So far, scientists across the world have identified over 200 genetic mutations in the SARS-CoV-2 that causes COVID-19. What does it tell us? Short answer: by itself, nothing much. Viruses mutate naturally, and mutations do not translate into a more dangerous or virulent form of the existing virus. There can, however, be advantages of identifying the mutations within the genome, a primary example being the development of vaccines. Mutations, which are essentially small genetic changes, are not evenly distributed across the virus genome—those invariant parts of the virus could be better targets for drug and vaccine development.
In the past week, there have been big developments in the scientific front in the topic of coronavirus evolution. One study, published in the journal Infection, Genetics and Evolution characterised patterns of diversity of the genome of the virus and highlighted how it has been adapting and evolving to its human hosts. Researchers from University College London (UCL) in the UK found that the largest proportion of the global genetic diversity of SARS-CoV-2 was found in the hardest-hit countries, suggesting extensive global transmission from early on in the epidemic and the absence of single 'patient zeroes' in most countries.
The findings further establish that the virus only emerged recently in late 2019, before quickly spreading across the globe. In that study, scientists identified 198 mutations that appear to have independently occurred more than once, which may hold clues to how the virus is adapting.
One strain a cause of worry
Preliminary research from Los Alamos National Laboratory in US's New Mexico, focussing on genetic changes or mutations in the "Spike" protein that gives the virus its distinctive "crown-like" shape, has identified 14 mutations in the Spike. The research was done using a database called the Global Initiative on Sharing All Influenza Data (GISAID). According to the researchers, one particular mutation—identified as D614G—is of "urgent concern". "It began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form," according to the study, which has not yet been peer-reviewed.
The Times of India reported that an analysis of 82 strains of the virus in India by India-born Prof S.S. Vasan and his colleagues from the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia showed that nearly 50 per cent of them have the new mutation, while globally, nearly two-thirds of all strains have displayed this mutation.
The researchers have proposed increased transmissibility of the virus due to the mutation. "D614G is increasing in frequency at an alarming rate, indicating a fitness advantage relative to the original Wuhan strain that enables more rapid spread," according to the study. This essentially means that viruses bearing the mutation D614G are replacing the original Wuhan form of the virus rapidly and repeatedly across the globe. "Based on currently available information, there are several ways the D614G mutation may impact Spike’s infectivity: it may improve receptor binding, fusion activation, or ADE antibody elicitation."
Will it affect vaccine development?
Experts have suggested it will not. Mutations, to an extent, will not affect vaccine development. Take seasonal influenza. Because of mutations, vaccines have to be tweaked every year to target it against the then dominant strain. Also, as mentioned before, scientists could target the unmutating or invariant parts of the virus for better vaccine development.
In the case of India, Head of Epidemiology and Communicable Diseases at ICMR, Dr Raman R. Gangakhedkar had earlier said, "It will take some time for us to know the predominant quasi-species of the novel coronavirus in the country. But mutations are not likely to make potential vaccines ineffective, as all sub-types of the virus have the same enzymes. Also, it has been in India for three months, and it does not mutate very fast."
A theory debunked?
A study by scientists at Britain's Glasgow University, analysing mutations in the SARS-CoV-2 genomes, claimed that the mutations found did not signal that there were completely different strains of the virus. This was in direct pushback against a previous Chinese study, which claimed there were two separate strains of the virus, one more infectious and virulent than the other.
The study, 'On the origin and continuing evolution of SARS-CoV-2', published in National Science Review, had hypothesised that there were two strains of the virus—'L' and 'S'. According to the study, the aggressive L type of coronavirus was found more in the early stages of Wuhan outbreak, but its frequency decreased due to human intervention. "Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure," according to the study.
According to the Glasgow study: "A recent study by Tang et al. (2020) claimed that two major types of SARS-CoV-2 had evolved in the ongoing COVID-19 pandemic and that one of these types was more “aggressive” than the other. Using examples from other viral outbreaks, we discuss the difficulty in demonstrating the existence or nature of a functional effect of a viral mutation, and we advise against overinterpretation of genomic data during the pandemic."
What does this mean for India?
The Indian Council of Medical Research (ICMR) is planning to study whether the novel coronavirus strain in India has undergone mutation while spreading within the country over the last two months. As per the Global Initiative on Sharing All Influenza Data (GISAID), so far, the maximum difference in the novel coronavirus strain in India has been found to be between 0.2 to 0.9 per cent, as compared to the strains in other countries. Official statements had claimed there are three strains of the virus traced in India so far. One was from Wuhan, and the other two from Italy and Iran. The sequence of the coronavirus strain from Iran was similar to that of China.
Experts in Gujarat had hypothesised that this more aggressive Wuhan L strain was one reason behind the higher COVID-19 mortality rates in Gujarat. "Analysis done by scientists abroad has shown that the L-type strain has been dominant where more mortality is reported among coronavirus patients. This strain was found to be more prevalent in Wuhan," director of state-run Gujarat Biotechnology Research Centre (GBRC) C.G. Joshi said.