SARS‐CoV‐2: Structural diversity, phylogeny, and potential animal host identification of spike glycoprotein

Abstract

To investigate the evolutionary history of the current pandemic outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a total of 137 genomes of coronavirus strains with release dates between January 2019 and 25 March 2020, were analyzed. To investigate the potential intermediate host of the SARS-CoV-2, we analyzed spike glycoprotein sequences from different animals, with particular emphasis on bats. We performed phylogenetic analysis and structural reconstruction of the spike glycoproteins with subsequent alignment and comparison. Our phylogenetic results revealed that SARS-CoV-2 was more similar to the bats' betacoronavirus isolates: HKU5-related from Pipistrellus abramus and HKU4-related from Tylonycteris pachypus. We also identified a yak betacoronavirus strain, YAK/ HY24/CH/2017, as the closest match in the comparison of the structural models of spike glycoproteins. Interestingly, a set of unique features has been described for this particular strain of the yak betacoronavirus. Therefore, our results suggest that the human SARS-CoV-2, responsible for the current outbreak of COVID-19, could also come from yak as an intermediate host.betacoronavirus, COVID-19, SARS-CoV-2, spike glycoprotein DABRAVOLSKI AND KAVALIONAK | 3 N-terminal domain (pfam16451), C-terminal S1 corresponds to the spike receptor-binding domain (pfam09408), and S2 domain contains coronavirus S1 glycoprotein (pfam01600), and coronavirus S2 glycoprotein (pfam01601) as subdomains ( Figure S1).Canonical spike glycoprotein contains four domains, each of which plays a specific function. It is known that both spike glycoprotein N-terminal domain (pfam16451) and spike receptorbinding domain (pfam09408) participate in specific receptor binding. The N-terminal domain binds to carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) in mouse hepatitis coronavirus, and binds sugar in porcine transmissible gastroenteritis virus. 13 Spike receptor-binding domain binds to the aminopeptidase N or angiotensin-converting enzyme 2 (ACE2) in coronaviruses. 14 An interplay between coronavirus S1 glycoprotein (pfam01600) and coronavirus S2 glycoprotein (pfam01601) is required for the attachment of spike to susceptible tissues and subsequent fusion. 15The phylogenetic data reported above show that the new human-delivered SARS-CoV-2 spike glycoproteins cluster with two betacoronaviruses, HKU4-and HKU5-related, delivered from the hosts T pachypus and P abramus, respectively. Also, as seen from the phylogenetic tree ( Figure S1), these two sequences deviate from the other bat coronavirus sequences, suggesting that these bat coronaviruses are homologous and genetically more similar to human-delivered SARS-CoV-2 than to the other bats' coronaviruses.In general, these data support phylogenetic results obtained by previous researches based on (a) whole-genome; (b) nonstructural proteins NS7b and NS8; (c) spike glycoprotein, and (d) nucleocapsid protein. 16For the next experiment, based on the alignment and comparison of the structures, MERS ...

A gapless unambiguous RNA metagenome-assembled genome sequence of a unique SARS-CoV-2 variant encoding spike S813I and ORF1a A859V substitutions

“…Brief genome description. We named the assembled genome CU002b-S3 (or CU_S3 for short).Its sequence has 29,792 bases with typical features of SARS-CoV-2 genomes (Dabravolski and Kavalionak, 2020;Li et al, 2020) and includes all its open reading frames (ORFs), ORF1a through ORF10, without any disruptive mutations. The genome has been classi ed as part of clade GR (according to GISAID classi cation); of the pangolin lineage B.1.1.1 (Rambaut et al, 2020); or of the major clade 20B (according to the new NextStrain classi cation (Had eld et al, 2018))-formerly known as clade A2a.…”

“…In spite of the millions of cases worldwide and the tens of thousands of sequenced genomes, SARS-CoV-2 genome is relatively stable with an estimated mutation rate of ~24 base per genome per year (GISAID); thus phylogenetic analyses do not lead to strongly distinct clusters, except for the major clades (Rambaut et al, 2020) that have been de ned so far in several studies (reviewed in Dabravolski and Kavalionak (2020) and monitored by NextStrain (Had eld et al, 2018)).…”

What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist

“…It is true that an impressive amount of data about the DNA sequencing of the virus has been gathered in a relatively short period of time and with that, the knowledge of its biological properties increased enormously (23,927 sequences in PUBMED) (19,(21)(22)(23)(24)(25)(26). However, for an urgent strategy, we could also take advantage of the lessons taught by the history of vaccinology in order to prevent the disease and save lives.…”

Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health

“…8 To ascertain the evolutionary origins of the current COVID-19 pandemic, a structural reconstruction of the spike glycoproteins with subsequent alignment and comparison was performed by Dabravolski and Kavalionak. 9 Their analysis identified a yak beta coronavirus strain YAK/HY24/CH/2017 as the closest match in the comparison of structural models of spike glycoproteins, thus proposing yaks as a potential intermediate host. 9 Their findings were supported by a report on the ACE2-spike glycoprotein complexes, suggesting Bovidae as potential hosts.…”