Complete genome sequence of Hepatitis C Virus isolated in Mexico

Abstract

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.