16条甲型肝炎病毒流行株基因型及全基因组特征分析

Genotyping and Whole Genome Characteristics of 16 Hepatitis A Virus Strains in China

为分析具有相同VP1-2A区基因序列的甲型肝炎病毒(Hepatitis A virus,HAV)流行株全基因组序列特征,收集我国6个省市不同年份同一起或不同起甲型肝炎(甲肝)暴发中,部分甲肝病例急性期血清标本,提取HAV RNA,进行VP1-2A区基因分型,RT-PCR分段扩增HAV近全基因组序列,构建系统进化树,分析基因组特征。本研究获得16条HAV近全基因组序列,均属于基因IA亚型,核苷酸和氨基酸序列同源性分别为95.81%~100%和99.23%~100%。与GenBank中HAV序列比较,15条序列与Man12-001(蒙古国株)最接近,核苷酸和氨基酸序列同源性分别为97.87%~99.81%和99.55%~99.95%;1条序列与HAJEF-K12(日本株)最接近,核苷酸和氨基酸序列同源性分别为99.37%和99.91%。本文中VP1-2A区序列完全相同的HAV流行株,来源于同一起甲肝暴发时,HAV近全基因组核苷酸序列差异为0%~0.03%;来源于不同起暴发时,核苷酸序列差异为0.18%~0.99%。16条HAV序列在已发表的中和抗原表位未发现变异,编码区氨基酸序列处于负向选择压力,16条序列间及与参考序列间未发现基因重组。本研究表明我国存在多株HAV流行株,主要为基因IA亚型;VP1-2A区序列完全相同的HAV流行株,来源于同一起甲肝暴发的HAV全基因组核苷酸序列同源性高于不同起暴发的HAV序列同源性。HAV基因分型及全基因序列分析与现场流行病学调查结果相结合,更有利于HAV溯源分析。

In order to analyze the whole genome sequence characteristics of Hepatitis A virus(HAV)strains with identical VP1-2A sequences,we collected serum samples of some acute hepatitis A cases from outbreaks at different times from six provinces of China,performed genotyping based on the VP1-2A region,amplified the nearly whole genome sequences by the segmental RT-PCR method,constructed phylogenetic trees,and analyzed the genetic characteristics of the sequences.We obtained 16 nearly full-length HAV sequences,all of which belonged to sub-genotype IA.The homology of nucleotide and amino acid sequences among the 16 HAV sequences were 95.81%-100%and 99.23%-100%,respectively.Compared with HAV sequences from GenBank,15 sequences were closer to HAV strain‘Man12-001’(derived from Mongolia),with nucleotide and amino acid sequence homologies of 97.87%-99.81%and 99.55%-99.95%,respectively.The other sequence was closer to HAV strain‘HAJEF-K12’(derived from Japan),with nucleotide and amino acid sequence homologies of 99.37%and 99.91%,respectively.Among the 16 HAV sequences with identical VP1-2A sequences,the nucleotide sequence differences of the nearly whole HAV genome from the same outbreak were 0%-0.03%;from different outbreaks,the nucleotide sequence differences were 0.18%-0.99%.No amino acid variation was found at the published neutralizing epitopes for the 16 HAV sequences,the amino acid sequences in the coding region were under negative selection pressure,and no recombination was found among our sequences or between our sequences and reference sequences.In conclusion,there are many HAV strains in China,mostly belonging to sub-genotype IA.For HAV strains with identical VP1-2A sequences,the whole genome sequences of HAVs derived from the same outbreak of Hepatitis A share higher homology than those from different outbreaks.Combining HAV genotyping and whole genome sequence analysis with the results of field epidemiological investigations is conducive to the traceability of epidemic situations.