Genomic Characterisation and Epidemiology of XBB Recombinant Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Uttarakhand using Next Generation Sequencing: A Retrospective Cross-sectional Study

Abstract

Introduction: Following the surge of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in late 2019, there was an 11-month period of relative evolutionary stability. However, since late 2020, SARS-CoV-2 evolution has been characterised by the emergence of mutation sets impacting virus characteristics like transmissibility and antigenicity, termed “variants of concern.” This shift likely responds to changing immune profiles within the human population. There is mounting evidence suggesting that post-vaccination serum is less effective in neutralising certain SARS-CoV-2 genotypes. XBB is a recombinant variant comprising sublineages BA.2.10.1 and BA.2.75 of the Omicron variant. Aim: To investigate the genomic characterisation and epidemiology of the XBB recombinant variant of SARS-CoV-2 in Uttarakhand, India. Materials and Methods: A retrospective cross-sectional study was conducted at the Viral Research Diagnostic Laboratory (VRDL Lab), Government Doon Medical College (GDMC), Dehradun, Uttarakhand, India. A total of 1,162 nasopharyngeal swabs received between September 2022 and February 2023 from various healthcare facilities were included for Next Generation Sequencing (NGS) of coronavirus. NGS was performed and all results were forwarded to the Indian SARS-CoV-2 Genomics Consortium (INSACOG) and the Indian Biological Data Centre (IBDC) for variant determination. Data collection occurred from March to April 2023, with data analysis following from May to June 2023. Statistical analysis was conducted using Microsoft Excel and Omnicalculator. Results: Among the 1,162 processed samples, 41 (3.53%) were identified as the XBB variant of Omicron. Within the XBB variants, XBB.2 was predominant 22 (53.7%). Maximum XBB samples (38, 92.7%) originated from District Dehradun, Uttarakhand, India. Conclusion: SARS-CoV-2 has been evolving and advancing with each new variant coming across. As XBB is impacting both previously infected individuals and those vaccinated, there is an imperative to develop new and efficacious vaccines against circulating variants to reduce associated risks of morbidity and mortality.

Keywords

• coronavirus variants
• coronavirus disease-2019 vaccines
• omicron variants