CoV are enveloped have a non-segmented, positive-sense RNA genome ranging from 26 to 32-kilo bases in length [21] and divided into four genera, including Alpha/Beta/Delta/Gamma. Evolutionary analyses have shown that bats, civet, camel, murine, canine, bovine, equine and rodents are the gene sources of most alpha-CoV and beta-CoV, while avian species, whale and porcine are the gene sources of most delta-CoV and gamma-CoV [22, 23]. Prior to December 2019, 6 CoV were described to be pathogenic to humans [24]. In this study, for the first time we have constructed the phylogenetic tree with all the species of the CoV and current outbreak of SARS-CoV-2, seventh human CoV infection belong to beta-CoV [lineage B].
The earliest genomic characterization of SARS-CoV-2 strains in Wuhan had 88–89% nucleotide identity with bat-SL-CoV (bat-SL-CoVZC45 and bat-SL-CoVzxc21), 79–89% nucleotide identity with human SARS-CoV and more distant from MERS-CoV (50%) [1, 23, 25, 26]. Although SARS-CoV-2 epidemic was linked to Wuhan seafood market, Huang C, et al. reported a total of 41 patients, and 14 cases are not related to the seafood market and no trace of bats has been found, so exact place of origin need to be studied in detail [27]. Subsequently, Zhou P. et al. from Wuhan institute of virology (Zheng Li Shi lab) showed that SARS-CoV-2 was highly similar throughout the genome to RaTG13 with an overall genome sequence identity of 96.2% and 93.1% nucleotide identity to S protein. Also, the author did not mention when it has been sequenced and RNA dependent RNA polymerase (RdRp) data not shown to compare SARS-CoV-2 [9]. RaTG13 was isolated from the bat (Rhinolophus affinis) on 24 July 2013 by Zheng Li Shi group and the reason unclear why they did not submit the sequence before instead on 27 Jan 2020, although it is proximal to bat-SL-CoV (accession number: AVP78042.1, AVP78031.1 and ACU31051.1) (Supplement-3). SARS-CoV (Rs806/2006) (accession number: ACU31051.1) already has proven for Intraspecies diversity and its implications for the origin of SARS coronaviruses in humans [28]. Hence, the detailed investigation needed for RaTG13 isolate and origin. Scientists report genetic sequences of viruses isolated from pangolins are 99% similar to that of the COVID-19 strains [7, 8, 10, 29]. Lam TT, et al. identified two sub-lineages of SARS-CoV-2-related CoV in Malayan pangolin, one that exhibits strong similarity to SARS-CoV-2 in the RBD [30]. Zhang C, et al., assembled a draft genome of the SARS-CoV-2 using the metagenomic samples from the lung of Manis javanica, showing an overall coverage of 73% of COVID-19 strains with 91% sequence identity [31]. However, Li X, et al. concluded that the human SARS-CoV‐2 virus, did not come directly from pangolins based on a unique peptide (PRRA) insertion seen in the human SARS‐CoV‐2 virus and not in pangolins carried CoV [32]. Also, a study demonstrated SARSCoV-2 is not a purposefully manipulated virus, based on high-affinity binding to human ACE2, polybasic cleavage site and the three adjacent predicted O-linked glycans are unique to SARS-CoV-2 and were not previously seen in lineage B beta-CoV [11]. Hence, we compared RaTG13 and pangolin-CoV with SARS-CoV-2 for an update and betterment of understanding.
RBD of S protein in SARS-CoV-2 binds strongly to human, pangolin and bat angiotensin-converting enzyme 2 (ACE2) receptors [19, 20, 33]. Studies have confirmed that S protein in the SARS-CoV-2 uses the ACE2, found in the lower respiratory tract of humans [1, 9], and other certain species (pangolin, civet, swine, cow, buffalo, goat, cat, sheep and pigeon) as cellular entry receptor [34, 35]. Liu Z, et al. indicated that, other than pangolins and snakes, turtles may act as the potential intermediate hosts transmitting SARS-CoV‐2 to humans based on the key amino acid interaction between RBD and ACE2 [36]. Choudhury A, et al. showed SARS-CoV-2 is close to bat-CoV, strongly binds with ACE2 receptor protein from both human and bat origin and TLR4 is most likely to be involved in recognizing molecular patterns from SARS-CoV-2 to induce inflammatory responses [37]. A study data support the natural origin of SARS-CoV-2, likely derived from bats, possibly transferred to pangolins, before spreading to man and it not artificial CoV, including the chimeric SL-SHC014-MA15 [38]. The study proposes a unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function [39]. Overall, we demonstrate the key residues of RBD (455, 486, 493, 494, 501 and 505) and polybasic cleavage sites varies significantly; need to be studied in detail for a better understanding of cross-species transmission. PubMed search result showed only three bats (Rhinolophus affinis) and five pangolin CoV sequences were available and more CoV isolation needs to verify the origin of RaTG13.