tetano
Editor, Senior Moderator
Genomic epidemiology of novel coronavirus (nCoV)
Built using github.com/nextstrain/ncov.
Showing 28 of 28 genomes sampled between Dec 2019 and Jan 2020.
Phylogeny
WuhanHangzhouShenzhenZhuhaiBangkokSeattleChicagoLo cation2019-Nov-292019-Dec-052019-Dec-112019-Dec-172019-Dec-232019-Dec-292020-Jan-042020-Jan-102020-Jan-162020-Jan-22Wuhan/WIV02/2019Wuhan/HBCDC-HB-01/2019Wuhan-Hu-1/2019Wuhan/WIV07/2019Wuhan/IPBCAMS-WH-03/2019Wuhan/IVDC-HB-05/2019Wuhan/IPBCAMS-WH-01/2019Wuhan/WIV05/2019Wuhan/IVDC-HB-04/2020USA/IL1/2020USA-WA1/2020HKU-SZ-005b_2020HKU-SZ-002a_2020Guangdong/20SF013/2020Guangdong/20SF012/2020Guangdong/20SF025/2020Nonthaburi/74/2020Zhejiang/WZ-02/2020Zhejiang/WZ-01/2020Guangdong/20SF028/2020Guangdong/20SF040/2020Guangdong/20SF014/2020Wuhan/WIV04/2019Wuhan/IPBCAMS-WH-02/2019Wuhan/IVDC-HB-01/2019Wuhan/IPBCAMS-WH-04/2019Wuhan/WIV06/2019Nonthaburi/61/2020
Geography
+−
Leaflet | ? OpenStreetMap contributors
Diversity
MNORF1aORF1bORF3aORF7aORF8SMNORF1aORF1bORF3aS02,00 04,0006,0008,00010,00012,00014,00016,00018,00020,0 0022,00024,00026,00028,00002,0004,0006,0008,00010, 00012,00014,00016,00018,00020,00022,00024,00026,00 028,0000.00.20.40.6
请点击这里查看中文版本
This phylogeny shows evolutionary relationships of viruses from the novel coronavirus (nCoV) outbreak. All samples are highly related with at most five mutations relative to a common ancestor, suggesting a shared common ancestor sometime in Nov 2019. This indicates an initial human infection in Nov 2019 followed by sustained human-to-human transmission leading to sampled infections.
We observe clustering of related infections. These are a cluster of two infections in Zhuhai (Guangdong/20SF028/2020 and Guangdong/20SF040/2020) and a cluster of three infections in Shenzhen (Guangdong/20SF013/2020, Guangdong/20SF025/2020, Guangdong/20SF012/2020). These are noted in GISAID as "family cluster infection". This represents clear direct human-to-human transmission.
Here, we estimate the time of the most recent common ancestor of sequenced viruses:
Site numbering and genome structure uses BetaCoV/Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 3 ? 10^-4 subs per site per year. There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. Full details on bioinformatic processing can be found here. The sample Wuhan/IPBCAMS-WH-05/2020 has been dropped from the analysis due to the appearance of clustered, spurious SNPs.
Phylogenetic context of nCoV in SARS-related betacoronaviruses can be seen here and phylogenetic context in betacoronaviruses can be seen here.
The nCoV genomes were generously shared by scientists at the Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China, at the National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China, at the Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China, at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, at the Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, at the Guangdong Provincial Center for Diseases Control and Prevention at the Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand, and at the US Centers for Disease Control and Prevention, Atlanta, USA, via GISAID. We gratefully acknowledge the Authors, Originating and Submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based.
Other nCoV genomes were shared by scientists at the University of Hong Kong and US Centers for Disease Control and Prevention via Genbank. We gratefully acknowledge their contributions.
https://nextstrain.org/ncov?fbclid=I...ewzZ4gsA3cRbzQ
Showing 28 of 28 genomes sampled between Dec 2019 and Jan 2020.
Phylogeny
WuhanHangzhouShenzhenZhuhaiBangkokSeattleChicagoLo cation2019-Nov-292019-Dec-052019-Dec-112019-Dec-172019-Dec-232019-Dec-292020-Jan-042020-Jan-102020-Jan-162020-Jan-22Wuhan/WIV02/2019Wuhan/HBCDC-HB-01/2019Wuhan-Hu-1/2019Wuhan/WIV07/2019Wuhan/IPBCAMS-WH-03/2019Wuhan/IVDC-HB-05/2019Wuhan/IPBCAMS-WH-01/2019Wuhan/WIV05/2019Wuhan/IVDC-HB-04/2020USA/IL1/2020USA-WA1/2020HKU-SZ-005b_2020HKU-SZ-002a_2020Guangdong/20SF013/2020Guangdong/20SF012/2020Guangdong/20SF025/2020Nonthaburi/74/2020Zhejiang/WZ-02/2020Zhejiang/WZ-01/2020Guangdong/20SF028/2020Guangdong/20SF040/2020Guangdong/20SF014/2020Wuhan/WIV04/2019Wuhan/IPBCAMS-WH-02/2019Wuhan/IVDC-HB-01/2019Wuhan/IPBCAMS-WH-04/2019Wuhan/WIV06/2019Nonthaburi/61/2020
Geography
+−
Leaflet | ? OpenStreetMap contributors
Diversity
MNORF1aORF1bORF3aORF7aORF8SMNORF1aORF1bORF3aS02,00 04,0006,0008,00010,00012,00014,00016,00018,00020,0 0022,00024,00026,00028,00002,0004,0006,0008,00010, 00012,00014,00016,00018,00020,00022,00024,00026,00 028,0000.00.20.40.6
请点击这里查看中文版本
This phylogeny shows evolutionary relationships of viruses from the novel coronavirus (nCoV) outbreak. All samples are highly related with at most five mutations relative to a common ancestor, suggesting a shared common ancestor sometime in Nov 2019. This indicates an initial human infection in Nov 2019 followed by sustained human-to-human transmission leading to sampled infections.
We observe clustering of related infections. These are a cluster of two infections in Zhuhai (Guangdong/20SF028/2020 and Guangdong/20SF040/2020) and a cluster of three infections in Shenzhen (Guangdong/20SF013/2020, Guangdong/20SF025/2020, Guangdong/20SF012/2020). These are noted in GISAID as "family cluster infection". This represents clear direct human-to-human transmission.
Here, we estimate the time of the most recent common ancestor of sequenced viruses:
Site numbering and genome structure uses BetaCoV/Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 3 ? 10^-4 subs per site per year. There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. Full details on bioinformatic processing can be found here. The sample Wuhan/IPBCAMS-WH-05/2020 has been dropped from the analysis due to the appearance of clustered, spurious SNPs.
Phylogenetic context of nCoV in SARS-related betacoronaviruses can be seen here and phylogenetic context in betacoronaviruses can be seen here.
The nCoV genomes were generously shared by scientists at the Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China, at the National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China, at the Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China, at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, at the Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China, at the Guangdong Provincial Center for Diseases Control and Prevention at the Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand, and at the US Centers for Disease Control and Prevention, Atlanta, USA, via GISAID. We gratefully acknowledge the Authors, Originating and Submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based.
Other nCoV genomes were shared by scientists at the University of Hong Kong and US Centers for Disease Control and Prevention via Genbank. We gratefully acknowledge their contributions.
https://nextstrain.org/ncov?fbclid=I...ewzZ4gsA3cRbzQ