Coronavirus | Different kinds of SARS-CoV-2 exist in India but none more lethal than the other: Indian Academy of Sciences President

Dr. Partha Majumder, in an interview with The Hindu’s Jacob Koshy, explains mutations in the novel coronavirus

Dr. Partha Majumder.

Dr. Partha Majumder , President, Indian Academy of Sciences, and scientist at the National Institute of Biomedical Genomics, explains mutations in the novel coronavirus in an interview with The Hindu’s Jacob Koshy .

Could you bring us up to speed on how many different strains or types of SARS-CoV-2 exist? Your own work in April had reported that one of them, called A2a, had become dominant globally.

First, these should not be called as ‘strains,’ but as lineages or clades or subtypes. Earlier, there was the ancestral type — the Wuhan virus type, from which 10 lineages had evolved. By reconsidering the mode and tempo of evolution of the virus and also to time-stamp a lineage, the earlier lineage definitions have been revised. Today, a lineage is given a name if its frequency reaches 20% globally. Further, an evolved lineage is given a separate identity if it differs from the existing lineages by at least two DNA changes (mutations). Based on the revised time-stamped nomenclature, there are now five lineages: 19A, 19B, 20A, 20B and 20C. The first two digits reflect the year in which the lineage evolved. Lineage 19 is an ancestral lineage that was present in China in 2019; subsequently, in 2020, three other lineages arose. A defining mutation of the former A2a lineage was D614G; meaning that at the 614th position in the viral sequence there was an amino acid substitution from aspartic acid in the pre-existing lineage to glycine in the evolved A2a lineage. In the new nomenclature, A2a is non-existent. The lineages 20A, 20B and 20C all have the D614G mutation. The D614G lineages have actually become dominant across India. But, interestingly, in the northern and eastern regions of India, the 20A lineage is dominant, while in southern and western India the 20B lineage is dominant. Even though both 20A and 20B contain the D614G mutation, there are other mutations that separate these two lineages. These mutations have been identified, but their impacts on the functional characteristics of the virus are not known yet.

You have in a paper described the D614G mutation and how it has a modification that allows it to take better hold in Europeans and North Americans but not as much in East Asians. However, there was a report from Malaysia recently that the D614G imported from an Indian had taken root in that country. So how worried should we be about D614G? Are there other prominent mutations inviting scientific attention?

The D614G mutant viruses are super-rapid spreaders. They transmit very efficiently. Our observation that the D614G mutant viruses have outcompeted and replaced all other lineages in Europe and North America with extreme rapidity, but have not done so in East Asia still holds true. This does not mean that the D614G mutant does not exist in East Asia. It did and still does, together with some other lineages. There is no cause of worry. The SARS-CoV-2 is a kind virus. It infects but does not usually kill. A vaccine must be efficacious to protect vaccine recipients against the entire diversity of the virus. Otherwise, it will afford limited protection.

Is there evidence that certain types are demonstrably more likely to kill?

Interestingly, even though scientists have looked, they have not been able to find credible evidence that different lineages are associated with different rates of mortality. As far as we can tell, all of the lineages are roughly similar in terms of their ability to cause death upon infecting a host.

Can chains of virus transmission really be broken or is it inevitable that countries of a certain size will see at least half of their populations infected? Also, is there anything in the structure of the virus that makes it seem impervious to the effects of temperature and humidity, or is it too early to take a call on that?

Without herd immunity to a certain level, I don’t see how one can contain the transmission of the coronavirus in a large, democratic country like India. I have not seen any credible data to show that temperature, humidity and other such environmental factors may have an impact on transmissibility of the virus.

Recently, Russia has announced the completion of phase-1 and phase-2 trials of a potential vaccine on a human adenovirus platform. The Oxford vaccine candidate (ChAdOx1) is based on a chimpanzee adenovirus vector. Do you think adenovirus platforms are a dependable bet for a virus of such novelty and infectiousness as SARS-CoV-2?

Honestly, I do not know much about vaccine vectors and therefore cannot give you any confident view on this question. Adenovirus-based vectors are excellent for delivering gene or antigens as vaccines. These vectors offer several advantages over other viral vectors because they can be manipulated easily, and accept large insertions in their genomes, and have the ability to induce specific antibody responses. They are also amenable to large-scale production. They are also known to produce inflammatory responses, which is a disadvantage.

Interactive map of confirmed coronavirus cases in India

We have had several viral outbreaks and epidemics before. Some like the Ebola virus and MERS (Middle Eastern Respiratory Syndrome) virus have far higher mortality rates. Some like H1N1 (that causes swine flu) did appear more infectious. However this is also a unique situation in that a virus was sequenced so rapidly, aiding the rapid development of rapid RT-PCR-based (Real Time Rapid Polymerase Chain Reaction) diagnostic kits and giving a large number of nations the ability to detect the virus. But science doesn't seem to have evolved commensurately quickly to develop new remedies or approaches to vaccine development. Does this mismatch contribute to the state of global panic that COVID-19 has triggered?

We have never faced a pandemic after 1918, when the Spanish flu was declared to be a pandemic. The Ebola and MERS were outbreaks of infections. Those viruses were far more efficient killers. Yes, we have been able to deploy RNA sequencing far more rapidly in the context of SARS-CoV-2, thanks to the development and spread of high-throughput sequencing technologies. However, the ability of scientists to develop treatment or vaccines do not always depend on availability of technologies, even if technologies can and do provide considerable amount of relevant data. There are many factors involved in the development of treatment or vaccines. Too many variable factors and uncertainties that preclude rapid development. I do agree that the lack of availability of treatment or vaccine has hugely contributed to the fear of infection and the resultant panic.

State-wise tracker for coronavirus cases, deaths and testing rates

There is research underway trying to answer why mortality rates in India are relatively low in spite of the high number of infections (even adjusting for under-reporting and our relatively more youthful demographic)? Can exposure to other endemic coronaviruses and influenza strains imply a more vigilant and responsive immunity?

I am not aware that the mortality rate in India is lower compared to other large geographical regions. I am not aware of any epidemiological study with a large sample size that has provided this evidence. The mortality rate is about 2% of all infected individuals in India, as in most other large geographical regions. Yes, prior exposure to other coronaviruses and related viruses can have an impact on lowering infection rates, but I am not sure about the impact of prior exposure on mortality.

As president of the Indian Academy of Sciences, what are your views on how effectively the Indian Council of Medical Research (ICMR) has managed to communicate, since March, the evolution of the pandemic in India and the extent of risk posed?

I believe that ICMR has done its best and has done well. The only time that the Academy got worried was when ICMR announced that India will make a vaccine within our Independence Day. The Academy protested.