In a recent interview, Dr. N K Arora, co-chair, Indian SARS-CoV-2 Genomics Consortium (INSACOG) elaborates about the Standard Operating Procedure (SOP) for testing and follow-up on variants, what makes the Delta variant so transmissible, how genomic surveillance can help contain its spread and reemphasises on the importance of COVID appropriate behaviour.
INSACOG is a consortium of 28 laboratories of the Ministry of Health & Family Welfare, Dept. of Biotechnology, Indian Council of Medical Research (ICMR), and Council of Scientific and Industrial Research (CSIR) for whole genome sequencing in the context of the COVID-19 pandemic. INSACOG was established by the Ministry of Health and Family Welfare, Govt of India on 25/12/2020.
Recently INSACOG expanded its reach. What is the thought behind its expansion?
There is a need to keep a strict vigil on the emergence of variants of concern and outbreaks so that they can be contained before they spread to a larger region. The Indian SARS-CoV-2 Genomics Consortium (INSACOG), established in December 2020, was a consortium of 10 laboratories. Recently 18 more laboratories became part of it.
The idea is to have a strong network of laboratories to do genomic surveillance of the SARS-CoV-2 and correlate whole genomics sequencing (WGS) data with clinical and epidemiological data to see whether or not a variant is more transmissible, causes more severe disease, escaping immunity or causing breakthrough infections, affecting vaccine efficacy, and diagnosed by current diagnostic tests.
Then National Center for Disease Control (NCDC) analyzes this data. The entire country has been divided into geographical regions and each lab is given the responsibility of one particular region. We have formed 180-190 clusters with around 4 districts in each cluster. Regular random swab samples and samples of patients who develop severe illness, vaccine breakthrough infections, and other atypical clinical presentations, are collected and sent to regional laboratories for sequencing. The current capacity of the country is to sequence over 50,000 samples per month; earlier it was approximately 30,000 samples.
What kind of mechanism country has for testing and follow-up on variants?
India has a well-established mechanism of Integrated Disease Surveillance. The IDSP coordinates sample collection and transportation from the districts/sentinel sites to Regional Genome Sequencing Laboratories (RGSL). The RGSLs are responsible for genome sequencing and identification of Variants of Concerns (VOC)/Variants of Interest (VOI), Potential Variants of Interest, and other mutations. Information on VOC/VOI is directly submitted to the Central Surveillance Unit for clinical-epidemiological correlation in coordination with State Surveillance Officers. The samples are then sent to the designated bio banks.
RGSLs, upon identification of a genomic mutation that could be of public health relevance, submit the same to the Scientific and Clinical Advisory Group (SCAG). SCAG thereafter discusses the Potential Variants of Interest and other mutations with experts and if necessary, recommends to the Central Surveillance Unit for further investigation.
Sharing of information and clinical-epidemiological correlation is done by IDSP, a unit of NCDC, along with the Ministry of Health, the Indian Council for Medical Research, the Department of Biotechnology, the Council for Scientific and Industrial Research, and state authorities.
Finally, the new mutations/variants of concern are cultured and scientific studies are undertaken to see the impact on infectiousness, virulence, vaccine efficacy, and immune escape properties.