The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Filter options prefixed with "(M)" are filters specific to the Measurements panel. They will have no effect on the phylogeny tree or other panels.
The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to gauge the uncertainty in the reconstruction of internal node dates.
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
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. The sample Wuhan/IPBCAMS-WH-05/2020 has been dropped from the analysis due to the appearance of clustered, spurious SNPs. Full details on bioinformatic processing can be found here.
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.
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