Omicron variant BA.4 found in TN sample studied by Neeri

Nagpur/Chennai: The Omicron sublineage BA.4, which is causing a spike in cases in South Africa beside being detected in European nations and United States, has been found in a Covid positive sample of a Tamil Nadu woman (age not disclosed).
This is the second known case of BA.4 in India after an international traveller tested positive in Hyderabad earlier this month. Another three Covid positive samples from Tamil Nadu tested positive for Omicron variant BA.2.12.1, which are being closely monitored.
TN health minister Ma Subramanian on Saturday said the patient, a 19-year-old in a gated community, who tested positive on May 9, has recovered. But her mother, who was also positive for the infection during the same time, was carrying BA.2 variant. Neither of them had a travel history.
“The patients self-isolated themselves at home and recovered in three days. They resumed work in a week,” said health secretary J Radhakrishnan. Two other family members — the teen’s father and grandmother — did not have symptoms. While the grandmother took one vaccine dose, others have taken two.
Samples of the teen and her mother were sent to National Environmental Engineering Research Institute (CSIR–NEERI) in Nagpur on May 13 for whole genome sequencing. On May 19, the mother showed BA.2 sub-lineage and the daughter BA.4. “We are awaiting confirmation by NCDC. Two members of a family usually carry the same variant if they are affected at the same time. In this case, we think the source of infection for mother and daughter could be different,” Radhakrishnan said.
The Omicron subvariant BA.4 was detected in whole genome sequencing at city's Neeri’s environmental virology cell led by scientist Krishna Khairnar. The sample was cross-checked for BA.4 by Indian SarsCov2 Consortium on Genomics (INSACOG) and the variant was reconfirmed, officials in the know said.
National Institute of Virology (NIV) has sought the BA.4 sample from Neeri for viral cultures. The viral culture allows further research in development of vaccine and drug in future. Early policy decision, further research, growing virus isolates are among some benefits of whole genome sequencing.
The BA.4, first detected on January 10, is a variant of concern because it is apprehended that it may evade immunity acquired from past infection or make population vulnerable due to waning immunity from vaccination, added the officials.
The Neeri lab had received 110 SarsCov2 positive samples detected between April 30 and May 18 from different districts in Vidarbha as well as through Integrated Disease Surveillance Programme (IDSP) Tamil Nadu for genome sequencing. IDSP Tamil Nadu alone accounted for 88 samples while 15 samples were from Nagpur, rest from Washim, Sawangi and Chandrapur. Out of total 110 samples received, only 87 samples qualified for whole genome sequencing.
This was the 19th series of study, designed to include samples of both symptomatic and asymptomatic Covid positive patients. BA.2, which replaced delta and its sublineages during the third wave in January, continued to remain the dominant Omicron variant. Among the studied samples BA.2 was found in 65.5% samples as compared to 1.14% of BA.4 and 3.44% of BA.2.12.1.
A total 54 samples studied belonged asymptomatic and 34 samples to symptomatic patients. Among asymptomatic cases, Omicron BA.2 was found in 59.61% and 74.28% in symptomatic cases. The lone BA.4 case had 1.92% share among asymptomatic cases.
The bioinformatic pipelines namely Pangolin-Scorpio were used to study the Sars-Cov-2 variants. The Neeri lab has completed whole genome sequencing of 1,466 Covid postive samples since January to May 19. It has published all data on GISAID, IDSP and INSACOG hub.