Scientists are looking for signs that another variant could emerge in Delta’s wake, but limited sampling capabilities are hindering the search.
In the state of Maharashtra, one of the first places struck by India’s devastating second wave of Covid-19 earlier this year, scientists are anxiously looking for signs of a third.
New laboratories in the financial capital, Mumbai, and in the city of Pune are searching for dangerous new variants. They have stepped up testing, to over 3,600 samples per month from 134 in December last year, as they search for mutations that could make the virus even harder to stop.
India is still far short of its goal to increase genome sequencing nationwide. While Covid-19 cases and deaths have plunged, according to official numbers, the virus is continuing to spread in some parts of the country. A low vaccination rate and other factors have left India especially vulnerable to variants like Delta, the strain that helped power India’s second wave this past spring.
“We need to track new variants to prepare ourselves for the next wave because waves will keep happening, much like the flu or common cold, which keep recurring because the virus mutates or recombines,” said Dr. Vinod Scaria, the principal scientist at the Institute of Genomics and Integrative Biology in New Delhi. “You can’t really prevent that. But you can always be prepared for it.”
The second wave, which exploded across the country in April and May, exposed both the Delta variant’s increased communicability and India’s inability to cope. Official figures show that about 430,000 people have died since the virus hit early last year, though the numbers are widely considered unreliable and experts say the true toll may be in the millions. The second wave pushed the country’s medical system past its limits and led to anger over the government’s inability to handle the crisis.
For now, the disaster appears to have ebbed. India’s daily official caseload has fallen to about 40,000, compared with the more than 300,000 it saw during the worst of the crisis. The hardest-hit urban centers like New Delhi, Mumbai and Pune have had a dramatic decline in cases. Covid-19 wards in many major cities have emptied.
Some hope that the sheer contagiousness of the Delta variant means that many people have already caught it and developed a measure of protection. A recent survey by the Indian Council of Medical Research, a government agency that funds and evaluates studies, found that two-thirds of blood samples surveyed had coronavirus antibodies, compared with about one-quarter in December and January. In some states, as many as three-quarters of samples surveyed carried antibodies.
But scientists cautioned that the survey, with a small sample size of 36,000, shouldn’t be read as an indication that India is out of the woods. Such tests can be prone to false positives. Also, the survey doesn’t represent all areas, said Giridhara Babu, professor of epidemiology at the government-affiliated Public Health Foundation of India, though it could help Indian officials better target areas for testing and vaccinations.
Even if the numbers are accurate, they suggest that 400 million people in India remain vulnerable to Covid-19.
“What is going to happen now is that areas with low sero prevalence and low vaccination will have more number of cases and more people getting hospitalized and higher deaths,” Dr. Babu said, referring to serology, or antibody, testing.
The potential for new variants complicates the picture even further. Places like India with low vaccination rates and other risk factors are particularly vulnerable to new strains.
After a chaotic and slow start, India has intensified its inoculation drive, regularly delivering five million doses per day. About half a billion doses have been administered so far, and more than 100 million citizens are now fully vaccinated. Indian medical experts hope the increased vaccinations will help blunt the impact of a third wave because even one shot can reduce the severity of infection.
Still, only 8.5 percent of the population is fully vaccinated. It remains to be seen whether the country can reach its goal of vaccinating all the adult population of roughly 900 million by the end of the year.
Low testing rates are another factor. India now administers an average of about 1.2 tests per thousand people per day, according to the Our World in Data project at Oxford University, well above levels at the beginning of the year. But its rate is still well below those of richer countries, coming in at a bit more than half of the level of the United States, for example.
Those low test rates make charting the course of the virus difficult. Currently, a large number of positive tests are coming from southern states like Kerala, which in general conduct more tests than in other parts of the country. That state accounts for nearly half of the total active cases. Infections in areas with lower testing rates would be hard to detect.
Researchers are particularly watching Kerala, which was hit later by the second wave than other parts of the country. A better-prepared health infrastructure helped reduce fatalities. But the circulation of the virus has been so steady that it gives opportunity for mutation.
“It is cause for satisfaction, in a way, that the mortality is not high,” said Dr. V.K. Paul, who leads the Indian government’s Covid-19 task force. “But when there is so much of virus replication, there are problems — variants can emerge, other areas can get infected, and vulnerable population in any part of the country remains susceptible.”
Kerala increased its genome sampling early, testing about 1,400 per month since December. Proactive genome sequencing has helped Kerala and Maharashtra in recent months to identify districts where a variant known as Delta Plus has emerged and immediately respond to contain the spread.
But broadly, India’s sampling effort is lagging. Under an initiative organized by the Indian SARS-CoV-2 Genomics Consortium, or Insacog, a group of national laboratories, each state was initially supposed to test 3 percent to 5 percent of samples. Currently, the country is sampling only about 0.1 percent of Covid-19 tests.
Should a third wave emerge, Indian officials say they have not let down a guard raised during the second wave. In New Delhi, which was the epicenter of the second wave, more than 95 percent of regular Covid beds as well as intensive care unit beds remain available. The state’s chief minister said that 27 oxygen plants had been added, and that tankers were being acquired, to avoid the oxygen shortage of the last wave. In Mumbai, about 85 percent of the regular Covid beds and nearly 70 percent of I.C.U. beds remain vacant. The number of vacant beds in Pune remains at about 77 percent.
The emergence of a third wave or another variant will ultimately depend on human behavior, said Dr. Scaria, of the Institute of Genomics and Integrative Biology. Testing may find the variant too late, as it did in the second wave, when the spread of the Delta variant did not become apparent in the country’s limited genome testing until April. Masks, vaccinations, social distancing and other precautions will be crucial to stopping new variants from emerging.
“A variant by itself cannot cause a wave, because variants can be tackled if you have the information in advance,” Dr. Scaria said. “Human behavior is as important, if not more, in creating a wave. If the right variant reaches the right population, it will create a wave.”
Hari Kumar contributed reporting.
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