Journal of Family Medicine and Primary Care (May 2024)

Genomic epidemiology of severe acute respiratory syndrome coronavirus 2 from Theni, Tamil Nadu

  • Gopinath Ramalingam,
  • Arundadhi Muthukumar,
  • Raju Sivadoss,
  • Gopinathan Rajan,
  • Dhanasezhian Aridass,
  • Amudhan Murugesan,
  • Krishnapriya Subramani,
  • Sucila Thangam Ganesan

DOI
https://doi.org/10.4103/jfmpc.jfmpc_1698_23
Journal volume & issue
Vol. 13, no. 5
pp. 1727 – 1733

Abstract

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Introduction: The coronavirus disease 2019 (COVID-19) is a viral infection characterized by respiratory and gastrointestinal symptoms. The causative agent of this infection is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic study helps in understanding the pathogenesis, epidemiology, and the development of therapeutic and preventive strategies in the combat against COVID-19. Materials and Methods: Nasopharyngeal and oropharyngeal swab samples were collected from asymptomatic and symptomatic patients during the time period of 2021–2022 for the detection of SARS-CoV-2 by employing real-time reverse transcriptase, cDNA synthesis, whole-genome sequencing by next-genome sequencing, analysis of SARS-CoV-2 sequence data and lineage and variant of concern assignment along with phylogenetic analysis. Results: Lineages BA.2.10 and BA.4.1.1 clustered with genomes from Senegal suggested the spread of infections. Similarly, high clustering among delta samples during the second wave showed possible importation and subsequent spread via local transmission. Conclusions: Studies like these are important to understand the characteristics and origins of locally circulating SARS-CoV-2 diversity in order to prevent further spread.

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