Abstract
BackgroundBat-borne viruses are relatively host specific. We hypothesize that this host specificity is due to coevolution of the viruses with their hosts. To test this hypothesis, we investigated the coevolution of coronavirus and paramyxovirus with their bat hosts. Published nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) gene of 60 coronavirus strains identified from 37 bat species, the RNA polymerase large (L) gene of 36 paramyxovirus strains from 29 bat species, and the cytochrome B (cytB) gene of 35 bat species were analyzed for coevolution signals. Each coevolution signal detected was tested and verified by global-fit cophylogenic analysis using software ParaFit, PACo, and eMPRess.ResultsSignificant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry closely related viruses.ConclusionsOur results suggest that paramyxovirus and coronavirus coevolve with their hosts.
Highlights
Phylogenetic relationship of bat coronaviruses with their bat hosts Phylogenetic analyses revealed that the bat coronavirus RaTG13/CN/MN996532 from Rhinolophus affinis found in Yunnan Province, China is on the same branch of the phylogenetic tree as the 18 human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains examined, suggesting that it is a relative of SARS-CoV-2 (Fig. 1)
The following 13 bat coronavirus strains are clustered on the same branch of phylogenetic tree as the six human Middle East respiratory syndrome coronavirus (MERS-CoV) strains examined, suggesting that they are evolutionarily close to each other: JPDB144/CHN/KU182965, HKU4-1/ CHN/EF065505, GX2012/CHN/KJ473822, HKU5-1/ CHN/EF065509, GD2013/CHN/KJ473820, PDF-2180/ UGA/KX574227, 5038/RSA/MF593268, PML-PHE1/ RSA/KC869678, SC2013/CHN/KJ473821, HKU25/CHN/ KX442565, NL13845/CHN/MG021451, 206645-40/ITA/ MG596802, and 206645-63/ITA/MG596803 (Fig. 1)
Since significant coevolution was found in both groups of the viruses by eMPRess and ParaFit and Procrustean Approach to Cophylogeny (PACo) Global tests, this low positive individual H–P link rate in paramyxoviruses may be due to small sample size
Summary
Phylogenetic relationship of bat coronaviruses with their bat hosts Phylogenetic analyses revealed that the bat coronavirus RaTG13/CN/MN996532 from Rhinolophus affinis found in Yunnan Province, China is on the same branch of the phylogenetic tree as the 18 human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains examined, suggesting that it is a relative of SARS-CoV-2 (Fig. 1). Strains CMR66/CMR/MG693170, HKU9-1/CHN/ EF065513, and GCCDC1-356/CHN/KU762338 with 78.03–96.24% RdRp gene sequence identity are clustered together on the same branch of the phylogenetic tree and are all from members of the Pteropodidae bat family (Fig. 2).
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