Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2

Abstract

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 −3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins. K E Y W O R D S COVID-19, cross-species transmission, evolutionary rate, potential intermediate animal host, SARS-CoV-2, TMRCA

Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species

“…Furthermore, the amino acid homologies of ORF1ab, N, S proteins of the two viruses are 98.55, 99.05 and 97.41% respectively. These results suggest the two viruses have a high genetic relationship, which is consistent with the results reported previously Li et al, 2020;Paraskevis et al, 2020;Zhou et al, 2020). Moreover, the N protein of SARS-CoV-2 and bat coronavirus RaTG13 had 4 different amino acids, which were 37S/P, 215G/S, 243G/S, and 267A/Q, respectively.…”

“…: MN996532), with 96.2% nucleotide homology in the whole genome Zhou et al, 2020). Other groups suggest that pangolin, mink, snake, turtle may be potential intermediate hosts for the virus (Association, 2020;Guo et al, 2020;Ji et al, 2020;Lam et al, 2020;Li et al, 2020;Liu et al, 2020a;Liu et al, 2020b;Xiao et al, 2020;Zhang et al, 2020a;Zhang et al, 2020b), which still need more evidence to be confirmed.…”

“…To date, a large number of studies have proved the pathogen of COVID-19 is a novel coronavirus, which belongs to the Coronavirus family, Betacoronavirus genus and Sarbecovirus subgenus, with a linear single-stranded positive-strand RNA genome of about 30 kb (Ceraolo and Giorgi, 2020;Jiang and Shi, 2020;Lai et al, 2020;Li et al, 2020;Lu et al, 2020;Zhou et al, 2020). However, so far, there are still controversies about the source of the virus and its intermediate host.…”

“…Notably, although the whole genome sequence of SARS-CoV-2 is almost identical, with a similarity rate of 99.9% (Ceraolo and Giorgi, 2020;Li et al, 2020;Lu et al, 2020;Paraskevis et al, 2020), the virus begins to mutate in patients . Mutations of different SARS-CoV-2 isolates mainly occurs in five genes, including S, N, ORF8, ORF3a, and ORF1ab, with about 42% of the variations are non-synonymous mutation ).…”

Identification of coronavirus sequences in carp cDNA from Wuhan, China

“…1 SARS-CoV-2 is also related to SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which cause severe disease that is associated with high mortality rates. 2,3 Coronaviruses originate in bats but are zoonotic and can circulate in a number of mammals and birds. 1 SARS-CoV emerged into the human population because of the exotic food trade in China, which allowed for a transmission event between a civet cat and a human.…”