Genome sequencing a challenge in rest of Karnataka

Lack of Covid-19 cases, swab collectors in rest of Karnataka region mars genome sequencing

Genome sequencing in Karnataka, except Bengaluru, has hit a hurdle owing to lack of Covid-positive samples and shortage of sample collectors in the region.

Genome sequencing is crucial to identify and track new variants of the coronavirus. While district and taluk hospitals outside Bengaluru are unable to send samples for genome sequencing due to lack of coronavirus cases, some districts point to shortage of sample collectors and transportation.

Chief Minister Basavaraj Bommai had on Thursday said that all Covid-19 positive samples would be sent for genome sequencing.

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Earlier in the month, Principal Health Secretary Anil K​umar TK issued a circular to the taluk and district hospitals stating that they should act as sentinel sites and its departments of medicine, paediatrics, ENT and OBG, should contribute to a daily Covid suspect sample size of 25 (in case of taluk hospitals) and 50 (in case of district hospitals).

If tested positive for coronavirus, the samples should be sent for genome sequencing to track emerging new variants of concern. For instance, there are three taluk hospitals in Dharwad district.

"But the positivity rate is zero per cent", said a district health official. "On an average, we have been testing 300 to 350 samples a day. We aren't getting any patients with ILI/SARI history. Also, unless the viral load in a sample is high and has a Ct value of less than 25, it can't be sent for sequencing."

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Meanwhile Kodagu district is grappling with a shortage of swab collectors and symptomatic cases. The last time the district sent samples for genome sequencing was two months ago.

"We have three taluk hospitals and sample collection is not happening in the districts due to various reasons: lack of swab collectors, lack of symptomatics, and even if we collect the samples, we are unable to transport it to the labs," Kodagu District Surveillance Officer Dr Anand N told DH.

Besides, there have been zero Covid cases in the district in the last 15-20 days, he added. "No symptomatics are visiting our hospitals. Even if they do, the results come negative. We are testing only 50 to 60 samples a day."

Kolar district surveillance officer Dr Charini MA said patient inflow was a challenge.

"There are no SARI/ILI cases even among the paediatric population. Among those tested, around 200 samples per day, positives are zero. From April 7, we had no Covid cases. We are not getting Covid samples with less than 25 Ct value so we can't send them for genome sequencing," she said.

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