. Respiratory disease in rhesus 222. Smits, S. L. et al. Exacerbated innate host response to 233. Zhou, J. et al. Infection of bat and human intestinal
macaques inoculated with SARS-CoV-2. Nature 585, SARS-CoV in aged non-human primates. PLoS Pathog. organoids by SARS-CoV-2. Nat. Med. 26, 1077–1083
268–272 (2020). 6, e1000756 (2010). (2020).
213. Woolsey, C. et al. Establishment of an African green 223. Carroll, T. et al. The B.1.427/1.429 (epsilon) 234. Sachs, N. et al. Long-term expanding human airway
monkey model for COVID-19 and protection against SARS-CoV-2 variants are more virulent than ancestral organoids for disease modeling. EMBO J. 38, e100300
re-infection. Nat. Immunol. 22, 86–98 (2021). B.1 (614G) in Syrian hamsters. PLoS Pathog. 18, (2019).
214. Chan, J. F. et al. Simulation of the clinical and e1009914 (2022). 235. Daniloski, Z. et al. Identification of required host
pathological manifestations of coronavirus disease 224. Halfmann, P. J. et al. SARS-CoV-2 Omicron virus factors for SARS-CoV-2 infection in human cells.
2019 (COVID-19) in a golden Syrian hamster causes attenuated disease in mice and hamsters. Cell 184, 92–105 e116 (2021).
model: implications for disease pathogenesis and Nature 603, 687–692 (2022). 236. Wang, R. et al. Genetic screens identify host factors
transmissibility. Clin. Infect. Dis. 71, 2428–2446 225. Liu, Y. et al. The N501Y spike substitution enhances for SARS-CoV-2 and common cold coronaviruses.
(2020). SARS-CoV-2 infection and transmission. Nature 602, Cell 184, 106–119 e114 (2021).
215. Osterrieder, N. et al. Age-dependent progression of 294–299 (2022). 237. Bailey, A. L. & Diamond, M. S. A Crisp(r) new perspective
SARS-CoV-2 infection in Syrian hamsters. Viruses 12, 226. Lau, S. Y. et al. Attenuated SARS-CoV-2 variants with on SARS-CoV-2 biology. Cell 184, 15–17 (2021).
779 (2020). deletions at the S1/S2 junction. Emerg. Microbes
216. Imai, M. et al. Syrian hamsters as a small animal Infect. 9, 837–842 (2020). Author contributions
model for SARS-CoV-2 infection and countermeasure 227. Klimstra, W. B. et al. SARS-CoV-2 growth, furin- The authors contributed equally to all aspects of the article.
development. Proc. Natl Acad. Sci. USA 117, cleavage-site adaptation and neutralization using
16587–16595 (2020). serum from acutely infected hospitalized COVID-19 Competing interests
217. Trimpert, J. et al. The Roborovski dwarf hamster is a patients. J. Gen. Virol. 101, 1156–1169 (2020). The authors declare no competing interests.
highly susceptible model for a rapid and fatal course 228. Bove, P. F. et al. Breaking the in vitro alveolar type II
of SARS-CoV-2 infection. Cell Rep. 33, 108488 cell proliferation barrier while retaining ion transport Peer review information
(2020). properties. Am. J. Respir. Cell Mol. Biol. 50, 767–776 Nature Reviews Microbiology thanks Lisa Gralinski, Malik
218. Wan, Y., Shang, J., Graham, R., Baric, R. S. & Li, F. (2014). Peiris and Stanley Perlman for their contribution to the peer
Receptor recognition by the novel coronavirus from 229. van der Vaart, J., Lamers, M. M., Haagmans, B. L. review of this work.
Wuhan: an analysis based on decade-long structural & Clevers, H. Advancing lung organoids for COVID-19
studies of SARS coronavirus. J. Virol. 94, e00127-20 research. Dis. Model. Mech. 14, dmm049060 (2021). Publisher’s note
(2020). 230. Zhou, J. et al. Differentiated human airway organoids Springer Nature remains neutral with regard to jurisdictional
219. Dinnon, K. H. 3rd et al. A mouse-adapted model to assess infectivity of emerging influenza virus. claims in published maps and institutional affiliations.
of SARS-CoV-2 to test COVID-19 countermeasures. Proc. Natl Acad. Sci. USA 115, 6822–6827
Nature 586, 560–566 (2020). (2018). © Springer Nature Limited 2022
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Abstract | The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-​CoV-2)

270 | May 2022 | volume 20 www.nature.com/nrmicro

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 271

Spike protein (S)

Nucleocapsid protein (N)

Membrane protein (M)

Target cell Protease

Type I/III IFN signal Type I IFN

272 | May 2022 | volume 20 www.nature.com/nrmicro

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 273

Platelets ↓ PAI1 ↑ Fibrinolysis ↓ Fibrin

Replication Cell death

274 | May 2022 | volume 20 www.nature.com/nrmicro

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 275

276 | May 2022 | volume 20 www.nature.com/nrmicro

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major role in coronavirus-​induced pathogenesis. In con- Mild or symptomatic case

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 279

Healthy alveolus COVID-19-associated ARDS

Surfactant IL-1β, IL-8, TNF,

280 | May 2022 | volume 20 www.nature.com/nrmicro

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 281

282 | May 2022 | volume 20 www.nature.com/nrmicro

NaTuRe RevIeWS | MICRObIOlOgy volume 20 | May 2022 | 283

284 | May 2022 | volume 20 www.nature.com/nrmicro

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Abstract | The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

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