Strand Life Sciences Sequenced 12,800 SARS-CoV-2 Samples from Bengaluru and Identifies 100 Lineages Circulating

Strand Life Sciences presents ‘Report on Genomic Surveillance of SARS-CoV-2 in the city of Bengaluru’

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 COVID19 genomic surveillance initiative of sequencing 12,800 SARS-CoV-2 samples from the city of Bengaluru on Sunday, 17th July 2022, as a part of the ‘Celebrating Covid Genomic Sequencing and Surveillance effort in Karnataka’ event at Sir Puttanna Chetty Townhall, JC Road, Bengaluru.

The event was presided over by Dr Ashwath Narayan CN, Minister of Higher Education, IT & BT, Govt 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.
12,800 samples sequenced from Jul 21 through Jun 22

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 analyzed 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.

L to R Naga karthik, IN covid support, Dr Balasundar CHO BBMP, Rajesh Sudaresan IISc Ashwath Narayan Ramesh Hariharan and Vishal US Rao

Key findings from the report 

A total of 12,800 RT PCR positive COVID-19 samples were sequenced at Strand Life Sciences during the time period between July 2021 and June 2022. These samples were collected from the various  wards across Karnataka, with a focus on Bengaluru.

Key findings

  • In the 12,800 samples sequenced, more than 100 lineages were found.
  • 44.4% of these were Delta and its 75 sub-lineages. 70% 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.
  • A.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%, albeit reduced from 94%. 
  • 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%.
  • 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.      

Key Contributions of the Initiative

  • Strand Life Sciences developed ‘CoviSurve™’, a dashboard for real-time integration of SARS-CoV-2 sequencing data with the clinical and epidemiological information. 
  • CoviSurve™ helps identify how many had a given variant and where and when it was detected. It also serves as a tool for early identification of novel variants. 
  • Strand Life Sciences played a key role in the detection of the first Omicron cases recorded in India from international travellers. Continuous monitoring in Bengaluru city allowed close tracking of the spread of Omicron in the community. 
  • Strand Life Sciences provided timely information that AY.4.2 was not a variant of concern in Bengaluru. AY.4.2 is a sub-lineage of the Delta variant. It was highlighted as a potential  variant of interest in the UK in late October 2021. However, only 1 out of 948 sequences in October 2021 from Bengaluru belonged to this  lineage. 
  • This information was shared with the relevant authorities in a timely manner.
  • Strand Life Sciences sequenced samples from high profile outbreaks in schools and colleges. In November 2021, as schools and colleges reopened, a number of COVID-19 clusters were observed in Karnataka. Strand’s analysis showed that sequences in these clusters were not related, reducing concerns of potential broader spread.
Commenting on the report, Dr. Ramesh Hariharan, CEO & Co-Founder, Strand Life Sciences, said, “We are proud to have contributed 38% of the samples submitted from Karnataka to major public databases. In hindsight, there was an opportunity to spot the emergence of the Delta strain at least a month before it caused its tragic mayhem. We learned from that and have since been tracking the virus closely and providing timely information to the Government of Karnataka and BBMP. We would like to thank the Government of Karnataka and BBMP officials as well as all our funding partners for their invaluable support, which allowed us as a society to stay on top of the virus.”

Dr Ashwath Narayan CN, Minister of Higher Education, IT & BT, Govt of Karnataka, “A vital component of managing public health is keeping up with virus mutations and lineages. We have taken active measures to encourage genomic sequencing to enable detection of new variants proactively. This effort by Strand Life Sciences has played a significant role in understanding the spread and identifying relevant solutions to control the spread of the virus.”

Dr. Vishal US Rao, Member of Genomic Surveillance Committee, Karnataka, and Director - Head and Neck Oncology, HCG Cancer Hospital, said, “As new variants of coronavirus 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”

Dr. K.V Thrilok Chandra, IAS, Special Commissioner Health, BBMP, said “Genomic Surveillance has played a central role in ramping up health infrastructure as well as in introducing new measures to curtail the spread of Covid-19. I would like to congratulate the entire team of Strand Life Sciences for undertaking this ambitious project and sharing key insights on SARS-CoV-2 variants”

Dr. Vijay Chandru, Member Genomic Surveillance Committee of GoK and Chairman of the Science Advisory Board, Strand Life Sciences, said,  “The success of the new PPP triumvirate of public health, private technology and philanthropy in the delivery of cutting-edge and world-class genomic surveillance during the last one year in Karnataka, is a remarkable achievement that needs to be talked about and celebrated. It is testimony to the cooperation we have between industry, academia and the government in Karnataka. Genomic surveillance of this class requires a remarkable convergence of prowess in biotechnology and information technology and sophistication in health systems delivery and it is Bengaluru’s excellence in all these spheres that have come together in response to the pandemic to demonstrate that pandemic preparedness can be a very positive outcome of this challenging period that we have lived through."

Strand Life Sciences is a genomics-based research and diagnostics company that combines a long track record in bioinformatics with cutting-edge laboratory assays and a vast hospital partner network to drive newer generations of patient care. Strand’s customers include global instrument, diagnostic and pharmaceutical companies. Strand is also a pioneer of genomic testing in India. Strand’s long global bioinformatics track record makes it the most trusted company for genomic diagnostics in the areas of oncology, rare diseases, fertility, women’s health, and infectious diseases.
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