Ask The Doctor: Active Genomic Surveillance, NGS Technologies Can Prepare Us for Next Pandemic

·3-min read

A year after the Coronavirus pandemic wrecked our collective lives, our society has been grappling with fear and insecurity. As a result, we have seen misinformation spread like wildfire, and many resorting to bizarre and incorrect methods of dealing with the virus. With this column, which will be published every Sunday, we aim to address any health or vaccine-related question our readers might have about the coronavirus pandemic.

In this week's column, the queries have been answered by Dr Anurag Agrawal, Director of Institute of Genomics and Integrative Biology, CSIR. Dr Agarwal talks about the ways to prepare for future pandemics, how big data and AI can help in that preparedness, and why the COVID-19 home testing kit won't be effective in India.

Technology-wise, what kind of preparedness is required to deal with future pandemics, especially in India?

Active genomic surveillance for the early discovery of potential pandemic pathogens is needed. Next-Generation Sequencing (NGS) technologies have the potential to improve the response to emerging infectious diseases when used alongside high-quality epidemiology.

Can big data and AI be used to fight COVID-19? If so, how?

Active genomic surveillance and large-scale molecular epidemiology are done by analysing big-data. Artificial Intelligence(AI) plays a critical role in finding mutant variants by NGS techniques and in predicting their behaviour. AI and big data are also accelerating the process of drug discovery, outbreak modelling, and diagnostics.

While we saw higher rates of people turning up to take the first dose of vaccine, the rates have fallen drastically, for those returning for the second and the final dose. How effective is the vaccine if all the doses are not taken?

The failure to take the second dose will critically reduce the effectiveness of the vaccine. Just like inadequate antibiotic treatment can lead to antibiotic resistance, inadequate immune responses may help the virus evade it.

After the initial dip in cases, the numbers have again begun to rise up, especially in a few states. What could be the reason for that?

I think the decline is fundamentally related to a high number of infected and recovered people. We are now seeing persisting outbreaks, mostly in Kerala and Maharashtra. In Kerala, it seems that they contained the infection better early on, and so they had a larger pool of people who remained unaffected by the end of 2020. Social interactions during Onam or New Year may have triggered the current outbreak.

In Maharashtra, there seem to be multiple reasons. First, pockets of susceptible people outside big cities. Second, declining immunity in places such as Mumbai where 7-8 months have passed since the initial big waves. Third, some reports of variants with immune escape ability, which needs confirmation. We have offered help with expanding sequencing there. In Kerala, IGIB has recently sequenced about 700 samples across the districts and we do not see immune escape variants to be the main reason although there has been an increase in one variant called N440K across South India.

When will home testing kits be available for COVID-19 in India?

Technologically, we can do it soon. Practically, it may not be an ideal solution for India. Local clinics or centres should be enabled to offer point- of- care tests. TATA MD Check, powered by FELUDA is now automated and is offered through mobile vans. A mobile van can conduct 3000+ tests daily. We are in discussion to use them for local testing during potential outbreaks.

Do you have questions about Coronavirus? Or the vaccines? Send us your questions: Tweet with #AskADoctor. Every week, we will have a public health expert to address your concerns through this column.