Why Covid variants seem to appear in Maharashtra first

Delta Plus variant, flagged as a 'variant of concern', seemingly first appeared in Maharashtra, where 21 cases have been detected so far. Its ancestor — the B.1.617 — also appeared first in the state in February.

A BMC health worker collects swab sample for Covid testing| PTI

Bengaluru/Mumbai: The central government Tuesday said the Delta Plus Covid variant is to be treated as a “variant of concern”, with new cases being detected in the country. The variant, also known as the AY.1 or B.1.617.2.1 is believed to be immune evasive and could be linked to resistance to monoclonal antibody therapies that are thought to hold promise for Covid treatment.

The variant (Delta Plus) seemingly first appeared in Maharashtra, where 21 such cases have been detected so far. It is believed that its ancestor — the B.1.617 — also appeared in Maharashtra, in February this year, and the Kappa, Delta, and Delta Plus variants all stemmed from it.

The B.1.617 is associated with immune evasive properties and is widely credited to have spread rapidly, leading to the second wave of infections in the country.

So, what gives rise to concerning variants and why are so many first detected in Maharashtra?

Evolution of variants

Tracking down the patients in whom variants evolved is difficult due to low rates of sampling. Even in places with very high rates of sampling and sequencing, such as the UK, tracking the index patient is difficult and the first sample that tested positive for the variant was likely of someone not even close to that person.

However, with data from places that sequence highly, experts are convinced that the most likely place variants with concerning immune escape mutations evolve in is within immunocompromised patients.

In such people, the illness does not resolve itself as it usually does in 10 days for others, since immune systems do not function optimally. So, the virus persists and mutates more, with a higher probability of evolving worrying mutations.

This has been observed in other viral infections as well, where viruses have recorded to have survived in, and then infected, immunodeficient individuals after many years.

There are a handful of instances which have led experts to pinpoint immunocompromised individuals as the most favourable hosts for concerning variants to develop.

One such was reported by Dr Ravindra Gupta, a virologist at the University of Cambridge, who studied a cancer patient who had been Covid positive for over a month. The results compiled by his team offered some of the earliest observations that confirmed the theory that immunocompromised people, such as cancer patients, may develop chronic infections that lead to variants.

What constitutes being immunocompromised is up for some debate, with some experts also sounding caution over autoimmune conditions, like rheumatoid arthritis.

The likelihood of newer variants rises with more infections. This is further evidenced by the fact that all the concerning variants come from the same lineage of the virus that is circulating in Maharashtra and the surrounding regions.

Dr Subhash Salunke, technical advisor to the Maharashtra government on Covid control, said the government machinery has been keenly watching for any troublesome mutations of the virus ever since the B.1.617 was found in Amravati in February.

Since then, Maharashtra has been sending about a hundred samples from each of its 36 districts for genome sequencing. It has sent 7,500 such samples until now, multiple state government officials said.

Salunke, who was one of the first healthcare experts to flag the possibility of the Delta variant back in February, told ThePrint, “We are testing samples in sufficient numbers, though there is always scope to do better. But, the main reason for Maharashtra always accounting for a high number of Covid cases and the prevalence of its variants is because of its social and geographic conditions. The population density is high in certain areas.”

He added: “This is not just limited to Covid. It can be seen in the way other viruses behave too in places such as Maharashtra, Kerala and Delhi”.

Variant of concern?

So far, there is no data to indicate that the Delta Plus variant is any more transmissible or deadly than the earlier Delta variant.

Of the 21 cases of Delta Plus variant found in Maharashtra so far, many were asymptomatic and those who had not received the Covid vaccine. Two districts — Ratnagiri and Jalgaon — account for 16 of the 21 cases reported.

Abhijit Raut, District Collector, Jalgaon, told ThePrint that the seven cases of the Delta Plus variant from Jalgaon all date back to May.

“They were all from a single village. They were all asymptomatic, and as of now they are all fit and fine. The age profile of the seven persons ranged from 24 to 62 years and none of them had any serious comorbidities,” he said.

The district administration conducted a mass screening camp in the village after it got the results confirming the presence of a new variant in the second week of June. Two persons tested positive in the camp.

“We have sent their samples again. We compared the average weekly positivity rate of the district to that of the village and the latter was marginally lower. We also studied if the rate of spread or the mortality rate was higher, but that too was not the case,” he added.

The Ratnagiri administration is studying the case profiles of the nine samples that tested positive for the Delta Plus variant. Meanwhile, it has started rigorous contact-tracing and screening of residents for Covid in the villages where these cases have been found, a district official said.

Origins in Maharashtra?

The high number of cases from sequences in Maharashtra do not confirm the origin of these variants in Maharashtra. Instead, they indicate a form of sampling bias, and the number of variants detected is expected to reflect proportionally with testing across the country. In fact, the Delta Plus variant (AY.1) has also been detected in multiple countries.

Maharashtra has one of the highest sequencing rates in the country, along with Kerala, and now more so thanks to its tie-up with CSIR for active genomic surveillance. The variants were detected as a part of routine surveillance, and increased surveillance is likely to flag newer variants across the country and the world.

While such active surveillance is crucial to catch a potentially concerning variant in time, experts say that so far there is no need to mark it a variant of concern.

Dr Shashank Joshi, a member of the state task force on Covid control, said in a tweet that there isn’t enough data to be alarmed.

Salunke, a public health expert, added that there needs to be more research to study its rate of transmission, virulence and whether the available vaccines are effective against it.

However, there is no data to indicate at the moment that vaccines do not work against the variant. Raut stated that all of the early cases that were detected in Jalgaon in May were in individuals who had not received either dose of the vaccine.

(Edited by Poulomi Banerjee)