Dr Vedam Ramprasad, a genetic scientist with many peer-reviewed publications to his name, is the chief executive officer of MedGenome. MedGenome claims to be the leading genomics and clinical data-driven diagnostics and drug discovery research company in South Asia.
Dr Ramprasad, while speaking to Outlook, says that large-scale genomic surveillance of SARS-CoV-2 is the answer to many questions that puzzle our virologists and vaccine scientists today. Excerpts:
Q) Why are we so clueless about the variant of Covid-19 which caused so much havoc in India in the second wave?
Let me tell you that today there are two things that everyone is interested in finding out about the new variants of Covid-19. First, has the virus mutated to become more infectious and virulent, and second, would that change the dynamics of testing and therapies that are currently available, including vaccines.
If we need the answers to these, we need to conduct large-scale genomic surveillance and co-relate it with the variants and their clinical outcomes. If you have a few lakh viral samples sequenced already, you should be able to do a statistical correlation to see whether individuals who had these viral variants were immune to the drugs given or did the vaccines not work for them or did it result in a larger number of deaths for people who are affected with mutant viruses.
Hence, unless and until you have data, it’s very difficult to get the answers. Invitro (in lab) experiments will help in some way.
Q) The Health Ministry constituted Indian SARS-CoV-2 Genomics Consortium (INSACOG) at the end of December last year to find out mutations and new variants of the virus. Wasn’t that INSACOG’s job to do that?
I don’t know what INSACOG’s constraints were but we should have sequenced at least 5% of all positive samples that were collected from two states, Delhi and Maharashtra. But I think it didn’t happen. It was quite important in view of the detection of the UK and other variants among people coming from abroad.
Q) Some reports also emerged that government didn’t provide adequate funds to the INSACOG and that hampered the work seriously. How far is it true?
I also read some such reports but I cannot comment on that.
Q) Even after receiving two doses of vaccines, many individuals have tested positive and some of them have even died? The most recent case is of Dr KK Aggarwal who was fully vaccinated but died of Covid-19. Do you think aggressive genome sequencing of the virus that infects a person post-vaccination is the only way to solve this mystery?
Yes, we need to have a large amount of data to get meaningful answers. Viruses will mutate and evolve and there are reports of variants of concerns and post-vaccination infections. It is important that we generate high-quality genomic data and other metadata in needed volumes. This will certainly facilitate our understanding in a significant way.
When doing statistical analysis at least 5% of the total positive individual must be sequenced. Along with that, we should know full clinical details of the host; starting from how many days it took to catch the infection? How severe was it? Did it result in fatality? Did they have any comorbidity? What was their gender? What was their age? Once enough data is collected, both the virus and the individual, meaningful interpretations are made.
Q) Do we have enough private labs that can partake and end up giving us good results?
If you put government and private labs, there will be about 15-20 labs that have the capacity and capability. Fortunately, the viral genome is very small. It is a 30KB genome which is almost 100 times smaller than the human genome.
In one sequencing run, you can run hundreds of samples. At this point in time, the two critical aspects are “from where you get the funding” and “how you can streamline so all this data collated at one place to ensure meaningful analysis is done.” Need for inclusive consortia.
Q) Being a private lab, can you carry out genome sequencing for an individual or for a company?
At this point, there is no official documentation from anybody including Indian Council of Medical Research (ICMR), that we should not do it. However, there are certain mandatory ICMR requirements that need to be fulfilled and we want everyone who wants to work with us on sequencing samples to align with those protocols.
Q) So, have you done any such work for any private company or hospital?
We have done sequencing for a few hundred samples. However, this has been done to support our collaborators. It is important to understand that currently, genome sequencing is at the surveillance level.
So, there is some sort of uncertainty among hospitals and other private players as they don’t know if they can send samples to us for genome sequencing.
Secondly, it is not being used for patient management at present. If a clinic/ hospital will send their samples to us, they first try to see how it can be applied to patient management.
Q) So, the government hasn’t collaborated with private labs for genome sequencing as of now?
No, since the first Covid wave broke, we were keen to be part of this initiative. We are South Asia’s largest genome sequencing lab and we have the capabilities. So ideally, public/private consortia are the best. We can offer the best in terms of capacity and capability.
Q) How expensive is genome sequencing? How much does it cost?
Depends on the number of samples that are being sequenced. If you’re doing a few 1000 samples, the cost can go as low as Rs 4000-5000 rupees per sample and if you’re doing lakhs of samples then the cost can go as low as Rs 3000 rupees per sample.