SARS-CoV-2 Genome Tree

How SARS-CoV-2 trees are constructed in Pathogenwatch.

About

Pathogenwatch will automatically generate a tree of SARS-CoV-2 genomes when a collection is created from the Genome Browser. When each genome is uploaded to Pathogenwatch an alignment against the Wuhan Hu 1 reference genome is stored. The selected genomes are aligned into a multiple sequence alignment and a dendrogram produced using FastTree. This tree is then displayed in the interactive collection viewer.

SARS-CoV-2 tree built using the Pathogenwatch pipeline.

Method

Alignment

• Each genome is mapped against the wuhan-hu-1 reference genome (NCBI Reference Sequence: NC_045512.2) using minimap2.

• The resulting SAM file from each genome is converted into FASTA format using goFASTA.

• The aligned FASTA output is stored in Pathogenwatch.

Tree Building

• The FASTA files are concatenated into a multiple sequence alignment along with the wuhan-hu-1 reference.

• Run FastTree with the options -gtr -nosupport -nt.

• Root the resulting tree to the reference.

• Remove the reference from the tree.

References

• FastTree: Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.

• goFASTA: https://github.com/cov-ert/gofasta

• minimap2: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. doi:10.1093/bioinformatics/bty191