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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.
J Med Virol. 2021 01; 93(1):499-505.JM

Abstract

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.

Authors+Show Affiliations

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.Central Research Facility, Meenakshi Medical College Hospital and Research Institute, Meenakshi Academy of Higher Education and Research, Kancheepuram, Tamilnadu, India.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.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.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32633815

Citation

Malaiyan, Jeevan, et al. "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." Journal of Medical Virology, vol. 93, no. 1, 2021, pp. 499-505.
Malaiyan J, Arumugam S, Mohan K, et al. 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. J Med Virol. 2021;93(1):499-505.
Malaiyan, J., Arumugam, S., Mohan, K., & Gomathi Radhakrishnan, G. (2021). 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. Journal of Medical Virology, 93(1), 499-505. https://doi.org/10.1002/jmv.26261
Malaiyan J, et al. 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. J Med Virol. 2021;93(1):499-505. PubMed PMID: 32633815.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Malaiyan,Jeevan, AU - Arumugam,Suresh, AU - Mohan,Kamalraj, AU - Gomathi Radhakrishnan,Gokul, Y1 - 2020/07/14/ PY - 2020/05/14/received PY - 2020/06/23/revised PY - 2020/07/04/accepted PY - 2020/7/8/pubmed PY - 2020/7/8/medline PY - 2020/7/8/entrez KW - COVID-19 KW - RaTg13 KW - SARS-CoV-2 KW - intermediate host KW - pangolins SP - 499 EP - 505 JF - Journal of medical virology JO - J Med Virol VL - 93 IS - 1 N2 - 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. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/32633815/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_ L2 - https://doi.org/10.1002/jmv.26261 DB - PRIME DP - Unbound Medicine ER -
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