Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico
Hepatitis E virus (HEV) is an emerging public health problem with an estimated 20 million infections each year. In Mexico, Orthohepevirus A, genotype 2, has been reported in humans, but genotype 3 has only been reported in swine (zoonotic). No diagnostic tests are publicly available in Mexico, and o...
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MDPI AG
2018-07-01
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| Series: | Viruses |
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| Online Access: | http://www.mdpi.com/1999-4915/10/8/391 |
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| author | Alicia Sotomayor-González María E. Trujillo-Ortega Blanca I. Taboada-Ramírez Carlos Sandoval-Jaime Rosa E. Sarmiento-Silva |
| author_facet | Alicia Sotomayor-González María E. Trujillo-Ortega Blanca I. Taboada-Ramírez Carlos Sandoval-Jaime Rosa E. Sarmiento-Silva |
| author_sort | Alicia Sotomayor-González |
| collection | DOAJ |
| description | Hepatitis E virus (HEV) is an emerging public health problem with an estimated 20 million infections each year. In Mexico, Orthohepevirus A, genotype 2, has been reported in humans, but genotype 3 has only been reported in swine (zoonotic). No diagnostic tests are publicly available in Mexico, and only partial sequences have been reported from swine samples. Hence, research is necessary to determine circulating strains, understand the features and dynamics of infection on pig farms, determine how to implement surveillance programs, and to assess public health risks. In this study, a next-generation sequencing (NGS) approach was applied to obtain a complete genome of swine HEV. Liver, feces, and bile samples were taken at slaughterhouses and a farm in Mexico. RT-PCR was used to determine positive samples and confirmed by Sanger sequencing. Of the 64 slaughterhouse samples, one bile sample was positive (B1r) (1.56%). Of 21 sample pools from farm animals, 14 were positive (66.66%), representing all stages of production. A complete sequence strain MXCDg3_B1c|_2016 was obtained from the bile of a domestic swine in the fattening stage. In addition, two partial sequences—MXCDg3_H2cons|_2016 (1473 nt) and MXCDg3_C3Acons|_2016 (4777 nt)—were obtained from sampled farm animals. Comparison with all reported genome HEV sequences showed similarity to genotype 3 subgenotype a (G3a), which has been previously reported in acute cases of human hepatitis in the US, Colombia, China, and Japan. |
| first_indexed | 2024-12-20T04:12:31Z |
| format | Article |
| id | doaj.art-ef39734253a9401ba832907fc22c61f4 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-20T04:12:31Z |
| publishDate | 2018-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-ef39734253a9401ba832907fc22c61f42022-12-21T19:53:52ZengMDPI AGViruses1999-49152018-07-0110839110.3390/v10080391v10080391Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from MexicoAlicia Sotomayor-González0María E. Trujillo-Ortega1Blanca I. Taboada-Ramírez2Carlos Sandoval-Jaime3Rosa E. Sarmiento-Silva4Laboratory of Virology, Microbiology and Immunology Department, Veterinary Medicine and Husbandry Faculty, National Autonomous University of Mexico (UNAM), Mexico City 04510, MexicoAcademic Council of the Biological, Chemical and Medical Sciences, National Autonomous University of Mexico (UNAM), Mexico City 04510, MexicoBiotechnology Institute (IBT), National Autonomous University of Mexico (UNAM), Cuernavaca 62209, Morelos, MexicoBiotechnology Institute (IBT), National Autonomous University of Mexico (UNAM), Cuernavaca 62209, Morelos, MexicoLaboratory of Virology, Microbiology and Immunology Department, Veterinary Medicine and Husbandry Faculty, National Autonomous University of Mexico (UNAM), Mexico City 04510, MexicoHepatitis E virus (HEV) is an emerging public health problem with an estimated 20 million infections each year. In Mexico, Orthohepevirus A, genotype 2, has been reported in humans, but genotype 3 has only been reported in swine (zoonotic). No diagnostic tests are publicly available in Mexico, and only partial sequences have been reported from swine samples. Hence, research is necessary to determine circulating strains, understand the features and dynamics of infection on pig farms, determine how to implement surveillance programs, and to assess public health risks. In this study, a next-generation sequencing (NGS) approach was applied to obtain a complete genome of swine HEV. Liver, feces, and bile samples were taken at slaughterhouses and a farm in Mexico. RT-PCR was used to determine positive samples and confirmed by Sanger sequencing. Of the 64 slaughterhouse samples, one bile sample was positive (B1r) (1.56%). Of 21 sample pools from farm animals, 14 were positive (66.66%), representing all stages of production. A complete sequence strain MXCDg3_B1c|_2016 was obtained from the bile of a domestic swine in the fattening stage. In addition, two partial sequences—MXCDg3_H2cons|_2016 (1473 nt) and MXCDg3_C3Acons|_2016 (4777 nt)—were obtained from sampled farm animals. Comparison with all reported genome HEV sequences showed similarity to genotype 3 subgenotype a (G3a), which has been previously reported in acute cases of human hepatitis in the US, Colombia, China, and Japan.http://www.mdpi.com/1999-4915/10/8/391hepatitis Ehepatitisswinezoonosisbilecharacterization |
| spellingShingle | Alicia Sotomayor-González María E. Trujillo-Ortega Blanca I. Taboada-Ramírez Carlos Sandoval-Jaime Rosa E. Sarmiento-Silva Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico Viruses hepatitis E hepatitis swine zoonosis bile characterization |
| title | Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico |
| title_full | Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico |
| title_fullStr | Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico |
| title_full_unstemmed | Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico |
| title_short | Phylogenetic Analysis and Characterization of the Complete Hepatitis E Virus Genome (Zoonotic Genotype 3) in Swine Samples from Mexico |
| title_sort | phylogenetic analysis and characterization of the complete hepatitis e virus genome zoonotic genotype 3 in swine samples from mexico |
| topic | hepatitis E hepatitis swine zoonosis bile characterization |
| url | http://www.mdpi.com/1999-4915/10/8/391 |
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