Strand Life Sciences presented insights from its COVID-19 genomic surveillance initiative of sequencing 12,800 SARS-CoV-2 samples in Bengaluru.

RTPCR +ve samples were collected between July, 2021 and June, 2022 from various laboratories in Bengaluru, Karnataka, with due permissions from BBMP. These samples were then sequenced and analysed for variants and strains at Strand’s laboratories, and the findings were conveyed to the Karnataka State and BBMP public health officials in conjunction with INSACOG (Indian SARS-CoV-2 Genetics Consortium) labs.

In the 12,800 samples sequenced, more than 100 lineages were found. 44.4 per cent of these were Delta and its 75 sub-lineages. 70 per cent of these were the main B.1.617.2 sub-lineage and the remaining were the various AY.

Delta and its sub-lineages were dominant from July to October 2021; the first Omicron presence in India was detected in late November 2021. Thereafter, Omicron grew rapidly to close to 100% by the end of January 2022 and the Delta sub-lineages were no longer visible.

There were a total of ~30 Omicron sub-lineages identified, of which BA.1, BA.2, BA.2.10, BA.3 were notable. BA.2 and its sub-lineages dominated from Jan to May 2022, while BA.1 and BA.3 also retained some presence. A small presence for BA.5 was detected in April and May 2022.

In June 2022, BA.2 and its sub-lineages continued to dominate at 74 per cent, albeit reduced from 94 per cent. BA.5 and its sub-lineages recorded substantial growth to 20% in Jun 2022 and appeared as the leading contenders to unseat BA.2 and its sub-lineages. BA.4 also appeared at 2 per cent. Continued genomic surveillance in the coming months will determine if BA.5 and its sub-lineages are able to phase out BA.2 and its sub-lineages, as has been the case in some other parts of the world.