New variants undetected as Kashmir sends less than 1% samples for genome sequencing

Suhail Bhat
Srinagar, May 7: The Valley is lagging in genome sequencing, even though there are strong indications that new variants are causing severe infections and hitting the younger population.
Even though more young people are getting consumed by the virus every day, the Valley is sending a few samples for genetic sequencing needed to detect new variants allowing them to proliferate quickly.
“With the second wave, we are seeing an aggressive behavior of the virus. In the firsts phase, the people with underlying medical conditions were the people who were experiencing severe symptoms or dying. In the second wave, we are seeing a different trend wherein the people in their 20s and 30s are dying,” Dr. Nissar-ul-Hassan, influenza expert told Excelsior. He added there are powerful signs that we are dealing with a mutant. “I am telling this because of a changed clinical spectrum of the virus,” he said.
A 30-year-old from Prichoo area of South Kashmir’s Pulwama died due to COVID-19 since last evening in Kashmir. Last month, an 18-year-old boy, who had no underlying disease, from Handwara died in SMHS hospital of Srinagar. Every other day, the death of people in their 20s, 30s is being reported in Valley since the second wave struck Valley.
“We have many people with bilateral pneumonia and patients with dipping oxygen. Even pregnant women are coming with severe infections. We already have one on the ventilator in SMHS. Pregnant women were not at all affected in the first wave. Even if they were affected, they were asymptomatic. This is the change in the virus’s behavior. Second, it has not only become infectious, but lethal,” he said.
As per guidelines, the States were supposed to send at least 5% of their samples for genome sequencing, but Kashmir has not even sent 1% of their samples. To make things worse, there is no data on the number of samples being sent for sequencing. “We don’t have anything on this,” Dr. Bashir Fomda, HoD Microbiology, SKIMS told Excelsior.
The experts, however, warned that the spread of the variants such as the one first spotted in the Valley, NH440K, which is an Indian variant, appears to be more lethal. They said that genetic sequencing of the test samples not only helps catch new variants quickly, but allow authorities to rework their virus strategies.
A virologist at the SKIMS claimed that they send only those samples for genome sequencing that comes from a person with foreign travel history. “The new strains can be documented through genomic sequencing and we are sending a few samples for genomic sequencing. Unless we don’t have studies, we can understand its behavior,” he said, adding that more samples need to be sent for sequencing.
He, however, lamented that while countries around the world are employing researchers to study the nature of diseases, authorities in SKIMS are asking them to do clerical jobs. “We are being asked to fill the details of the patients on the computer while we must analyze the samples at the labs. They could have easily used our services to understand the nature of this virus,” a PG student at SKIMS said.
Another reason is, there is a need to ramp up genome sequencing is that many tests show negative RTPCR. “Most times we have seen that while CT-scan is consistent with COVID but RTPCR is falsely negative which shows that we are dealing with a mutant,” he said.
Genomic sequencing has to be extensive which means not only positive cases have to be sent, but suspected patients also need to be checked. “Only then can we know the magnitude of the problem. We may also have some locally emerging deadly variants. All this is possible only because of genomic sequencing of these samples,” Dr. Nissar said.