Isolation and genome characterization of SARS-CoV-2 recombinant Omicron variant XBB.1.16 from Central India

Despite the World Health Organization's declaration in May 2023 of the end of the Public Health Emergency of International Concern (PHEIC), COVID-19 continues to circulate globally. As such, the continued transmission across the different parts of the globe resulted in the emergence of variants which could pose a constant challenge to public health. The isolation of circulating virus variants during these times is essential to assess the impact of the strains and establish effective counter-measures if necessary. This study focuses on the isolation and characterization of the SARS-CoV-2 recombinant Omicron variant XBB.1.16 from a clinical sample in Central India, collected during an early 2023 surge. Using a throat swab, confirmation of the variant by qRT-PCR and distinctive Cytopathic Effects (CPE) were observed on the Vero E6 cell line. The isolation by passages of the virus was found to be successful through positive qRT-PCR and next-generation sequencing (NGS). The isolate was found to be XBB.1.16, Clade GRA, a Variant of Interest (VOI) after sequencing. Detailed analysis of the spike gene indicated 53 mutations leading to 45 amino acid substitutions compared to the original Wuhan strain.

The online version contains supplementary material available at https://doi.org/10.1007/s13337-026-00974-w.