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<p>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.</p>

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

  • 期刊论文

  • 发表日期：

    2026年7月22日

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  • Rohit Menon,
  • Sushil Kumar Sharma,
  • Anshuman Behera,
  • Ambuj Shrivastava,
  • Shashi Sharma,
  • Jyoti S. Kumar,
  • Paban Kumar Dash,
  • Manmohan Parida

摘要

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.