BENGALURU: Karnataka has been entrusted with a target of genome sequencing 10,000 samples in the next 20 days. Samples from the Indian Council of Medical Research (ICMR)-approved government and private RT-PCR labs in the state have been instructed to select 10 per cent of their daily samples for special whole genome sequencing (WGS), along with relevant data, in an appropriate format from district hospital laboratories.
The WGS is a process of determining the DNA sequence of an organism’s genome — in this case that of the SARS-CoV-2 virus — to understand the nature of the variant and whether it has undergone mutations. The order was issued by the Department of Health & Family Welfare on Monday, on the instruction of the Union Health Secretary.
All district surveillance officers and officers at sentinel sites will have to now send the samples to the National Institute of Mental Health & Neuro Sciences (NIMHANS) and IN-Stem in Bengaluru for sequencing.
“As per the Union Health Secretary’s instructions given during the video conference held on December 31, a target of 10,000 samples have to be sequenced. Though the routine whole genome sequencing is undertaken with 15 samples fortnightly from each district, the state has now been instructed to conduct a special genomic sequencing surveillance of Covid-19 with a larger proportion of daily positive samples to be sequenced from 2nd to 28th February,” the order stated.
State health officials said keeping track of any new variant of concern is now of extreme importance, and also the spread of Omicron’s sub-lineage BA.2 — also known as the “stealth variant” — has been leading to an increase in the number of Covid-19 cases in many countries, including India. This sampling will help in not only identifying the dominating lineage in the state, but also track any new variant, the officials said. The accessibility to data upload was initially with sentinel sites but is now extended to District Surveillance Officers.
Patients with international travel history (irrespective of CT value)
Representative samples from clusters/focal outbreaks with severe morbidity and/or mortality
Seriously sick, hospitalised patients and prolonged hospital admissions
Cases of Covid-19 re-infection
Individuals who are fully vaccinated and have completed 15 days after second dose
Covid-19 death cases