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Genome sequencing is a recent technique and hence focus must be put on creating awareness for both people as well as clinicians

The rollout of vaccines to tackle the spread of the novel coronavirus has brought relief to the entire world. However, inequity in vaccine distribution has created opportunities for new variants to emerge. A robust genomic surveillance program must be developed in India and then scaled up by December 2021, to rapidly detect and evaluate new variants. This will be essential to manage and mitigate threats to collective public health.

What is genome surveillance?

Genomic surveillance allows researchers to examine and compare the genome sequence of the viral strains infecting the population. This characterisation is necessary to pre-empt and prevent new COVID-19 waves and future epidemics/pandemics. Public labs put into action by the Indian SARS-CoV-2 Genome Sequencing Consortia (INSACOG) for this purpose are not adequately funded. These public labs have the capacity to process 30,000 samples a month.

To achieve the five percent sequencing target, India must process 75,000 samples a month which is 2.5 times the current scale. Increasing the effort to a magnitude of over five times, will quickly use up spare capacity in the public labs. Making private sector labs a part of the genome sequencing process can help India build a better response to the impending third wave as well as future pandemics.

How does genome sequencing help?

Sequencing the viral genome helps public health specialists track the spread and trajectory of the mutated virus, called variants, and design effective strategies. Failure to characterize the variant affects diagnosis and reduces our ability to stop the infection and treat patients in the right manner.

This partially explains negative RT-PCRs in infected people in the second wave. Vaccines, the most effective control mechanism today, can also have a reduced response to variants. With existing drugs and vaccines reducing their beneficial effects on variants, the possibility of more severe disease will increase. For it to be effective, the surveillance needs to be done at a global scale since that is how the pandemic spreads.

India lags behind

An open-source collaborative initiative called Global Initiative on Sharing All Influenza Data or GISAID, already collects, shares and analyses data on all viral infections including COVID. Through its efforts, GISAID has become a credible source for researchers around the world to track the trajectory of the virus and help governments create the most appropriate responses. As of 13th July, India had submitted 34,997 samples to this initiative. This amounts to 0.113 percent of the database.

In India, where less than one percent of the population is infected, sampling of five percent of its positive cases can help identify and track new mutations of the virus. With 45,000-50,000 new cases, sampling five percent requires 2,500 samples to be collected and analysed every single day. We now average 450-500 samples a day.

Increasing the speed and scale of genome sequencing in India is therefore absolutely essential. This includes identifying the right people, collecting good quality samples (through a nasal or oral swab), submitting the samples to the right labs that are equipped to carry out the test, and sequencing the viral genome. Finally, the results must be shared with INSACOG and GISAID, the Indian and global bodies tracking the mutation. This process is exhaustive but necessary, because it helps to track and control the spread of the delta- or any other emerging variant that could well result in a third wave of the pandemic.

To speed up results we should get representative samples from hotspots or areas of unusual outbreaks, particularly focusing on people getting re-infected. Samples from vaccinated people getting infected will also be required to fully understand the degree of mutation in the variant. To achieve scale, investing to increase the capacities of public genome-sequencing labs would be ideal. However, since the need is immediate and urgent, a more practical approach would be to utilise private sector capacity in collaboration with the union government. An order from the ICMR has, however, banned this for the moment.

Including the private sector, leverages untapped capacity while requiring minimal investment in infrastructure and human capital. Private lab chains say each lab can sequence between 100-2000 samples a day depending on its size. Considering that India has several such companies, large and small, this will be a welcome addition in capacity. Assuming the daily number of cases stays constant, 2500 samples a day, will not prove difficult to sequence. In the event of cases escalating, private labs can scale to two to three times their current capacity with adequate funding from the government. Since these are a handful of companies, managing the agreements and executing this plan also seems relatively simple.

A central nodal agency to ensure data is anonymised and stored securely, while not the best option, could work in the immediate term to address concerns about data storage, privacy and security. ICMR or the NCDC may be required to create a standardized protocol for processing and storing samples to ensure the highest data quality and standardization.

Regular check-ins with private players can ensure that targets are met and that costs do not escalate. One way to do this is to focus sample collection on infection hotspots, containment zones and travel hubs. This will ensure that the aim is on the quality of the samples and not the quantity.

Conclusion

This is by no means an all-encompassing idea. The approach will have to be multi-pronged. The government will have to invest in upscaling INSACOG’s public labs in parallel while opening more of them. Adding this capacity may seem a long and tedious process, but is absolutely necessary for a coherent response to fend off future waves or other pandemics. Given the urgency in the immediate term, involving private players seems to be an effective, efficient, affordable, and quick turnaround solution.

Genome sequencing is a recent technique and hence focus must be put on creating awareness for both people as well as clinicians. Cultural issues around privacy and sharing genome samples could create barriers for this very important but niched practice, to go mainstream. As we can see, it is critical for genomic sequencing hubs to become a permanent part of India’s pandemic preparedness policy.

The author was formerly Executive Vice President at GlaxoSmithKline and a participant in the Graduate Certificate in Public Policy (Health & Lifesciences) program at the Takshashila Institution.