Strand Life Sciences has sequenced a total of 12800  samples from July, 2021 to June,  2022, and identified more than a 100 lineages circulating in Bengaluru

Strand Life Sciences, a genomics-based research and diagnostics company, presented insights from its COVID-19 genomic surveillance initiative of sequencing 12,800 SARS-CoV-2 samples from the city of Bengaluru as a part of the ‘Celebrating Covid Genomic Sequencing and Surveillance effort in Karnataka’ event.

The event was presided over by Dr Ashwath Narayan CN, Minister of Higher Education, IT & BT, Government of Karnataka, Dr Thrilok Chandra, IAS, Special Health Commissioner, BBMP, Dr Ramesh Hariharan, CEO & Co-Founder, Strand Life Sciences, Prof. Rajesh Sundaresan, IISc, Professor, Dr Vishal US Rao, Member of Genomic Surveillance Committee, Karnataka, and Director – Head and Neck Oncology, HCG Cancer Hospital, and Prof. Rakesh Mishra, Director, Tata Institute for Genetics and Society.

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 like InStem, the key stakeholders for this project. The project was supported primarily by philanthropic funding from IN Covid Support, supplemented with funding from organisations like ACT Covid Response Collective.

Key findings

• In the 12,800 samples sequenced, more than 100 lineages were found.
• 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.* sub-lineages.
• Delta and its sub-lineages were dominant from July to Oct 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.
• 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.
• 5 and its sub-lineages recorded substantial growth to 20 per cent 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.