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Cited by 0SARS-CoV-2 and COVID-19 ResearchEvolution and Genetic DynamicsSARS-CoV-2 detection and testing

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Mutational and evolutionary dynamics of non-structural and spike proteins from variants of concern (VOC) of SARS-CoV-2 in India

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Chaudhuri, Ankur, Das, Subhrangshu, Chakrabarti, Saikat·2024·International Journal of Biological Macromolecules
DOI 10.1016/j.ijbiomac.2024.137154

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Abstract

Monitoring the genetic diversity and emerging mutations in SARS-CoV-2 remains crucial for understanding its evolution, given the virus's persistence in India. This study analyzes lineage dynamics, mutation screening, structural analysis, and phylodynamics of SARS-CoV-2 variants of concern (VOC) in India from October 2020 to September 2023. The predominant variants identified were alpha, beta, delta, and omicron, with delta and omicron making up 76.05 % of sequenced genomes. The B.1.617.2 lineage of the delta variant was the major contributor to COVID-19 cases before the rise of omicron. Mutation screening of non-structural proteins (NSPs) and spike proteins revealed distinct profiles for each VOC. Co-mutation patterns were analyzed, showing structural and energetic alterations. Phylogenetic analysis indicated that nsp1, nsp3, nsp4, nsp13, and nsp14 were strongly associated with increased mutation load. The study also highlighted that nsp14 and spike have similar mutability patterns, underscoring nsp14's critical role in SARS-CoV-2 infectivity and persistence. This research provides a comprehensive view of SARS-CoV-2's evolution and persistence in India.

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Metadata

Authors
Chaudhuri, A., Das, S., & Chakrabarti, S.
Affiliations
Indian Institute of Chemical Biology (IN)
Corresponding author
  • Chaudhuri, Ankur
  • Chakrabarti, Saikat
ORCID
Chakrabarti, Saikat
Venue
International Journal of Biological Macromolecules
Publisher
Elsevier BV
Published
2024-12
Volume
282
Issue
Pt 4
Pages
137154
ISSN
0141-8130 (ISSN-L)
DOI
10.1016/j.ijbiomac.2024.137154
OpenAlex
W4403966378
Cited by
0
References
2
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Biological Macromolecules (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • Department of Biotechnology, Ministry of Science and Technology, India (BT/PR40137/BTIS/137/35/2022)
  • CSIR - Indian Institute of Chemical Biology
  • Indian Council of Medical Research (BMI/11(55)2022)
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
Keywords
SARS-CoV-2, variants of concern, non-structural proteins, spike protein, viral mutations, co-mutation patterns, nsp14, phylodynamics, Omicron variant, Delta variant, India, viral evolution
MeSH terms
COVID-19, SARS-CoV-2, Humans, India, Mutation, Phylogeny, Genome, Viral, Viral Nonstructural Proteins, Evolution, Molecular, Spike Glycoprotein, Coronavirus

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