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
APA StyleSotomayor-González, A., Trujillo-Ortega, M. E., Taboada-Ramírez, B. I., Sandoval-Jaime, C., & Sarmiento-Silva, R. E. (2018). Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico. Viruses, 10(8), 391. https://doi.org/10.3390/v10080391