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Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

Selvavinayagam ST 1 , Sankar S 2 , Yong YK 3 , Murugesan A 4 , Suvaithenamudhan S 5 , Hemashree K 1 Show all authors , Rajeshkumar M 1 , Kumaresan A 1 , Pandey RP 6 , Shanmugam S 7 , Arthydevi P 1 , Kumar MS 1 , Gopalan N 8 , Kannan M 9 , Cheedarla N 10 , Tan HY 11 , Zhang Y 12 , Larsson M 13 , Balakrishnan P 7 , Velu V 10 , Byrareddy SN 14 , Shankar EM 15 , Raju S 1

Affiliations 

  • 1 State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai 600 006, Tamil Nadu, India
  • 2 Department of Microbiology, Centre for Infectious Diseases, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 600 077, Tamil Nadu, India
  • 3 Laboratory Center, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
  • 4 Department of Microbiology, Government Theni Medical College and Hospital, Theni-625 512, India
  • 5 School of Biomedical Sciences, Sri Balaji Vidyapeeth, (Deemed to be University), Pondicherry 607 402, India
  • 6 School of Health Sciences and Technology, UPES, Dehradun 248007, Uttarakhand, India
  • 7 Center for Infectious Diseases, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 602105, Tamil Nadu, India
  • 8 Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur 610 005, India
  • 9 Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
  • 10 Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA, 30329, USA
  • 11 School of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Selangor, Malaysia
  • 12 Chemical Engineering, Xiamen University Malaysia, Sepang, Malaysia
  • 13 Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 58 183 Linköping, Sweden
  • 14 Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
  • 15 Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
medRxiv, 2024 Apr 19.
PMID: 38699322 DOI: 10.1101/2024.04.16.24305882

Abstract

In December 2023, we observed a notable shift in the COVID-19 landscape, when the JN.1 emerged as a predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive samples, followed by sequence analysis. Mutations within the spike protein sequences were analyzed and compared with the previous lineages and sublineages of SARS-CoV-2, to identify the potential impact of these unique mutations on protein structure and possible functionality. Several unique and dynamic mutations were identified herein. Our data provides key insights into the emergence of newer variants of SARS-CoV-2 in our region and highlights the need for robust and sustained genomic surveillance of SARS-CoV-2.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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