The Prevalence and Gene Characteristics Analysis of Human Coronavirus 229E Among Acute Respiratory Infection Cases
In order to the population-based prevalence and viral genetic characteristics of Human coronavirus 229E(HCoV-229E)infection among the cases with acute respiratory infection(ARI)in China,a descriptive epidemiological analysis of HCoV-229E positive cases was conducted among 15,335 ARI cases in eleven provinces of China from 2009 to 2021.S gene amplification was performed on the clinical specimens obtained from HCoV-229E-positive cases for phylogenetic and evolutionary analysis.Among the 15,335 ARI cases,316 were identified to be positive for HCoV,with the detection rate of 2.06％.Of 207 cases identified for subtype,38 were confirmed to be positive for HCoV-229E.The detection rate of HCoV-229E exhibited no statistically significant differences across different seasons(x2=2.345,P=0.504).The detection rate of males is higher than that of females(x2=4.546,P＜0.05).Among different age groups,except for the 5～17 age group where HCoV-229E was not detected,no statistically significant differences in HCoV-229E detection rate were observed(x2=1.927,P=0.588).Of the 38 HCoV-229E positive cases,a total of 23(60.53％)were co-infected cases,compared with HCoV-229E single infection cases,the proportion of lower respiratory tract infection and pneumonia cases increased in co-infection cases.Nine spike protein(S)gene sequences of HCoV-229E were obtained from 2019 to 2021,and together with 90 HCoV-229E S gene sequences downloaded from GenBank,a phylogenetic tree was constructed.The results indicated that HCoV-229E worldwide could be classified into 6 genogroups,showing clear temporal clustering.The 9 HCoV-229E S gene sequences all belong to genogroup 6 but occupied different clades,the genogroup 6 was also the predominant lineage worldwide and located at the end of the phylogenetic tree.The molecular evolution rate of the S gene is about 7.32 × 10-4 substitutions/site/year.Most amino acid sites of the S protein are under negative selection pressure(w＜1),but there are still individual positive selection sites.During the evolution of the virus,multiple amino acid mutations and N-glycosylation site mutations occurred in the S protein,with some mutations located in the 3 receptor-binding loops of the S protein's receptor-binding domain.This study investigates the epidemiological features and molecular evolution characteristics of HCoV-229E in parts of China,offering fundamental data essential for the control and prevention of HCoV-229E infections.
Human coronavirus 229EEpidemiological characteristicsPhylogenetic analysisMolecular evolution
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NSTL
万方数据
