India to begin sequencing genes from Covid + go 5% samples
India will soon begin sequencing the genes of at least 5% of all Covid-19 positive samples in an attempt to better track mutations, officials from the Union Ministry of Health said, detailing a new genomic surveillance exercise to be able to better detect if there are worrisome variants of the virus.
The measures come weeks after the UK found a variant with an unusually high number of changes, including some that are believed to make the virus between 56% and 70% more transmissible. As of yet, the new strain is not known to cause more serious disease or render the current class of vaccines ineffective.
With India reporting 22,383 cases per day on average over the last week, it would mean sequencing1,120genomes a day. To do this, the government has established a genomic surveillance consortium under the National Center for Disease Control (NCDC), the union health ministry said.
Currently, the consortium’s laboratories have 50 samples from people who returned from the UK.
On the other hand, the National Working Group on Covid-19 that met on Saturday recommended that whole genome sequencing also be carried out in cases where the S gene does not appear in an RT-PCR or other molecular tests.
Eight of the 23 mutations that have been identified in the new UK variant are in the S gene, including one in the receptor-binding domain that the virus uses to enter human cells.
All molecular tests, such as RT PCR, CBNAAT, and TrueNat, amplify the genetic material of the virus present in the swab samples and compare it to two or three Sars-CoV-2 genes to give a positive result. With the new mutations, some tests may not recognize the S gene in a patient sample.
The NTF has also recommended that sequencing be performed if there is a proven case of reinfection.
“The UK performs whole genome sequencing for about 10% of its positive samples, which is one of the highest in the world. This is how they were able to detect the new variant that was spreading rapidly in London and some other regions. Sequencing the 5% of the total sample will be a very large exercise, but it will be very useful in giving us information on which variant is in circulation, where we should implement restrictions to stop the spread of a particular variant, and whether vaccines in development will continue. working against the variant, ”said Dr. Rakesh Mishra, director of the Center for Cellular and Molecular Biology. Experts have said that vaccines and natural immunity are likely to work against the new UK variant.
To quickly detect and isolate people who could carry the mutant variant which is believed to spread 70% faster, the NCDC had already directed all agencies to send positive samples from the UK returnees for full sequencing of the genome. Whole genome sequencing was also mandatory for anyone who tested positive in the community after returning from the UK in the last 28 days.
The consortium will be made up of laboratories from the National Institute of Virology-Pune, the Institute for Genomics and Integrative Biology-Delhi, the Center for Cellular and Molecular Biology-Hyderabad, the National Institute of Mental Health and Neuroscience-Bangalore, among others.
“A genomic surveillance consortium, INSACOG, has been formed under the leadership of NCDC, New Delhi, for epidemiological and laboratory surveillance of circulating strains of SARS-CoV-2 in the country,” said a statement from the Ministry of Health. of the Union. Most of these labs were already sequencing Sars-CoV-2 genomes, however it is likely to scale up and coordinate efforts.