Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Molecular Detection of HEV
2.3. HEV Sequencing
2.4. Computer Sequence Analysis
2.5. Phylogenetic Analysis
3. Results
3.1. Molecular Detection of Hepatitis E
3.2. HEV Sequencing
- (i)
- Bile sample B1. We were able to assemble one complete hepatitis E virus genome, denoted MXCDg3a_B1c|_2016 with a coverage of 354.62. This genome is 7241 nucleotides (nt) long, excluding the poli-A tail (12 nt) at the 3’ termini. The genome consisted of 5’ UTR of 27 nt (1–27); three open reading frames—ORF1 of 5120 nt (27–5147), ORF2 of 1979 nt (5185–7164), ORF3 of 365 nt (5147–5512)—and a 3’ UTR of 77 nt (7164–7241), followed by the poli-A tail (Figure 1). This sequence had been deposited at GenBank under accession no. MG833836.
- (ii)
- Liver sample H2 was denoted MXCDg3a_H2cons|_2016; a partial sequence was obtained of 1473 nt covering the 3’ end (5766–7239) with a coverage of 6.30. The GenBank accession number is MH003296.
- (iii)
- Feces sample C3A was identified as MXCDg3a_C3Acons|_2016; a partial sequence of 4777 nt was obtained covering the 3’ end (2464–7241) with a coverage of 18.35; GenBank no. MG980615.
3.3. Complete Genome Characterization
3.4. Phylogenetic Analysis
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Ethics Approval
References and Note
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ID | # of Samples | Type of Sample | Origin | Production Stage | RT-PCR Result |
---|---|---|---|---|---|
1 | 16 | Liver, bile, feces | Slaughterhouse | Finishers | N |
2 | 16 | Liver, bile, feces | Slaughterhouse | Finishers | N |
3 | 16 | Liver, bile, feces | Slaughterhouse | Finishers | P* |
4 | 16 | Liver, bile, feces | Slaughterhouse | Finishers | N |
G1 | 10 | Feces | Farm | Gestation | P |
G2 | 10 | Feces | Farm | Gestation | N |
G3 | 10 | Feces | Farm | Gestation | P |
D1 | 10 | Feces | Farm | Weaning | P |
D2 | 10 | Feces | Farm | Weaning | P |
D3 | 10 | Feces | Farm | Weaning | P |
E1 | 10 | Feces | Farm | Finishers | N |
E2 | 10 | Feces | Farm | Finishers | P |
E12 | 10 | Feces | Farm | Finishers | P |
M1 | 10 | Feces | Farm | Nursing | N |
M2 | 10 | Feces | Farm | Nursing | P |
M3 | 10 | Feces | Farm | Nursing | N |
R | 10 | Feces | Farm | Breeding | N |
S | 10 | Feces | Farm | Boars | N |
H1 | 3 | Liver | Farm | Finishers | P |
H2 | 4 | Liver | Farm | Finishers | P |
H3 | 1 | Liver | Farm | Finishers | P |
B1 | 4 | Bile | Farm | Finishers | P |
B2 | 4 | Bile | Farm | Finishers | P |
C1 | 4 | Feces | Farm | Finishers | P |
C2 | 4 | Feces | Farm | Finishers | N |
* only 1 bile positive |
Sequence Identification | Genome | ORF1 | ORF2 | ORF3 | |||
---|---|---|---|---|---|---|---|
ID | Full-Length% (nt) | % (nt) | % (aa) | % (nt) | % (aa) | % (nt) | % (aa) |
USHM|AF060669.1|g3a|_1998 | 91 | 90 | 97 | 92 | 98 | 98 | 98 |
JPHM|AB089824.1|g3|_1993 | 91 | 90 | 98 | 92 | 98 | 96 | 98 |
USHM|JQ679014.1|g3|_2010 | 91 | 90 | 97 | 92 | 98 | 96 | 98 |
USCD|AY575857.1|g3|_1997 | 91 | 90 | 98 | 92 | 98 | 96 | 98 |
USMN|JN837481.1|g3|_2008 | 91 | 90 | 97 | 92 | 99 | 97 | 97 |
JPHM|AB074920.3|g3|_2002 | 91 | 90 | 98 | 92 | 99 | 98 | 98 |
JPHM|AB074918.2|g3|_2002 | 91 | 90 | 98 | 93 | 99 | 98 | 98 |
CNCD|KJ507955.1|g3|_2003 | 90 | 90 | 98 | 92 | 98 | 97 | 99 |
KRCD|FJ426403.1|g3|_2007 | 90 | 90 | 96 | 93 | 97 | 96 | 98 |
KRCD|FJ426404.1|g3|_2007 | 90 | 89 | 96 | 92 | 98 | 97 | 98 |
SGHM|KT447526.1|g3|_2010 | 90 | 89 | 97 | 91 | 98 | 96 | 96 |
USHM|JQ679013.1|g3|_2010 | 90 | 90 | 93 | 92 | 98 | 94 | 97 |
CHCD|KX981911.1|g3|_2015 | 89 | 89 | 96 | 91 | 98 | 97 | 98 |
CNCD|AY115488.1|g3|_2002 | 87 | 86 | 95 | 90 | 98 | 96 | 98 |
JPHM|AB091394.1|g3|_2002 | 87 | 86 | 97 | 89 | 99 | 97 | 97 |
JPCD|AB740232.1|g3|_2013 | 87 | 86 | 96 | 89 | 98 | 96 | 98 |
JPHM|LC131066.1|g3|_2016 | 87 | 86 | 96 | 90 | 99 | 96 | 96 |
JPHM|AB437317.1|g3|_2003 | 87 | 86 | 97 | 89 | 99 | 97 | 96 |
JPHM|LC176492.1|g3k|_2015 | 87 | 86 | 96 | 90 | 98 | 96 | 96 |
JPHM|AB369689.1|g3|_2004 | 87 | 86 | 96 | 90 | 99 | 97 | 97 |
JPHM|AB291963.1|g3|_2005 | 87 | 86 | 96 | 90 | 98 | 95 | 93 |
JPJB|AB222184.1|g3|_2004 | 87 | 86 | 96 | 88 | 98 | 96 | 96 |
JPMN|AB236320.1|g3|_2002 | 87 | 86 | 97 | 89 | 98 | 97 | 97 |
JPJB|AB222182.1|g3|_2004 | 87 | 86 | 96 | 89 | 98 | 96 | 96 |
CNCD|KJ507956.1|g3|2003 | 87 | 86 | 97 | 89 | 98 | 96 | 93 |
JPJB|AB222183.1|g3|_2004 | 87 | 86 | 97 | 89 | 98 | 96 | 93 |
JPCD|AB073912.1|g3|_2001 | 87 | 86 | 96 | 89 | 98 | 96 | 96 |
JPJB|AB189070.1|g3|_2004 | 87 | 85 | 96 | 89 | 98 | 96 | 96 |
JPHM|AB437319.1|g3|2003 | 87 | 91 | 97 | 89 | 99 | 96 | 95 |
JPHM|AB291960.1|g3|_2006 | 86 | 86 | 97 | 89 | 98 | 96 | 95 |
JPHM|AB291952.1|g3|_2005 | 86 | 86 | 97 | 88 | 99 | 97 | 96 |
JPHM|AB369691.1|g3|_2005 | 86 | 86 | 97 | 89 | 99 | 98 | 96 |
JPHM|AP003430.1|g3|_2001 | 86 | 86 | 96 | 88 | 98 | 97 | 98 |
JPHM|AB291962.1|g3|_2004 | 86 | 85 | 96 | 89 | 98 | 96 | 97 |
CHCD|FJ527832.2|g3|2008 | 86 | 86 | 96 | 88 | 98 | 97 | 98 |
JPND|AB246676.1|g3|_2006 | 86 | 85 | 97 | 89 | 98 | 99 | 93 |
ALJB|FJ998008.1|g3|_2007 | 85 | 84 | 96 | 87 | 99 | 95 | 94 |
CHCD|FJ610232.1|G4|_2008 | 78 | 79 | 85 | 81 | 93 | 87 | 85 |
TWHM|HQ634346.1|G4|_2010 | 78 | 78 | 86 | 81 | 94 | 90 | 88 |
CHCD|KC692453.1|G4|_2011 | 78 | 78 | 85 | 80 | 94 | 88 | 86 |
EACM|KJ496143.1|g7|_2013 | 78 | 78 | 87 | 80 | 92 | 87 | 80 |
CHCD|GU119960.2|G4a|_2009 | 78 | 77 | 85 | 81 | 94 | 89 | 88 |
JPJB|AB573435.2|G5|_2009 | 78 | 77 | 84 | 80 | 91 | 86 | 80 |
CDCH|GU206559.1|G4|_2008 | 78 | 79 | 85 | 81 | 92 | 86 | 85 |
INHM|JF443724.1|G1|_2005 | 77 | 77 | 82 | 80 | 92 | 85 | 82 |
CHHM|NC_001434.1|G1|_1987 | 77 | 77 | 82 | 80 | 92 | 85 | 82 |
CHHM|JQ655734.1|G1|_2012 | 77 | 77 | 82 | 79 | 91 | 86 | 82 |
MXHM|M74506.1|g2|_1992 | 76 | 77 | 81 | 79 | 91 | 85 | 80 |
JPWB|AB602441.1|g6|_2006 | 76 | NS | 83 | 79 | 91 | 84 | 73 |
* NS. No similarity found |
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Sotomayor-González, A.; Trujillo-Ortega, M.E.; Taboada-Ramírez, B.I.; Sandoval-Jaime, C.; Sarmiento-Silva, R.E. Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico. Viruses 2018, 10, 391. https://doi.org/10.3390/v10080391
Sotomayor-González A, Trujillo-Ortega ME, Taboada-Ramírez BI, Sandoval-Jaime C, Sarmiento-Silva RE. Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico. Viruses. 2018; 10(8):391. https://doi.org/10.3390/v10080391
Chicago/Turabian StyleSotomayor-González, Alicia, María E. Trujillo-Ortega, Blanca I. Taboada-Ramírez, Carlos Sandoval-Jaime, and Rosa E. Sarmiento-Silva. 2018. "Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico" Viruses 10, no. 8: 391. https://doi.org/10.3390/v10080391