Whole-genome and quasispecies sequences analysis of three hepatitis A virus isolates in China / 中华实验和临床病毒学杂志

ABSTRACT

Objective@#To analyze the genetic characteristics of whole-genome and quasispecies sequences from three hepatitis A virus (HAV) strains in China.@*Methods@#Serum samples from acute hepatitis A patients were collected and viral RNA extraction, transcription, nested PCR, sequencing and assembling were performed to gain near full-length sequences; cloning-based sequencing of the full-length VP1-2 A region was also performed.@*Results@#Genotyping showed that the nucleotide and amino acid identities among three strains on VP1-2 A junction region were both 100% and all belonged to subgenotype IA; the nucleotide and amino acid identities on whole-genome region were 99.9%-100% and 100% respectively, and shared the highest identities with AH2 strain from GenBank of 98.5% in nucleotide and 99.7% in amino acid level; no amino acid variation was found among published neutralizing antigenic sites. Within cloning sequences from each strain, the nucleotide and amino acid identities were 99.0%-100% and 98.1%-100%, while among all cloning sequences were 99.0%-100% and 97.2%-100%. The variation rate of nucleotide and amino acid in VP1-2 A junction region were both higher than that of partial VP1 region.@*Conclusions@#Sequences among three strains in VP1-2 A region were identical, the nucleotide and amino acid identities in both whole-genome region and among quasispecies sequences were relatively high to deduce that they were from the same outbreak. This study provides new insight for identification of HAV transmissions and tracing investigations.