Three districts focus on genome sequencing as State registers 6,000+ COVID cases

Amravati will send 90 more samples of Covid-19 patients, including those of the deceased, to look for prevalence of mutation in them. Yavatmal will send 100 samples, while Akola sent its first 75 samples on Thursday for genome sequencing to check if mutation is responsible for rapid rise in cases in the district.

Maharashtra on Friday recorded 6,112 cases. The last time daily case load crossed 6,000 in the state was 114 days ago on October 28. The state now has 20.87 lakh cases with 44,765 active infections.

Maharashtra on Friday could immunise only 14,880 people, far below its usual tally of 30,000-40,000 a day. Dr Archana Patil, state director (family welfare), said less vaccination camps were held because of Shiv Jayanti celebrations. The decision to send samples for genome sequencing comes after four of 12 samples from Amravati showed a point mutation (E484Q) similar to the one found in South Africa, Brazil and the UK. One of four samples from Yavatmal showed a local mutation (N440K). All samples were sequenced in BJ Medical College.

District officials fear the mutation could be linked to the widespread transmission and sudden rise in cases in parts of Vidarbha. The State Government has however questioned the validity of BJ Medical College’s report. “This explains the rise in cases in cluster pattern in Amravati and Yavatmal. The pattern indicates a mutation is passing through these districts,” said Dr Shashank Joshi, state task force member. He added that so far, 241 mutations have been reported in India in Sars-CoV-2. The size of Sars-CoV-2 genomic makeup is 30kb, a change anywhere in the RNA strand can lead to mutation.

Interestingly, another common mutation – widespread in Europe, US, Canada, Australia, China and Germany – has been found by BJ Medical College (Pune) in 11 of 12 samples randomly picked for genome sequencing in the state. The D614G mutation has a higher rate of transmission although its severity is low. This is now common in several parts of Maharashtra. Dr Prashant Thakare, in-charge of molecular lab in Amravati, said they have selected 90 samples for genome sequencing to further assess mutations’ prevalence. “We have selected samples for genome sequencing from severely and mildly-ill patients, few asymptomatic cases and those who died of Covid-19,” he said.

The four cases with E484Q mutation had no travel history outside of Amravati and they were unrelated to each other. However, the entire families contracted Covid-19, Dr Thakare said. Similarly, where a person tested for N440K mutation in Yavatmal, there is no travel history outside the district and the entire family tested positive. BJ Medical College initially labelled the four Amravati mutations as E484K. On Thursday, it corrected them to E484Q.

“E484Q and E484K mutations are both similar in nature. There was an error in reporting, it has been corrected now,” said Dr Rajesh Karyakarte, head of microbiology in BJ Medical. He added that both mutations have the ability to evade antibody response. On Friday, the Maharashtra health department issued a statement saying, “it has found no foreign variant” in the samples tested from Pune, Amravati or Yavatmal, but the department did not officially comment on mutations found by BJ Medical College.

Dr Pradeep Vyas, State Health Secretary, said the public health department had not authorised the genome sequencing in BJ Medical College. He added, “To label a UK variant, there must be at least 17 types of specific point mutations, and to label a South African variant, there must be nine types point mutations. E484K is one of the mutations. We have sent more samples to NIV (National Institute of Virology) in Pune. We are waiting for their report.”

“BJ Medical College is not authorised to do genome sequencing by the Centre. They also need to use a new nomenclature for sequencing. They themselves corrected their report later on. There are few technical issues in sequencing. We asked them to submit their reports to us,” said state epidemiologist Dr Pradeep Awate. Of 10 labs authorised by the Centre, two in NIV and National Centre for Cell Science (NCCS) in Pune are approved to perform sequencing. As per the state’s epidemiology cell, so far, 12 cases of the UK variant in passengers with foreign travel history have been officially found. All the cases were isolated and have recovered.