Medicina Tropical y Cirugía

Abstracto

Whole Genome Sequencing of Omicron Identified Multiple Outbreaks and Introduction Events in India during November 2021 and January 2022

Shreedhanya D. Marathe, Varun Shamanna, Geetha Nagaraj, Nischita S, Muthumeenakshi Bhaskaran, K.L Ravi Kumar

The Variant of Concern (VOC), Omicron is the predominant variant circulating throughout the world of the SARS CoV-2 pandemic during the third wave including India. The world health organisation has designated this highly mutated variant as a VOC due to its high transmissibility and risk of reinfection. Whole genome sequencing and analysis were performed for SARS-CoV-2 PCR positive samples between December 2021 to January 2022. From the 133 Omicron variants detected, genomic analysis was carried out by contextualizing them with 1586 complete genomes of Omicron from India obtained from GISAID. The Omicron variant prevalence in India has increased in a log phase within 3 months in most of the metropolitan cities. With the limited sequencing data available, it was identified that the sublineage BA.1 was predominant in India from November 2021 to January 2022. Further, the first sequence of BA.2 sublineage was submitted from Delhi only in the mid of December 2021. The two outbreaks observed were of BA.2 variant and were found to spread to multiple cities in a short time. The rapid spread and specific mutations in the outbreak samples of Omicron indicate that the variant is highly transmissible when compared to previous variants. The study shows the importance of genomic sequence to identify the emergence of clusters and take actions to prevent further spreading events.