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Article(id=1320442617985356134, tenantId=1146029695717560320, journalId=1319373219989389464, issueId=1320442616123081022, articleNumber=null, orderNo=null, doi=10.11847/zgggws1147360, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1741622400000, receivedDateStr=2025-03-11, revisedDate=1752508800000, revisedDateStr=2025-07-15, acceptedDate=1754064000000, acceptedDateStr=2025-08-02, onlineDate=1792747652764, onlineDateStr=2026-10-23, pubDate=1767974400000, pubDateStr=2026-01-10, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1792747652764, onlineIssueDateStr=2026-10-23, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1792747652764, creator=13701087609, updateTime=1792747652764, updator=13701087609, issue=Issue{id=1320442616123081022, tenantId=1146029695717560320, journalId=1319373219989389464, year='2026', volume='42', issue='1', pageStart='1', pageEnd='128', issueExtLink='null', onlineDate='null', pubDate='1767974400000', pubDateStr='2026-01-10', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1792747652321, creator='13701087609', updateTime=1792748136930, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1320444648791851086, tenantId=1146029695717560320, journalId=1319373219989389464, issueId=1320442616123081022, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1320444648791851087, tenantId=1146029695717560320, journalId=1319373219989389464, issueId=1320442616123081022, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=23, endPage=29, ext={EN=ArticleExt(id=1320442618199265639, articleId=1320442617985356134, tenantId=1146029695717560320, journalId=1319373219989389464, language=EN, title=Whole genome sequencing and population evolution analysis of monkeypox viruses from four cases in Guizhou province from 2023 to 2024, columnId=1320442616970330431, journalTitle=Chinese Journal of Public Health, columnName=Special Report—Prevention and Control of Infectious Diseases, runingTitle=null, highlight=null, articleAbstract=
Objective

To analyze the whole genome sequences and the population evolution characteristics of monkeypox viruses from four cases in Guizhou province from 2023 to 2024.

Methods

Samples were collected from four monkeypox cases in Guizhou province, and the whole genome sequences of the viruses were obtained by amplicon sequencing. High-quality genome sequences of monkeypox viruses in Asia from 2022 to 2024 were screened and downloaded from the GISAID database to construct a population dataset containing 173 sequences. This dataset was used for divergence time estimation, phylogenetic analysis, and mutation site identification.

Results

In the population dataset, the number of sequences was the largest in 2023 (126), followed by that in 2022 (33) and 2024 (14). It was estimated that the time to the most recent common ancestor (TMRCA) of monkeypox viruses emerged in 2013, with an evolutionary rate of 3.77×10−5 subs/site/year. From 2022 to 2024, the diversity of monkeypox virus lineages declined, with the dominant lineage changing from IIb.A.2 to IIb.C.1. China had the most diverse monkeypox virus lineages, including IIb.C.1, IIb.B.1.3, IIb.B.1.20, IIb.B.1, IIb.B.1.5, and IIb.A.1. The phylogenetic analysis revealed that the prevalent strains in 2022 were mainly related to lineage A of clade IIb. In 2023, IIb.C.1 became the dominant lineage, and it further evolved to be dominated by sublineage IIb.C.1.1 with the emergence of IIb.B.1. Due to the limited data volume of the 2024 samples, no significant new clusters were formed. The viruses from the four cases in Guizhou province all belonged to the clade IIb.C.1. Nine to 20 mutation sites were identified in each sample. Among them, N3R_R84K was the common mutation site of the four cases, and amino acid mutations and back mutations were observed at this site.

Conclusions

Monkeypox viruses present variations and diversity in China, and its evolutionary dynamics show obvious time dependence. The monkeypox viruses from all the four cases in Guizhou province from 2023 to 2024 belonged to the lineage IIb.C.1 and all carried the key mutation site N3R_R84K. Continuous monitoring of the viral genome should be carried out, with close attention paid to the sources, transmission chains, and variations of the virus.

, authors=Ping WU, Lin FU, Chunting LIU, Suye ZHAO, authorsList=Ping WU, Lin FU, Chunting LIU, Suye ZHAO, authorCompany=null, correspAuthors=Suye ZHAO, authorNote=null, correspAuthorsNote=
ZHAO Suye, E-mail:
, copyrightStatement=Copyright © 2026 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=1320442621349187954, articleId=1320442617985356134, tenantId=1146029695717560320, journalId=1319373219989389464, language=CN, title=2023—2024年贵州省4例猴痘病例病毒全基因组测序及群体进化分析, columnId=1320442617125519681, journalTitle=中国公共卫生, columnName=专题报道——传染病预防与控制, runingTitle=null, highlight=null, articleAbstract=
目的

分析2023—2024年贵州省4例猴痘病例病毒全基因组序列及其群体进化特征。

方法

收集贵州省4例猴痘病例样本，采用扩增子测序技术获取病毒全基因组序列。从GISAID数据库筛选并下载2022—2024年亚洲地区高质量的猴痘病毒基因组序列，构建包含173条序列的群体数据集，利用该数据集进行分化时间估算、系统发育和突变位点分析。

结果

在群体数据集中，2023年序列最多（126条），其次为2022年（33条）和2024年（14条）。估算猴痘病毒最近共同祖先时间（TMRCA）出现在2013年，进化速率为3.77×10−5 subs/site/year。2022—2024年，猴痘病毒型别多样性降低，优势型别由IIb.A.2转变为IIb.C.1。中国猴痘病毒型别多样性最丰富，包含IIb.C.1、IIb.B.1.3、IIb.B.1.20、IIb.B.1、IIb.B.1.5、IIb. A.1。系统发育分析显示，2022年流行株以IIb分支A型相关谱系为主；2023年IIb.C.1型成为优势谱系，并伴随IIb.B.1型的出现，进一步演化为以IIb.C.1.1型为主导；2024年样本因数据量有限，未形成显著新聚类。贵州省4例病例病毒均属于IIb.C.1进化分支，各样本分别鉴定出9～20个突变位点，其中N3R_R84K为4例猴痘病毒共有的突变位点，并观察到该位点存在氨基酸突变和回突变现象。

结论

猴痘病毒在中国存在变异和多样性，其进化动态呈现明显的时间依赖性。2023—2024年贵州省4例猴痘病毒均属于IIb.C.1进化分支，均携带N3R_R84K关键位点变异。应持续开展病毒基因组监测，密切关注病毒来源、传播链及变异情况。

, authors=吴萍, 付琳, 刘淳婷, 赵苏晔*, *, authorsList=吴萍, 付琳, 刘淳婷, 赵苏晔, authorCompany=null, correspAuthors=赵苏晔, authorNote=

吴萍（1992—），副主任技师，硕士，研究方向：呼吸道病毒和自然疫源性疾病检测

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赵苏晔，E-mail：
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吴萍（1992—），副主任技师，硕士，研究方向：呼吸道病毒和自然疫源性疾病检测

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吴萍（1992—），副主任技师，硕士，研究方向：呼吸道病毒和自然疫源性疾病检测

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注：第1圈层表示国家；第2圈层表示年份；红点表示4条待测序列，蓝色外群表示天花病毒

, figureFileSmall=d5B8h/DEuhaS4lfSbfER5w==, figureFileBig=Wac+q13FgVFFRE9hq42yZQ==, tableContent=null), ArticleFig(id=1320442627208630680, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Fig.3, caption=Divergence time of monkeypox virus genomes, figureFileSmall=VfgPsOuhFPvk1NDyEe0+lA==, figureFileBig=tY9bwp5sG2XEF/bGG8C4Qg==, tableContent=null), ArticleFig(id=1320442628856992154, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=图3, caption=猴痘病毒全基因组时间分化图

注：红点表示4条待测序列

, figureFileSmall=VfgPsOuhFPvk1NDyEe0+lA==, figureFileBig=tY9bwp5sG2XEF/bGG8C4Qg==, tableContent=null), ArticleFig(id=1320442628936683931, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Fig.4, caption=Heat map of monkeypox virus genome mutation sites, figureFileSmall=PfC4yJjAcx4xzBuPAYzkZA==, figureFileBig=8KTZA6ZcVD7EyvSpNp5AqQ==, tableContent=null), ArticleFig(id=1320442629024764316, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=图4, caption=猴痘病毒全基因组突变位点热图, figureFileSmall=PfC4yJjAcx4xzBuPAYzkZA==, figureFileBig=8KTZA6ZcVD7EyvSpNp5AqQ==, tableContent=null), ArticleFig(id=1320442629087678877, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Fig.5, caption=Tertiary protein structure of monkeypox virus N3R_R84K, figureFileSmall=rtlsQ0DPAoR8kPwtHuQjBQ==, figureFileBig=FXtM4XrCe0DbBYGJsxkF6Q==, tableContent=null), ArticleFig(id=1320442629318365598, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=图5, caption=猴痘病毒N3R_R84K的蛋白质三级结构图, figureFileSmall=rtlsQ0DPAoR8kPwtHuQjBQ==, figureFileBig=FXtM4XrCe0DbBYGJsxkF6Q==, tableContent=null), ArticleFig(id=1320442629389668767, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Tab.1, caption=

Statistics of sequencing information of monkeypox viruses from four cases

, figureFileSmall=null, figureFileBig=null, tableContent=
编号样本类型Ct值数据量/Mbreads数基因组覆盖度（测序深度≥10×/%）分型
hMpxV/China/GuiZhou/20 230 718阴茎分泌物21363348 78099.58Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 230 810咽拭子27444280 00099.98Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 230 914咽拭子25872671 99799.96Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 240 912痘疱渗出物20647412 740 00099.98Ⅱb.C.1.1
), ArticleFig(id=1320442629456777632, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=表1, caption=

4例猴痘病例测序结果

, figureFileSmall=null, figureFileBig=null, tableContent=
编号样本类型Ct值数据量/Mbreads数基因组覆盖度（测序深度≥10×/%）分型
hMpxV/China/GuiZhou/20 230 718阴茎分泌物21363348 78099.58Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 230 810咽拭子27444280 00099.98Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 230 914咽拭子25872671 99799.96Ⅱb.C.1.1
hMpxV/China/GuiZhou/20 240 912痘疱渗出物20647412 740 00099.98Ⅱb.C.1.1
), ArticleFig(id=1320442629523886497, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Tab.2, caption=

Statistics of collection sites of monkeypox virus genomes in Asian countries during 2022–2024

, figureFileSmall=null, figureFileBig=null, tableContent=
国家2022年2023年2024年总计
日本045449
印度尼西亚140344
韩国614020
泰国1010020
中国313016
印度5128
菲律宾1135
巴基斯坦0224
新加坡4004
以色列1001
格鲁吉亚1001
越南1001
合计3312614173
), ArticleFig(id=1320442629603578274, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=表2, caption=

2022—2024年亚洲不同国家猴痘基因组序列数量分布（条）

, figureFileSmall=null, figureFileBig=null, tableContent=
国家2022年2023年2024年总计
日本045449
印度尼西亚140344
韩国614020
泰国1010020
中国313016
印度5128
菲律宾1135
巴基斯坦0224
新加坡4004
以色列1001
格鲁吉亚1001
越南1001
合计3312614173
), ArticleFig(id=1320442629683270051, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=EN, label=Tab.3, caption=

Statistics of monkeypox virus genotypes in Asian countries during 2022–2024

, figureFileSmall=null, figureFileBig=null, tableContent=
Clade/Lineage2022年2023年2024年总计
IIb.C.1087693
IIb.C.1.1029130
IIb.A.2.1103417
IIb.B.19009
IIb.A.26006
IIb.B.1.200235
IIb.B.1.30404
IIb.B.1.23003
IIb.B.1.12002
IIb.A.10101
IIb.A1001
IIb.B.1.51001
IIb.B.1.71001
合计3312614173
), ArticleFig(id=1320442629809099172, tenantId=1146029695717560320, journalId=1319373219989389464, articleId=1320442617985356134, language=CN, label=表3, caption=

2022—2024年亚洲地区国家猴痘基因组型别统计（条）

, figureFileSmall=null, figureFileBig=null, tableContent=
Clade/Lineage2022年2023年2024年总计
IIb.C.1087693
IIb.C.1.1029130
IIb.A.2.1103417
IIb.B.19009
IIb.A.26006
IIb.B.1.200235
IIb.B.1.30404
IIb.B.1.23003
IIb.B.1.12002
IIb.A.10101
IIb.A1001
IIb.B.1.51001
IIb.B.1.71001
合计3312614173
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2023—2024年贵州省4例猴痘病例病毒全基因组测序及群体进化分析
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吴萍 , 付琳 , 刘淳婷 , 赵苏晔 *, *
中国公共卫生 | 专题报道——传染病预防与控制 2026,42(1): 23-29
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中国公共卫生 |专题报道——传染病预防与控制 2026 , 42 (1) : 23 -29
2023—2024年贵州省4例猴痘病例病毒全基因组测序及群体进化分析
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吴萍, 付琳, 刘淳婷, 赵苏晔*, *
作者信息
  • 贵州省疾病预防控制中心，贵阳 550000
通讯作者:
赵苏晔，E-mail：
作者简介:

吴萍（1992—），副主任技师，硕士，研究方向：呼吸道病毒和自然疫源性疾病检测

Whole genome sequencing and population evolution analysis of monkeypox viruses from four cases in Guizhou province from 2023 to 2024
Ping WU, Lin FU, Chunting LIU, Suye ZHAO
Affiliations
  • Guizhou Center for Disease Control and Prevention, Guiyang 550000, China
    • Corresponding Author:
    ZHAO Suye, E-mail:
出版时间: 2026-01-10 doi: 10.11847/zgggws1147360
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摘要
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目的

分析2023—2024年贵州省4例猴痘病例病毒全基因组序列及其群体进化特征。

方法

收集贵州省4例猴痘病例样本，采用扩增子测序技术获取病毒全基因组序列。从GISAID数据库筛选并下载2022—2024年亚洲地区高质量的猴痘病毒基因组序列，构建包含173条序列的群体数据集，利用该数据集进行分化时间估算、系统发育和突变位点分析。

结果

在群体数据集中，2023年序列最多（126条），其次为2022年（33条）和2024年（14条）。估算猴痘病毒最近共同祖先时间（TMRCA）出现在2013年，进化速率为3.77×10−5 subs/site/year。2022—2024年，猴痘病毒型别多样性降低，优势型别由IIb.A.2转变为IIb.C.1。中国猴痘病毒型别多样性最丰富，包含IIb.C.1、IIb.B.1.3、IIb.B.1.20、IIb.B.1、IIb.B.1.5、IIb. A.1。系统发育分析显示，2022年流行株以IIb分支A型相关谱系为主；2023年IIb.C.1型成为优势谱系，并伴随IIb.B.1型的出现，进一步演化为以IIb.C.1.1型为主导；2024年样本因数据量有限，未形成显著新聚类。贵州省4例病例病毒均属于IIb.C.1进化分支，各样本分别鉴定出9～20个突变位点，其中N3R_R84K为4例猴痘病毒共有的突变位点，并观察到该位点存在氨基酸突变和回突变现象。

结论

猴痘病毒在中国存在变异和多样性，其进化动态呈现明显的时间依赖性。2023—2024年贵州省4例猴痘病毒均属于IIb.C.1进化分支，均携带N3R_R84K关键位点变异。应持续开展病毒基因组监测，密切关注病毒来源、传播链及变异情况。

猴痘病毒  /  全基因组测序  /  群体进化  /  分化时间  /  贵州省
Objective

To analyze the whole genome sequences and the population evolution characteristics of monkeypox viruses from four cases in Guizhou province from 2023 to 2024.

Methods

Samples were collected from four monkeypox cases in Guizhou province, and the whole genome sequences of the viruses were obtained by amplicon sequencing. High-quality genome sequences of monkeypox viruses in Asia from 2022 to 2024 were screened and downloaded from the GISAID database to construct a population dataset containing 173 sequences. This dataset was used for divergence time estimation, phylogenetic analysis, and mutation site identification.

Results

In the population dataset, the number of sequences was the largest in 2023 (126), followed by that in 2022 (33) and 2024 (14). It was estimated that the time to the most recent common ancestor (TMRCA) of monkeypox viruses emerged in 2013, with an evolutionary rate of 3.77×10−5 subs/site/year. From 2022 to 2024, the diversity of monkeypox virus lineages declined, with the dominant lineage changing from IIb.A.2 to IIb.C.1. China had the most diverse monkeypox virus lineages, including IIb.C.1, IIb.B.1.3, IIb.B.1.20, IIb.B.1, IIb.B.1.5, and IIb.A.1. The phylogenetic analysis revealed that the prevalent strains in 2022 were mainly related to lineage A of clade IIb. In 2023, IIb.C.1 became the dominant lineage, and it further evolved to be dominated by sublineage IIb.C.1.1 with the emergence of IIb.B.1. Due to the limited data volume of the 2024 samples, no significant new clusters were formed. The viruses from the four cases in Guizhou province all belonged to the clade IIb.C.1. Nine to 20 mutation sites were identified in each sample. Among them, N3R_R84K was the common mutation site of the four cases, and amino acid mutations and back mutations were observed at this site.

Conclusions

Monkeypox viruses present variations and diversity in China, and its evolutionary dynamics show obvious time dependence. The monkeypox viruses from all the four cases in Guizhou province from 2023 to 2024 belonged to the lineage IIb.C.1 and all carried the key mutation site N3R_R84K. Continuous monitoring of the viral genome should be carried out, with close attention paid to the sources, transmission chains, and variations of the virus.

monkeypox virus  /  whole genome sequencing  /  population evolution  /  divergence time  /  Guizhou province
吴萍, 付琳, 刘淳婷, 赵苏晔. 2023—2024年贵州省4例猴痘病例病毒全基因组测序及群体进化分析. 中国公共卫生, 2026 , 42 (1) : 23 -29 . DOI: 10.11847/zgggws1147360
Ping WU, Lin FU, Chunting LIU, Suye ZHAO. Whole genome sequencing and population evolution analysis of monkeypox viruses from four cases in Guizhou province from 2023 to 2024[J]. Chinese Journal of Public Health, 2026 , 42 (1) : 23 -29 . DOI: 10.11847/zgggws1147360
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猴痘是由猴痘病毒（monkeypox virus, MPXV）所引起的一种人兽共患病，症状为发热、皮疹以及淋巴结肿大等，病死率约0.1%～10%[1–2]，目前尚无特效治疗方法。自2022年9月我国报告首例猴痘输入病例以来，多个省份发现猴痘病例，并引发本土续发疫情和隐匿传播。猴痘病毒属痘病毒科正痘病毒属双链DNA病毒，大小为200 nm×250 nm，约196 858个碱基（bp）。猴痘病毒分为中非分支或刚果盆地分支（Clade I）和西非分支（Clade Ⅱ），但目前已出现较多亚分支[3–5]。猴痘病毒的传播模式在不断演变，研究显示猴痘病毒可能自2016年以来就在人群中传播且不断进化，以逃避人类免疫系统[6]。比较2018年与2022年的MPXV基因组序列表明，双链DNA病毒的突变率远高于预期，且大多数突变与人类免疫系统中抗病毒酶活性有关，这表明持续的人际传播促使了病毒的进化[7]。猴痘病毒不同分支的特征差异，Clade I的猴痘病毒引起的病情较重，病死率可达10.6%；而Clade Ⅱ猴痘的症状较轻，全球病死率约为0.22%。近期还发现Clade I分支已经演化出Clade Ib分支，并在非洲大规模传播[8–10]。分析猴痘病毒群体进化有助于深入了解这些分支的演化关系以及其特征差异的形成机制[11]，而全基因组扩增测序并结合系统进化分析，可以阐明猴痘病毒在当地可能的来源。本研究对2023—2024年贵州省4例猴痘病例样本进行病毒全基因组测序分析，并与亚洲地区173条样本的比对分析，有助于深入认识该病毒的流行特征、传播模式、不同分支关系等多方面内容，为贵州省猴痘疫情的防控和应对提供科学依据。
1　材料与方法
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1.1　样本来源
来自2023年7月—2024年9月贵州省报告的4例猴痘病例，样本类型包括2份咽拭子、1份阴茎分泌物和1份痘疱渗出物拭子。参照《猴痘防控技术指南（2022年版）》[2]和《猴痘防控方案》采集并检测所有的样本，样本编号遵循“病原体/国家/地区/日期”的分级格式。
1.2　猴痘病毒核酸提取与实时荧光定量PCR检测
取4例猴痘病例样本各200 μL，使用病毒DNA/RNA提取试剂盒T035（中国天隆科技公司）提取样本中的病毒核酸。以实时荧光定量PCR（荧光PCR法猴痘病毒核酸检测试剂盒：SJ-XQ-0191-2，中国上海伯杰公司）检测病毒核酸，根据试剂盒说明书判定实验结果。
1.3　全基因组扩增与测序
使用MPXV全基因组捕获试剂盒BK-MPXV024（中国柏熠公司）对实时荧光定量PCR检测Ct值≤32的样本进行病毒全基因组扩增，获得的全基因组片段使用连接法测序多样本DNA建库辅助试剂盒2.0（货号AM024，中国柏熠公司）三代测序仪上进行病毒全基因组测序。
1.4　数据整理与分析
从GISAID数据库（https://gisaid.org/）检索并下载2022—2024年亚洲各国具有明确采样日期、高覆盖率的猴痘病毒近全长高质量基因组序列。为保证猴痘病毒型别、所选地区、采集时间等在数量上的无偏差性，最终挑选出173条样本纳入本研究。使用中国柏熠猴痘病毒全基因组分析系统V1.0初步处理数据，以Mafft软件比对猴痘全基因组序列，应用IQTREE软件根据GTR+I+G4模型为全基因组数据构建最大似然树，并使用iTOL网站美化进化树。以BEAST1.8.4软件的MCMC方法估算猴痘病毒全基因组序列的分歧时间并分析进化速率。基于严格分子钟模型和Bayesian Skyline作为优先种群增长模式进行分析；依Bayesian Skyline作为优先种群增长模式，后验概率依Metropolis-Hastings-Green算法通过马尔科夫链运行500 000 000代，使用Tracer v1.7软件检验收敛程度。当所有参数的有效取样大小均大于200时，认为迭代运算达到收敛。将本研究中的4例猴痘病毒基因组上传Nextclade网站（https://clades.nextstrain.org/），以hMpxV/USA/MA-CDC-001/2022为参考序列确定MPXV的型别并获取相关变异位点。
2　结　果
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2.1　测序数据基本信息（表1）
为分析2023—2024年贵州省4例猴痘病例病毒全基因组序列及其群体进化特征，本研究对2023—2024年收集的4例猴痘病例的样本进行了高通量全基因组测序。测序基本数据显示，4条序列数据量均大于300 M，reads数均≥280 000，基因组覆盖度（测序深度≥10×）99.58%～99.98%，基因分型均归属于Ⅱb.C.1.1亚分支。
2.2　亚洲各国猴痘病毒基因组序列数量分布（表2）
本研究分析的数据集中，来自各国的猴痘病毒基因组序列数量分别为：日本49条、印度尼西亚44条、韩国20条、泰国20条、印度8条、菲律宾5条、巴基斯坦4条、新加坡4条、以色列1条、格鲁吉亚1条、越南1条。按年份统计，该数据集中于2023年的猴痘病毒基因组序列数量最多（126条），其次是2022年（33条）和2024年（14条）。
2.3　2022—2024年亚洲地区猴痘基因型别分布（表3）
2022年猴痘病毒主要基因型别为IIb.A.2.1和IIb.B.1，2023主要型别为IIb.C.1和IIb.C.1.1，2024年则以IIb.C.1型别为主。从2022年到2024年，型别的多样性逐年降低，主要型别由IIb.A.2变为IIb.C.1。
2.4　亚洲各国猴痘病毒基因型别多样性及分布（图1）
中国最具型别多样性，包含IIb.C.1、IIb.B.1.3、IIb.B.1.20、IIb.B.1、IIb.B.1.5、IIb.A.1。其次是日本、韩国和泰国，这3个国家均含有4种型别猴痘型别。IIb.C.1在印度尼西亚出现最多，IIb.C.1.1、IIb.B.1.1和IIb.B.1.3在韩国出现最多，IIb.B.1.20在中国和菲律宾则出现最多，IIb.B.1、IIb.A.2在泰国出现最多，IIb.A.2.1在印度出现最多，IIb.B.1.1在韩国出现最多，IIb.A.1和IIb.B.1.5只在中国出现，IIb.B.1.7和IIb.B.1.2只出现在新加坡，IIb.A则出现在越南。
2.5　系统发育分析（图2）
比对177条猴痘全基因组序列，其中包含2条外群序列、4条待测序列和173条参考序列。2022年以IIb.A型别为主；从2023年开始，IIb.C.1型别作为主要型别，随后小部分IIb.B.1出现后，IIb.C.1.1作为主要型别出现；但2024年因数据较少，未形成较好的聚集性。根据最大似然树显示，不同年份的病毒序列在时间维度上呈现出明显的连续性和时间依赖性进化模式。具体而言，外群（蓝色）最早出现在2022年（橙色），随后依次进化出2023年（绿色）和2024年（褐色）的毒株。值得注意的是，2024年的样本由于数据量相对较少，在系统树中呈现分散分布的特征。
2.6　分化时间分析（图3）
以BEAST1.8.4软件的MCMC方法估算猴痘病毒全基因组序列的分歧时间并分析进化速率。基于严格分子钟模型和Bayesian Skyline作为优先种群增长模式进行分析；依Bayesian Skyline作为优先种群增长模式，后验概率依Metropolis-Hastings-Green算法通过马尔科夫链运行500 000 000代，使用Tracer v1.7软件检验收敛程度。当所有参数的有效取样大小均大于200时，认为迭代运算达到收敛。本研究表明猴痘病毒所有现存株系的最近共同祖先时间（TMRCA）为2013年，其进化速率是3.77×10−5 subs/site/year。本研究整合GISAID数据库收录的2022—2024年全球173株猴痘病毒全基因组序列，结合本研究测序获得的贵州省4例基因组数据，构建了系统发育时间树。亚洲地区猴痘病毒呈现明显的谱系动态更替规律：2022年流行初期以IIb.A亚分支为主导，随后其进化分支Ⅱb.A.2成为优势流行株；至2023—2024年，IIb.B.1和IIb.C.1亚分支呈现交替流行模式。值得注意的是，2023—2024年贵州省检出的4例猴痘病毒均归属于Ⅱb.C.1.1亚分支，提示该亚分支可能已在本地区形成局部传播链。这一基于系统发育分析揭示的谱系动态更替特征，为贵州省本地流行株的监测溯源提供了关键的分子流行病学标记。
2.7　病毒突变位点分析（图4）
本研究中的4例猴痘病毒基因组序列分别识别出9～20个不等的突变位点，其中hMpxV/China/GuiZhou/20240912突变位点最多，共计20个。这些突变位点中，有2个已知突变位点N3R_R84K和A28L_D372del；新增23个突变位点，主要有P.0、C4L_E417K、M4R_S188F、E12L_L16F、A47R_S52L、A50R_D59N、B17R_E532K、R1R_S90L、D7L_C512R、C4L_D122N、F4L_H97I、F4L_E99N、F4L_T96Q、F4L_Y100I、G5R_M175R、L3R_G105A、L3R_L106stop、E3R_E191K、A11L_I416T、B4R_Y251F、B5R_S381L、O1L_S185F、M4R_S216L，其中hMpxV/China/GuiZhou/20240912的L3R_L106stop变异位点测序深度为368，L106stop突变型reads数187条（占总reads的50%），L106野生型reads数181条（占总reads的50%），表明在该感染者的病毒群体中，同时存在携带L106stop突变株和野生型毒株的混合感染。
2.8　病毒N3R_R84K的蛋白质（图5）
由于本研究的4例样本均出现了已知突变N3R_R84K，为了进一步探究该突变位点的进化史，通过https://swissmodel.expasy.org/interactive在线网站对MPXV N3R同源建模，N3R蛋白的球状结构域与牛痘病毒N3R蛋白（PDB ID：4ffe.1.A）具有一定的相似性（61.49%），使用Pymol开展可视化分析，通过R包sitePath和系统进化树对突变位点R84K变化趋势实施可视化，亚洲地区的N3R蛋白序列集，在2022—2024年其第84位氨基酸经历了由精氨酸（R）突变为赖氨酸（K），再回突变为精氨酸（R）的过程。
3　讨　论
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本研究对2023—2024年贵州省4例猴痘病例样本进行病毒全基因组测序，并与亚洲各国173条全基因组序列进行群体进化分析。在本研究数据集中，从2022年到2024年，型别的多样性逐年降低，主要型别由IIb.A.2转移至IIb.C.1。这种型别的转移和多样性的降低，可能与病毒的生物学特性、传播方式以及人群免疫状况等多种因素有关。同时，随着全球对猴痘疫情的防控措施不断加强，以及人群免疫水平的提高，其他型别的病毒可能逐渐被抑制或清除，从而进一步降低了病毒的多样性[12]。使用猴痘全基因组数据集构建的最大似然树的结论，与我国2023年猴痘病例病毒Clade IIb的进化轨迹和特征一致[13]。意味着猴痘病毒传播并不受地理因素的显著影响，或者病毒在不同地理区域间的传播已经足够广泛，以至于在基因组层面上无法观察到明显的地理聚类特征。为进一步理解猴痘病毒进化规律，本研究推算猴痘病毒的TMRCA（time to most recent common ancestor）和进化速率；TMRCA指最近共同祖先的时间，即病毒所有现存株系的最后一个共同祖先出现的时间[14]。本研究中，TMRCA为2013年，即猴痘病毒所有现存株系的最近共同祖先存在于2013年。这个信息表明，自那时以来，猴痘病毒已经经历了一段时间的进化。进化速率3.77×10–5 subs/site/year则描述了病毒进化的速度，即每年每个位点发生突变的概率。这个速率相对较低，说明猴痘病毒的进化并不是非常迅速，但是持续进行的。这种持续的进化可能导致病毒特性的变化，比如传播能力、致病性或者对治疗措施的敏感性等。
2023—2024年贵州省4例猴痘病毒均为IIb.C.1亚分支，分别识别出9～20个不等的突变位点，其中hMpxV/China/GuiZhou/20240912突变位点最多，2022—2023年全球暴发的猴痘疫情中，猴痘病例主要是分支IIb感染[14–15]，而贵州省报告的这4例猴痘病毒均属于该分支，表明它们与这一时期的全球流行病例在遗传上具有一致性。值得注意的是，虽然猴痘病毒属于双链DNA病毒，相对稳定，不会像新型冠状病毒和流感等病毒那样突变得特别快或产生特别多的变种，但病毒变异是持续存在的，比如本研究中的2024年贵州省猴痘病例（hMpxV/China/GuiZhou/20240912）突变位点最多，这可能是病毒适应环境、逃避宿主免疫机制的一种方式。因此，对于猴痘病毒的监测和防控工作仍然不能松懈，需要密切关注病毒的变异情况，以及时采取应对措施。此外，4例样本均出现了已知突变N3R_R84K，为了进一步探究该突变位点的进化史，本研究发现亚洲地区的N3R蛋白序列集，在2022—2024年其第84位氨基酸经历了由精氨酸突变为赖氨酸，再回突变为精氨酸的过程，可能意味着精氨酸在这个位置上对病毒的生存或传播更为重要。病毒的遗传变异是病毒进化的基础，而选择压力则是推动病毒进化的动力。猴痘病毒在复制和传播过程中，会不断面临来自宿主免疫系统、抗病毒药物等外部压力。这些压力会促使病毒发生突变，以适应新的环境或逃避宿主的免疫攻击。因此，猴痘病毒第84位氨基酸的突变和回突变，也可能是病毒在遗传变异和选择压力共同作用下的结果。这种变化可能对病毒的生物学特性、传播能力、致病性等方面产生影响，因此需要密切关注和研究。

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doi: 10.11847/zgggws1147360
  • 接收时间：2025-03-11
  • 首发时间：2026-10-23
  • 出版时间：2026-01-10
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  • 收稿日期：2025-03-11
  • 修回日期：2025-07-15
  • 录用日期：2025-08-02
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    贵州省疾病预防控制中心，贵阳 550000

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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
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
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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