India hit global headlines recently for sharing less than ‘one-tenth of one per cent’ daily Covid cases. That translates to a mere 0.06 per cent of over 3 lakh cases recorded each day. Why this lack?
CHENNAI: India ranks a distant 102 in genetic sequencing of coronavirus and sharing that data with the rest of the world, says Global Initiative on Sharing Avian Influenza Data (GISAID). Only 3,636 genome sequences have been shared with the GISAID between January 12, 2020, and April 28, 2021.
Sequencing genomes of daily cases will help determine the impact of new variants in the second wave, including the infamous double mutant. The international community has criticised India for not sequencing enough genomes each day, and for what they call “poor infrastructure” in genomic labs.
However, scientists here say the real reason is not the lack of capacity at genomic labs. It is the lack of background data on samples, thanks to the burden on the healthcare system. The labs in India have capacity to sequence far more samples each day than the current rate, says Rakesh Kumar Mishra, director of CSIR-Centre for Cellular and Molecular Biology (CCMB) in Hyderabad. “The problem lies elsewhere.”
The main reasons for this, according to Mishra, are poor logistics and inadequate metadata. Last December, Indian government put together 10 labs under the name Indian SARS-CoV-2 Genomics Consortium (INSACOG), to ramp up the process of sequencing across the country. Mishra’s lab is part of this consortium.
There is extensive speculation that the prime culprit behind the second wave of cases is a double mutant, dubbed B.1.617. Each day, India submits a count of only a couple of hundred sequences of this variant to the GISAID database, while almost four lakh sequences of the UK-origin B.1.1.7 variant is on the database.
Given that many scientists have found the double mutant sequence variant in their respective countries, they are anxious to know the impact it is causing in India, where it was first detected last October. This way, countries can brace for what they may face in the future and develop better vaccines and drugs. But, why is India struggling to get this data? To understand that, one must know how the genomic study is used to combat the pandemic.
FROM VIRUS TO DATA
When people go for a Covid test, their swab samples are collected. The samples are then analysed using an RT-PCR test. If a sample tests positive, it is sent to a genomic lab along with patient’s records containing metadata – their age, sex, co-morbid conditions, vaccination history, symptoms, and mortality among others.