COVID-19: Delta, sub-lineages dominant from July to October 2021, reveals genomic surveillance initiative

The first Omicron presence in India was detected in late November 2021, it was revealed

Chief Minister Basavaraj Bommai launching free vaccination programme for people above 18 years in Karnataka as part of Amruta Mahaotsava programme, in Bengaluru on July 16, 2022. The Chief Minister is flanked by Minister for Industries Murugesh Nirani and Health Minister K. Sudhakar. | Photo Credit: HANDOUT E MAIL

The Delta variant and its sub-lineages were dominant from July to October 2021 and the first Omicron presence in India was detected in late November 2021, revealed the findings of a COVID-19 genomic surveillance initiative, of sequencing 12,800 SARS-CoV-2 samples from Bengaluru, which were released here on Sunday.

The findings were released by Strand Life Sciences, a genomics-based research and diagnostics company, as a part of the ‘Celebrating Covid Genomic Sequencing and Surveillance effort in Karnataka’ event.

RT-PCR positive samples were collected between July, 2021, and June, 2022, from various laboratories in Bengaluru, sequenced, and analysed.

According to a release, in the 12,800 samples sequenced, over 100 lineages were found. As many as 44.4% of these were Delta and its 75 sub-lineages.

After the Omicron variant was first detected in November, it 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 January to May 2022, while BA.1 and BA.3 also retained some presence. A small presence of BA.5 was detected in April and May 2022. In June 2022, BA.2 and its sub-lineages continued to dominate at 74%, albeit reduced from 94%,” said the release.

It went on to say that BA.5 and its sub-lineages recorded substantial growth to 20% in June 2022 and appeared as the leading contenders to unseat BA.2 and its sub-lineages. BA.4 also appeared at 2%.

The findings were conveyed to the State government and the BBMP public health officials in conjunction with INSACOG (Indian SARS-CoV-2 Genetics Consortium) labs like InStem, the key stakeholders for the project, said the release.

Vishal U.S. Rao, member of Genomic Surveillance Committee, Karnataka, and Director, Head and Neck Oncology, HCG Cancer Hospital, said, “As new variants of the virus continue to emerge, genomic surveillance has an important role to play in bringing the pandemic under control. In order to contribute effectively, we must continue to build tools and sustainable systems for genomic surveillance which can then be leveraged to other pathogens. We plan to continue sequencing of human SARS-CoV-2 cases to ensure that public health officials stay informed and implement appropriate measures”.