Govt’s top scientific advisor responds to online petition for Covid datasets
The office of the Principal Scientific Advisor (PSA) has asked research collaboratives to create a mechanism to widely share available and new datasets and asked the Indian SARS-CoV-2 Genomic Consortia (INSACOG) to reach out to more partners, including independently supported ones, to expand genomic sequencing in India, according to a note from the government’s top scientific advisor.
“Issues such as vaccine hesitancy, nature of variants, re-infection, extent, and nature of post-vaccination protection, etc. can all be addressed better by collaborative research. While this is being done by some groups now, our broader research community needs to be much more facilitated by our research agencies to be involved in addition to ‘bottom-up’ efforts,” read a note from the office of Principal Scientific Advisor Prof K VijayRaghavan.
The note also sought “wider involvement of teams in data analysis, bioinformatics, and decision-making” by INSACOG.
The communication comes in response to an online petition by scientists to seek open sharing of granular epidemiological and genomic surveillance data. The petition, signed by scientists from various fields across the country, demanded that the government collect and release key epidemiological data to help scientists in developing “data-driven mitigation strategies.”
“Our inability to adequately manage the spread of infections has, to a large extent, resulted from epidemiological data not being systematically collected and released in a timely manner to the scientific community,” the online petition said. It has been signed by top scientists including the country’s top vaccinologist Dr Gagandeep Kang, biologist Dr Mukund Thattai, and epidemiologist Dr Jacob John.
They also asked that restrictions on imports under “Atmanirbhar Bharat” policy be removed as they hampered scientific study for the want of imported scientific equipment and reagents. The note from the PSA office responded to this concern. “Delegation for clearances for imports have already been given, some months ago, to Secretaries ofDepartments/Ministries and decisions can be taken at the level of Deans and Institution directors. This will be examined, and specific steps taken to remove bottlenecks”.
The scientists have made four major demands: large-scale genomic surveillance of new variants (the INSACOG sequences only 1% of the positive cases), release of granular data on testing and clinical outcome of Covid-19 cases, release of anonymised data on the clinical outcomes of hospitalised patients, and data on the immune response to vaccination in Indian population.
“The ICMR database is inaccessible to anyone outside of the government and perhaps also to many within the government. Most scientists – including several identified by DST and NITI Aayog to develop new prediction models for India – do not have access to this data. Public health measures in India should necessarily vary from one local area to another, because there is a great geographical variability in patterns of spread of the infection due to local conditions,” the petition read.
Data that is available to researchers are often scattered and available in different formats, thus preventing them from drawing meaningful conclusions. “As a computational biologist, the data I have been working with mainly involve the new case numbers and outcomes (recovery/death) over the course of the first and second wave. At the moment, the datasets are fragmented across different states and local authorities,” said Dr Thattai.
He cites the example of Bengaluru where he depends on data from the government of Karnataka and Bruhat Bengaluru Mahanagara Palike (BBMP). The data that they put out are in different formats and are presented as an aggregate.
“They will give the total number of positive cases in a given day, or the total number of tests that are positive, or the fraction of cases that are under-60s, and so on. But these aggregate statistics, while useful for seeing trends, do not permit further detailed analysis. Suppose I want to know whether the fatality rate for over-60s is lower in the second wave than the first (as we might expect, if the vaccination campaign has been effective). We cannot obtain these data from the aggregate statistics. We will need to wait for the MoHFW itself to test this question,” he said.
He said, the granular data – anonymised age, gender, district, date of positive test, date of hospitalisation, date of recovery or death, vaccination status, previous infection status if any – should be made available to all scientists. “From these granular raw data we can extract meaningful information. The ICMR which has been tasked with collecting this data nationwide, should have the most comprehensive dataset. We are asking for this dataset to be made available for other researchers to also use,” he said.