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Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades.
Infect Genet Evol. 2021 Sep; 93:104973.IG

Abstract

SARS-CoV-2 is currently causing major havoc worldwide with its efficient transmission and propagation. To track the emergence as well as the persistence of mutations during the early stage of the pandemic, a comparative analysis of SARS-CoV-2 whole proteome sequences has been performed by considering manually curated 31,389 whole genome sequences from 84 countries. Among the 7 highly recurring (percentage frequency≥10%) mutations (Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and N protein:G204R), N protein:R203K and N protein: G204R are co-occurring (dependent) mutations. Nsp12:P323L and Spike:D614G often appear simultaneously. The highly recurring Spike:D614G, Nsp12:P323L and Nsp6:L37F as well as moderately recurring (percentage frequency between ≥1 and <10%) ORF3a:G251V and ORF8:L84S mutations have led to4 major clades in addition to a clade that lacks high recurring mutations. Further, the occurrence of ORF3a:Q57H&Nsp2:T85I, ORF3a:Q57H and N protein:R203K&G204R along with Nsp12:P323L&Spike:D614G has led to 3 additional sub-clades. Similarly, occurrence of Nsp6:L37F and ORF3a:G251V together has led to the emergence of a sub-clade. Nonetheless, ORF8:L84S does not occur along with ORF3a:G251V or Nsp6:L37F. Intriguingly, ORF3a:G251V and ORF8:L84S are found to occur independent of Nsp12:P323L and Spike:D614G mutations. These clades have evolved during the early stage of the pandemic and have disseminated across several countries. Further, Nsp10 is found to be highly resistant to mutations, thus, it can be exploited for drug/vaccine development and the corresponding gene sequence can be used for the diagnosis. Concisely, the study reports the SARS-CoV-2 antigens diversity across the globe during the early stage of the pandemic and facilitates the understanding of viral evolution.

Authors+Show Affiliations

Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502285, India.Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502285, India.Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502285, India.Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502285, India. Electronic address: tr@bt.iith.ac.in.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34147651

Citation

Patro, L Ponoop Prasad, et al. "Global Variation in SARS-CoV-2 Proteome and Its Implication in Pre-lockdown Emergence and Dissemination of 5 Dominant SARS-CoV-2 Clades." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 93, 2021, p. 104973.
Patro LPP, Sathyaseelan C, Uttamrao PP, et al. Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Infect Genet Evol. 2021;93:104973.
Patro, L. P. P., Sathyaseelan, C., Uttamrao, P. P., & Rathinavelan, T. (2021). Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 93, 104973. https://doi.org/10.1016/j.meegid.2021.104973
Patro LPP, et al. Global Variation in SARS-CoV-2 Proteome and Its Implication in Pre-lockdown Emergence and Dissemination of 5 Dominant SARS-CoV-2 Clades. Infect Genet Evol. 2021;93:104973. PubMed PMID: 34147651.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. AU - Patro,L Ponoop Prasad, AU - Sathyaseelan,Chakkarai, AU - Uttamrao,Patil Pranita, AU - Rathinavelan,Thenmalarchelvi, Y1 - 2021/06/18/ PY - 2021/03/08/received PY - 2021/05/29/revised PY - 2021/06/15/accepted PY - 2021/6/21/pubmed PY - 2021/9/14/medline PY - 2021/6/20/entrez KW - Highly recurring mutations KW - Moderately recurring mutations KW - Mutational susceptibility KW - Phyloproteomics KW - Proteome analysis KW - SARS-CoV-2 viromics SP - 104973 EP - 104973 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 93 N2 - SARS-CoV-2 is currently causing major havoc worldwide with its efficient transmission and propagation. To track the emergence as well as the persistence of mutations during the early stage of the pandemic, a comparative analysis of SARS-CoV-2 whole proteome sequences has been performed by considering manually curated 31,389 whole genome sequences from 84 countries. Among the 7 highly recurring (percentage frequency≥10%) mutations (Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and N protein:G204R), N protein:R203K and N protein: G204R are co-occurring (dependent) mutations. Nsp12:P323L and Spike:D614G often appear simultaneously. The highly recurring Spike:D614G, Nsp12:P323L and Nsp6:L37F as well as moderately recurring (percentage frequency between ≥1 and <10%) ORF3a:G251V and ORF8:L84S mutations have led to4 major clades in addition to a clade that lacks high recurring mutations. Further, the occurrence of ORF3a:Q57H&Nsp2:T85I, ORF3a:Q57H and N protein:R203K&G204R along with Nsp12:P323L&Spike:D614G has led to 3 additional sub-clades. Similarly, occurrence of Nsp6:L37F and ORF3a:G251V together has led to the emergence of a sub-clade. Nonetheless, ORF8:L84S does not occur along with ORF3a:G251V or Nsp6:L37F. Intriguingly, ORF3a:G251V and ORF8:L84S are found to occur independent of Nsp12:P323L and Spike:D614G mutations. These clades have evolved during the early stage of the pandemic and have disseminated across several countries. Further, Nsp10 is found to be highly resistant to mutations, thus, it can be exploited for drug/vaccine development and the corresponding gene sequence can be used for the diagnosis. Concisely, the study reports the SARS-CoV-2 antigens diversity across the globe during the early stage of the pandemic and facilitates the understanding of viral evolution. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/34147651/Global_variation_in_SARS_CoV_2_proteome_and_its_implication_in_pre_lockdown_emergence_and_dissemination_of_5_dominant_SARS_CoV_2_clades_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(21)00270-7 DB - PRIME DP - Unbound Medicine ER -