India detects new 'double mutant' variant as COVID-19 cases spike, raising fears of a second wave

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India has discovered a new "double mutant" variant of COVID-19, as the country struggles to contain a spike in cases that's raising fears of a second wave. (FILE PHOTO)

(CNN) — India has discovered a new "double mutant" variant of COVID-19, as the country struggles to contain a spike in cases that's raising fears of a second wave.

"VOCs (variants of concern) and a new double mutant variant have been found in India," the country's Ministry of Health said in a news release on Wednesday, adding that "genomic sequencing and epidemiological studies are continuing to further analyze the situation."

A "double mutant" variant is a virus strain that carries two mutations. It's not yet clear how many infections have been linked to this double mutant variant, or whether the strain is any more dangerous, but the ministry said "such mutations confer immune escape and increased infectivity."

According to the ministry, the number of known cases linked to the double mutation was not high enough to explain the current nationwide surge in infections,

India recorded 53,476 new COVID-19 cases on Thursday — the highest single-day rise in five months. The last time the daily count was this high was October 23, according to a CNN tally of figures from the Ministry of Health.

The country's first wave of infections started climbing last summer and peaked in September, with numbers slowly declining since then. By February this year, the number of daily cases had fallen by nearly 90%, to about 10,000 a day.

But by the start of March, it became clear that cases were slowly on the increase again — and they have exploded in the past few weeks.

India has now reported a total of more than 11.7 million cases and 160,000 related deaths, according to Johns Hopkins University data.

"I would say that it is the beginning of a second wave," Randeep Guleria, director at the All India Institute of Medical Sciences, said Wednesday. "It is something that has already been seen in many European countries; we seem to be following them."

There are a number of factors — one being Covid fatigue, and the possibility people are being less cautious due to the winter decline in infections. "You see that in the community, when you go out, wearing a mask has become less and less," Guleria said. "We see crowds developing, partying, a lot of marriage ceremonies are happening in India."

Another factor could be the rise of "variants which will come to India from other parts of the world," he said, pointing to the strain first detected in the UK, which has since spread in numerous Indian states...

Variants and mutations

All viruses evolve over time, and sometimes make changes when they replicate, causing mutations. Some mutations have little effect — but others could make the variant more easily transmissible, or cause infections with more severe symptoms.

From around 10,787 samples analyzed by the Indian SARS-CoV-2 Consortium on Genomics from 18 states, 771 cases of variants of concern were detected, the majority of which were the UK strain, according to the Ministry of Health. Thirty-four were the variant first identified in South Africa and one was variant P.1 from Brazil.

Although the ministry said these are not correlated to the recent spike in cases, the variants have mostly been detected in states of "grave concern" that are seeing the highest numbers, including Punjab and Maharashtra. And now double mutations have been reported.

So far this year in Maharashtra, "there has been an increase in the fraction of samples with the E484Q and L452R mutations," the ministry said in its news release. They were found in 15-20% of samples and do not match any previously cataloged variants of concern, the ministry said, adding "such mutations confer immune escape and increased infectivity."

It's not unusual to see multiple mutations in one variant. "All of these viruses (variants) which we are dealing with are already mutants," said virologist T Jacob John. The strain that became globally prevalent was already different from the first strain that originated in Wuhan, China he added.

The strain first found in the UK, formally called the B.1.1.7 variant, has 23 mutations compared to the original strain found in Wuhan, according to the American Society of Microbiology.

The Brazil variant known as P.1 has 17 mutations, and the South Africa variant known as B.1.351 also has multiple mutations, according to the US Centers for Disease Control and Prevention (CDC).

How dangerous a mutation is depends on where in the virus it's happening. For instance, the South Africa variant has mutations that change the structure of the spike protein, which appear to affect the receptor binding domain — the part of the spike protein most important for attaching to and infecting cells. Researchers are now investigating whether it could help the virus partly escape the effects of vaccines.

Guleria cautioned that a double mutation was not necessarily cause for alarm, since researchers are still investigating the effect of the mutations.

"They are not clear as to what is the significance of this," he said. "Does it have clinical significance or is it just an observation? And that has to be linked to epidemiological data, which is what is being done."

One question is which variants — and which mutations — might be able to evade the effects of our existing vaccines.

"If somebody was infected with coronavirus six months ago, that person is immune to the non-mutated coronavirus," John said. "But is the person still immune against the variants? (That has to be) studied."

India's vaccination drive

In the meantime, Indian authorities are working to control the spike by implementing new restrictions and stepping up the country's vaccine program.

India is administering two vaccines domestically. One is Covishield, a vaccine developed by Oxford University and AstraZeneca and produced by the Serum Institute of India, the world's largest vaccine maker. The other is India's first homegrown coronavirus vaccine, Covaxin, developed jointly by Bharat Biotech and the government-run Indian Council of Medical Research.

So far, India has administered more than 50 million doses of vaccines, with more than 8.1 million people fully vaccinated, according to Johns Hopkins University.

The Serum Institute of India not only produces most of the vaccines for India — it is also responsible for many of the vaccines distributed to the rest of the world. In September last year, SII pledged to manufacture and deliver 200 million doses for COVAX — a WHO vaccine alliance set up to ensure fair access to COVID-19 vaccines.

But SII has had to halt or delay its exports several times in recent months as global and domestic demand surged.

On January 4, India restricted the export of the AstraZeneca vaccine produced by SII until at least March. "We were given a restricted license only to give it and provide it to the government of India because they want to prioritize for the most vulnerable and needy segments first," SII CEO Adar Poonawalla said at the time. "The only condition is that we can only supply to the government of India, we can't sell it in the private market, and we can't export it."

On Thursday, Reuters reported that India would likely delay deliveries of AstraZeneca vaccines to COVAX, citing UNICEF. India had put a temporary hold on all major exports of AstraZeneca shots made by SII to meet domestic demand, according to Reuters.

CNN has reached out to SII, UNICEF and the Ministry of External Affairs for comment, but has not yet received a response.

The Ministry of Home Affairs also introduced new infection control guidelines on Tuesday, which will be in place until the end of April. Some of the measures include quickly isolating positive cases and tracing their contacts within 72 hours.

Several cities and states including Mumbai, Delhi and Odisha have banned gatherings during Holi, the upcoming festival of colors, on March 28.

This story was first published on "India detects new 'double mutant' variant as Covid-19 cases spike, raising fears of a second wave"