265 samples from Yavatmal, Amravati, Akola up for genome sequencing

On Thursday, The Indian Express reported that district officials fear the mutation could be linked to 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 make up 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. Last year, genome sequencing of few reinfection cases in Mumbai too found this mutation.

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 labeled 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 Central, 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.