Omicron BA.2 lineage dominant in symptomatic cases, finds Neeri study

NAGPUR: After replacing Delta variant in the district, new Omicron lineage BA.2 is turning out to be the new dominant variant strain among symptomatic patients, as per Neeri’s latest genome sequencing study. The Omicron variant thus far was known to cause mild disease and most of those found Covid positive in the last 30 days have remained asymptomatic or mildly symptomatic patients.

The earlier three genome sequencing series conducted by Neeri were done on total 201 samples randomly collected between January 1 and 16 from different parts of the city. In this fourth series, sequencing was done on 89 samples of symptomatic cases, including six admitted at a private hospital. These samples were collected between January 17 and 21 by Nagpur Municipal Corporation (NMC).

The BA.2 doesn’t exhibit ‘S’ gene deletion, thus making it difficult to detect the strain without genome sequencing. Authorities had been relying on ‘S’ gene target failure (SGTF) RT-PCR kits to look out for Omicron suspects among new Covid cases.

The Neeri study also dispels doubts among doctors regarding patients admitted in ICUs. Doctors had assumed Delta variant patients required oxygen support or intensive care in third wave. The findings have led to change in treatment protocol too.

Dr Krishna Khairnar, head of environmental virology cell, Neeri, said, “The Sars-Cov-2 study showed distribution of Omicron lineage B.1.1.529, BA.1, and BA.2 among the studied symptomatic patients. The percentage share was B.1.1.529 (31.5%), BA.1 (2.3%) and BA.2 (66.2%).”

Dr Khairnar added that two genome bioinformatics software pipelines viz Scorpion and Pangolin were deployed to reach a consensus on calling the SarCov2 variants, for making the callings robust. The software can assign or fix SarsCov2 lineages and variants.

Asked about aggressive sequencing, Dr Khairnar said, “It was a concern that the BA.2 lineage was not picked up in SGTF run. Our concern was addressed in this finding that it is not Delta but Omicron lineage. Identification of 66% cases may have been missed.”

The six samples of ICU patients came from those under treatment of infectious disease specialist Dr Ashwini Tayade. “The study has removed our doubts regarding severe disease among Covid patients. Another misconception was that if ‘S’ gene is not detected then it is not Omicron. But the Neeri study has found two lineages BA.1 and BA.2. The BA.2 variant doesn’t exhibit S gene failure in RT-PCR. The BA.2 strain can presently be picked up by either whole genome sequencing or Omisure kit,” said Dr Tayade.

Dr Tayade added that assuming Delta variant, cocktail therapy was given to the ICU patients. “Monoclonal antibodies will hardly have any role now,” she said.

Dr Tayade added that BA.2 is more infectious. “We are in peak week where soon BA.2 variant will take over,” she said.