Complete genome sequence of Hepatitis C Virus isolated in Mexico
Introduction and Objective: Death due to liver damage caused by the hepatitis C virus (HCV) represents one of the most frequent health threats in Mexico. However, the complete genome of HCV has not yet been sequenced. The aim of this study was to obtain the complete genome sequence of HCV isolated f...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Annals of Hepatology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1665268122001909 |
| _version_ | 1811320231821312000 |
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| author | K López-Riojas KA Galán-Huerta AF Ruiz-Higareda L Muñoz-Espinosa P Cordero-Pérez D Arellanos-Soto S Lozano-Sepulveda AM Rivas-Estilla |
| author_facet | K López-Riojas KA Galán-Huerta AF Ruiz-Higareda L Muñoz-Espinosa P Cordero-Pérez D Arellanos-Soto S Lozano-Sepulveda AM Rivas-Estilla |
| author_sort | K López-Riojas |
| collection | DOAJ |
| description | Introduction and Objective: Death due to liver damage caused by the hepatitis C virus (HCV) represents one of the most frequent health threats in Mexico. However, the complete genome of HCV has not yet been sequenced. The aim of this study was to obtain the complete genome sequence of HCV isolated from patients in Mexico. Materials and Methods: We evaluated patients with hepatitis C who sought medical care at the “Liver Unit” that belongs to the “Hospital Universitario Dr. José Eleuterio” in Monterrey, Mexico from May 2016 to August 2019. We extracted RNA from five samples and amplified the whole genome of HCV with tiled-PCR. Amplicons were sequenced with MinION, a third-generation sequencer technology. Obtained sequences were assembled with the Genome Detective program and posteriorly analyzed with IQtree platform. Results: We obtained four partial and one complete VHC genome that corresponded to genotype 1b. The average coverage of the complete genome was 600X. The phylogenetic analysis of the complete genome showed that this sequence from Mexico was related to viruses isolated in the United States of America, Indonesia, and Japan. Because there is not a full HCV complete genome sequenced before in our country, we used the partial viral genomes reported before in Mexico to compare NS3 and NS5A genes with our reported sequences. The NS3 gene alignment showed that the newly sequenced viruses grouped in a clade different from the previously sequenced viruses. When NS5A gene was used, the newly obtained sequences grouped with the previously sequenced viruses in Mexico. Conclusion: We were able to obtain the first complete and four partial HCV genomes from Mexican patients. This newly sequenced virus will improve the molecular epidemiology of HCV in Mexico. Funding: The resources used in this study were from the hospital without any additional financing Declaration of interest: The authors declare no potential conflicts of interest. |
| first_indexed | 2024-04-13T12:56:21Z |
| format | Article |
| id | doaj.art-0bcaa6c80c7f4158bd00d1a717f752f7 |
| institution | Directory Open Access Journal |
| issn | 1665-2681 |
| language | English |
| last_indexed | 2024-04-13T12:56:21Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Annals of Hepatology |
| spelling | doaj.art-0bcaa6c80c7f4158bd00d1a717f752f72022-12-22T02:46:03ZengElsevierAnnals of Hepatology1665-26812022-12-0127100848Complete genome sequence of Hepatitis C Virus isolated in MexicoK López-Riojas0KA Galán-Huerta1AF Ruiz-Higareda2L Muñoz-Espinosa3P Cordero-Pérez4D Arellanos-Soto5S Lozano-Sepulveda6AM Rivas-Estilla7Center for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoCenter for Research and Innovation in Medical Virology. Medical Faculty, UANL. MexicoIntroduction and Objective: Death due to liver damage caused by the hepatitis C virus (HCV) represents one of the most frequent health threats in Mexico. However, the complete genome of HCV has not yet been sequenced. The aim of this study was to obtain the complete genome sequence of HCV isolated from patients in Mexico. Materials and Methods: We evaluated patients with hepatitis C who sought medical care at the “Liver Unit” that belongs to the “Hospital Universitario Dr. José Eleuterio” in Monterrey, Mexico from May 2016 to August 2019. We extracted RNA from five samples and amplified the whole genome of HCV with tiled-PCR. Amplicons were sequenced with MinION, a third-generation sequencer technology. Obtained sequences were assembled with the Genome Detective program and posteriorly analyzed with IQtree platform. Results: We obtained four partial and one complete VHC genome that corresponded to genotype 1b. The average coverage of the complete genome was 600X. The phylogenetic analysis of the complete genome showed that this sequence from Mexico was related to viruses isolated in the United States of America, Indonesia, and Japan. Because there is not a full HCV complete genome sequenced before in our country, we used the partial viral genomes reported before in Mexico to compare NS3 and NS5A genes with our reported sequences. The NS3 gene alignment showed that the newly sequenced viruses grouped in a clade different from the previously sequenced viruses. When NS5A gene was used, the newly obtained sequences grouped with the previously sequenced viruses in Mexico. Conclusion: We were able to obtain the first complete and four partial HCV genomes from Mexican patients. This newly sequenced virus will improve the molecular epidemiology of HCV in Mexico. Funding: The resources used in this study were from the hospital without any additional financing Declaration of interest: The authors declare no potential conflicts of interest.http://www.sciencedirect.com/science/article/pii/S1665268122001909 |
| spellingShingle | K López-Riojas KA Galán-Huerta AF Ruiz-Higareda L Muñoz-Espinosa P Cordero-Pérez D Arellanos-Soto S Lozano-Sepulveda AM Rivas-Estilla Complete genome sequence of Hepatitis C Virus isolated in Mexico Annals of Hepatology |
| title | Complete genome sequence of Hepatitis C Virus isolated in Mexico |
| title_full | Complete genome sequence of Hepatitis C Virus isolated in Mexico |
| title_fullStr | Complete genome sequence of Hepatitis C Virus isolated in Mexico |
| title_full_unstemmed | Complete genome sequence of Hepatitis C Virus isolated in Mexico |
| title_short | Complete genome sequence of Hepatitis C Virus isolated in Mexico |
| title_sort | complete genome sequence of hepatitis c virus isolated in mexico |
| url | http://www.sciencedirect.com/science/article/pii/S1665268122001909 |
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