India has sequenced over 100,000 viral genomes as part of its surveillance effort – Hindustan Times

At least 100,000 genomes of the Sars-CoV-2 virus that causes coronavirus disease (Covid-19) has been sequenced by the consortium of laboratories that keep an eye out for variants that might lead to a surge in infection. The Indian SARS-CoV-2 Genomics Consortium (INSACOG), which consists of 10 central laboratories and 28 regional ones, has sequenced 115,101 samples since January this year.

Of the total samples, over 65,000 samples were assigned lineages by the Pangolin software used by the researchers to determine which variant family they belong to. Of these, 69% of samples are known variants of interest (VOI) or variants of concern (VOC), according to the latest bulletin of the consortium.

At present, delta and its sub-lineage continue to be the dominant variant. Delta (B.1.617.2 and AY.x) continues to be the main VOC in India. No new VOI or VOC are noted and other VOC and VOI other than Delta are now negligible in sequencing data from India, the bulletin states. A previous bulletin had clarified the delta sub-lineage AY4.2 that was declared as a variant of interest by the UK was found in 0.1% of the samples. It is too low to be of a concern at the time, the bulletin from November 1 states.

The original delta variant (B1.617.2) continues to be the most dominant one in India, found in 66% of all the samples sequenced, according to data from outbreak.info, which compiles data from the global GISAID database. Delta is followed by five sub-lineages of it AY.43 (7%), AY.39 (5%), AY.44 (3%), AY.20 (3%), and AY.33 (2%).

In October-end, HT reported that there were 17 genome sequences that were being re-looked by researchers from INSACOG in order to see whether they can be classified as AY4.2. There are two mutations in the spike protein and one in the ORF region of the viral genome; if a sequence contains two of the three mutations coupled with the ones for delta variant they are considered to be AY4.2.

The scrutiny around AY.4.2 arose after the latest technical briefing by the Public Health England (PHE) upgraded the variant as being under investigation. The PHE document, dated October 22, said the key decision is based on AY.4.2 having a modestly increased growth rate and a higher secondary rate of attack the ability to pass the infection on to someone was higher than Deltas (12.4% versus 11.1%).

Among the total samples that have been assigned lineages so far this year, Alpha accounts for 6.4%, beta 0.33%, gamma 0.003%, delta 43.9%, close relatives of delta (B1.617.1 and B1.617.3) account for 8.2% of the sequences, and the AY sub-lineage of delta accounts for 10%, according to INSACOG data.

Dr Ekta Gupta, head of the regional INSACOG laboratory at the Institute of Liver and Biliary Sciences in Delhi said, So far, there is no clinical significance of the AY variants that we are seeing. These are also similar to the delta variant that a large proportion of the population has been exposed to, so these are unlikely to cause a huge surge.

Union minister of state for science and technology Dr Jitendra Singh, in a high-level review meeting on the current status of Covid-19 research, took note that over 100,000 samples have been sequenced so far and over 57,000 patient samples have been stored at five bio-repositories across the country that will be made available to researchers and private players for the development of vaccines and therapeutics.

A vaccine testing and research facility will come up at the second campus of the Rajiv Gandhi Centre for Biotechnology (RGCB) and this centre will also have a BSL-3 facility which is capable of handling airborne viruses like Covid-19. This facility will be the first of its kind in South India. The RGCB will be developed as a hub for research and testing of multiple vaccines such as cancer vaccines and those for infectious diseases, including Covid-19. This will bring huge recognition for the RGCB in the specific area of vaccine research and development, the minister said.

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India has sequenced over 100,000 viral genomes as part of its surveillance effort - Hindustan Times