Since the first case of SARS-CoV-2 in March 2020, India has witnessed three pandemic waves. Delta (B.1.617.2) and its sublineages caused the second wave, and Omicron (B.1.1.529) and its sublineages (BA.1 and BA.2) are driving the third wave. After the waning of the third wave, India saw a surge in COVID-19 cases from May 2022. On sequencing, these variants were characterised as BA.2 by Pangolin. However, the predominance of BA.2 after the waning of the third COVID wave was unexplainable. Subsequently, the Indian isolates of BA.2 were further classified into sub-lineages BA.2.74, BA.2.75 and BA.2.76.
Since their designation, these new sub-lineages have already spread to over 40 countries. They have acquired additional mutations in their spike protein compared to BA.2. These added mutations, over and above those of the parental BA.2 variant, have raised concerns about their impact on viral pathogenicity, transmissibility, and immune evasion properties of the new variants.
We have been the coordinating laboratory for the surveillance of the SARS-CoV-2 virus in the community in Maharashtra. We receive samples from its attached hospital and various RT-PCR testing laboratories across the State for whole genome sequencing. During our study, a total of 990 RT-PCR positive SARS-CoV-2 samples, with a cycle threshold value (Ct) of less than 25, were processed for whole genome sequencing between June 3 and August 7, 2022. A set of individual-level data was obtained corresponding to the samples. Additional information on the presence of any symptoms, hospitalisation, treatment, comorbidities and vaccination status was collected via a telephonic interview with each patient.
