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SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.
Muttineni, Radhakrishna; R N, Binitha; Putty, Kalyani; Marapakala, Kavitha; K P, Sandra; Panyam, Jaslin; Vemula, Aravind; Singh, Shashi Mohan; Balachandran, Subin; S T, Viroji Rao; Kondapi, Anand Kumar.
  • Muttineni R; Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India.
  • R N B; Department of Zoology, Mar Athanasius College (Autonomous), Kothamangalam, Kerala, India.
  • Putty K; Department of Veterinary Biotechnology, PVNR Telangana Veterinary University, Hyderabad, Telangana, India.
  • Marapakala K; Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India.
  • K P S; Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Telangana, India.
  • Panyam J; Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India.
  • Vemula A; Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India.
  • Singh SM; Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India.
  • Balachandran S; Department of Zoology, Mar Athanasius College (Autonomous), Kothamangalam, Kerala, India.
  • S T VR; Department of Animal Genetics and Breeding, PVNR Telangana Veterinary University, Hyderabad, Telangana, India.
  • Kondapi AK; Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Telangana, India.
Transbound Emerg Dis ; 69(5): e1721-e1733, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1735979
ABSTRACT
Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1 January 2021 to 31 August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N-terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralizing antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Vaccines / Variants Limits: Animals Language: English Journal: Transbound Emerg Dis Journal subject: Veterinary Medicine Year: 2022 Document Type: Article Affiliation country: Tbed.14508

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Vaccines / Variants Limits: Animals Language: English Journal: Transbound Emerg Dis Journal subject: Veterinary Medicine Year: 2022 Document Type: Article Affiliation country: Tbed.14508