CoVID-19 outbreak phylogeographic network

PURPOSE: to help identify "patient zero" (the index patient who was the source of a local outbreak).

DISCLAIMER: This is no medical device or software. For use only at your own risk and your own responsibility. In no event will Fluxus Technology Ltd or its officers be liable for any expenses, losses, or damages resulting from the use or interpretation of the data or the phylogeographic network. This network has not been peer-reviewed.

ACKNOWLEDGEMENT: Sequence data were provided by the GISAID COVID-19 sequence database. In accordance with GISAID's data usage terms we are currently endeavoring to contact the sequence data contributors to invite them to join in the analysis and further development thereof with the aim to publish a paper. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu(TM) Database on which this research is based. The sequence data contributors are listed in this Excel table.

METHODS: GISAID provided COVID-19 FASTA sequences. We produced a quality controlled data set, an alignment and a phylogenetic network analysis. We produced PDFs and screenshots and Network Publisher fdi files with nodes coloured by geographic origin of virus sequence for interactive exploration. The fdi files can also be read into the free Network Draw program but the geographic colouring is not displayable there.

RESULTS: The root node according to the bat corona virus outgroup is node 13, distinguished from the Wuhan-1 reference sequence at positions 8782, 28144, and 29095. The root cluster contains only Chinese, Japanese and two Americans. results data (zip file), world phylogeographic network (screenshot), English COVID-19 virus in phylogeographic network (screenshot).

CONTACT: Dr. Peter Forster, pf223 (at) cam (dot) ac (dot) uk

DATE: 29 Feb 2020