Phylogenetic network of 160 SARS-CoV-2 genomes.

A previous paper, Zhou et al. (7) recently reported a closely related bat coronavirus, with 96.2% sequence similarity to the human virus.  The sequence of the corona virus 19 at the A node in Wuhan is 96.2% similar to the sequence reported by Zhou et al from a bat in Yunnan Province over 1000 miles from Wuhan.  Details in the full paper at the link below.

Node A is the root cluster obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from Yunnan Province. The other nodes (circles) are mutational derivatives of node A.

Circle areas are proportional to the number of taxa (a), and each notch on the links [tiny hash marks on the lines] represents a mutated nucleotide position. The 161 taxa (160 human viruses and one bat virus) yield 101 distinct genomic sequences.

Sequence is identified by comparison to reference standard sequence .  The sequence range under consideration is 56 to 29,797, with nucleotide position (np) numbering according to the Wuhan 1 reference sequence (8). The median-joining network algorithm (2) and the Steiner algorithm (9) were used, both implemented in the software package Network5011CS (https://www.fluxus-engineering.com/), with the parameter epsilon set to zero, generating this network containing 288 most-parsimonious trees of length 229 mutations.

The reticulations (b) are mainly caused by recurrent mutations at np11083.

The phylogenetic diagram is available for detailed scrutiny in A0 poster format (SI Appendix, Fig. S5) and in the free Network download files. (see full paper at the link below.)

Definitions:

(a) Taxa (plural of taxon) are any group or rank in a biological classification (i.e. taxonomy) into which related organisms are grouped, for example, species, families, phylums, orders, genus, race, etc.
(b) Reticulations are the crossing and intersecting net-like patterns. Reticulate evolution, or network evolution, describes the origination of a lineage through the partial or entire merging of two ancestor lineages.  Imagine two tree limbs which grew out of a single tree trunk and then later grew back together wholly or partially and a new, third limb emerges or the two limbs could merge into one.

Citation:  Phylogenetic network analysis of SARS-CoV-2 genomes