India records spike in Covid-19 cases as several variants detected, prompting fears of a second wave

India on Thursday recorded 53,476 new Covid-19 cases, marking the highest single-day rise in cases since October 23, according to a CNN tally of figures from the Indian Ministry of Health.

The country has been reporting more than 35,000 new cases daily for over a week in a recent surge in cases after they fell in January and February this year.

Randeep Guleria, director at the All India Institute of Medical Sciences, told CNN on Wednesday that “it is the beginning of a second wave.”

The rise in cases comes as the country’s top researchers announced that there are nearly 800 variants of concern present in the country.

The Indian SARS-CoV-2 Consortium on Genomics – which has been carrying out genome sequencing and analysis of coronavirus strains since December – says 771 cases of variants of concern have been detected in India. Most of the cases are the coronavirus variant first identified in the UK, according to a statement from the Indian Ministry of Health on Wednesday.

While the Health Ministry has not correlated these to the recent rise in cases, these variants have been primarily detected in states such as Punjab and Maharashtra, two states that the health ministry has called states of “grave concern,” given that they are contributing to most of the nation’s case load.

Guleria said the emergence of the more infectious UK variant in some states may be one of the factors contributing to the recent surge in case numbers.

The Health Ministry has said “such mutations confer immune escape and increased infectivity,” while adding that further analysis is being conducted.

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

A health worker checks the body temperature of arriving passengers as they are mandated to undergo Covid-19 coronavirus screening at a railway terminus in Mumbai on January 6, 2021. (Photo by INDRANIL MUKHERJEE / AFP) (Photo by INDRANIL MUKHERJEE/AFP via Getty Images)

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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.

Guleria said the second wave “is something that has already been seen in many European countries; we seem to be following them.”

A number of factors are contributing to that rise, Guleria explained.

“One of the factors is that today it’s been one year since India had the lockdown and there are people who seem to have gone into Covid fatigue,” he said, adding that “you see that in the community, when you go out, wearing a mask has become less and less.

“We see crowds developing, partying, a lot of marriage ceremonies are happening in India,” he added.

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.

The Ministry of Health and Family Welfare also said it has found a variant with mutations that don’t match previously identified variants of concern.

Critical Care staff carry out a tracheostomy procedure on a Covid-19 patient on the Christine Brown ward at King's College Hospital in London on January 27, 2021.

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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, 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 new variant 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.

A Health official takes part in dry run or a mock drill for Covid-19 coronavirus vaccine at a Urban Community Health Centre in Ajmer, Rajasthan, India on 02 January 2021. (Photo by Himanshu Sharma/NurPhoto via Getty Images)

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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.”

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 Tuesday that 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.

CNN’s Kara Fox contributed to this report.