Episode 4: A hotspot of coronavirus variants

(Lightly edited for readability)

Speakers

Chitra Pattabiraman, Anurag Agrawal, John Pickrell, Subhra Priyadarshini

00:00 Partner announcement: This episode is produced with support from DBT Wellcome Trust India Alliance.

00:10 Subhra Priyadarshini: Welcome to the Nature India podcast, I am Subhra Priyadarshini.

It's June 2021, 15 months into our living with the COVID-19 pandemic. In many parts of the world, the pandemic continues to rage on. Here in India, a deadly second wave peeked in May, with more than 400,000 new cases being recorded every day. That graph of course is plunging now. Through the pandemic, India has reported nearly 350,000 people dead and millions more infected. The recent surge in coronavirus cases has overwhelmed the country's healthcare system. It has alarmed researchers, policymakers, and of course the general public. As losses mount, scientists are trying their best to understand the variants now circulating in India. The World Health Organization recently renamed the variants of the novel Coronavirus to Greek letters for simplicity, and to remove any stigma that might be attached to naming them with their country of origin.

In this episode of the Nature India podcast, we will explore how variants arise, what sets the Delta variant, earlier called the B.1.617.2 variant, that originated in India, apart from the others? Will our existing vaccines provide immunity against emerging variants? So how exactly does a COVID-19 variant evolve?

We ask Chitra Pattabiraman to explain. Chitra is an early career fellow at the National Institute of Mental Health and Neurosciences, Bangalore. She works on novel or emerging viruses in human populations and Her research focuses on how viruses mutate.

02:17 Chitra Pattabiraman: So actually, we can think of the virus as having inside it the instructions to make itself. And those instructions are what we would call the genome of the virus. So when the virus makes copies of itself, it can make mistakes while copying. So think of it like you're doing a Xerox copy of a page, right? When you're copying it out. You can make mistakes. And so this is what happens when a virus makes a copy of itself or replicates. And for SARS-CoV-2, this rate is roughly one mistake every two weeks is what we get to see. So by now it has been in the population enough that you will start seeing a variety of these genomes, just based on differences from what was originally circulating in Wuhan, China in 2019.

03:16 Subhra Priyadarshini: Okay, so the variant of concern on top of everyone's minds right now is, of course, Delta B.1.617.2, which was first detected in India. Anurag Agrawal, Director of the Institute of Genomics and Integrative Biology in Delhi, was part of the consortium that first reported the Delta variant of SARS-CoV-2, as a potential variant of concern. It has become the dominant strain across India. And as we speak, it has spread to at least 62 countries, including the United Kingdom, Fiji, Singapore, and Australia.

03:56 Anurag Agrawal: The current variant that everybody's interested in which WHO has now called Delta – we are stopping using complicated nomenclatures, and we certainly don't want to use name of countries – is the one that was originally found in India, and appears to be much more transmissible than previous variants. Transmissibility means if one person is infected, how many more people can be determined by something called R0 (R nought). So what we can see is that the new variants infect about half to one more person compared to the original ones. Now it sounds like a small amount, but because it's an exponential growth, anything with an effect of, you know, half more or one more person can lead to a large increase at the rate at which an outbreak spreads.

04:45 Chitra Pattabiraman: While we don't know what are the factors that makes them emerge, it is probably just the fact that so many people are infected. And we believe that things like immunosuppression, having like these large number of people infected, long transmission chains, gives the virus the opportunity to change itself, and some of those changes or advantageous, and then you start seeing those take over the population.

05:17 Subhra Priyadarshini: Alright, so how they're taking over the population has a lot to do with the changes in the virus’ Spike protein, the protrusions on its surface that make it look like a crown or corona under the microscope, as everybody knows by now. Last month, my colleagues Benjamin Thompson and John Pickrell produced an episode of Coronapod on the variants in India. Here's a quick snippet from John Pickrell. Nature's Asia Pacific bureau chief.

05:58 John Pickrell: Viruses constantly evolving and new variants are appearing in different places, some of these variants pose kind of a new threat and other mutations and changes in the viral genome are relatively benign. But one area that scientists are particularly interested in is the virus’ spike protein, which allows it to gain entry into cells. So one of the groups in India who has been studying the virus, they looked at the spike protein, and they found eight mutations in that spike protein. And a number of these have been kind of concerning because two of them look similar to mutations that have allowed other variants of concern to become more transmissible and a third resembles a mutation that was found in another variant called P1, which, you know, caused outbreak in Brazil early this year. And they found that that third mutation resembles one that may have allowed the P1 variants, sort of, partially evade immunity and lead to that outbreak among people who'd already been infected with the virus in Brazil. So the genomic work is really important to show us some of these different mutations. But then to kind of actually see whether these mutations are allowing the virus to be able to enter cells more efficiently or have other effects, we have to actually test it. There's some experiments in hamsters that seem to show it causes some more damage and inflammation in the lungs.

07:20 Subhra Priyadarshini: Okay, so the studies are still very preliminary, as John says. going forward, what will help prevent the emergence of more new variants? And more importantly, new surges? Everyone, of course, rightly so is asking the question, when is the third wave of coronavirus infections expected in India.

07:43 Anurag Agrawal: The primary mechanism of preventing new variants is preventing infection. This can be done in only two ways. One is normal public health measures of containment and the second is vaccination. At the end of the day, I see these two as the two main pillars on which any strategy to contain variants would be built.

08:05 Subhra Priyadarshini: Okay, so there's concern among general people as well as public health managers about whether the current crop of vaccines will be effective against all these emerging variants or not. What do we know so far? So John Pickrell actually did explain this a bit in Coronapod earlier.

08:23 John Pickrell: So there have been very preliminary studies, which actually tested the two vaccines that are currently being used in India. So one of those is the Covaxin vaccine, made by Indian firm Bharat Biotech, and the other one is the locally produced version of the Oxford AstraZeneca vaccine, which is called Covishield. And certainly, at the moment, it appears that those vaccines are still effective against the very, very small studies with small sample sizes. So really, they're just the beginning of trying to work out what's going on with this variant.

08:59 Subhra Priyadarshini: We went back to Anurag Agrawal and Chitra Pattabiraman to tell us a little more.

09:04 Anurag Agrawal What we can see is the rest for Public Health England is single dose of AstraZeneca vaccine, what we call COVID Shield, give around 33% protection, while two doses gave around 60% protection, so it is not very bad. If you were to see how bad these things can be. You can look at the South African variant p dot 1.351. Now called Peter, in which the study showed that the AstraZeneca vaccine had gone down to 10 to 20% effectiveness. So the variants currently circulating in India have some loss of immunity, but not a tremendous one. And most importantly, whether in Public Health England or in hospitals, they are very few reports of people developing severe disease or death after being double vaccinated.

09:54 Chitra Pattabiraman: So while we can expect that in the future, this will be a challenge and vaccines may need to be revised, and companies are already planning their changes and the booster doses and so on. At the same time, it looks like the current vaccines do protect.

10:09 Subhra Priyadarshini: Okay, good to know. So we are there to the public health measures that we are already following, basically masking and physical distancing, and getting vaccinated as soon as possible. But there's another crucial intervention, and that is finding the variants early. That's why sequencing or genomic surveillance is key, right?

10:30 Anurag Agrawal: If you have large number of infections, but you never sequence anything, you will never find a variant, we must continue our efforts to find them. By sequencing continuously.

10:39 Chitra Pattabiraman: I can tell you that genomic surveillance across the world has been incredibly fruitful in tracking variants. So for example, the variant in the UK was tracked, because you get a lot of sequencing. So they were able to catch this, sort of, new variant quite early, we were able to inform the world quite reasonably fast.

11:03 Anurag Agrawal: I think the current average time around the world has been three months of finding a variant of concern. I'm very certain we can tick at least three to four weeks off that number.

11:13 Subhra Priyadarshini: Now, that's some progress. Of course, we need more to track emerging variants rapidly. For instance, COVID tests could help diagnose which variants people have, not just whether they're infected with SARS-CoV-2 or not. Development of these technologies is underway. As scientists keep doing their part, let's make sure we do ours. Stay masked, stay physically distanced, and if we can, please let's get vaccinated?

We'll be back soon with another insightful episode around science in India. Until then, you can tune in to Nature's podcast Coronapod for more. And of course, come back to Nature India podcast for new episodes in Hindi and in English. I'm Subhra Priyadarshini and this is the Nature India podcast.

12:18 Partner announcement: Thanks to the DBT Wellcome Trust India Alliance for their support in producing this episode.

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