Isolation and Genome Characterisation of Omicron variant (BA.2) of SARS-CoV-2 from Central India

The COVID-19 pandemic has been causing enormous damage to humankind in terms of morbidity, mortality and huge economic losses since 2020. The continued high rate of transmission globally is leading to the advent of newer variants. The virus culture of emerging variants is critical for the evaluation of existing and future medical countermeasures. Most parts of India including Central India witnessed an explosive rise in cases in early 2022 marked as the third wave of the pandemic. In this study, The SARS-CoV-2 Omicron (BA.2) variant was successfully isolated from a COVID-19 patient. The qRT-PCR-positive clinical samples were serially passaged in Vero E6 cells, which showcased characteristic cytopathic effects. The successful virus isolation was confirmed through a battery of tests including qRT-PCR and sequencing through Next-Generation Sequencing (NGS). The genome sequencing revealed that the virus isolate belonged to Omicron BA.2 (GRA, B.1.1.529), during time of its emergence declared as Variant of Concern (VOC). The spike region of this isolate, namely, DRDE-03/2022 exhibited 24 amino acid changes when compared to the SARS-CoV-2 prototype Wuhan sequence in its spike region (Spike hCoV-19/Wuhan/WIV04/2019). This study reports the successful isolation of the Omicron BA.2 variant of SARS-CoV-2 from Central India.