Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement and Specimens
2.2. Sputum Pre-Treatment
2.3. Extraction
2.4. In Vitro Transcription
2.5. PBV RT-qPCR Assay
2.6. mNGS Library Prep and Sequencing
2.7. mNGS Analysis
2.8. Pairwise Amino Acid Identity
2.9. Phylogenetics
2.10. Phylogeny-Trait Association Analysis
2.11. Statistics
2.12. NCBI Accessions
3. Results
3.1. Discovery of a Novel Picobirnavirus
3.2. ABT3406 RdRp Branches with Respiratory PBV Strains
3.3. Quantitative PCR Screen Reveals High Prevalence of PBV among Hospitalized
3.4. Emergence of a Distinct PBV Genotype
3.5. RdRp and Capsid Are Both Associated with Respiratory Disease
3.6. PBV Is Typically Present as a Co-Infection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Capsid-FAM | RdRp-FAM | RdRp-CY3 | RdRp-CY5 | PBV Segment 1 | PBV Capsid Only | PBV Segment 2-RdRp | NGS Reads | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample ID | Country | Year | Ct | Ct | Ct | Ct | NGS Reads | % Coverage | Closest Reference | NGS Reads | % Coverage | NGS Reads | % Coverage | Closest Reference | Total |
NYB4466 | USA-NY | 2018 | −1 | 29.41 | −1 | −1 | 3394 | 99% | ABT3406 | 2539 | 100% | 2616 | 97% | ABT3406 | 8,048,648 |
NYB4468 | USA-NY | 2018 | −1 | 33.36 | −1 | 30.34 | 35 | 62% | ABT3406 | 28 | 70% | 35 | 67% | ABT3406 | 14,782,666 |
NYB4138 | USA-NY | 2018 | −1 | 26.4 | −1 | 23.87 | 201 | 96% | ABT3406 | 143 | 97% | 266 | 94% | ABT3406 | 7,321,340 |
MRN001 | COL | 2019 | 26.53 | 30.78 | −1 | 24.06 | 178 | 100% | ABT3406 | 139 | 100% | 288 | 97% | ABT3406 | 3,749,428 |
MRN006 | COL | 2019 | 22.18 | 28.33 | −1 | 20.42 | 2229 | 100% | ABT3406 | 1655 | 100% | 2905 | 100% | ABT3406 | 3,541,114 |
MRN012 | COL | 2019 | −1 | 23.36 | 22.78 | −1 | 111 | 42% | KY928792 | 111 | 50% | 215 | 96% | KY928727 | 9,517,318 |
MRN012 | COL | 2019 | −1 | 23.36 | 22.78 | −1 | 3202 | 100% | MRN012 | 2190 | 100% | 3020 | 100% | KM285233 | 9,517,318 |
MRN015 | COL | 2019 | 24.69 | 23.1 | 24.15 | 25.5 | 7518 | 100% | ABT3406 | 5425 | 100% | 5793 | 99% | ABT3406 | 4,685,264 |
MRN015 | COL | 2019 | 24.69 | 23.1 | 24.15 | 25.5 | 15,340 | 100% | MRN012 | 10,584 | 100% | 11,053 | 100% | KM285233 | 4,685,264 |
MRN016 | COL | 2019 | −1 | 28.71 | −1 | 25.56 | 675 | 100% | ABT3406 | 586 | 100% | 812 | 100% | ABT3406 | 14,733,470 |
MRN020 | COL | 2019 | −1 | 35.51 | −1 | −1 | 169 | 87% | ABT3406 | 131 | 89% | 72 | 67% | ABT3406 | 34,621,664 |
MRN021 | COL | 2019 | 35.59 | 35.25 | −1 | 31.49 | 36 | 54% | ABT3406 | 22 | 54% | 72 | 92% | ABT3406 | 34,481,740 |
MRN023 | COL | 2019 | −1 | 25.12 | 24.22 | −1 | 3233 | 100% | MRN012 | 2533 | 100% | 3925 | 100% | KM285233 | 8,746,944 |
MRN031 | COL | 2019 | −1 | 32.26 | −1 | 30.16 | 25 | 62% | MK204396 | 22 | 71% | 20 | 47% | ABT3406 | 6,175,024 |
MRN032 | COL | 2019 | −1 | 27.69 | −1 | 25.94 | 66 | 92% | MK204396 | 56 | 89% | 57 | 95% | ABT3406 | 5,853,846 |
MRN033 | COL | 2019 | −1 | 25.35 | 26.91 | 34.56 | 28 | 48% | MK204396 | 14 | 40% | 307 | 100% | MH933835 | 16,786,708 |
MRN033 | COL | 2019 | −1 | 25.35 | 26.91 | 34.56 | 1880 | 99% | MRN012 | 1439 | 100% | 1361 | 100% | KM285233 | 16,786,708 |
MRN034 | COL | 2019 | −1 | 26.41 | 27.39 | 35.75 | 12 | 30% | MK204396 | 10 | 33% | 957 | 100% | MH933835 | 9,571,150 |
MRN034 | COL | 2019 | −1 | 26.41 | 27.39 | 35.75 | 2627 | 100% | MRN012 | 2071 | 100% | 1315 | 100% | KM285233 | 9,571,150 |
MRN035 | COL | 2019 | 35.84 | 29.3 | −1 | 26.64 | 458 | 100% | ABT3406 | 431 | 100% | 437 | 92% | ABT3406 | 8,335,936 |
MRN038 | COL | 2019 | 26.57 | 30.67 | −1 | 29.08 | 352 | 100% | ABT3406 | 300 | 100% | 280 | 97% | ABT3406 | 1,585,992 |
MRN039 | COL | 2019 | 34.43 | 21.56 | 25.45 | 29.43 | 545 | 100% | MK204396 | 363 | 100% | 417 | 89% | MH933835 | 4,737,986 |
MRN039 | COL | 2019 | 34.43 | 21.56 | 25.45 | 29.43 | 1416 | 97% | MRN012 | 1372 | 100% | 2387 | 99% | KM285233 | 4,737,986 |
MRN044 | COL | 2019 | 22.58 | 31.48 | −1 | 26.95 | 5395 | 99% | ABT3406 | 4823 | 98% | 5603 | 100% | ABT3406 | 8,691,792 |
MRN044 | COL | 2019 | 22.58 | 31.48 | −1 | 26.95 | 40 | 56% | MRN012 | 36 | 67% | 109 | 70% | KM285233 | 8,691,792 |
MRN046 | COL | 2019 | 19.61 | 27.14 | −1 | 23.29 | 2490 | 99% | ABT3406 | 1786 | 99% | 2302 | 100% | ABT3406 | 4,679,714 |
Patient ID | Age | Sex | RdRp FAM Ct | Log Titer cp/mL | Sputum Color | Viral Coinfection | Bacterial Coinfection | Medical Diagnosis | Symptoms |
---|---|---|---|---|---|---|---|---|---|
NYB4466 | 52 | M | 29.41 | 4.34 | Yellow | HHV-4 | Stenotrophomonas, Mycoplasma | n.d. | n.d. |
NYB4468 | 40 | F | 33.36 | 3.15 | Clear | Influenza, Strep phage | Streptococcus pneumonia, Bacillus | n.d. | n.d. |
NYB4138 | 71 | M | 26.4 | 5.25 | Brown/yellow | Klebsiella phage | Klebsiella pneumonia | n.d. | n.d. |
NYB4477 | 51 | F | 36.26 | 2.28 | Brown/yellow | none | None | n.d. | n.d. |
NYB4470 | 62 | F | 34.6 | 2.23 | Yellow | HHV-1, coronavirus OC43 | None | n.d. | n.d. |
BBL46722 | 57 | F | 35.04 | 2.10 | Brown | None | None | n.d. | n.d. |
MRN001 | 32 | F | 30.78 | 3.38 | Brown | None | Treponema, Bacteroides | Myco TB+ | Multidrug resistance, 2nd phase of treatment, fever, weight loss, chest pain, pain with breathing |
MRN006 | 36 | M | 28.33 | 4.12 | Clear | None | none | Pulmonary TB | Smear microscopy (+), BARR (++), chest pains, fever, weight loss, fatigue |
MRN012 | 18 | F | 23.36 | 5.62 | Clear | Respirovirus 3 | none | Pulmonary TB | Smear microscopy (−), Radiography (+), chest pains, cough, fever, weight loss |
Sptm Ctrl | 36.34 | 1.71 | n.d. | None | Klebsiella pneumonia | n.d. | n.d. | ||
MRN015 | 36 | M | 23.1 | 5.96 | Clear | None | Bordetalla, Burkholderia, Pseudomonas, Serretia | Pulmonary TB | Smear microscopy (+), BARR++, severe cough, fever, weight loss, chills, fatigue |
MRN016 | 28 | F | 28.71 | 4.27 | Clear | Pseudomonas phage | Pseudomonas aeruginosa | Pulmonary TB | Smear microscopy (+), BARR+++, 2nd phase of treatment |
MRN020 | 83 | M | 35.51 | 2.22 | Clear | None | Mycoplasma, Treponema, Streptococcus | Negative | Coughing up blood, fatigue, weight loss |
MRN021 | 68 | F | 35.25 | 2.30 | Yellow/clear | Enterovirus D | None | Negative | Fever, night sweats, pain when breathing |
MRN023 | 60 | M | 25.12 | 5.35 | Brown/yellow | None | Haemophilus parainfluenza | Negative | Night sweats, fever, coughing up blood |
MRN031 | 86 | M | 32.26 | 3.20 | Clear | Rhinovirus A | Clostridium | Smear(−), Rad(+) | Fatigue, fever, night sweats |
MRN032 | 71 | M | 27.69 | 4.58 | Yellow | Rhinovirus A, Haemophilus virus | Haemophilus influenzae | Pneumonia | Chest pains, coughing up blood, pain when breathing |
MRN033 | 52 | M | 25.35 | 5.28 | Clear | None | Bacillus, Treponema | Chronic bronchitis (−) | Chest pains, Chest pains when coughing |
MRN034 | 61 | M | 26.41 | 4.96 | Clear | None | Bacillus, Mycoplasma, Treponema | EPOC BARR(+) | Night sweats |
MRN035 | 68 | M | 29.3 | 4.09 | Clear | None | Spirochaeta, Treponema, Bacteroides, Mycoplasma | Pulmonary TB, Barr(++) | Coughing up blood, fatigue, chest pains |
MRN036 | 71 | F | 34.19 | 2.62 | Yellow | None | None | Bronchopneumonia (−) | Chest pains, hest pains when coughing |
MRN038 | 69 | M | 30.67 | 3.68 | Clear | None | Burkholderia, Serretia, Pseudomonas | EPOC BARR (−) | Fatigue, night sweats |
MRN039 | 20 | M | 21.56 | 6.42 | Clear | None | Treponema | Chronic bronchitis (−) | Chest pains when coughing and breathing |
MRN044 | 72 | M | 31.48 | 3.44 | Clear | None | None | EPOC BARR (−) | Night sweats, chills, fatigue |
MRN046 | 72 | F | 27.14 | 4.74 | Clear | None | None | Pneumonia (−) | Chest pains when coughing, weight loss, chills |
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Berg, M.G.; Forberg, K.; Perez, L.J.; Luk, K.-C.; Meyer, T.V.; Cloherty, G.A. Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness. Viruses 2021, 13, 2534. https://doi.org/10.3390/v13122534
Berg MG, Forberg K, Perez LJ, Luk K-C, Meyer TV, Cloherty GA. Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness. Viruses. 2021; 13(12):2534. https://doi.org/10.3390/v13122534
Chicago/Turabian StyleBerg, Michael G., Kenn Forberg, Lester J. Perez, Ka-Cheung Luk, Todd V. Meyer, and Gavin A. Cloherty. 2021. "Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness" Viruses 13, no. 12: 2534. https://doi.org/10.3390/v13122534