“下一个病毒株”网站上的2019新冠病毒基因序列数据更新很快。一周前的3月26号有1442例,今天4月5月已经翻倍还多,已有3370例。网站在3月27日和4月3日已经给出两份周分析报告。小编结合4月3日报告,继续为大家“看图翻译”来解读新冠病毒传播和系统发育树情况。
目前网站GISAID数据库有来自 6 大洲 53 个国家的病毒样本序列。 这是一项令人难以置信的壮举-- 在病毒大流行期间对一种未知的大型 RNA 病毒进行测序是很困难的,只有通过世界各地的科学家和医生令人难以置信的工作和及时共享数据才有可能。地图上每个圆圈的大小表示的是该区域当前有多少数据可用,而不是疫情的真实严重程度。其中来自欧洲、北美、中国和澳大利亚的病例样本比较多。最近新上传的中国样本有一些,使得许多分支根部溯源更清晰。
(3370例COVID-19系统发育树矩形图)
(3370例COVID-19系统发育无根树)
(546例全球簇2系统发育矩形图)
(546例全球簇2样例分布与传播)
这个簇有几个重要特点。特点一是大部分样本突变步数都比较少,基本都在8步以内,欧美地区的样本又在6步以内。只有香港的几个单倍型分支突变步数比较大,最大的一个序列突变了15步。
(546例全球簇2系统发育突变雷达图)
(546例全球簇2系统发育时钟图)
荷兰独立支系根部以杭州地区的样本为主,也包括有上海、广东、重庆、日本等地的样本。这个分支的根部又衍生出其他地区的几个本地社区传播分支,包括澳大利亚、马来西亚和美国加利福尼亚州等本地社区传播分支。从美国加州社区分支又衍生出冰岛本地社区传播分支,可能来源于美国游客的传播。
(“长三角”亚簇的一个分支X系统发育树)
(“长三角”亚簇的一个分支X无根树)
2. 全球簇1状况分析
(448例全球簇1系统发育矩形图)
(448例全球簇1样例分布与传播)
(448例全球簇1系统发育无根树)
3. 环太簇状况分析
(727例环太簇系统发育矩形图)
(727例环太簇样例分布与传播)
(环太簇内的西班牙簇分支)
(环太簇西班牙簇样例分布和传播)
下图显示环太簇727例样本无根树。
(727例环太簇无根树)
4. 欧洲主簇状况分析
(1628例欧洲主簇系统发育矩形图)
(1628例欧洲主簇样例分布与传播)
(欧洲主簇内增加日本样本的一个分支片段)
5. 美国疫情状况分析
(来自美国样例在新冠病毒系统发育树上的位置)
现在美国成为疫情新的震中,如果各国旅行仍然没加限制,那么美国又会成为新的输出中心。比如加拿大邻近的序列大多数来自美国,表明这两个国家之间存在显著传播。但是,同样,这也不能作为它是起源地的证据。这些都是实事求是。除非有人真能开棺验尸,证明在11月之前,美国就有新冠病毒在流行。
虽然这些数据使我们能够推断出这场疫情的许多有用的特征并实时跟踪其传播,但需要强调的是,这些结论受到现有数据的限制。比如,地图上显示来自南半球的序列很少。这既不是因为 COVID-19 没有在这些地区传播,也不是因为理解这些病例不重要,而仅仅是因为从这些地区上传的数据相对较少。
Beijing Institute of Microbiology and Epidemiology
pangolin/Guangdong/P2S/2019
pangolin/Guangxi/P1E/2017
pangolin/Guangxi/P2V/2017
pangolin/Guangxi/P3B/2017
pangolin/Guangxi/P4L/2017
pangolin/Guangxi/P5E/2017
pangolin/Guangxi/P5L/2017
Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital
HongKong/Case23_26012020/2020
HongKong/Case27_30012020/2020
HongKong/Case29_01022020/2020
HongKong/Case30_29012020/2020
HongKong/Case31_28012020/2020
HongKong/Case32_04022020/2020
HongKong/Case33_02022020/2020
HongKong/Case34_30012020/2020
HongKong/Case35_04022020/2020
HongKong/Case36_07022020/2020
HongKong/HKPU39-3001/2020
HongKong/HKPU40-2801/2020
HongKong/HKPU41-0802/2020
HongKong/HKPU44-0102/2020
HongKong/HKPU52-3101/2020
HongKong/HKPU54-0302/2020
HongKong/HKPU57-0702/2020
HongKong/HKPU60-0802/2020
HongKong/HKPU64-1202/2020
Department of Clinical Pathology, Tuen Mun Hospital, 23 Tsing Chung Koon Road, Tuen Mun, N.T.
HongKong/HKPU63-1402/2020
Centers for Disease Control, R.O.C. (Taiwan)
Taiwan/2/2020
Department of microbiology laboratory,Anhui Provincial Center for Disease Control and Prevention
Anhui/SZ005/2020
Fujian Center for Disease Control and Prevention
Fujian/13/2020
Fujian/8/2020
General Hospital of Central Theater Command of People's Liberation Army of China
Wuhan/WH01/2019
Wuhan/WH02/2019
Wuhan/WH03/2020
Wuhan/WH04/2020
Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Public Health
Foshan/20SF207/2020
Foshan/20SF210/2020
Foshan/20SF211/2020
Guangdong/20SF012/2020
Guangdong/20SF013/2020
Guangdong/20SF014/2020
Guangdong/20SF025/2020
Guangdong/20SF028/2020
Guangdong/20SF040/2020
Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provinical Public Health
Guangdong/20SF174/2020
Guangzhou/20SF206/2020
Guangdong Provincial Center for Diseases Control and Prevention;Guangdong Provincial Institute of Public Health
Guangdong/20SF201/2020
Guangdong Provincial Institution of Public Health, Guangdong Provinical Center for Disease Control and Prevention
Guangdong/2020XN4239-P0034/2020
Guangdong/2020XN4243-P0035/2020
Guangdong/2020XN4273-P0036/2020
Guangdong/2020XN4276-P0037/2020
Guangdong/2020XN4291-P0038/2020
Guangdong/2020XN4373-P0039/2020
Guangdong/2020XN4433-P0040/2020
Guangdong/2020XN4448-P0002/2020
Guangdong/2020XN4459-P0041/2020
Guangdong/2020XN4475-P0042/2020
Guangdong/DG-S2-P0054/2020
Guangdong/DG-S41-P0056/2020
Guangdong/DG-S6-P0055/2020
Guangdong/DG-S9-P0045/2020
Guangdong/FS-S29-P0051/2020
Guangdong/FS-S30-P0052/2020
Guangdong/FS-S34-P0015/2020
Guangdong/FS-S42-P0046/2020
Guangdong/FS-S48-P0047/2020
Guangdong/FS-S50-P0053/2020
Guangdong/GD2020012-P0022/2020
Guangdong/GD2020016-P0011/2020
Guangdong/GD2020080-P0010/2020
Guangdong/GD2020085-P0043/2020
Guangdong/GD2020086-P0021/2020
Guangdong/GD2020087-P0008/2020
Guangdong/GD2020115-P0009/2020
Guangdong/GD2020134-P0031/2020
Guangdong/GD2020139-P0007/2020
Guangdong/GD2020227-P0029/2020
Guangdong/GD2020233-P0027/2020
Guangdong/GD2020234-P0023/2020
Guangdong/GD2020241-P0013/2020
Guangdong/GD2020246-P0028/2020
Guangdong/GD2020258-P0018/2020
Guangdong/GDFS2020052-P0025/2020
Guangdong/GDFS2020054-P0005/2020
Guangdong/GDFS2020056-P0044/2020
Guangdong/GDFS2020127-P0026/2020
Guangdong/GDSZ202004-P0004/2020
Guangdong/GDSZ202008-P0020/2020
Guangdong/GDSZ202009-P0032/2020
Guangdong/GDSZ202013-P0014/2020
Guangdong/GDSZ202015-P0019/2020
Guangdong/GZ-S6-P0050/2020
Guangdong/JM-S1-P0062/2020
Guangdong/MM-S1-P0048/2020
Guangdong/SZ-N128-P0057/2020
Guangdong/SZ-N59-P0049/2020
Guangdong/ZH-N22-P0059/2020
Guangdong/ZH-S33-P0058/2020
Guangdong/ZQ-S2-P0061/2020
Guangdong/ZS-S6-P0060/2020
Hong Kong Department of Health
HongKong/VB20024950/2020
HongKong/VB20026565/2020
HongKong/VM20001061/2020
HongKong/case42_VM20002493/2020
HongKong/case48_VM20002507/2020
HongKong/case49_VM20002508/2020
HongKong/case52_VM20002582/2020
HongKong/case78_VM20002849/2020
HongKong/case85_VM20002868/2020
HongKong/case90_VM20002907/2020
Hangzhou Center for Disease and Control Microbiology Lab
Hangzhou/HZ-1/2020
Hangzhou Center for Disease Control and Prevention
Hangzhou/HZ162/2020
Hangzhou/HZ178/2020
Hangzhou/HZ185/2020
Hangzhou/HZ477/2020
Hangzhou/HZ48/2020
Hangzhou/HZ481/2020
Hangzhou/HZ49/2020
Hangzhou/HZ551/2020
Hangzhou/HZ576/2020
Hangzhou/HZ60/2020
Hangzhou/HZ62/2020
Hangzhou/HZ638/2020
Hangzhou/HZ79/2020
Hangzhou/HZ90/2020
Hangzhou/HZ91/2020
Hangzhou/HZCDC0001/2020
Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
Wuhan/IPBCAMS-WH-01/2019
Wuhan/IPBCAMS-WH-02/2019
Wuhan/IPBCAMS-WH-03/2019
Wuhan/IPBCAMS-WH-04/2019
Wuhan/IPBCAMS-WH-05/2020
Institute of Viral Disease Control and Prevention, China CDC
Wuhan/IVDC-HB-envF13-20/2020
Wuhan/IVDC-HB-envF13-21/2020
Wuhan/IVDC-HB-envF13/2020
Wuhan/IVDC-HB-envF54/2020
Jiangxi province Center for Disease Control and Prevention
NanChang/JX216/2020
Jingzhou Center for Disease Control and Prevention
Jingzhou/HBCDC-HB-01/2020
Laboratory Medicine
Taiwan/CGMH-CGU-01/2020
Taiwan/CGMH-CGU-02/2020
Taiwan/CGMH-CGU-03/2020
Taiwan/CGMH-CGU-04/2020
Taiwan/CGMH-CGU-05/2020
Taiwan/CGMH-CGU-06/2020
Taiwan/CGMH-CGU-07/2020
Taiwan/CGMH-CGU-08/2020
Taiwan/CGMH-CGU-09/2020
Taiwan/CGMH-CGU-10/2020
Taiwan/CGMH-CGU-11/2020
Taiwan/CGMH-CGU-12/2020
NHC Key laboratory of Enteric Pathogenic Microbiology, Institute of Pathogenic Microbiology
Jiangsu/JS01/2020
Jiangsu/JS02/2020
Jiangsu/JS03/2020
National Institute for Viral Disease Control and Prevention, China CDC
Beijing/IVDC-BJ-005/2020
Chongqing/IVDC-CQ-001/2020
Henan/IVDC-HeN-002/2020
Jiangsu/IVDC-JS-001/2020
Jiangxi/IVDC-JX-002/2020
Shandong/IVDC-SD-001/2020
Shanghai/IVDC-SH-001/2020
Sichuan/IVDC-SC-001/2020
Wuhan/IVDC-HB-01/2019
Wuhan/IVDC-HB-04/2020
Wuhan/IVDC-HB-05/2019
Yunnan/IVDC-YN-003/2020
Prince of Wales Hospital
HongKong/case2_VB20017970/2020
Second Hospital of Anhui Medical University
Hefei/2/2020
Shandong Provincial Center for Disease Control and Prevention
Shandong/LY001/2020
Shandong/LY002/2020
Shandong/LY003/2020
Shandong/LY004/2020
Shandong/LY005/2020
Shandong/LY006/2020
Shandong/LY007/2020
Shandong/LY008/2020
Shanghai Public Health Clinical Center, Shanghai Medical College, Fudan University
Shanghai/SH0002/2020
Shanghai/SH0003/2020
Shanghai/SH0004/2020
Shanghai/SH0005/2020
Shanghai/SH0007/2020
Shanghai/SH0008/2020
Shanghai/SH0009/2020
Shanghai/SH0010/2020
Shanghai/SH0011/2020
Shanghai/SH0012/2020
Shanghai/SH0013/2020
Shanghai/SH0014/2020
Shanghai/SH0017/2020
Shanghai/SH0020/2020
Shanghai/SH0021/2020
Shanghai/SH0022/2020
Shanghai/SH0023/2020
Shanghai/SH0024/2020
Shanghai/SH0025/2020
Shanghai/SH0026/2020
Shanghai/SH0027/2020
Shanghai/SH0028/2020
Shanghai/SH0029/2020
Shanghai/SH0030/2020
Shanghai/SH0031/2020
Shanghai/SH0032/2020
Shanghai/SH0033/2020
Shanghai/SH0034/2020
Shanghai/SH0035/2020
Shanghai/SH0036/2020
Shanghai/SH0037/2020
Shanghai/SH0038/2020
Shanghai/SH0039/2020
Shanghai/SH0040/2020
Shanghai/SH0041/2020
Shanghai/SH0042/2020
Shanghai/SH0043/2020
Shanghai/SH0044/2020
Shanghai/SH0045/2020
Shanghai/SH0047/2020
Shanghai/SH0048/2020
Shanghai/SH0049/2020
Shanghai/SH0050/2020
Shanghai/SH0051/2020
Shanghai/SH0052/2020
Shanghai/SH0053/2020
Shanghai/SH0054/2020
Shanghai/SH0055/2020
Shanghai/SH0056/2020
Shanghai/SH0058/2020
Shanghai/SH0059/2020
Shanghai/SH0060/2020
Shanghai/SH0065/2020
Shanghai/SH0066/2020
Shanghai/SH0067/2020
Shanghai/SH0068/2020
Shanghai/SH0069/2020
Shanghai/SH0070/2020
Shanghai/SH0071/2020
Shanghai/SH0072/2020
Shanghai/SH0073/2020
Shanghai/SH0074/2020
Shanghai/SH0075/2020
Shanghai/SH0076/2020
Shanghai/SH0077/2020
Shanghai/SH0079/2020
Shanghai/SH0080/2020
Shanghai/SH0081/2020
Shanghai/SH0083/2020
Shanghai/SH0085/2020
Shanghai/SH0086/2020
Shanghai/SH0088/2020
Shanghai/SH0091/2020
Shanghai/SH0093/2020
Shanghai/SH0094/2020
Shanghai/SH0098/2020
Shanghai/SH0100/2020
Shanghai/SH0101/2020
Shanghai/SH0102/2020
Shanghai/SH0104/2020
Shanghai/SH0106/2020
Shanghai/SH0107/2020
Shanghai/SH0109/2020
Shanghai/SH0110/2020
Shanghai/SH0112/2020
Shanghai/SH0114/2020
Shanghai/SH0115/2020
Shanghai/SH0117/2020
Shanghai/SH0119/2020
Shanghai/SH0121/2020
Shanghai/SH0125/2020
Shanghai/SH0126/2020
Shanghai/SH0127/2020
Shanghai/SH0128/2020
Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
Shenzhen/SZTH-002/2020
Shenzhen/SZTH-003/2020
Shenzhen/SZTH-004/2020
Shenzhen Third People's Hospital
Shenzhen/SZTH-001/2020
South China Agricultural University
pangolin/Guangdong/1/2019
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China 310003
Hangzhou/ZJU-010/2020
Hangzhou/ZJU-011/2020
Hangzhou/ZJU-03/2020
Hangzhou/ZJU-04/2020
Hangzhou/ZJU-06/2020
Hangzhou/ZJU-07/2020
Hangzhou/ZJU-08/2020
Hangzhou/ZJU-09/2020
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. 310003
Hangzhou/ZJU-01/2020
Hangzhou/ZJU-02/2020
Hangzhou/ZJU-05/2020
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University
Guangzhou/GZMU0014/2020
Guangzhou/GZMU0016/2020
Guangzhou/GZMU0030/2020
Guangzhou/GZMU0031/2020
Guangzhou/GZMU0042/2020
Guangzhou/GZMU0044/2020
Guangzhou/GZMU0047/2020
Guangzhou/GZMU0048/2020
Tai Lung Veterinary Laboratory, Agriculture, Fisheries and Conservation Department
canine/HongKong/20-02756/2020
Taiwan Centers for Disease Control
Taiwan/3/2020
Taiwan/4/2020
The Central Hospital Of Wuhan
Wuhan/HBCDC-HB-02/2020
The University of Hong Kong - Shenzhen Hospital
Shenzhen/HKU-SZ-002/2020
Shenzhen/HKU-SZ-005/2020
Tianmen Center for Disease Control and Prevention
Tianmen/HBCDC-HB-07/2020
Union Hospital of Tongji Medical College, Huazhong University of Science and Technology
Wuhan/HBCDC-HB-03/2020
Wuhan/HBCDC-HB-04/2020
Weifang Center for Disease Control and Prevention
China/WF0001/2020
China/WF0002/2020
China/WF0003/2020
China/WF0004/2020
China/WF0006/2020
China/WF0009/2020
China/WF0012/2020
China/WF0014/2020
China/WF0015/2020
China/WF0016/2020
China/WF0017/2020
China/WF0018/2020
China/WF0019/2020
China/WF0020/2020
China/WF0021/2020
China/WF0023/2020
China/WF0024/2020
China/WF0026/2020
China/WF0028/2020
China/WF0029/2020
Wuhan Fourth Hospital
Wuhan/WH05/2020
Wuhan Institute of Virology, Chinese Academy of Sciences
bat/Yunnan/RaTG13/2013
Wuhan Jinyintan Hospital
Wuhan/HBCDC-HB-01/2019
Wuhan/HBCDC-HB-02/2019
Wuhan/HBCDC-HB-03/2019
Wuhan/HBCDC-HB-04/2019
Wuhan/WIV02/2019
Wuhan/WIV04/2019
Wuhan/WIV05/2019
Wuhan/WIV06/2019
Wuhan/WIV07/2019
Wuhan Lung Hospital
Wuhan/HBCDC-HB-06/2020
Yongchuan District Center for Disease Control and Prevention
Chongqing/YC01/2020
Zhejiang Provincial Center for Disease Control and Prevention
Zhejiang/WZ-01/2020
Zhejiang/WZ-02/2020
Zhongxian Center for Disease Control and Prevention
Chongqing/ZX01/2020
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