Article(id=1321169610964058648, tenantId=1146029695717560320, journalId=1319373219989389464, issueId=1321169578152014376, articleNumber=null, orderNo=null, doi=10.11847/zgggws1148021, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1750867200000, receivedDateStr=2025-06-26, revisedDate=1752422400000, revisedDateStr=2025-07-14, acceptedDate=1754236800000, acceptedDateStr=2025-08-04, onlineDate=1792920981398, onlineDateStr=2026-10-25, pubDate=1760025600000, pubDateStr=2025-10-10, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1792920981398, onlineIssueDateStr=2026-10-25, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1792920981398, creator=13701087609, updateTime=1792920981398, updator=13701087609, issue=Issue{id=1321169578152014376, tenantId=1146029695717560320, journalId=1319373219989389464, year='2025', volume='41', issue='10', pageStart='1153', pageEnd='1280', issueExtLink='null', onlineDate='null', pubDate='1760025600000', pubDateStr='2025-10-10', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1792920973575, creator='13701087609', updateTime=1792920973575, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext=null, issueFiles=null, downloadFileDto=null}, startPage=1232, endPage=1239, ext={EN=ArticleExt(id=1321169611207328281, articleId=1321169610964058648, tenantId=1146029695717560320, journalId=1319373219989389464, language=EN, title=Molecular epidemiological characterization of SARS-CoV-2 Omicron variants in Quzhou, 2023–2024, columnId=1320427686514770171, journalTitle=Chinese Journal of Public Health, columnName=Survey and Report, runingTitle=null, highlight=null, articleAbstract=
Objective

To understand the epidemiological trends of SARS-CoV-2 Omicron variants and evolutionary variations of the spike protein in Quzhou city of Zhejiang province from 2023 to 2024.

Methods

Respiratory specimens (including nasopharyngeal swabs and sputum specimens) were collected from COVID-19 cases at sentinel surveillance sites for SARS-CoV-2 variants and influenza in Quzhou between January 2023 and September 2024. The whole genome sequences of SARS-CoV-2 from 267 cases were obtained by nanopore sequencing. The genotypes and amino acid variations were analyzed through Pangolin v4.3 and Nextclade v3.13.1 platforms. Heatmaps of amino acid mutations in the key domains of the spike protein were generated by TBtools-Ⅱ v2.222, while the impact of amino acid mutations on viral adaptability was assessed by the VarEPS system.

Results

All the 246 sequences were Omicron variants of SARS-CoV-2, showing the turnover of BA.5-XBB-BA.2 lineages. These variants were classified into ten sub-lineages, with JN.1 and its sub-lineages showing the highest prevalence (42.28%, 104/246). This classification was consistent with the results of the phylogenetic analysis. The distribution of SARS-CoV-2 genotypes across different age groups showed differences (P < 0.001). Amino acid mutation analysis revealed frequent mutations in the spike protein, with the number of mutation sites gradually increasing over time and involving substitutions, insertions, and deletions. JN.1, XDV.1, and their sub-lineages exhibited higher mutation frequency in the spike protein, accumulating novel mutations (K356T, R403K, N450D, N481K, E544K, A570V, P621S, etc.) in key domains. Functional assessments indicated that multiple spike protein mutations (R346T, S371F, S373P, T376A, D405N, R408S, K417N, G446S, F456L, Y505H, etc.) may reduce the binding stability between the spike protein with neutralizing antibodies.

Conclusion

The Omicron variants were the predominant circulating variants in Quzhou during 2023–2024, exhibiting diverse genotypes. Monitoring and analyzing amino acid mutations in the spike protein facilitate timely understanding of the evolutionary characteristics of SARS-CoV-2, providing a theoretical basis for risk assessment of COVID-19 variant prevalence and the implementation of epidemic prevention and control measures.

, authors=Shiteng HUANG, Bingdong ZHAN, Lei LYU, Jialing YOU, Chenghua YE, Sheng WAN, Ruijun YANG, authorsList=Shiteng HUANG, Bingdong ZHAN, Lei LYU, Jialing YOU, Chenghua YE, Sheng WAN, Ruijun YANG, authorCompany=null, correspAuthors=Ruijun YANG, authorNote=null, correspAuthorsNote=
YANG Ruijun, E-mail:
, copyrightStatement=Copyright © 2025 Chinese Journal of Public Health. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1321169613883294241, articleId=1321169610964058648, tenantId=1146029695717560320, journalId=1319373219989389464, language=CN, title=2023—2024年衢州市新型冠状病毒Omicron变异株分子流行病学特征分析, columnId=1320427686770622717, journalTitle=中国公共卫生, columnName=调查报告与分析, runingTitle=null, highlight=null, articleAbstract=
目的

了解2023—2024年浙江省衢州市新冠病毒(SARS-CoV-2)Omicron变异株流行趋势及刺突蛋白(S)变异进化规律。

方法

收集2023年1月—2024年9月衢州市各新冠病毒变异监测哨点和流感监测哨点医院送检的新冠病毒感染者鼻咽拭子、痰液等呼吸道样本;采用纳米孔测序技术对收集的267份呼吸道样本进行新冠病毒全基因组测序。运用Pangolin v4.3和Nextclade v3.13.1在线分析平台进行基因分型,并获取氨基酸变异等信息;通过 TBtools-Ⅱ v2.222 绘制S蛋白关键结构域的氨基酸变异热图,利用VarEPS系统评估氨基酸变异对病毒适应性的影响。

结果

共获得246条新冠病毒全基因组有效序列,均为Omicron变异株,可分为10个进化分支,总体呈BA.5-XBB-BA.2谱系进行顺序更替,其中JN.1及其亚分支占比最高(42.28%,104/246),与系统发育分析结果一致。不同年龄组的新冠病毒基因型分布差异有统计学意义(P<0.001)。氨基酸变异分析显示,S蛋白氨基酸变异最为频繁,其变异位点数随时间逐步增加,并存在氨基酸更替/插入/缺失变异,其中JN.1和XDV.1及其亚分支S蛋白氨基酸突变频率更高,并在关键结构域新增多个变异位点(K356T、R403K、N450D、N481K、E544K、A570V、P621S等)。评估显示,S蛋白多个氨基酸变异位点(R346T、S371F、S373P、T376A、D405N、R408S、K417N、G446S、F456L、Y505H等)可在一定程度上降低S蛋白与中和抗体的结合稳定性。

结论

2023—2024年衢州地区以Omicron变异株为优势变异株,其基因型呈现多样性,对S蛋白的氨基酸变异监测与分析,有助于及时了解新冠病毒的进化特征,为新冠病毒变异株的流行风险评估及疫情防控提供理论依据。

, authors=黄世腾, 占炳东, 吕磊, 游佳玲, 叶承华, 万圣, 杨瑞军*, *, authorsList=黄世腾, 占炳东, 吕磊, 游佳玲, 叶承华, 万圣, 杨瑞军, authorCompany=null, correspAuthors=杨瑞军, authorNote=

黄世腾(1984—),主管技师,硕士,研究方向:微生物检测

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杨瑞军,E-mail:
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PLoS One, 2023, 18(10): e0289432., articleTitle=null, refAbstract=null), Reference(id=1321169624482300542, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=31, rfOrder=30, authorNames=null, journalName=null, refType=null, unstructuredReference=Khatri R, Siddqui G, Sadhu S, et al. Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity[J]. Medical Microbiology and Immunology, 2023, 212(1): 103-122., articleTitle=null, refAbstract=null), Reference(id=1321169624561992319, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=32, rfOrder=31, authorNames=null, journalName=null, refType=null, unstructuredReference=Li P, Faraone J N, Hsu C C, et al. Neutralization and spike stability of JN. 1-derived LB. 1, KP. 2.3, KP. 3, and KP. 3.1. 1 subvariants[J]. mBio, 2025, 16(5): e00464-25., articleTitle=null, refAbstract=null), Reference(id=1321169624650072704, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=33, rfOrder=32, authorNames=null, journalName=null, refType=null, unstructuredReference=Wu A P, Wang L L, Zhou H Y, et al. One year of SARS-CoV-2 evolution[J]. Cell Host and Microbe, 2021, 29(4): 503-507., articleTitle=null, refAbstract=null)], funds=null, companyList=[AuthorCompany(id=1321169614139146786, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, xref=null, ext=[AuthorCompanyExt(id=1321169614147535395, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, companyId=1321169614139146786, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=Microbiology Laboratory, Quzhou Center for Disease Control and Prevention, Quzhou 324000, China), AuthorCompanyExt(id=1321169614155924004, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, companyId=1321169614139146786, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=衢州市疾病预防控制中心微生物检验科,衢州 324000)])], figs=[ArticleFig(id=1321169619067454035, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Fig.1, caption=Time distribution of different genotypes of 246 Omicron variants in Quzhou, figureFileSmall=ewBOxp/xFqbvDyQJSwJ7Bg==, figureFileBig=I74E/QDEMxFOqR77OqY0Ng==, tableContent=null), ArticleFig(id=1321169619147145812, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=图1, caption=衢州市246例Omicron变异株各基因型检出时间分布, figureFileSmall=ewBOxp/xFqbvDyQJSwJ7Bg==, figureFileBig=I74E/QDEMxFOqR77OqY0Ng==, tableContent=null), ArticleFig(id=1321169619348472405, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Fig.2, caption=Phylogenetic tree of 246 Omicron variants in Quzhou, 2023–2024 based on whole genome sequences, figureFileSmall=RfE5hJ2nDhHB7WhtPYu6XQ==, figureFileBig=afj3a/AcxVbgGUgqAGW4oQ==, tableContent=null), ArticleFig(id=1321169619423969878, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=图2, caption=2023—2024年衢州市246例Omicron变异株全基因组系统发育树, figureFileSmall=RfE5hJ2nDhHB7WhtPYu6XQ==, figureFileBig=afj3a/AcxVbgGUgqAGW4oQ==, tableContent=null), ArticleFig(id=1321169619503661655, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Fig.3, caption=Cluster heatmap for amino acid mutation frequency in the S protein of 246 Omicron variants in Quzhou, figureFileSmall=4BEUDYxxQoTWq+j7rSDvGQ==, figureFileBig=A8NfWxBF3XqzdYi85fqJDw==, tableContent=null), ArticleFig(id=1321169619574964824, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=图3, caption=衢州市246例Omicron变异株S蛋白氨基酸突变频率聚类分析热图, figureFileSmall=4BEUDYxxQoTWq+j7rSDvGQ==, figureFileBig=A8NfWxBF3XqzdYi85fqJDw==, tableContent=null), ArticleFig(id=1321169619650462297, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Tab.1, caption=

Population distribution of Omicron variants infecting 246 patients in Quzhou

, figureFileSmall=null, figureFileBig=null, tableContent=
特征BA.5.2及其亚分支XBB.1.9及其亚分支XBB.1.16及其亚分支JN.1及其亚分支XDV.1及其亚分支其他分支aχ2值P值
例数构成比/%例数构成比/%例数构成比/%例数构成比/%例数构成比/%例数构成比/%
性别0.8410.974
 男性945.002551.021045.454543.271144.001246.15
 女性1155.002448.981254.555956.731456.001453.85
年龄/岁<0.001b
 <20420.00612.24313.631615.38312.00415.38
 20~420.001224.49522.733129.811040.00519.23
 30~210.00918.3729.091514.4228.00519.23
 40~15.0048.1614.5543.8528.00311.54
 50~315.00510.21313.641312.50312.0027.69
 ≥60630.001326.53836.362524.04520.00726.93
), ArticleFig(id=1321169619751125594, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=表1, caption=

衢州市246例Omicron变异株感染者人群分布

, figureFileSmall=null, figureFileBig=null, tableContent=
特征BA.5.2及其亚分支XBB.1.9及其亚分支XBB.1.16及其亚分支JN.1及其亚分支XDV.1及其亚分支其他分支aχ2值P值
例数构成比/%例数构成比/%例数构成比/%例数构成比/%例数构成比/%例数构成比/%
性别0.8410.974
 男性945.002551.021045.454543.271144.001246.15
 女性1155.002448.981254.555956.731456.001453.85
年龄/岁<0.001b
 <20420.00612.24313.631615.38312.00415.38
 20~420.001224.49522.733129.811040.00519.23
 30~210.00918.3729.091514.4228.00519.23
 40~15.0048.1614.5543.8528.00311.54
 50~315.00510.21313.641312.50312.0027.69
 ≥60630.001326.53836.362524.04520.00726.93
), ArticleFig(id=1321169619839205979, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Tab.2, caption=

Amino acid mutations in the S protein of SARS-CoV-2 in Quzhou (refer to SARS-CoV-2 Wuhan-Hu-1/2019_MN908947)

, figureFileSmall=null, figureFileBig=null, tableContent=
进化分支NTDRBDRBMCTD1+CTD2FPHR1HR2CT
BA.5.2及
其亚分支
T19I, A27S, G142D,
V213G
G339D, R346T, S371F, S373P,
S375F, T376A, D405N, R408S,
K417N
N440K, L452R, S477N,
T478K, E484A, F486V,
Q498R, N501Y, Y505H
D614G, H655Y,
N679K, P681H,
D796YQ954H,
N969K
—C1243F
XBB.1.9及
其亚分支
T19I, A27S, Q52H, V83A,
G142D, H146Q, Q183E,
V213E, G252V
G339H, R346T, L368I, S371F,
S373P, S375F, T376A, D405N,
R408S, A411S, K417N
N440K, V445P, G446S,
L455F, F456L, N460K, S477N,
T478K, E484A, F486P, F490S,
Q498R, N501Y, Y505H
D614G, H655Y,
N679K, P681H
D796YQ954H,
N969K
—D1259Y
XBB.1.16及
其亚分支
T19I, A27S, V83A, L84I,
G142D, H146Q, E180V,
Q183E, V213E, G252V
G339H, R346T, L368I, S371F,
S373P, S375F, T376A, D405N,
R408S, K417N
N440K, V445P, G446S, L455F,
F456L, N460K, S477N, T478R,
E484A, F486P, F490S, Q498R,
N501Y, Y505H
T547I, D614G,
H655Y, N679K,
P681H
D796YQ954H,
N969K
—D1259Y
JN.1及其
亚分支
T19I, R21T, A27S, S50L,
F59S, V127F, G142D, H146Q,
F157S, R158G, Q183H, L212I,
V213G, L216F, H245N, S255F,
A264D, V16insMPLF
I332V, G339H, R346T, K356T,
S371F, S373P, S375F, T376A,
R403K, D405N, R408S, K417N
N440K, V445H, G446S, N450D,
L452W, L455S, F456L, N460K,
S477N, T478K, N481K, E484K,
F486P, Q498R, N501Y, Y505H
E554K, A570V,
D614G, P621S,
H655Y, N679K,
P681R
D796YS939F,
Q954H,
N969K,
I934V
G1171DG1251E
XDV.1及
其亚分支
T19I, R21T, A27S, S50L,
V127F, G142D, F157S,
R158G, L212I, V213G,
L216F, H245N, A264D,
V16insMPLF
I332V, G339H, K356T, S371F,
S373P, S375F, T376A, R403K,
D405N, R408S, K417N
N440K, V445H, G446S, N450D,
L452W, L455S, F456L, N460K,
S477N, T478K, N481K, E484K,
F486P, Q498R, N501Y, Y505H
E554K, A570V,
D614G, P621S,
H655Y, N679K,
P681R
D796YS939F,
Q954H,
N969K
L1203F—
), ArticleFig(id=1321169619939869277, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=表2, caption=

衢州市新冠病毒S蛋白氨基酸变异情况(参考新冠病毒Wuhan-Hu-1/2019_MN908947)

, figureFileSmall=null, figureFileBig=null, tableContent=
进化分支NTDRBDRBMCTD1+CTD2FPHR1HR2CT
BA.5.2及
其亚分支
T19I, A27S, G142D,
V213G
G339D, R346T, S371F, S373P,
S375F, T376A, D405N, R408S,
K417N
N440K, L452R, S477N,
T478K, E484A, F486V,
Q498R, N501Y, Y505H
D614G, H655Y,
N679K, P681H,
D796YQ954H,
N969K
—C1243F
XBB.1.9及
其亚分支
T19I, A27S, Q52H, V83A,
G142D, H146Q, Q183E,
V213E, G252V
G339H, R346T, L368I, S371F,
S373P, S375F, T376A, D405N,
R408S, A411S, K417N
N440K, V445P, G446S,
L455F, F456L, N460K, S477N,
T478K, E484A, F486P, F490S,
Q498R, N501Y, Y505H
D614G, H655Y,
N679K, P681H
D796YQ954H,
N969K
—D1259Y
XBB.1.16及
其亚分支
T19I, A27S, V83A, L84I,
G142D, H146Q, E180V,
Q183E, V213E, G252V
G339H, R346T, L368I, S371F,
S373P, S375F, T376A, D405N,
R408S, K417N
N440K, V445P, G446S, L455F,
F456L, N460K, S477N, T478R,
E484A, F486P, F490S, Q498R,
N501Y, Y505H
T547I, D614G,
H655Y, N679K,
P681H
D796YQ954H,
N969K
—D1259Y
JN.1及其
亚分支
T19I, R21T, A27S, S50L,
F59S, V127F, G142D, H146Q,
F157S, R158G, Q183H, L212I,
V213G, L216F, H245N, S255F,
A264D, V16insMPLF
I332V, G339H, R346T, K356T,
S371F, S373P, S375F, T376A,
R403K, D405N, R408S, K417N
N440K, V445H, G446S, N450D,
L452W, L455S, F456L, N460K,
S477N, T478K, N481K, E484K,
F486P, Q498R, N501Y, Y505H
E554K, A570V,
D614G, P621S,
H655Y, N679K,
P681R
D796YS939F,
Q954H,
N969K,
I934V
G1171DG1251E
XDV.1及
其亚分支
T19I, R21T, A27S, S50L,
V127F, G142D, F157S,
R158G, L212I, V213G,
L216F, H245N, A264D,
V16insMPLF
I332V, G339H, K356T, S371F,
S373P, S375F, T376A, R403K,
D405N, R408S, K417N
N440K, V445H, G446S, N450D,
L452W, L455S, F456L, N460K,
S477N, T478K, N481K, E484K,
F486P, Q498R, N501Y, Y505H
E554K, A570V,
D614G, P621S,
H655Y, N679K,
P681R
D796YS939F,
Q954H,
N969K
L1203F—
), ArticleFig(id=1321169620019561054, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=EN, label=Tab.3, caption=

Risk assessment of amino acid mutations in the S protein

, figureFileSmall=null, figureFileBig=null, tableContent=
氨基酸变异Provean评分a非同义密度b抗体亲和力c结合稳定性(ACE2)d氨基酸替换风险e
S:V213E−1.0160.000★★☆
S:V213G−0.9360.000★★☆☆
S:G339D−0.3440.001★★☆
S:G339H−0.982★▲☆☆
S:V445P−0.148★★☆
S:V445H0.117★★☆☆
S:L455F0.4620.003★
S:L455S0.8120.000★★☆☆
S:T478R−0.7160.002★★☆
S:T478K−0.3060.485★★☆
S:F486V−0.3880.000★★☆
S:F486P−0.713★★☆☆
), ArticleFig(id=1321169620124418655, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1321169610964058648, language=CN, label=表3, caption=

S蛋白氨基酸位点变异风险评估结果

, figureFileSmall=null, figureFileBig=null, tableContent=
氨基酸变异Provean评分a非同义密度b抗体亲和力c结合稳定性(ACE2)d氨基酸替换风险e
S:V213E−1.0160.000★★☆
S:V213G−0.9360.000★★☆☆
S:G339D−0.3440.001★★☆
S:G339H−0.982★▲☆☆
S:V445P−0.148★★☆
S:V445H0.117★★☆☆
S:L455F0.4620.003★
S:L455S0.8120.000★★☆☆
S:T478R−0.7160.002★★☆
S:T478K−0.3060.485★★☆
S:F486V−0.3880.000★★☆
S:F486P−0.713★★☆☆
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2023—2024年衢州市新型冠状病毒Omicron变异株分子流行病学特征分析
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黄世腾 , 占炳东 , 吕磊 , 游佳玲 , 叶承华 , 万圣 , 杨瑞军 *, *
中国公共卫生 | 调查报告与分析 2025,41(10): 1232-1239
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中国公共卫生 |调查报告与分析 2025 , 41 (10) : 1232 -1239
2023—2024年衢州市新型冠状病毒Omicron变异株分子流行病学特征分析
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黄世腾, 占炳东, 吕磊, 游佳玲, 叶承华, 万圣, 杨瑞军*, *
作者信息
  • 衢州市疾病预防控制中心微生物检验科,衢州 324000
通讯作者:
杨瑞军,E-mail:
作者简介:

黄世腾(1984—),主管技师,硕士,研究方向:微生物检测

Molecular epidemiological characterization of SARS-CoV-2 Omicron variants in Quzhou, 2023–2024
Shiteng HUANG, Bingdong ZHAN, Lei LYU, Jialing YOU, Chenghua YE, Sheng WAN, Ruijun YANG
Affiliations
  • Microbiology Laboratory, Quzhou Center for Disease Control and Prevention, Quzhou 324000, China
  • Corresponding Author:
    YANG Ruijun, E-mail:
出版时间: 2025-10-10 doi: 10.11847/zgggws1148021
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目的

了解2023—2024年浙江省衢州市新冠病毒(SARS-CoV-2)Omicron变异株流行趋势及刺突蛋白(S)变异进化规律。

方法

收集2023年1月—2024年9月衢州市各新冠病毒变异监测哨点和流感监测哨点医院送检的新冠病毒感染者鼻咽拭子、痰液等呼吸道样本;采用纳米孔测序技术对收集的267份呼吸道样本进行新冠病毒全基因组测序。运用Pangolin v4.3和Nextclade v3.13.1在线分析平台进行基因分型,并获取氨基酸变异等信息;通过 TBtools-Ⅱ v2.222 绘制S蛋白关键结构域的氨基酸变异热图,利用VarEPS系统评估氨基酸变异对病毒适应性的影响。

结果

共获得246条新冠病毒全基因组有效序列,均为Omicron变异株,可分为10个进化分支,总体呈BA.5-XBB-BA.2谱系进行顺序更替,其中JN.1及其亚分支占比最高(42.28%,104/246),与系统发育分析结果一致。不同年龄组的新冠病毒基因型分布差异有统计学意义(P<0.001)。氨基酸变异分析显示,S蛋白氨基酸变异最为频繁,其变异位点数随时间逐步增加,并存在氨基酸更替/插入/缺失变异,其中JN.1和XDV.1及其亚分支S蛋白氨基酸突变频率更高,并在关键结构域新增多个变异位点(K356T、R403K、N450D、N481K、E544K、A570V、P621S等)。评估显示,S蛋白多个氨基酸变异位点(R346T、S371F、S373P、T376A、D405N、R408S、K417N、G446S、F456L、Y505H等)可在一定程度上降低S蛋白与中和抗体的结合稳定性。

结论

2023—2024年衢州地区以Omicron变异株为优势变异株,其基因型呈现多样性,对S蛋白的氨基酸变异监测与分析,有助于及时了解新冠病毒的进化特征,为新冠病毒变异株的流行风险评估及疫情防控提供理论依据。

新型冠状病毒  /  Omicron  /  刺突蛋白  /  全基因组测序  /  衢州市
Objective

To understand the epidemiological trends of SARS-CoV-2 Omicron variants and evolutionary variations of the spike protein in Quzhou city of Zhejiang province from 2023 to 2024.

Methods

Respiratory specimens (including nasopharyngeal swabs and sputum specimens) were collected from COVID-19 cases at sentinel surveillance sites for SARS-CoV-2 variants and influenza in Quzhou between January 2023 and September 2024. The whole genome sequences of SARS-CoV-2 from 267 cases were obtained by nanopore sequencing. The genotypes and amino acid variations were analyzed through Pangolin v4.3 and Nextclade v3.13.1 platforms. Heatmaps of amino acid mutations in the key domains of the spike protein were generated by TBtools-Ⅱ v2.222, while the impact of amino acid mutations on viral adaptability was assessed by the VarEPS system.

Results

All the 246 sequences were Omicron variants of SARS-CoV-2, showing the turnover of BA.5-XBB-BA.2 lineages. These variants were classified into ten sub-lineages, with JN.1 and its sub-lineages showing the highest prevalence (42.28%, 104/246). This classification was consistent with the results of the phylogenetic analysis. The distribution of SARS-CoV-2 genotypes across different age groups showed differences (P < 0.001). Amino acid mutation analysis revealed frequent mutations in the spike protein, with the number of mutation sites gradually increasing over time and involving substitutions, insertions, and deletions. JN.1, XDV.1, and their sub-lineages exhibited higher mutation frequency in the spike protein, accumulating novel mutations (K356T, R403K, N450D, N481K, E544K, A570V, P621S, etc.) in key domains. Functional assessments indicated that multiple spike protein mutations (R346T, S371F, S373P, T376A, D405N, R408S, K417N, G446S, F456L, Y505H, etc.) may reduce the binding stability between the spike protein with neutralizing antibodies.

Conclusion

The Omicron variants were the predominant circulating variants in Quzhou during 2023–2024, exhibiting diverse genotypes. Monitoring and analyzing amino acid mutations in the spike protein facilitate timely understanding of the evolutionary characteristics of SARS-CoV-2, providing a theoretical basis for risk assessment of COVID-19 variant prevalence and the implementation of epidemic prevention and control measures.

SARS-CoV-2  /  Omicron  /  spike protein  /  whole genome sequencing  /  Quzhou city
黄世腾, 占炳东, 吕磊, 游佳玲, 叶承华, 万圣, 杨瑞军. 2023—2024年衢州市新型冠状病毒Omicron变异株分子流行病学特征分析. 中国公共卫生, 2025 , 41 (10) : 1232 -1239 . DOI: 10.11847/zgggws1148021
Shiteng HUANG, Bingdong ZHAN, Lei LYU, Jialing YOU, Chenghua YE, Sheng WAN, Ruijun YANG. Molecular epidemiological characterization of SARS-CoV-2 Omicron variants in Quzhou, 2023–2024[J]. Chinese Journal of Public Health, 2025 , 41 (10) : 1232 -1239 . DOI: 10.11847/zgggws1148021
自2019年底,新型冠状病毒感染疫情(coronavirus disease 2019, COVID-19, 简称“新冠疫情”)出现以来,迅速引发全球大流行,对人类生命健康和社会公共卫生安全造成巨大威胁[1]。随着新冠病毒疫情的持续流行,不断有新的变异株出现,从Alpha、Beta、Gamma、Delta到Omicron,其分支已达数百种[2];其中Omicron变异株于2021年11月在南非首次被发现,其免疫逃逸能力显著增强,并迅速成为全球流行的优势株[3]。新冠病毒基因组全长约30 kb,可编码至少4种结构蛋白和多种非结构蛋白,其中结构蛋白主要包括核壳蛋白(nucleocapsid protein, N)、基质蛋白(matrix protein, M)、包膜蛋白(envelop protein, E)和刺突表面蛋白(spike protein, S)[4]。S蛋白在识别并结合宿主细胞受体血管紧张素转化酶2(angiotensin converting enzyme 2, ACE2)、介导细胞膜融合及诱导中和抗体产生中起到重要作用[5]。相关研究表明,S蛋白的氨基酸位点变异能直接导致新冠病毒传播力和致病力的改变[6–7]。因此,对S蛋白变异位点的研究具有重要意义。本研究对2023—2024年浙江省衢州市新冠病毒Omicron变异株流行趋势和遗传进化特征进行分析,重点关注S蛋白关键位点的变异趋势;旨在为浙江省衢州地区新冠疫情防控提供科学依据。
本研究样本来源于2023年1月—2024年9月浙江省衢州地区各新冠病毒变异监测哨点和流感监测哨点医院送检的新冠病毒感染者鼻咽拭子、痰液等呼吸道样本;同时收集病例的基本资料(包括姓名、性别、年龄、发病日期、采样日期等)。
使用核酸提取试剂盒(西安天隆科技有限公司)CqEx-RNA/DNA病毒(CDC)提取病毒RNA;使用新冠病毒核酸检测荧光法PCR试剂盒(上海伯杰医疗科技有限公司)进行新冠病毒核酸检测(ABI 实时荧光PCR仪QuantStudio5,美国赛默飞)。选取CT值<32的阳性样本,采用ULSEN®超灵敏度新冠病毒全基因组捕获试剂盒(北京微未来科技有限公司)(低载量),进行新冠病毒全基因组特异性捕获扩增。
采用连接法测序多样本DNA建库辅助试剂盒(杭州柏熠科技有限公司)A+B(BK-AUX024)和快速条形码测序试剂盒(SQK-RBK114-24, Oxford Nanopore)构建文库、使用MinON or GridlON测序芯片(R10, Oxford Nanopore)和Nanopore纳米孔测序仪(GridION MK1,英国牛津公司)对新冠病毒进行全基因组测序。
采用杭州柏熠病原微生物分析平台上的新冠病毒分析模块,进行新冠病毒全基因组序列的拼接组装,并对测序数据进行质量评估。将获取的新冠病毒全基因组序列通过Pangolin v4.3(https://pangolin.cog-uk.io/)和Nextclade v3.13.1(https://clades.nextstrain.org/)在线分型平台进行基因分型。选取覆盖度在98%以上、Overall QC status 评级在mediocre及以上的序列进行后续分析。
以新冠病毒Wuhan-Hu-1/2019(GenBank: MN908947)为参考序列,将选取的序列通过Nextclade v3.13.1在线分析平台获取核苷酸和氨基酸变异位点等参数信息;应用TBtools-Ⅱ v2.222软件绘制S蛋白氨基酸突变聚类分析热图;使用MAFFT v7.487软件进行序列多重比对,通过IQ-TREE v2.1.4软件基于最大似然法构建系统发育树,Bootstrap值设置为1000;最后通过iTOL(https://itol.embl.de/)对系统发育树进行美化。
通过新冠病毒变异评估与预警系统(variations evaluation and prewarning system, VarEPS)(https://nmdc.cn/ncovn/variationsite)[8]评估S蛋白关键结构域氨基酸突变对S蛋白与ACE2受体结合稳定性和S蛋白与中和抗体亲和力等生物学功能的影响,并对氨基酸突变进行风险评估。
采用Excel 2016和SPSS 26.0软件对数据进行统计分析,组间比较运用χ2检验或Fisher确切概率法。以 P<0.05 为差异有统计学意义。
对267份新冠病毒感染病例样本进行全基因组测序,经质量评估及数据过滤,共获得246条覆盖度在98%以上、评级在mediocre及以上的新冠病毒全基因组序列。分型结果显示,246条新冠病毒全基因组序列均为Omicron变异株,可分为10个进化分支,其中BA.5谱系占比8.13%(20/246),包括13例BF.7及其亚分支,7例DY及其亚分支;XBB谱系占比38.62%(95/246),包括49例XBB.1.9及其亚分支,22例XBB.1.16及其亚分支,11例XBB.1.5及其亚分支,9例XBB.1.22及其亚分支,4例XBB其他进化分支;BA.2谱系占比43.09%(106/246),包括104例JN.1及其亚分支, 2例BA.2.75及其亚分支;XDV.1及其亚分支25例(占比10.16%)。
2023年1月—2024年9月有246例新冠病毒感染病例,其中2023年12月未监测到新冠病毒阳性病例;2023年1月—2023年4月以BA.5.2及其亚分支为优势基因型;2023年5月—2023年6月为过渡期,XBB.1分支出现并与BA.5.2及其亚分支共存;2023年7月—2023年11月以XBB.1.9及其亚分支为优势基因型;2024年主要以JN.1及其亚分支为优势基因型。在246例新冠病毒感染病例中,71例来源于新冠病毒变异监测哨点,175例来源于流感监测哨点医院;其中男女比例0.84:1(112:134),年龄范围在2~92岁,中位数为34(23,60)岁。不同性别的新冠病毒基因型分布差异无统计学意义(χ2=0.841,P=0.974);不同年龄组基因型分布差异有统计学意义(Fisher确切概率法,P<0.001);其中BA.5.2、XBB.1.9和XBB.1.16及其亚分支在≥60岁人群分布较高,JN.1和XDV.1及其亚分支在20~29岁人群分布较高。
从GISAID数据库下载16条国内同期的新冠病毒Omicron变异株参考序列,与本研究的246条新冠病毒全基因组序列及武汉参考株Wuhan-Hu-1/2019(GenBank:MN908947)序列构建系统发育树。结果显示,246条序列主要聚集为10个进化群,包括BA.5.2及其亚分支、XBB.1.5及其亚分支、XBB.1.9及其亚分支、XBB.1.16及其亚分支、XBB.1.22及其亚分支、XBB其他进化分支、JN.1及其亚分支、BA.2.75及其亚分支和XDV.1及其亚分支;与Pangolin 分型结果基本一致;相同分支聚成一簇,其中JN.1及其亚分支与武汉参考株的遗传距离最远。
与新冠病毒Wuhan-Hu-1/2019(GenBank:MN908947)序列相比,衢州市246例新冠病毒全基因组序列平均有核苷酸变异位点109个(76~137个)、氨基酸变异位点80个(53~100个);并随着时间的推移,其氨基酸变异位点数从BA.5.2及其亚分支(53~69个)到XBB.1及其亚分支(66~78个),再到JN.1和XDV.1及其亚分支(82~100个),呈现上升趋势;其中S蛋白氨基酸变异(29~57个)最为频繁,其共同变异位点28个,主要集中于S1亚基的N端结构域(N-terminal domain, NTD)和受体结合域(receptor-binding domain, RBD,包括受体结合基序(receptor-binding motif, RBM);其余变异位点依次位于C端核心结构域(C-terminal core domain, CTD),包括630loop、七肽重复区1(heptad repeat domain 1, HR1)、融合肽(fusion peptide, FP)、胞质尾区(cytoplasmic tail, CT)和七肽重复区2(heptad repeat domain 2, HR2);而跨膜结构域(transmembrane domain, TM)未发现氨基酸变异位点。
相较于BA.5.2及其亚分支,BF.7及其亚分支在S蛋白均增加了R346T(RBD区)氨基酸变异位点,XBB.1.9及其亚分支在NTD(共增加4个:Q52H、V83A、Q183E、G252V;转换1个:V213E)、RBD(共增加8个:L368I、A411S、V445P、G446S、L455F、F456L、N460K、F490S;减少1个:L452R;转换2个:G339H、F486P)。而相较于XBB.1.9及其亚分支,EG.5.1及其亚分支在S蛋白均增加了Q52H、F456L氨基酸变异位点,HK.3及其亚分支相较于EG.5.1及其亚分支在S蛋白又增加了L455F氨基酸变异位点。JN.1及其亚分支相较于XBB.1.9及其亚分支在NTD(共增加11个:R21T、S50L、F59S、V127F、F157S、R158G、L212I、L216F、H245N、S255F、A264D;减少3个:Q52H、V83A、G252V;转换2个:Q183H、V213G)、RBD(共增加6个:I332V、K356T、R403K、N450D、L452W、N481K;减少3个L368I、F456L、F490S;转换3个:V445H、L455S、E484K)。此外,本研究所有JN.1和XDV.1及其亚分支均发生了V16insMPLF氨基酸插入(NTD区),在KP.2.3和LB.1及其亚分支中均出现了S31氨基酸位点的缺失(S31del)。根据各基因型S蛋白氨基酸位点突变检出率绘制的聚类分析热图显示,不同基因型的氨基酸突变频率有所差异,其中JN.1和XDV.1及其亚分支的S蛋白氨基酸突变最为频繁。
通过VarEPS系统对S蛋白高频变异位点进行变异评估与预测分析。结果显示,多个变异位点(G142D、R346T、S371F、S373P、T376A、D405N、R408S、K417N、G446S、F456L、Y505H、N969K等)可在一定程度上降低S蛋白与中和抗体的亲和力(★~★★);部分变异位点(G339H、S371F、S373P、S375F、N450D、L452R等)还可降低S蛋白与ACE2受体的结合稳定性(~▲),这些变异位点广泛分布于EG.5.1、HK.3、JN.1、XDV.1等多种基因型及其亚分支中。此外,部分多重变异位点(V213E/G、G339D/H、V445P/H、L455F/S、F486V/P等)在JN.1和XDV.1及其亚分支中表现为更高的氨基酸替换风险(☆☆),其对S蛋白与中和抗体的亲和力及ACE2受体结合稳定性的影响也有所差异。
新冠病毒Omicron变异株是目前传染性最强的变异株,具有传播速度快、免疫逃逸能力强等显著特点[9–10],也是目前全球流行的主要变异株[11]。衢州市新冠病毒变异株监测结果显示,2023—2024年新冠病毒流行株均为Omicron变异株,与全球流行趋势一致[11]。从分型结果看,可分为10个进化分支,不同时期优势分支有所不同,并随着病毒的进化逐渐变迁,从BA.5.2及其亚分支到XBB谱系的出现,再逐渐进化出EG.5.1和HK.3及其亚分支并成为优势分支;衢州市从2024年1月JN.1及其亚分支开始出现,并迅速占据主导地位,该变异株也引发了多起全球性疫情, 可能具有更强的感染性和免疫逃逸能力[12]。此外,不同分支在变异变迁过程中存在共存现象,提示病毒的变异可能是在生存压力下逐渐选择的结果,通过不断进化,从而实现免疫逃逸[13]。依据中国疾病预防控制中心发布的《全国新型冠状病毒感染疫情情况》[14],2023—2024年衢州市新冠病毒各分支流行趋势与全国趋势基本一致,但稍有滞后,国内XBB谱系和JN.1及其亚分支均出现更早,这可能与衢州市的地理位置和人员流动性有关,但作为内陆城市,衢州市素有“四省通衢、五路总头”之称,其监测数据仍具有较好的代表性。
在监测的246例病例中,不同性别的新冠病毒基因型分布差异无统计学意义,这与国内部分研究结果一致[15],符合人群对新冠病毒普遍易感的特征[16]。从年龄分布看,本研究覆盖范围在2~92岁,各基因型的年龄分布广泛,但不同年龄组新冠病毒基因型分布差异有统计学意义,并与国内部分研究结果存在一定差异 [15,17]。这可能是受到样本来源及CT值限制,导致不同年龄组的测序样本数存在偏差所致。但广泛的年龄分布同样表明除老年人外,社交活动频繁的青年人群也应加强个人防护,及时接种疫苗。
新冠病毒的持续流行以及庞大的感染群体,为病毒的不断进化创造了条件;并在宿主免疫压力的选择下,形成适应性更强的变异株[18]。研究表明,Omicron变异株S蛋白携带有大量变异位点,包括多个片段的缺失与插入[19]。参考新冠病毒Wuhan-Hu-1/2019(GenBank:MN908947)序列,本研究的246例Omicron变异株平均有核苷酸变异位点109个(76~137个)、氨基酸变异位点80个(53~100个),相较于前期研究[20],呈现明显上升趋势,提示病毒可能通过持续积累突变来提升自身适应能力。有研究显示,S蛋白氨基酸变异位点主要集中于S1亚基的NTD结构域和RBD区域,其中RBD区域直接作用于细胞受体ACE2,而NTD结构域可通过调节S蛋白构象辅助受体结合[21]。因此,NTD和RBD区域的氨基酸位点变异可能对病毒感染力和免疫逃逸能力造成直接影响。
本研究通过对246例Omicron变异株S蛋白氨基酸变异位点分析显示,从BA.5.2到XBB谱系再到JN.1和XDV.1及其亚分支,其S蛋白氨基酸变异位点逐步增加,不同基因型之间氨基酸位点突变频率存在差异。其中,BF.7及其亚分支主要增加了R346T氨基酸变异位点,相较于BA.5及其亚分支有着更强的免疫逃逸能力[22]。 在XBB谱系中新增的G446S、F456L、N460K、F490S等氨基酸变异位点可增强病毒的免疫逃逸能力,但也会削弱病毒与ACE2受体的亲和力[23–24]。同时存在N440K、T478K、Q498R、N501Y等增强受体亲和力的变异位点,以维持病毒感染力与免疫逃逸能力之间的平衡,其中Q498R与N501Y可通过协同作用改变S蛋白的构象,使RBD呈现“向上位效应”,以显著提升受体亲和力[25]。HK.3及其亚分支中的L455F-F456L可通过协同作用增强病毒免疫逃逸能力的同时,逆转对ACE2受体亲和力的不利因素[26],这可能是HK.3及其亚分支在2023年底成为优势基因型的原因之一;也提示位点之间存在复杂的协同作用关系,其分子机制还有待深入研究。JN.1及其亚分支作为目前发现的感染力和免疫逃逸能力最强的进化分支之一,其S蛋白相较于XBB谱系携带有更多的氨基酸变异位点[27],其中K356T、N450D、L452W、L455S、E544K、A570V等氨基酸变异位点可增强病毒的免疫逃逸能力,同时L455S进一步提升了JN.1及其亚分支对 RBD-1类抗体的抗性,使其表现出广泛耐受性,具有强大的免疫逃逸能力[28]。研究表明,E544K突变可使靶向CTD的小鼠源抗体S3H3完全失效[29]。此外,E484K可通过增强受体结合所需的静电互补性从而增加受体亲和力,并可与N501Y协同作用进一步提升病毒感染力[30]。位于S1/S2结构域交界处的P681R突变可通过增强弗林蛋白酶对S蛋白的切割效率,从而提高病毒感染性,并可与D614G协同作用进一步促进S蛋白的活化[31]。此外,本研究中LB.1与KP.2.3基因型均存在S31del变异,其在增强病毒免疫逃逸能力的同时进一步提升病毒的稳定性[32],这可能是衢州市2024年8—9月LB.1与KP.2.3成为优势基因型的原因之一。强大的感染力和免疫逃逸能力促使JN.1及其亚分支迅速成为全球流行的主导变异株,衢州市自2024年1月JN.1及其亚分支取代XBB.1.9及其亚分支以来,也迅速成为绝对优势分支。
新冠病毒作为一种RNA病毒有着较高的突变率,尤其是S蛋白作为介导病毒与宿主细胞受体识别及免疫逃逸的相关蛋白,有着更高的突变率[33],其关键结构域的突变可能会直接影响病毒的感染力和免疫逃逸能力。通过VarEPS系统分析显示,在本研究的S蛋白关键结构域中多数变异位点可不同程度地降低S蛋白与中和抗体的亲和力,从而增加病毒的免疫逃逸能力,这可能也是病毒不断进化的主要方向;但对S蛋白与ACE2受体的结合稳定性影响有限,提示病毒与ACE2受体的结合稳定性可能主要通过多位点间的协同作用得以维持甚至加强,从而保持病毒感染力与免疫逃逸能力之间的平衡。此外,在S蛋白中还存在多个氨基酸位点变异更替(V213E到V213G、G339D到G339H、V445P到V445H、L455F到L455S、F486V到F486P等),这些变异位点的更替在影响抗体亲和力和受体结合稳定性的同时还显示出更高的氨基酸替换风险,应予以重点关注。
综上所述,本研究揭示了衢州市新冠病毒Omicron变异株流行趋势及分子遗传进化特征,通过对新冠病毒变异株的持续监测,有助于及时发现新的变异株及关键变异位点,为新冠疫情溯源、流行风险评估及防控策略的制定提供科学指导,同时对于疫苗及抗病毒药物的研发也具有重要意义。本研究也存在一定的局限性,首先受到样本CT值限制,序列测定未能做到样本全覆盖;其次缺乏完善的临床资料数据,仅在分子层面对衢州市新冠病毒变异株进行分析。后期应进一步提高样本覆盖率及完善临床资料数据,将流行病学研究与分子进化研究相结合,为衢州市新冠疫情的风险研判及精准防控提供科学依据。

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doi: 10.11847/zgggws1148021
  • 接收时间:2025-06-26
  • 首发时间:2026-10-25
  • 出版时间:2025-10-10
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  • 收稿日期:2025-06-26
  • 修回日期:2025-07-14
  • 录用日期:2025-08-04
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    衢州市疾病预防控制中心微生物检验科,衢州 324000

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鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
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红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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