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Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study

Selvavinayagam ST 1 , Karishma SJ 2 , Hemashree K 1 , Yong YK 3 , Suvaithenamudhan S 2 , Rajeshkumar M 1 Show all authors , Aswathy B 2 , Kalaivani V 1 , Priyanka J 1 , Kumaresan A 1 , Kannan M 4 , Gopalan N 5 , Chandramathi S 6 , Vignesh R 7 , Murugesan A 8 , Anshad AR 2 , Ganesh B 9 , Joseph N 10 , Babu H 11 , Govindaraj S 11 , Larsson M 12 , Kandasamy SL 13 , Palani S 1 , Singh K 13 , Byrareddy SN 14 , Velu V 11 , Shankar EM 2 , Raju S 1

Affiliations 

  • 1 State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
  • 2 Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
  • 3 Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor 43 900, Malaysia
  • 4 Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
  • 5 Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur 610 005, India
  • 6 Department of Medical Microbiology, University of Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
  • 7 Faculty of Medicine, Preclinical Department, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak 30450, Malaysia
  • 8 Department of Microbiology, The Government Theni Medical College and Hospital, Theni, India
  • 9 National Institute of Epidemiology, Indian Council of Medical Research, Ayappakkam, Chennai 600 077, India
  • 10 Department of Medical Microbiology, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
  • 11 Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
  • 12 Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
  • 13 Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
  • 14 Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
Lancet Reg Health Southeast Asia, 2023 Dec;19:100272.
PMID: 38076717 DOI: 10.1016/j.lansea.2023.100272

Abstract

BACKGROUND: Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India.

METHODS: Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients.

FINDINGS: Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population.

INTERPRETATION: Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the 'next' predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants.

FUNDING: National Health Mission (India), SIDASARC, VINNMER (Sweden), ORIP/NIH (USA).

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

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