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An update on the origin of SARS-CoV-2: Despite closest identity, bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O-linked glycan residues.

Jeevan Malaiyan1 Suresh Arumugam2 Kamalraj Mohan1 Gokul Gomathi Radhakrishnan3
Affiliations 3 institutions
  1. Division of Virology, Department of Microbiology, Sri Muthukumaran Medical College Hospital and Research Institute, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Chikkarayapuram, Chennai, India.
  2. Central Research Facility, Meenakshi Medical College Hospital and Research Institute, Meenakshi Academy of Higher Education and Research, Kancheepuram, Tamilnadu, India.
  3. Department of General Medicine, Sri Muthukumaran Medical College Hospital and Research Institute, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Chikkarayapuram, Chennai, India.
PMID 32633815 2021 J Med Virol eng ppublish
PubMed DOI Browse context

Article

Publication summary

The initial cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8 993 659 active cases, 469 587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS-CoV-2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. The key residues of the receptor-binding domain (RBD) and O-linked glycan were compared. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forms a new clade-2 in lineage B of beta-CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS-CoV-2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin-CoV. SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.

COVID-19 intermediate host pangolins RaTg13 SARS-CoV-2 Animals Binding Sites China Chiroptera Communicable Disease Control Coronavirus Coronavirus Envelope Proteins Gene Expression Regulation, Viral Host Specificity Humans Models, Molecular Pangolins Phylogeny

Structured evidence records

Evidence records

5 total
Genomic Evolution 3 records
Genomic Evolution Extraction confidence 0.90
Key finding

Phylogenetic analysis showed that SARS-CoV-2 is closely related to bat RaTG13 and pangolin-CoV, forming a new clade within lineage B of betacoronaviruses, indicating genomic evolutionary relationships relevant to its origin.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forming a new clade-2 in lineage B of beta-CoV.

Genes or proteins
receptor-binding domain; spike glycoprotein
Analysis methods
phylogenetic analysis; sequence identity comparison
Genomic Evolution Extraction confidence 0.90
Key finding

Comparative genomic analysis identified differences in the spike protein cleavage site and O-linked glycan residues between SARS-CoV-2, bat RaTG13, and pangolin-CoV, highlighting adaptive genomic variation among these viruses.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13.

Genes or proteins
spike glycoprotein; receptor-binding domain; O-linked glycan region
Analysis methods
comparative genomics; sequence alignment
Genomic Evolution Extraction confidence 0.90
Key finding

Genomic evidence suggests that bat and pangolin coronaviruses are closely related to SARS-CoV-2 and potentially represent its evolutionary source.

Virus
SARSr-CoV
Location
Not specified
Supporting text

Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2.

Genes or proteins
receptor-binding domain; spike glycoprotein
Analysis methods
phylogenetic comparison
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.95
Key finding

SARS-CoV-2 spike glycoprotein shows an inserted PRRA polybasic cleavage site and variations in receptor-binding domain residues compared to bat RaTG13 and pangolin CoV, suggesting molecular adaptation related to ACE2 receptor binding.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. The alignments of RBD contact residues to ACE2 justified that SARS-CoV-2 sequences were 100% identical but significantly varied in RaTG13 and pangolin-CoV.

Genes or proteins
Spike glycoprotein
Receptors
ACE2
Mutations
PRRA insertion
Mechanism types
receptor_binding; pathogenicity
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.85
Key finding

SARS-CoV-2, bat RaTG13, and pangolin CoV differ in receptor-binding domain residues interacting with ACE2, suggesting varying receptor compatibility.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

The alignments of RBD contact residues to ACE2 justified that SARS-CoV-2 strains were 100% identical to each other but significantly varied in RaTG13 and pangolin-CoV, indicating differences in receptor-binding residues.

Method
phylogenetic analysis; sequence alignment
Receptors
ACE2