Zhao Fei-Fei, Lu Yi-Yu, Feng Yan, Xu Chang-Ping, Mo Shi-Hua
Medical School of Ningbo University, Ningbo 315211, China.
Zhonghua Yu Fang Yi Xue Za Zhi. 2011 Jul;45(7):612-8.
To analyze the consistency of evolution condition between HA gene and the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province from 1998 to 2009, and to study the potential antigenic region on the whole genome.
The sequences of whole genome of 19 Zhejiang influenza virus isolates circulated from 1998 to 2009, which conserved by influenza laboratory of Zhejiang Provincial Centre for Disease Prevention and Control, were amplified using RT-PCR assays. The obtained sequences were used to conduct phylogenetic analysis with 10 contemporaneous vaccine strains. Three methods, including comparison of the amino acid substitutions, calculation of the entropy value and the filtering of positive selection sites, were used to confirm the mutable sites on each gene.
The whole genome of influenza virus subtype A/H3N2 was 4466 amino acids in length, with 137 stable mutations. The 144, 158 aa of HA gene mutate four and three times respectively; 93, 143, 307, 370, 372 aa of NA gene and 450 aa of NP gene mutate twice, and there were 29% (12/41) and 77% (24/31) mutations of HA and NA genes occurred on the non-epitope regions respectively. Analysis of the entropy value suggest that many amino acid sites on the non-epitope regions were prone to mutation, including 3, 225, 361 aa of HA gene; 93, 143, 147, 150, 372 aa of NA gene; 113, 576, 586 aa of PB1 gene; 101,256, 382, 421, 437 aa of PA; 377, 450 aa of NP gene; 218 aa of M1 gene and 31 aa of M2 gene.
Based on the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province in 1998 to 2009, there may be several unknown or new antigen sites existing on the non-epitope regions of HA and NA genes and parts of internal genes. The phylogenetic tree constructed based on the complete sequence was more comprehensive than on the HA gene to reflect the genetic relationship and law of evolution among the influenza virus strains.
分析1998年至2009年浙江省分离的甲型H3N2流感病毒株HA基因与全基因组进化情况的一致性，并研究全基因组上潜在的抗原区域。
采用RT-PCR方法扩增浙江省疾病预防控制中心流感实验室保存的1998年至2009年流行的19株浙江省流感病毒分离株的全基因组序列。将获得的序列与10株同期疫苗株进行系统发育分析。采用氨基酸替换比较、熵值计算和正选择位点筛选3种方法确定各基因上的可变位点。
甲型H3N2流感病毒全基因组长度为4466个氨基酸，有137个稳定突变。HA基因的144、158位氨基酸分别突变4次和3次；NA基因的93、143、307、370、372位氨基酸和NP基因的450位氨基酸突变2次，HA和NA基因分别有29%（12/41）和77%（24/31）的突变发生在非抗原表位区域。熵值分析表明，非抗原表位区域的许多氨基酸位点易于突变，包括HA基因的3、225、361位氨基酸；NA基因的93、143、147、150、372位氨基酸；PB1基因的113、576、586位氨基酸；PA的101、256、382、421、437位氨基酸；NP基因的377、450位氨基酸；M1基因的218位氨基酸和M2基因的31位氨基酸。
基于1998年至2009年浙江省分离的甲型H3N2流感病毒株全基因组，HA和NA基因及部分内部基因的非抗原表位区域可能存在一些未知或新的抗原位点。基于完整序列构建的系统发育树比基于HA基因构建的系统发育树更能全面反映流感病毒株间的亲缘关系和进化规律。
