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Explained: Which are the Covid-19 variants in India, and do they explain the surge?

Over 320 coronavirus samples have been found to have the UK lineage in Punjab. Does this explain the recent surge? And how widespread are the South Africa and Brazil variants, besides others in India?

Written by Amitabh Sinha | Pune |
Updated: March 30, 2021 8:34:52 am
Coronavirus, Covid India update, Coronavirus news, India Coronavirus, India Covid strains, India Covid variants, India variant Covid, Indian ExpressAt a mall in Pune (Express Photo: Ashish Kale, File)

More than 320 coronavirus samples from Punjab have been found to have the “UK lineage”, a reference to a new strain of the virus that had emerged in the UK in December, with genetic mutations that have enabled it to spread faster. This is the most widespread occurrence of the UK variant in the Indian population found till date, and could possibly explain the rapid surge in cases in Punjab in the last few weeks.

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A government statement on Wednesday said 736 samples from across the country had so far been found to have UK lineage. Apart from these, 34 samples were found to have the “South African lineage”, and one had the “Brazilian lineage”. The South African and Brazilian variants are two other dominant strains of coronavirus circulating around the world. The genetic mutations in these two variants make them more likely to escape the human immune system. The apprehension, therefore, is that current vaccines might be comparatively less effective against them, although this is still being investigated.

Variants in India

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The UK, Brazilian and South African variants are not the only ones currently circulating in the Indian population. Like any other organism, the coronavirus is also constantly mutating, with some changes in its genetic structure happening in every replication cycle. Most of these mutations are inconsequential, and do not alter the overall nature or behaviour of the coronavirus. But a few of them, possibly one in thousands, can introduce important changes, helping the virus to adapt or survive better.

During this epidemic, three kinds of changes are being keenly watched — those that increase the ability of the virus to spread faster, those that cause more severe disease in the infected person, and those that help the virus escape the immune response.

The UK, Brazilian and South African variants are such strains. Each of them now has its own families, meaning there have been many subsequent mutations in these but with the original defining mutation remaining intact. These three variant families, or lineages, have been found in multiple countries, and are mainly responsible for the surge in cases in Europe and Brazil.

Besides these, several other variants are circulating in the Indian population, those that have originated locally as well as others that have been brought by travellers from abroad. But none of these has been classified as a “variant of concern”.

Covid-19 variants detected in India

UK Covid-19 variant & concerns

Scientists have maintained that none of the three ‘variants of concern’ — UK, Brazilian or South African — can be linked to the present rise in cases in India. Their level of prevalence in the community, as of now, is not so high that the current surge could be attributed to them.

Even in Punjab, where 80% of 400 samples analysed turned out to be the UK variant, it is too early to blame it for the extraordinary rise in cases in the last few weeks. The results of genome sequencing have been revealed now, and a clinical correlation needs to be done to assess whether they are responsible for the rise in cases.

As scientists have pointed out, if the people infected with the UK strain in Punjab are all travellers, or their direct contacts, then their occurrences could be easily explained, and are not too much of a worry. However, if it has been found in people in the wider community as well, then there is the danger of it spreading to others very quickly. It would also mean that the isolation and quarantine procedures being followed in the state, especially for travellers, have not been very followed strictly.

A few specific mutations found in the UK strain, like one named E484Q and another called N440K, have been seen in some other variants as well, and these have been circulating in the Indian population for several months. At present, there is no evidence to suggest that either of these could have led to the second surge, or caused re-infection in patients.

However, much more detailed scientific investigations are required to assess their impact on the spread of the disease in India.

Genome sequencing…

India has the second highest number of people infected with the coronavirus during the epidemic. But it has done very few genome sequences of the different variants in circulation. So far, it has carried out gene analysis of 19,092 samples from across the country, according to a statement made by the government in Parliament last week. This includes the sequencing of 10,787 samples since the government set up INSACOG (Indian SARS-CoV2 Consortium on Genomics) in December specifically for this purpose. Many other countries, including the United States and China, have analysed more than 100,000 gene sequences.

Studying genetic changes in the organism is important clues to understand the origin, transmission and impact of the virus on patients. The stated objective of INSACOG is to sequence the samples from at least 5% of all the infected cases through a network of ten laboratories. That looks like a very tall order right now. India has so far recorded over 1.17 crore positive cases. The 19,092 samples that have sequenced till now form just 0.16% of that number.

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… and why it’s been slow

One of the major reasons for the slow pace of genome sequencing has been a lack of funds. So far, no money has been allocated for INSACOG, although officials said approval for funds was now expected any day. The laboratories have been using money from their own annual budgets to do the sequencing work. It takes between Rs 3,000 and Rs 5,000 to extract the gene sequence of one sample. The cost is mainly of the chemical reagents that are required in the process.

Also, states have not been proactively sending their samples to the laboratories for sequencing. Maharashtra, which has recorded more than 25 lakh infections till now, has sent only about 2,800 samples for sequencing, according to government data presented in Parliament. That’s just about 0.11% of all the cases. Kerala has sent the highest number of samples for sequencing, about 5,200, but Karnataka, which has a comparable number of cases, has sent only 137 samples. Such a low rate of genome sequencing might not be statistically significant to draw conclusions about the changing nature and behaviour of the virus, or in designing appropriate interventions to contain the spread of the epidemic.

This article first appeared in the print edition on March 25, 2021 under the title ‘Cracking the virus strain’.

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