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Emergence of a unique SARS-CoV-2 Delta sub-cluster harboring a constellation of co-appearing non-Spike mutations.
Banerjee, Anindita; Mazumder, Anup; Roy, Jayita; Das, Jagyashila; Majumdar, Agniva; Chatterjee, Ananya; Biswas, Nidhan K; Chawla Sarkar, Mamta; Das, Saumitra; Dutta, Shanta; Maitra, Arindam.
  • Banerjee A; National Institute of Biomedical Genomics, Kalyani, India.
  • Mazumder A; National Institute of Biomedical Genomics, Kalyani, India.
  • Roy J; National Institute of Biomedical Genomics, Kalyani, India.
  • Das J; National Institute of Biomedical Genomics, Kalyani, India.
  • Majumdar A; ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
  • Chatterjee A; ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
  • Biswas NK; National Institute of Biomedical Genomics, Kalyani, India.
  • Chawla Sarkar M; ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
  • Das S; National Institute of Biomedical Genomics, Kalyani, India.
  • Dutta S; Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.
  • Maitra A; ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
J Med Virol ; 95(1): e28413, 2023 01.
Article in English | MEDLINE | ID: covidwho-2173199
ABSTRACT
Accumulation of diverse mutations across the structural and nonstructural genes is leading to rapid evolution of SARS-CoV-2, altering its pathogenicity. We performed whole genome sequencing of 239 SARS-CoV-2 RNA samples collected from both adult and pediatric patients across eastern India (West Bengal), during the second pandemic wave in India (April-May 2021). In addition to several common spike mutations within the Delta variant, a unique constellation of eight co-appearing non-Spike mutations was identified, which revealed a high degree of positive mutual correlation. Our results also demonstrated the dynamics of SARS-CoV-2 variants among unvaccinated pediatric patients. 41.4% of our studied Delta strains harbored this signature set of eight co-appearing non-Spike mutations and phylogenetically out-clustered other Delta sub-lineages like 21J, 21A, or 21I. This is the first report from eastern India that portrayed a landscape of co-appearing mutations in the non-Spike proteins, which might have led to the evolution of a distinct Delta subcluster. Accumulation of such mutations in SARS-CoV-2 may lead to the emergence of "vaccine-evading variants." Hence, monitoring of such non-Spike mutations will be significant in the formulation of any future vaccines against those SARS-CoV-2 variants that might evade the current vaccine-induced immunity, among both the pediatric and adult populations.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Topics: Vaccines / Variants Limits: Adult / Child / Humans Language: English Journal: J Med Virol Year: 2023 Document Type: Article Affiliation country: Jmv.28413

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Topics: Vaccines / Variants Limits: Adult / Child / Humans Language: English Journal: J Med Virol Year: 2023 Document Type: Article Affiliation country: Jmv.28413