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                       2019新型冠状病毒信息库

              遗传, 2020, 42(2): 212-221 doi: 10.16288/j.yczz.20-030

              http://www.chinagene.cn/article/2020/0253-9772/0253-9772-42-2-212.shtml

赵文明,1,2,3宋述慧,1,2陈梅丽,1,2邹东,1,2马利娜,1,2马英克1,2李茹姣1,2郝丽丽1,2李翠萍1,2田东梅1,2唐碧霞1,2王彦青1,2朱军伟1,2陈焕新1,2章张1,2,3薛勇彪,1,3鲍一明,1,2,3

1. 国家生物信息中心&中国科学院北京基因组研究所国家基因组科学数据中心, 北京 100101;

2. 中国科学院北京基因组研究所基因组科学与信息重点实验室,北京 100101 3. 中国科学院大学,北京 100049

3. 中国科学院大学,北京 100049


The 2019 novel coronavirus resource

Wenming Zhao,1,2,3Shuhui Song,1,2Meili Chen,1,2Dong Zou,1,2Lina Ma,1,2Yingke Ma1,2Rujiao Li1,2Lili Hao1,2Cuiping Li1,2Dongmei Tian1,2Bixia Tang1,2Yanqing Wang1,2Junwei Zhu1,2Huanxin Chen1,2Zhang Zhang1,2,3Yongbiao Xue,1,3Yiming Bao,1,2,3

1. China National Center for Bioinformation & National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;

2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

3. University of Chinese Academy of Sciences, Beijing 100049, China

摘要

2019年12月在中国武汉开始爆发的新型肺炎已造成全球25个国家/地区的31516人感染、638人死亡(截止2020年2月7日16时),引起该肺炎的病毒被世界卫生组织命名为2019新型冠状病毒(2019-nCoV)。为促进2019-nCoV数据共享应用并及时向全球公众提供病毒的相关信息,国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建立了2019新型冠状病毒信息库(2019nCoVR,https://bigd.big.ac.cn/ncov)。该信息库整合了来自德国全球流感病毒数据库、美国国家生物技术信息中心、深圳(国家)基因库、国家微生物科学数据中心及CNCB/NGDC等机构公开发布的2019-nCoV核苷酸和蛋白质序列数据、元信息、学术文献、新闻动态、科普文章等信息,开展了不同冠状病毒株的基因组序列变异分析并提供可视化展示。同时,2019nCoVR无缝对接CNCB/NGDC的相关数据库,提供新测序病毒株系的基因组原始测序数据、组装后序列的在线汇交、管理与共享、国际数据库同步发布等数据服务。本文对2019nCoVR数据汇交、管理、发布及使用等进行全面阐述,以方便用户了解该信息库各项功能及数据状况,为加速开展病毒的分类溯源、变异演化、快速检测、药物研发以及新型肺炎的精准预防与治疗等研究提供重要基础。

关键词: 冠状病毒数据库 ; 2019新型冠状病毒 ; 国家生物信息中心 ; 国家基因组科学数据中心 ; 基因组数据共享

Abstract


An ongoing outbreak of a novel coronavirus infection in Wuhan, China since December 2019 has led to 31,516 infected persons and 638 deaths across 25 countries (till 16:00 on February 7, 2020). The virus causing this pneumonia was then named as the 2019 novel coronavirus (2019-nCoV) by the World Health Organization. To promote the data sharing and make all relevant information of 2019-nCoV publicly available, we construct the 2019 Novel Coronavirus Resource (2019nCoVR, https://bigd.big.ac.cn/ncov). 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the Global Initiative on Sharing All Influenza Data, National Center for Biotechnology Information, China National GeneBank, National Microbiology Data Center and China National Center for Bioinformation (CNCB)/National Genomics Data Center (NGDC). It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains. Moreover, by linking seamlessly with related databases in CNCB/NGDC, 2019nCoVR offers virus data submission and sharing services for raw sequence reads and assembled sequences. In this report, we provide comprehensive descriptions on data deposition, management, release and utility in 2019nCoVR, laying important foundations in aid of studies on virus classification and origin, genome variation and evolution, fast detection, drug development and pneumonia precision prevention and therapy.

Keywords: 2019nCoVR ; 2019 novel coronavirus ; China National Center for Bioinformation (CNCB) ; National Genomics Data Center (NGDC) ; genomic data sharing

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本文引用格式

赵文明, 宋述慧, 陈梅丽, 邹东, 马利娜, 马英克, 李茹姣, 郝丽丽, 李翠萍, 田东梅, 唐碧霞, 王彦青, 朱军伟, 陈焕新, 章张, 薛勇彪, 鲍一明. 2019新型冠状病毒信息库遗传[J], 2020, 42(2): 212-221 doi:10.16288/j.yczz.20-030

Wenming Zhao. The 2019 novel coronavirus resourceHereditas(Beijing)[J], 2020, 42(2): 212-221 doi:10.16288/j.yczz.20-030


2019年12月以来,中国湖北省武汉市部分医院陆续发现了多例不明原因肺炎病例,后被证实是由一种先前尚未发现的冠状病毒(coronavirus)感染引起的急性呼吸道传染病,这种病毒被世界卫生组织(World Health Organization, WHO)命名为2019新型冠状病毒(2019 novel coronavirus, 2019-nCoV)*[1]( *注:2020年2月11日,2019新型冠状病毒(2019-nCoV)被国际病毒分类委员会(the International Committee on Taxonomy of Viruses)冠状病毒研究小组(Coronavirus Study Group, CSG)命名为“SARS-CoV-2” (severe acute respiratory syndrome coronavirus 2),同时,由该病毒感染引起的疾病被WHO命名为“COVID-19” (corona virus disease 2019)。),该病毒与中东呼吸综合征相关冠状病毒(middle east respiratory syndrome-related coronavirus, MERSr-CoV)和严重急性呼吸综合征相关冠状病毒(severe acute respiratory syndrome-related coronavirus, SARSr-CoV)同属于β冠状病毒属[2]

利用快速发展的基因组学方法与技术,全球的科研人员已经获得了多个2019-nCoV基因组序列,并且开展了多项相关研究[2,3,4,5,6,7]。因此,收集整合已有的2019-nCoV数据,构建统一完整的信息库系统,实现对数据的动态发布与共享对于防控病毒疫情、制定病毒性肺炎治疗方案具有重要意义[8,9]。自2020年1月5日,复旦大学张永振教授向美国国家生物技术信息中心(National Center for Biotechnology Information, NCBI)[10]的GenBank数据库提交第一条新型冠状病毒基因组序列(Acc. No. MN908947)至2020年2月5日,共有86条2019-nCoV序列数据在全球多个数据库发布,主要分布于德国全球流感病毒数据库(Global Initiative on Sharing All Influenza Data, GISAID)[11]、美国NCBI、深圳(国家)基因库(China National GeneBank, CNGB)[12]、国家微生物科学数据中心(National Microbiology Data Center, NMDC)[13]及国家生物信息中心(China National Center for Bioinformation, CNCB)/国家基因组科学数据中心(National Genomics Data Center, NGDC)[14]等相关数据库。然而,2019-nCoV序列数据分散在这些数据库中,未形成完整、统一访问的数据集,这给科研人员检索、预览和获取数据带来诸多不便。

为了缓解当前数据多源的局面和问题,帮助科研人员便捷地获取数据,同时提供高效的基因组序列递交与发布共享系统,CNCB/NGDC通过整合全球2019-nCoV相关数据,构建了2019新型冠状病毒信息库(2019nCoVR, https://bigd.big.ac.cn/ncov),并于2020年1月22日正式公开上线。2019nCoVR动态发布基因组序列、元数据信息以及相关新闻、学术文献、科普文章,提供冠状病毒基因组的变异分析结果与可视化展示,提供已知冠状病毒科的核 苷酸和蛋白质序列信息的搜索和下载。同时,2019nCoVR无缝对接NGDC的原始组学数据归档库(Genome Sequence Archive, GSA)[15,16]和基因组数据库(Genome Warehouse, GWH)[14,17,18],提供新病毒的基因组原始测序数据和组装后序列的在线汇交、管理、共享以及与国际数据库同步发布等服务。本文主要介绍2019nCoVR的数据资源、数据汇交与审核机制以及数据发布、管理与使用规范等内容,为加速开展病毒分类溯源、变异演化、快速检测、药物研发以及新型肺炎的精准预防与治疗等研究提供重要数据基础。

1 2019nCoVR数据资源

1.1 基因组序列发布动态

基于严格的质控审编流程,2019nCoVR收集整合多个数据平台(CNCB/NGDC、CNGB、GISAID、NCBI、NMDC)的2019-nCoV序列信息和元数据信息(包括病毒株名、序列号、数据来源、宿主、采样日期、采样地点、样本提供单位、数据递交单位等),持续更新序列发布动态,为开展相关科学研究提供完备准确的第一手数据。自2019年12月2019-nCoV疫情爆发至2020年2月5日,已收录来自16个国家/地区的81株病毒的86条基因组序列(附表1),其中67株具有全基因组序列(人体中分离66株,蝙蝠中分离1株)。

在数据获取与访问权限方面,遵守不同数据共享平台的数据管理规则,提供最大限度的数据集成与访问。可公开访问的数据已整合录入2019nCoVR,包括NCBI、CNCB/NGDC、NMDC、CNGB中相关基因组序列,任何人可不受限访问并下载;受限访问的数据,主要为GISAID数据库中序列,用户需到GISAID系统注册、登录后才可访问并下载(图1)。

图1

图1   2019新型冠状病毒基因组元信息相关统计结果

A:数据共享平台;B:采样国家/地区;C:样本提供单位;D:数据递交单位。

Fig. 1   Statistics of 2019-nCoV genome meta information


在病毒来源方面,所收录的病毒株主要来自湖北省武汉市,部分来自广东省和浙江省等地区,还有一小部分来自美国、泰国和日本等国家。病毒样本采集单位主要包括香港大学深圳医院、广东省疾病预防控制中心(Center for Disease Control and Prevention, CDC)、广东省公共卫生研究院、武汉金银潭医院、中国医学科学院病原生物学研究所等国内外28家医疗卫生或科研单位。基因组测序和数据递交主要由香港大学深圳医院、中国CDC、广东省CDC、湖北省CDC、华大基因(Beijing Genomics Institute, BGI)等30家单位完成(图1)。

1.2 基因组序列资源整合与信息检索

基于CNCB/NGDC的GWH数据平台,2019nCoVR收录并整合国内外公共数据平台中可开放获取的冠状病毒序列数据,形成冠状病毒序列数据集。截止到2020年2月5日,已审编收录冠状病毒科的核苷酸序列7566条和蛋白质序列29039条,以及相应的元数据信息(图2)。基于标准化的信息整合与发布,2019nCoVR提供多方位信息检索、条件查询、批量下载等功能,用户亦可在FTP网站公开访问和下载数据(ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/)。

图2

图2   冠状病毒科基因组序列信息汇总

Fig. 2   Coronaviridae genome sequence information


1.3 基因组序列变异分析与可视化

2019nCoVR分别选取可感染人的两种冠状病毒,即SARS (NC_004718)和最先公布的2019-nCoV基因组序列(MN908947),以及一种从蝙蝠中分离采集到的SARS样冠状病毒(bat-SL-CoVZC45, MG772933)作为参考基因组,整合“发布动态”中汇总可获取的全基因组序列,用Muscle软件[19,20]逐一进行全基因组序列比较和多序列比对,比较发现2019-nCoV与NC_004718、bat-SL-CoVZC45和蝙蝠中检测到的冠状病毒(bat/Yunnan/RaTG13/2013)的基因组序列相似度分别为80%、88%和96%,而2019-nCoV内部不同株系间的序列相似性约为99.9%。基于从人体中分离的65株病毒全基因组序列,在去除序列变异数量异常和变异位点集中(有5个突变发生在20 bp的区域内)的3株序列后,对剩余的62株序列采用基于距离的UPGMA法构建系统发育树,显示其遗传关系非常近且有所分化(图3)。

图3

图3   新型冠状病毒序列的系统进化树

Fig. 3   Phylogenetics tree of 2019-nCoV


通过提取基因组序列比对中发现的变异位置、类型及信息,并配置GBrowse浏览器[21],可视化展示了每个病毒分离株与不同参考序列的变异(图4A)。此外,统计包括插入、删除、Indel和单核苷酸多态位点(SNP)的各类变异总数,提供了每个病毒株变异统计信息检索及下载。汇总各株变异信息发现主要的变异类型是SNP。经统计,与2019-nCoV参考序列相比,有14株病毒的序列无变异,49株平均有1~9个SNP变异(图4B),1株有27个SNP变异,因此推测该株(Acc. No. EPI_ISL_406592)的基因组序列质量存在问题。此外,检测到的少数序列删除变异(deletion)主要发生在基因组的5ʹUTR和3ʹUTR区域,有可能与测序准确率、基因组拼接等有关。初步提示已发布的65株病毒可能来源于近期出现的同一个病毒源。

图4

图4   基因组序列变异在线展示示意图及变异信息统计与注释

A:全基因组序列变异在线展示示意图;B:病毒株SNP变异数统计;C:SNP变异在各注释基因及UTR区的数量统计;D:SNP变异效应统计。

Fig. 4   Snapshot of genome sequence variants on GBrowse as well as SNP statistics and annotations


通过计算每个变异位点的群体发生频率并采用VEP软件[22]对上述变异进行注释,网站提供了所有变异位点注释信息(包括碱基变异、密码子及氨基酸变化、变异注释类型)的查询、浏览与下载。经统计发现2019-nCoV群体内的序列变异主要发生在5个基因,即产生病毒表面糖蛋白的S基因、编码病毒核衣壳磷蛋白的N基因、orf8基因、orf3a和最大的基因orf1ab。其中,orf1ab基因的变异位点数高达39 (图4C)。经分析,约42%的变异是非同义突变(图4D),且发现多株病毒的非同义突变主要发生在S蛋白的第32位(F→I,c.94Ttc>Atc)和第49位(H→Y,c.145Cat>Tat)及ORF8蛋白的第84位(L→S,c.251tTa>tCa),而发生在ORF1ab蛋白上的非同义突变位点数量最多(附表2)。

1.4 关联信息整合

2019nCoVR整合了来源于公共数据库及公共媒体的相关信息,主要包括:(1) NCBI冠状病毒科的所有序列、冠状病毒全基因组序列、感染人的冠状病毒全基因组序列、2019-nCoV序列等;(2)PubMed中冠状病毒相关的学术文献及Europe PMC针对2019-nCoV的最新学术报道;(3)中国CDC及WHO等权威机构对2019-nCoV的新闻报道、病毒解读及其相关的科普知识。这些内容为全球科研人员和普通民众开展学术研究、了解科研进展、掌握新闻动态与科学知识提供一站式数据资源与信息窗口。

2 数据汇交与审核机制

依托CNCB/NGDC的GSA系统,2019nCoVR提供新型冠状病毒原始测序数据的汇交服务,汇交内容主要包括元数据信息和序列文件。数据递交完成后,GSA系统会对用户递交的元数据信息和序列文件进行质量控制与审核,校验文件大小和内容、统计序列信息、评估数据质量,以此确保递交数据的完整性和可靠性。审核通过后,系统会为该数据分配唯一的数据编号(accession number),并通过邮件通知递交者。数据编号可作为数据检索和访问的标识,也可在文章中使用。

与之类似,2019nCoVR依托CNCB/NGDC的GWH数据库,汇交新型冠状病毒基因组序列和蛋白质序列,主要包括元数据、序列信息和注释文件。

为严格把控病毒基因组数据入库质量,针对用户递交的数据,GWH建立了严格的质量控制标准,审核检查数据的合法性和一致性,主要包括序列合法性、基因结构与信息完整性、基因结构内部的一致性、序列内容与注释信息的一致性以及载体、接头、index、污染序列等。数据审核通过后,GWH系统会为该数据分配正式的数据编号,方便数据检索、访问和下载。截止到2020年2月5日,已经收录了中国医学科学院病原生物学研究所和中国科学院武汉病毒研究所提交的11株冠状病毒全基因组序列。为了进一步扩大2019-nCoV基因组序列的国际影响力和应用范围,CNCB/NGDC与国际生物信息数据库建立了数据同步共享机制,第一批5个2019-nCoV全基因组序列已经在NCBI发布(Acc. No. MT019529~ MT019533)。

3 数据发布、管理与使用规范

2019nCoVR遵循CNCB/NGDC的相关数据管理制度及领域内数据管理惯例,即数据的所有权属于数据递交者,数据的公开与发布由数据提交者(submitter)自行管理。递交至2019nCoVR的新型冠状病毒数据(包括元信息和关联的序列数据),将分为公开(public)、受控(controlled)和私有(confidential)三种类型,数据提交者根据其数据的密级、保密期限、开放条件、开放对象和审核程序等,在提交数据时选择一种数据访问类型,数据提交完成并审核通过后,系统将按照数据提交者选择的数据访问类型进行管理(表1)。三类数据访问类型的管理规则具体如下:

(1)公开类型:元信息和关联序列数据都公开共享,任何用户可查询、访问与下载;

(2)受控类型:元信息公开共享,但关联序列数据受控访问。数据申请者须向数据提交者提出序列数据使用请求,由数据提交者向数据申请者发放访问权限。数据提交者可根据情况动态调整数据访问类型。

(3)私有类型:元信息和关联数据不会在数据平台上展示,用户无法查询、访问或下载。当私有数据符合开放共享条件时,如相关科研论文已发表或者达到约定公开时限,系统会通知数据提交者公开其数据。私有类型数据亦可由数据提交者动态管理。

表1   三类数据访问类型的基本规则

Table 1  Fundamental rules for three types of data access

数据类型 汇交内容 公开程度 开放对象 开放条件
公开* 元信息
关联数据
公开 所有用户 审核通过即公开
受控 元信息
关联数据
公开
受控
所有用户
申请用户
相关科研论文已发表或达到约定公开时限
私有 元信息
关联数据
受控 相关科研论文已发表或达到约定公开时限

*:凡是类似2019-nCoV等涉及国家或全球公共卫生安全,呼吁基因序列数据在测序完成后第一时间采用“公开”数据类型开放共享。

新窗口打开下载CSV


4 结语与展望

2019nCoVR整合来自CNCB/NGDC、CNGB、GISAID、NCBI及NMDC 的新型冠状病毒数据资源,无缝对接CNCB/NGDC的相关数据库,为新型冠状病毒基因组数据的快速发布与开放共享提供公共平台,也为加速开展病毒分类溯源、基因组演化、快速检测、药物研发、新型肺炎的精准预防与治疗等研究提供重要基础。随着2019-nCoV科研工作的深入开展,2019nCoVR将持续更新并发布相关基因组序列及其元数据信息,为攻坚2019-nCoV提供数据保障与信息支撑。同时,特此呼吁科研人员和医务工作者加快推进2019-nCoV基因组数据的汇交、共享与发布,建立实现全球数据共同体,协同战胜病毒疫情。

致谢

该信息库由国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建设并维护。在建设过程中,得到了北京大学罗静初教授的支持和帮助,在此表示感谢!信息库所有数据来源于用户直接递交或国内外公共数据平台,包括GISAID、NCBI/GenBank、NMDC、CNGB/CNGBdb等(附表1),在此,对所有样本收集和数据递交的单位和个人表示感谢!

附录

附表1和附表2见网站电子版www.chinagene.cn。

附表1   病毒基因组元信息表。信息统计截至2020年2月5日。

Table S1  

Virus Isolate Name Accession ID Data Source Related ID Host Sample Collection Date Location Nuc.Completeness Originating Lab Submitting Lab
BetaCoV/USA/WA1-F6/2020 EPI_ISL_407215 GISAID Human 2020-1-25 USA / Washington Complete WA State Department of Health Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Dieases Control and Prevention
BetaCoV/Korea/KCDC03/2020 EPI_ISL_407193 GISAID Human 2020-1-25 Korea / Gyeonggi-do Complete Korea Centers for Disease Control & Prevention (KCDC) Center for Laboratory Control of Infectious Diseases Division of Viral Diseases Korea Centers for Disease Control & Prevention (KCDC) Center for Laboratory Control of Infectious Diseases Division of Viral Diseases
BetaCoV/Japan/AI/I-004/2020 EPI_ISL_407084 GISAID Human 2020-1-25 Japan / Aichi Complete Department of Virology III, National Institute of Infectious Diseases Pathogen Genomics Center, National Institute of Infectious Diseases
BetaCoV/USA/WA1-A12/2020 EPI_ISL_407214 GISAID Human 2020-1-25 USA / Washington Complete WA State Department of Health Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Dieases Control and Prevention
BetaCoV/Singapore/1/2020 EPI_ISL_406973 GISAID Human 2020-1-23 Singapore Complete Singapore General Hospital National Public Health Laboratory
BetaCoV/England/02/2020 EPI_ISL_407073 GISAID Human 2020-1-29 England Complete Respiratory Virus Unit, Microbiology Services Colindale, Public Health England Respiratory Virus Unit, Microbiology Services Colindale, Public Health England
BetaCoV/England/01/2020 EPI_ISL_407071 GISAID Human 2020-1-29 England Complete Respiratory Virus Unit, Microbiology Services Colindale, Public Health England Respiratory Virus Unit, Microbiology Services Colindale, Public Health England
BetaCoV/Finland/1/2020 EPI_ISL_407079 GISAID Human 2020-1-29 Finland / Lapland Partial/scaffold level Lapland Central Hospital Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
BetaCoV/Hangzhou/HZ-1/2020 EPI_ISL_406970 GISAID Human 2020-1-20 China / Zhejiang / Hangzhou Complete Hangzhou Center for Disease Control and Prevention, Microbiology Lab Hangzhou Center for Disease Control and Prevention, Microbiology Lab
2019 nCoV/Italy-INMI1 MT008022 GenBank EPI_ISL_406959 Human 2020-01 Italy / Rome Partial/gene level Virology Laboratory, INMI L. Spallanzani
2019 nCoV/Italy-INMI2 MT008023 GenBank EPI_ISL_406960 Human 2020-01 Italy / Rome Partial/gene level Virology Laboratory, INMI L. Spallanzani
BetaCoV/Wuhan/WH19002/2019 NMDC60013002-05 NMDC Human 2019-12-30 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Wuhan/WH19008/2019 NMDC60013002-06 NMDC Human 2019-12-30 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Wuhan/YS8011/2020 NMDC60013002-07 NMDC Human 2020-1-7 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Wuhan/WH19001/2019 NMDC60013002-08 NMDC Human 2019-12-30 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Wuhan/WH19004/2020 NMDC60013002-09 NMDC Human 2020-1-1 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Wuhan/WH19005/2019 NMDC60013002-10 NMDC Human 2019-12-30 China / Hubei Province / Wuhan City Complete China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention; BGI PathoGenesis Pharmaceutical Technology Co., Ltd
BetaCoV/Germany/BavPat1/2020 EPI_ISL_406862 GISAID Human 2020-1-28 Germany / Bavaria / Munich Complete Charité Universitätsmedizin Berlin, Institute of Virology; Institut für Mikrobiologie der Bundeswehr, Munich Charité Universitätsmedizin Berlin, Institute of Virology
BetaCoV/Wuhan/WH-01/2019 NMDC60013002-01 NMDC LR757998, EPI_ISL_406798, CNA0007332 Human 2019-12-26 China / Hubei Province / Wuhan City Complete General Hospital of Central Theater Command of People's Liberation Army of China BGI PathoGenesis Pharmaceutical Technology Co., Ltd; China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention
BetaCoV/Wuhan/WH-02/2019 NMDC60013002-02 NMDC LR757997, CNA0007333 Human 2019-12-31 China / Hubei Province / Wuhan City Partial/scaffold level BGI PathoGenesis Pharmaceutical Technology Co., Ltd; China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention
BetaCoV/Wuhan/WH-03/2019 NMDC60013002-03 NMDC LR757996, EPI_ISL_406800, CNA0007334 Human 2020-1-1 China / Hubei Province / Wuhan City Complete General Hospital of Central Theater Command of People's Liberation Army of China BGI PathoGenesis Pharmaceutical Technology Co., Ltd; China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention
BetaCoV/Wuhan/WH-04/2019 NMDC60013002-04 NMDC LR757995, EPI_ISL_406801, CNA0007335 Human 2020-1-5 China / Hubei Province / Wuhan City Complete General Hospital of Central Theater Command of People's Liberation Army of China BGI PathoGenesis Pharmaceutical Technology Co., Ltd; China CDC; Shandong First Medical University & Shandong Academy of Medical Sciences; Hubei Provincial Center for Disease Control and Prevention
BetaCoV/Australia/VIC01/2020 MT007544 GenBank EPI_ISL_406844 Human 2020-1-25 Australia / Victoria / Clayton Complete Monash Medical Centre Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
WIV02 GWHABKK00000000 Genome Warehouse EPI_ISL_402127, MN996527 Human 2019-12-30 China/ Hubei / Wuhan Complete Wuhan Jinyintan Hospital CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
WIV04 GWHABKL00000000 Genome Warehouse EPI_ISL_402124, MN996528 Human 2019-12-30 China / Hubei / Wuhan Complete Wuhan Jinyintan Hospital CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
WIV05 GWHABKM00000000 Genome Warehouse EPI_ISL_402128, MN996529 Human 2019-12-30 China / Hubei / Wuhan Complete Wuhan Jinyintan Hospital CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
WIV06 GWHABKN00000000 Genome Warehouse EPI_ISL_402129, MN996530 Human 2019-12-30 China / Hubei / Wuhan Complete Wuhan Jinyintan Hospital CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
WIV07 GWHABKO00000000 Genome Warehouse EPI_ISL_402130, MN996531 Human 2019-12-30 China / Hubei / Wuhan Complete Wuhan Jinyintan Hospital CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
TG13 GWHABKP00000000 Genome Warehouse EPI_ISL_402131, MN996532 Rhinolophus affinis 2013-7-24 China / Yunnan / Pu'er Complete Wuhan Institute of Virology CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences
BetaCoV/Guangdong/20SF174/2020 EPI_ISL_406531 GISAID Human 2020-1-22 China / Guangdong Province Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Guangzhou/20SF206/2020 EPI_ISL_406533 GISAID Human 2020-1-22 China / Guangdong Province / Guangzhou City Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Foshan/20SF207/2020 EPI_ISL_406534 GISAID Human 2020-1-22 China / Guangdong Province Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Foshan/20SF210/2020 EPI_ISL_406535 GISAID Human 2020-1-22 China / Guangdong Province Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Foshan/20SF211/2020 EPI_ISL_406536 GISAID Human 2020-1-22 China / Guangdong Province Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Guangdong/20SF201/2020 EPI_ISL_406538 GISAID Human 2020-1-23 China / Guangdong Province Complete Guangdong Provincial Center for Diseases Control and Prevention;Guangdong Provincial Institute of Public Health Guangdong Provincial Center for Diseases Control and Prevention
BetaCoV/Shenzhen/SZTH-001/2020 EPI_ISL_406592 GISAID Human 2020-1-13 China/ Guangdong Province / Shenzhen City Complete Shenzhen Third People's Hospital Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
BetaCoV/Shenzhen/SZTH-003/2020 EPI_ISL_406594 GISAID Human 2020-1-16 China/ Guangdong Province / Shenzhen City Complete Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
BetaCoV/Shenzhen/SZTH-004/2020 EPI_ISL_406595 GISAID Human 2020-1-16 China/ Guangdong Province / Shenzhen City Complete Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
BetaCoV/Shenzhen/SZTH-002/2020 EPI_ISL_406593 GISAID Human 2020-1-13 China/ Guangdong Province / Shenzhen City Complete Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
BetaCoV/France/IDF0373/2020 EPI_ISL_406597 GISAID Human 2020-1-23 France / Ile-de-France / Paris Complete Department of Infectious and Tropical Diseases, Bichat Claude Bernard Hospital, Paris National Reference Center for Viruses of Respiratory Infections, Institut Pasteur, Paris
BetaCoV/France/IDF0372/2020 EPI_ISL_406596 GISAID Human 2020-1-23 France / Ile-de-France / Paris Complete Department of Infectious and Tropical Diseases, Bichat Claude Bernard Hospital, Paris National Reference Center for Viruses of Respiratory Infections, Institut Pasteur, Paris
2019-nCoV_HKU-SZ-001_2020 MN938387 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-001_2020 MN938385 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-002b_2020 MN938388 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-004_2020 MN938389 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-004_2020 MN938386 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-005_2020 MN938390 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007a_2020 MN975266 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007a_2020 MN975263 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007b_2020 MN975264 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007b_2020 MN975267 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007c_2020 MN975268 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-007c_2020 MN975265 GenBank Human 2020-01 China / Guangdong / Shenzhen Partial/gene level University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
SI200040-SP MN970003 GenBank Human 2020-1-8 Thailand Partial/gene level Faculty of Medicine, Chulalongkorn University
SI200121-SP MN970004 GenBank Human 2020-1-13 Thailand Partial/gene level Faculty of Medicine, Chulalongkorn University
BetaCoV/Taiwan/2/2020 EPI_ISL_406031 GISAID Human 2020-1-23 Taiwan/Kaohsiung City Complete Centers for Disease Control (Taiwan) Centers for Disease Control (Taiwan)
2019-nCoV/USA-CA1/2020 MN994467 GenBank EPI_ISL_406034 Human 2020-1-23 USA / California / Los Angeles Complete California Department of Public Health Division of Viral Diseases, Centers for Disease Control and Prevention
2019-nCoV/USA-CA2/2020 MN994468 GenBank EPI_ISL_406036 Human 2020-1-22 USA / California / Orange County Complete California Department of Public Health Division of Viral Diseases, Centers for Disease Control and Prevention
2019-nCoV/USA-AZ1/2020 MN997409 GenBank EPI_ISL_406223 Human 2020-1-22 USA / Arizona / Phoenix Complete Arizona Department of Health Services Division of Viral Diseases, Centers for Disease Control and Prevention
2019-nCoV WHU01 MN988668 GenBank EPI_ISL_406716 Human 2020-1-2 China / Hubei / Wuhan Complete State Key Laboratory of Virology, Wuhan University State Key Laboratory of Virology, Wuhan University
2019-nCoV WHU02 MN988669 GenBank EPI_ISL_406717 Human 2020-1-2 China / Hubei / Wuhan Complete State Key Laboratory of Virology, Wuhan University State Key Laboratory of Virology, Wuhan University
2019-nCoV/USA-WA1/2020 MN985325 GenBank EPI_ISL_404895 Human 2020-1-19 USA / Washington / Snohomish County Complete Providence Regional Medical Center Division of Viral Diseases, Centers for Disease Control and Prevention
2019-nCoV/USA-IL1/2020 MN988713 GenBank EPI_ISL_404253 Human 2020-1-21 USA / Illinois /Chicago Complete Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Dieases Control and Prevention IL Department of Public Health Chicago Laboratory
BetaCoV/Wuhan/IPBCAMS-WH-01/2019 GWHABKF00000000 Genome Warehouse EPI_ISL_402123 Human 2019-12-23 China / Hubei Province / Wuhan City Complete Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College; Vision Medicals Co., Ltd
BetaCoV/Wuhan/IPBCAMS-WH-02/2019 GWHABKG00000000 Genome Warehouse EPI_ISL_403931 Human 2019-12-30 China / Hubei Province / Wuhan City Complete Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
BetaCoV/Wuhan/IPBCAMS-WH-03/2019 GWHABKH00000000 Genome Warehouse EPI_ISL_403930 Human 2019-12-30 China / Hubei Province / Wuhan City Complete Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
BetaCoV/Wuhan/IPBCAMS-WH-04/2019 GWHABKI00000000 Genome Warehouse EPI_ISL_403929 Human 2019-12-30 China / Hubei Province / Wuhan City Complete Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
BetaCoV/Wuhan/IPBCAMS-WH-05/2020 GWHABKJ00000000 Genome Warehouse EPI_ISL_403928 Human 2020-1-1 China / Hubei Province / Wuhan City Complete Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College; China National Center for Bioinformation
2019-nCoV_HKU-SZ-002a_2020 MN938384 GenBank EPI_ISL_406030 Human 2020-1 China / Guangdong / Shenzhen Complete University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
2019-nCoV_HKU-SZ-005b_2020 MN975262 GenBank EPI_ISL_405839 Human 2020-1 China / Guangdong / Shenzhen Complete University of Hong Kong-Shenzhen Hospital University of Hong Kong-Shenzhen Hospital
BetaCoV/Guangdong/20SF040/2020 EPI_ISL_403937 GISAID Human 2020-1-18 China / Guangdong Province / Zhuhai City Complete Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Guangdong/20SF028/2020 EPI_ISL_403936 GISAID Human 2020-1-17 China / Guangdong Province / Zhuhai City Complete Guangdong Provincial Center for Diseases control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Guangdong/20SF025/2020 EPI_ISL_403935 GISAID Human 2020-1-15 China / Guangdong Province / Shenzhen City Complete Guangdong Provincial Center for Diseases control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Guangdong/20SF014/2020 EPI_ISL_403934 GISAID Human 2020-1-15 China / Guangdong Province / Shenzhen City Complete Guangdong Provincial Center for Diseases control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Guangdong/20SF013/2020 EPI_ISL_403933 GISAID Human 2020-1-15 China / Guangdong Province / Shenzhen City Complete Guangdong Provincial Center for Diseases control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Guangdong/20SF012/2020 EPI_ISL_403932 GISAID Human 2020-1-14 China / Guangdong Province / Shenzhen City Complete Guangdong Provincial Center for Diseases control and Prevention; Guangdong Provincial Institute of Public Health Department of Microbiology, Guangdong Provincial Center for Diseases control and Prevention
BetaCoV/Zhejiang/WZ-01/2020 EPI_ISL_404227 GISAID Human 2020-1-16 China / Zhejiang Province Complete Zhejiang Provincial Center for Disease Control and Prevention Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention
BetaCoV/Zhejiang/WZ-02/2020 EPI_ISL_404228 GISAID Human 2020-1-17 China / Zhejiang Province Complete Zhejiang Provincial Center for Disease Control and Prevention Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention
BetaCoV/Wuhan/HBCDC-HB-01/2019 EPI_ISL_402132 GISAID Human 2019-12-30 China/Hubei Province Complete Wuhan Jinyintan Hospital Hubei Provincial Center for Disease Control and Prevention
BetaCoV/Nonthaburi/74/2020 EPI_ISL_403963 GISAID Human 2020-1-13 Thailand/ Nonthaburi Province Complete Bamrasnaradura Hospital Department of Medical Sciences, Ministry of Public Health, Thailand; Thai Red Cross Emerging Infectious Diseases - Health Science Centre; Department of Disease Control, Ministry of Public Health, Thailand
BetaCoV/Nonthaburi/61/2020 EPI_ISL_403962 GISAID Human 2020-1-8 Thailand/ Nonthaburi Province Complete Bamrasnaradura Hospital Department of Medical Sciences, Ministry of Public Health, Thailand; Thai Red Cross Emerging Infectious Diseases - Health Science Centre; Department of Disease Control, Ministry of Public Health, Thailand
BetaCoV/Wuhan/IVDC-HB-04/2020 EPI_ISL_402120 GISAID Human 2020-1-1 China / Hubei Province / Wuhan City Complete National Institute for Viral Disease Control and Prevention, China CDC National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-01/2019 EPI_ISL_402119 GISAID Human 2019-12-30 China / Hubei Province / Wuhan City Complete National Institute for Viral Disease Control and Prevention, China CDC National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-05/2019 EPI_ISL_402121 GISAID Human 2019-12-30 China / Hubei Province / Wuhan City Complete National Institute for Viral Disease Control and Prevention, China CDC National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Kanagawa/1/2020 EPI_ISL_402126 GISAID Human 2020-1-14 Kanagawa Prefecture / Japan Partial Dept. of Virology III, National Institute of Infectious Diseases Dept. of Virology III, National Institute of Infectious Diseases
Wuhan-Hu-1 MN908947 GenBank NC_045512 Human 2019-12 China / Hubei Province / Wuhan City Complete Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China

新窗口打开下载CSV


附表2   2019-nCoV基因组序列变异注释信息

Table S2  Genome variants and annotations

基因组位置 基因/区域名称 变异病毒株数 碱基变化及病毒株数 变异注释类型 蛋白名称.位置.氨基酸变化 基因名.CDS位置.序列变化 效应类型
2019-nCoV_16 5'UTR 1 C->T:1 intergenic_variant - - MODIFIER
2019-nCoV_31 5'UTR 1 A->G:1 intergenic_variant - - MODIFIER
2019-nCoV_104 5'UTR 1 T->A:1 intergenic_variant - - MODIFIER
2019-nCoV_111 5'UTR 1 T->C:1 intergenic_variant - - MODIFIER
2019-nCoV_112 5'UTR 1 T->G:1 intergenic_variant - - MODIFIER
2019-nCoV_119 5'UTR 1 C->G:1 intergenic_variant - - MODIFIER
2019-nCoV_120 5'UTR 1 T->C:1 intergenic_variant - - MODIFIER
2019-nCoV_124 5'UTR 1 G->A:1 intergenic_variant - - MODIFIER
2019-nCoV_241 5'UTR 1 C->T:1 upstream_gene_variant QHD43415.1 gene-orf1ab MODIFIER;DISTANCE=25
2019-nCoV_358 gene-orf1ab 1 TGGAGACTCCGTGGAGGAGGTCTTA->T:1 inframe_deletion QHD43415.1:p.32-39GDSVEEVL>- gene-orf1ab:c.94-117GGAGACTCCGTGGAGGAGGTCTTA>- MODERATE
2019-nCoV_490 gene-orf1ab 1 T->W:1 coding_sequence_variant QHD43415.1:p.75- gene-orf1ab:c.225gaT>gaW MODIFIER
2019-nCoV_583 gene-orf1ab 1 C->T:1 synonymous_variant QHD43415.1:p.106V gene-orf1ab:c.318gtC>gtT LOW
2019-nCoV_709 gene-orf1ab 1 G->A:1 synonymous_variant QHD43415.1:p.148E gene-orf1ab:c.444gaG>gaA LOW
2019-nCoV_1548 gene-orf1ab 1 G->A:1 missense_variant QHD43415.1:p.428S>N gene-orf1ab:c.1283aGc>aAc MODERATE
2019-nCoV_1912 gene-orf1ab 1 C->T:1 synonymous_variant QHD43415.1:p.549S gene-orf1ab:c.1647tcC>tcT LOW
2019-nCoV_3037 gene-orf1ab 1 C->T:1 synonymous_variant QHD43415.1:p.924F gene-orf1ab:c.2772ttC>ttT LOW
2019-nCoV_3177 gene-orf1ab 1 C->Y:1 coding_sequence_variant QHD43415.1:p.971- gene-orf1ab:c.2912cCt>cYt MODIFIER
2019-nCoV_3778 gene-orf1ab 1 A->G:1 synonymous_variant QHD43415.1:p.1171T gene-orf1ab:c.3513acA>acG LOW
2019-nCoV_4402 gene-orf1ab 1 T->C:1 synonymous_variant QHD43415.1:p.1379L gene-orf1ab:c.4137ctT>ctC LOW
2019-nCoV_5062 gene-orf1ab 1 G->T:1 missense_variant QHD43415.1:p.1599L>F gene-orf1ab:c.4797ttG>ttT MODERATE
2019-nCoV_6846 gene-orf1ab 1 T->C:1 missense_variant QHD43415.1:p.2194M>T gene-orf1ab:c.6581aTg>aCg MODERATE
2019-nCoV_6968 gene-orf1ab 1 C->A:1 missense_variant QHD43415.1:p.2235L>I gene-orf1ab:c.6703Cta>Ata MODERATE
2019-nCoV_6996 gene-orf1ab 1 T->C:1 missense_variant QHD43415.1:p.2244I>T gene-orf1ab:c.6731aTc>aCc MODERATE
2019-nCoV_7016 gene-orf1ab 1 G->A:1 missense_variant QHD43415.1:p.2251G>S gene-orf1ab:c.6751Ggt>Agt MODERATE
2019-nCoV_7866 gene-orf1ab 1 G->T:1 missense_variant QHD43415.1:p.2534G>V gene-orf1ab:c.7601gGt>gTt MODERATE
2019-nCoV_8001 gene-orf1ab 1 A->C:1 missense_variant QHD43415.1:p.2579D>A gene-orf1ab:c.7736gAt>gCt MODERATE
2019-nCoV_8388 gene-orf1ab 1 A->G:1 missense_variant QHD43415.1:p.2708N>S gene-orf1ab:c.8123aAc>aGc MODERATE
2019-nCoV_8782 gene-orf1ab 16 C->T:15;C->Y:1 synonymous_variant;coding_sequence_variant QHD43415.1:p.2839S;QHD43415.1:p.2839- gene-orf1ab:c.8517agC>agT;gene-orf1ab:c.8517agC>agY LOW;MODIFIER
2019-nCoV_8987 gene-orf1ab 1 T->A:1 missense_variant QHD43415.1:p.2908F>I gene-orf1ab:c.8722Ttt>Att MODERATE
2019-nCoV_9534 gene-orf1ab 1 C->T:1 missense_variant QHD43415.1:p.3090T>I gene-orf1ab:c.9269aCt>aTt MODERATE
2019-nCoV_9561 gene-orf1ab 1 C->T:1 missense_variant QHD43415.1:p.3099S>L gene-orf1ab:c.9296tCa>tTa MODERATE
2019-nCoV_11083 gene-orf1ab 1 G->T:1 missense_variant QHD43415.1:p.3606L>F gene-orf1ab:c.10818ttG>ttT MODERATE
2019-nCoV_11707 gene-orf1ab 1 A->G:1 synonymous_variant QHD43415.1:p.3814L gene-orf1ab:c.11442ttA>ttG LOW
2019-nCoV_11764 gene-orf1ab 1 T->A:1 missense_variant QHD43415.1:p.3833N>K gene-orf1ab:c.11499aaT>aaA MODERATE
2019-nCoV_15324 gene-orf1ab 1 C->T:1 synonymous_variant QHD43415.1:p.5020N gene-orf1ab:c.15060aaC>aaT LOW
2019-nCoV_15607 gene-orf1ab 1 T->C:1 synonymous_variant QHD43415.1:p.5115L gene-orf1ab:c.15343Tta>Cta LOW
2019-nCoV_16188 gene-orf1ab 1 G->T:1 missense_variant QHD43415.1:p.5308W>C gene-orf1ab:c.15924tgG>tgT MODERATE
2019-nCoV_17000 gene-orf1ab 1 C->T:1 missense_variant QHD43415.1:p.5579T>I gene-orf1ab:c.16736aCa>aTa MODERATE
2019-nCoV_17373 gene-orf1ab 2 C->T:2 synonymous_variant QHD43415.1:p.5703A gene-orf1ab:c.17109gcC>gcT LOW
2019-nCoV_18060 gene-orf1ab 3 C->T:3 synonymous_variant QHD43415.1:p.5932L gene-orf1ab:c.17796ctC>ctT LOW
2019-nCoV_18488 gene-orf1ab 2 T->C:2 missense_variant QHD43415.1:p.6075I>T gene-orf1ab:c.18224aTa>aCa MODERATE
2019-nCoV_18512 gene-orf1ab 1 C->T:1 missense_variant QHD43415.1:p.6083P>L gene-orf1ab:c.18248cCt>cTt MODERATE
2019-nCoV_19065 gene-orf1ab 1 T->C:1 synonymous_variant QHD43415.1:p.6267P gene-orf1ab:c.18801ccT>ccC LOW
2019-nCoV_19959 gene-orf1ab 1 A->C:1 missense_variant QHD43415.1:p.6565E>D gene-orf1ab:c.19695gaA>gaC MODERATE
2019-nCoV_20670 gene-orf1ab 2 G->A:2 synonymous_variant QHD43415.1:p.6802A gene-orf1ab:c.20406gcG>gcA LOW
2019-nCoV_20679 gene-orf1ab 2 G->A:2 synonymous_variant QHD43415.1:p.6805P gene-orf1ab:c.20415ccG>ccA LOW
2019-nCoV_21137 gene-orf1ab 1 A->G:1 missense_variant QHD43415.1:p.6958K>R gene-orf1ab:c.20873aAg>aGg MODERATE
2019-nCoV_21316 gene-orf1ab 1 G->A:1 missense_variant QHD43415.1:p.7018D>N gene-orf1ab:c.21052Gat>Aat MODERATE
2019-nCoV_21656 gene-S 1 T->A:1 missense_variant QHD43416.1:p.32F>I gene-S:c.94Ttc>Atc MODERATE
2019-nCoV_21707 gene-S 3 C->T:3 missense_variant QHD43416.1:p.49H>Y gene-S:c.145Cat>Tat MODERATE
2019-nCoV_22303 gene-S 1 T->G:1 missense_variant QHD43416.1:p.247S>R gene-S:c.741agT>agG MODERATE
2019-nCoV_22586 gene-S 1 T->Y:1 coding_sequence_variant QHD43416.1:p.342- gene-S:c.1024Ttt>Ytt MODIFIER
2019-nCoV_22622 gene-S 1 A->G:1 missense_variant QHD43416.1:p.354N>D gene-S:c.1060Aac>Gac MODERATE
2019-nCoV_22652 gene-S 1 G->T:1 missense_variant QHD43416.1:p.364D>Y gene-S:c.1090Gat>Tat MODERATE
2019-nCoV_22661 gene-S 2 G->T:2 missense_variant QHD43416.1:p.367V>F gene-S:c.1099Gtc>Ttc MODERATE
2019-nCoV_23403 gene-S 1 A->G:1 missense_variant QHD43416.1:p.614D>G gene-S:c.1841gAt>gGt MODERATE
2019-nCoV_23569 gene-S 2 T->C:2 synonymous_variant QHD43416.1:p.669G gene-S:c.2007ggT>ggC LOW
2019-nCoV_23605 gene-S 2 T->G:2 synonymous_variant QHD43416.1:p.681P gene-S:c.2043ccT>ccG LOW
2019-nCoV_24034 gene-S 2 C->T:1;C->Y:1 synonymous_variant;coding_sequence_variant QHD43416.1:p.824N;QHD43416.1:p.824- gene-S:c.2472aaC>aaT;gene-S:c.2472aaC>aaY LOW;MODIFIER
2019-nCoV_24325 gene-S 2 A->G:2 synonymous_variant QHD43416.1:p.921K gene-S:c.2763aaA>aaG LOW
2019-nCoV_25060 gene-S 1 A->G:1 synonymous_variant QHD43416.1:p.1166L gene-S:c.3498ttA>ttG LOW
2019-nCoV_25645 gene-ORF3a 1 T->C:1 synonymous_variant QHD43417.1:p.85L gene-ORF3a:c.253Ttg>Ctg LOW
2019-nCoV_25964 gene-ORF3a 1 A->G:1 missense_variant QHD43417.1:p.191E>G gene-ORF3a:c.572gAa>gGa MODERATE
2019-nCoV_26144 gene-ORF3a 5 G->T:5 missense_variant QHD43417.1:p.251G>V gene-ORF3a:c.752gGt>gTt MODERATE
2019-nCoV_26729 gene-M 2 T->C:1;T->Y:1 synonymous_variant;coding_sequence_variant QHD43419.1:p.69A;QHD43419.1:p.69- gene-M:c.207gcT>gcC;gene-M:c.207gcT>gcY LOW;MODIFIER
2019-nCoV_27493 gene-ORF7a 2 C->T:2 missense_variant QHD43421.1:p.34P>S gene-ORF7a:c.100Cct>Tct MODERATE
2019-nCoV_27577 gene-ORF7a 1 C->T:1 stop_gained QHD43421.1:p.62Q>* gene-ORF7a:c.184Caa>Taa HIGH
2019-nCoV_28077 gene-ORF8 2 G->S:1;G->C:1 coding_sequence_variant;missense_variant QHD43422.1:p.62-;QHD43422.1:p.62V>L gene-ORF8:c.184Gtg>Stg;gene-ORF8:c.184Gtg>Ctg MODIFIER;MODERATE
2019-nCoV_28144 gene-ORF8 16 T->C:15;T->Y:1 missense_variant;coding_sequence_variant QHD43422.1:p.84L>S;QHD43422.1:p.84- gene-ORF8:c.251tTa>tCa;gene-ORF8:c.251tTa>tYa MODERATE;MODIFIER
2019-nCoV_28253 gene-ORF8 2 C->T:2 synonymous_variant QHD43422.1:p.120F gene-ORF8:c.360ttC>ttT LOW
2019-nCoV_28291 gene-N 1 C->T:1 synonymous_variant QHD43423.2:p.6P gene-N:c.18ccC>ccT LOW
2019-nCoV_28716 gene-N 1 C->T:1 missense_variant QHD43423.2:p.148T>I gene-N:c.443aCc>aTc MODERATE
2019-nCoV_28792 gene-N 1 A->T:1 synonymous_variant QHD43423.2:p.173A gene-N:c.519gcA>gcT LOW
2019-nCoV_28854 gene-N 3 C->T:2;C->Y:1 missense_variant;coding_sequence_variant QHD43423.2:p.194S>L;QHD43423.2:p.194- gene-N:c.581tCa>tTa;gene-N:c.581tCa>tYa MODERATE;MODIFIER
2019-nCoV_29095 gene-N 7 C->T:7 synonymous_variant QHD43423.2:p.274F gene-N:c.822ttC>ttT LOW
2019-nCoV_29303 gene-N 1 C->T:1 missense_variant QHD43423.2:p.344P>S gene-N:c.1030Cca>Tca MODERATE
2019-nCoV_29596 gene-ORF10 1 A->G:1 missense_variant QHI42199.1:p.13I>M gene-ORF10:c.39atA>atG MODERATE
2019-nCoV_29749 3'UTR 1 ACGATCGAGTG->A:1 downstream_gene_variant QHI42199.1 gene-ORF10 MODIFIER;DISTANCE=76
2019-nCoV_29854 3'UTR 1 C->T:1 intergenic_variant - - MODIFIER
2019-nCoV_29856 3'UTR 1 T->A:1 intergenic_variant - - MODIFIER
2019-nCoV_29868 3'UTR 1 GA->G:1 intergenic_variant - - MODIFIER
2019-nCoV_29877 3'UTR 1 A->T:1 intergenic_variant - - MODIFIER

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