Phylogenetic tree of 2019-nCoV and identifying positive/negative selection sites
Coronaviridae family
Variety of RNA viruses sizes from several species.
MERS-CoV
2019-nCoV
SARS-CoV
Belongs to Orthocoronavirinae subfamily
Possible origin of epidemic
Wuhan, China
Animal to human transmission, which leads to interhuman transmission of virus
Basic local alignment search tool
&
Multiple sequence alignment online tool
Dataset built using 5 similar SARS sequences, 2 MERS sequences, and 5 close sequences for bat SARS-like coronavirus
Maximum likelihood (ML) tested different phylogenetic hypotheses using the probability of a model
Downloaded the 15 genomes of 2019-nCoV
Dataset of 27 sequences were aligned after duplicates were removed
Regions of virus
A bat
Region E
Region S
Region N
Region M
FUBAR analysis: Two sites (380th & 410th nucleotides position) showed significant pervasive selection.
Six sites (14%) showed a significant pervasive negative selection.
FUBAR analysis: No positive selection found
FUBAR analysis: Two sites (536th & 644th nucleotide) showed significant pervasive selection. There is a significant pervasive
negative selection in 1065 sites (87%). This means the S region might be highly conserved.
FUBAR analysis: No positive selection found.
Clade II
FUBAR analysis: 409th aminoacidic spot for Wuhan coronavirus had glutamine residue. 380th aminoacidic spot for Wuhan coronavirus had threonine residue, Six sites (14%) showed a significant pervasive negative selection.
FUBAR analysis: The 536th aminoacidic in Wuhan coronavirus sequence has threonine residue. The 644th aminoacidic has threonine residue.
2019‐nCoV homology model: found to be the most stable and similar to the SARS coronavirus nucleocapsid protein structure.
2019‐nCoV homology model: found to be the most stable and similar to the SARS coronavirus spike glycoprotein.
Results regarding 2019-nCoV
The 2019‐nCoV and bat SARS‐like coronavirus share the 309th&380th position on the aminoacidic sequences
2019‐nCoV: polar amino acid
SARS: nonpolar amino acid
2019‐nCoV positive selective pressure on spike glycoprotein: 536th aminoacidic position with asparagine residue. 644th aminoacidic position with threonine residue.
Bat-SARS-like coronavirus 536th aminoacidic position with glutamine residue. 644th aminoacidic position with serine residue.
SARS virus: 536th aminoacidic position with aspartic acid residue. 644th aminoacidic position with alanine residue.
Reference
Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M. 2020. The 2019-new coronavirus epidemic: Evidence for virus evolution. Journal of Medical Virology. 92(4):455–459. doi:https://doi.org/10.1002/jmv.25688.
Overall findings
2019‐nCoV is very similar to a sequence from the bat SARS‐like coronavirus.
Bat SARS‐like coronavirus is homologous and is found to be more similar to the 2019-nCoV.
Hypothesis is supported showing that the transmission chain started from a bat and reached a human.