Genetic variation and evolutionary characteristics of hemagglutinin-neuraminidase (HN) gene in human parainfluenza virus 3 in China
10.3760/cma.j.cn112866-20220209-00024
- VernacularTitle:我国人副流感病毒3型HN基因的遗传变异及进化特征分析
- Author:
Jie JIANG
1
;
Linqing ZHAO
;
Min MU
;
Wenyang WANG
;
Jin XU
;
Liang CAI
;
Zhengde XIE
;
Zhen ZHU
;
Yan ZHANG
;
Shanshan ZHOU
;
Yi FENG
;
Naiying MAO
Author Information
1. 国家卫生健康委员会医学病毒和病毒病重点实验室 世界卫生组织西太平洋地区麻疹/风疹参比实验室 中国疾病预防控制中心病毒病预防控制所麻疹室，北京 102206
- Keywords:
Human parainfluenza virus 3;
Hemagglutinin-neuraminidase protein;
Gene signature;
Bayesian evolutionary analysis
- From:
Chinese Journal of Experimental and Clinical Virology
2022;36(2):141-149
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the gene variation and evolutionary characteristics of human parainfluenza virus 3 (HPIV3) circulating in China based on hemagglutinin-neuraminidase (HN) gene.Methods:Multiple qPCR was used to screen nucleic acid of common pathogens in throat swabs from acute respiratory tract infection cases in five provinces (Beijing, Zhejiang, Anhui, Henan, Hunan) from 2007 to 2020. Subsequently, the HN gene sequence of HPIV3 positive samples was determined and compared with the HN gene sequence of HPIV3 strains from 10 provinces in China and abroad in the GenBank database. The molecular evolution analysis was carried out using a variety of bioinformatics method.Results:A total of 49 strains of HPIV3 HN gene sequences were obtained from 5 provinces, with nucleotide homology ranging from 96.6% to 100%. Among them, 48 strains were subtype C3 and 1 strain was subtype C5. Phylogenetic analysis showed that there were co-epidemics of C1, C3 and C5 strains in 12 provinces of China during 2003—2020, and the nucleotide and amino acid homology among the strains were 95.4%-99.8% and 97.9%-100%, respectively. Among them, C3 is the dominant subtype in China, which is divided into five evolutionary branches of C3a, C3b, C3c, C3e and C3f, and the C3f has the widest range and time of spread. The evolutionary analysis of the C3 subtype showed that the estimated time to the most recent common ancestor (tMRCA) of it dated back to 1990, and its effective population size tended to be stable after expansion from 2002 to 2010. The HN gene evolution rate of the evolutionary branches of C3 HPIV3 varied from 3.69×10 -4 to 5.82×10 -4 substitutions/sites/year; the HN protein of C3 subtype strains shared four potential N-glycosylation sites N308, N351, N485 and N523, and the selection pressure was mainly negative. Conclusions:The C3 is an endemic dominant genotype, which has been widely spread and continuously circulating in China, and has formed different evolutionary clades during epidemic.
