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8.7 per cent variants of concern found in COVID-19 genome sequencing, experts suggest more research

Of the samples detected with variants of concern, 1109 have been found with the UK variant, 79 with the South African variant and one with the Brazil variant.

Published: 17th April 2021 02:18 AM  |   Last Updated: 17th April 2021 09:58 AM   |  A+A-

A health worker sorts swab samples at a testing centre, as coronavirus cases surge across the national capital, at MCD dispensary, Mehrauli, in New Delhi.

A health worker sorts swab samples at a testing centre, as coronavirus cases surge across the national capital, at MCD dispensary, Mehrauli, in New Delhi. (Photo | PTI)

By Express News Service

NEW DELHI: Of the over 13,614 samples of Covid-19 whose whole genomic sequencing has been carried out, 1,189 (8.77%) have tested positive for variants of concern, the Centre said on Friday. But it refrained from linking the rise in cases to the mutant pathogen.

Of the samples detected with variants of concern, 1109 have been found with the UK variant, 79 with the South African variant and one with the Brazil variant. The details have been put out amid concerns that Covid-19 with double mutation may be responsible for the aggressive spike in cases.

Criticised for the delay in carrying out thorough genomic surveillance when the second wave of the pandemic has caused havoc, the health ministry also maintained that the National Centre for Disease Control has also communicated state-specific results from time to time.

It, however, also blamed states like Maharashtra, Kerala and MP for not sharing clinical data of samples being sent for genome sequencing. 

Meanwhile, a global mutation tracker on Friday suggested the 'double mutant' coronavirus, first identified in Maharashtra, has a cumulative prevalence of 10 per cent in India, a finding that some scientists here said is based on insufficient data and needs more research.

Genome sequencing with representative samples from all states seeing a COVID-19 surge is necessary before any conclusion can be drawn, experts said after a tracker by US-based Scripps Research suggested the B.1.617 lineage, also called a double mutant, has the highest cumulative prevalence of all mutant variants analysed in India.

Though the double mutant' has drawn attention, and some degree of panic, it is difficult to say if it is the most common or abundant variant or even if it is responsible for the raging second Covid wave in India, said Anurag Agrawal, director of the CSIR-Institute of Genomics and Integrative Biology in New Delhi, and virologist Upasana Ray.

The report is an incomplete representation of Indian data and different areas in the country have different dominant variants, they said.

In the 265 lineages from India, the cumulative prevalence of the B.1.617 variant was 10 per cent, the Scripps researchers found.

The results in Scripps 'outbreak. info' tracker are based on data provided by science initiative GISAID, which had identified 408 B.1.617 sequences worldwide since the lineage was identified in October last.

The B.1.617 variant has been detected in 11 countries, according to the tracker.

The cumulative prevalence of the B.1.1.7 variant first identified in the UK was 8 per cent.

For the South Africa variant, it was just 5 per cent.

Cumulative prevalence is the ratio of the sequences containing a mutant to all sequences collected since the identification of the variant in that location.

"Most of the recent sequences have not been deposited and the representation is not proportionate," Agrawal told PTI while referring to the Scripps findings.

Ray agreed and noted that the double mutant is definitely one of the dominant variants in the mutated SARS-COV2 variant pool but may not the most abundant.

"To say that it is the most dominant or abundant variation, we need to be sure that sequencing has been done as similar representations from all the states with COVID-19 surge," the senior scientist at the Kolkata-based CSIR-Indian Institute of Chemical Biology explained.

Amid mounting concerns, health authorities in UK said they have identified 77 cases of the B.1.617 variant of coronavirus and designated it a Variant Under Investigation (VUI).

Public Health England (PHE), which releases weekly updates on the number of confirmed new cases of Variants of Concern (VOC) and VUI in the UK, reported on Thursday that the variant first detected in India includes a number of mutations.

"PHE has identified 77 cases of this variant in the UK and all appropriate public health interventions will be undertaken, including enhanced contact tracing," it said.

Although the double mutant is one of the mutants that has drawn attention, it is not established that it is the cause of the rapid transmission during the current COVID-19 wave, scientists here said.

"Not only the double mutant, but all the other dominant variants of concern are also increasing. So it is too early to say which one will out-compete all others," Ray told PTI.

"Remember, pandemic fatigue might by itself be contributing to the spread," she added.

The B.1.617 variant of SARS-CoV-2 carries two mutations, E484Q and L452R.

Both are separately found in many other coronavirus variants, but have been reported together for the first time in India.

The two mutations are found in the virus's spike protein, which helps the virus to bind itself to the human cell's receptors and gain entry into a host cell.

Concerns surrounding new strains of SARS-CoV-2, the virus behind the COVID-19 pandemic, have been mounting.

Agrawal said over 15,000 samples have been sequenced in India, including over 12,000 community samples, in 2021.

He noted that in India, different areas have different variants that are dominant.

For example, he said, in Punjab and surrounding areas, the B.1.1.7 variant is common.

In Maharashtra and Gujarat, the B.1.167 variant is dominant.

Similarly, in southern India, the N440K mutation is more dominant, although it does not have a variant name yet.

"All variants are starting to be seen across India also. The most common strains are the normal ones. Only in few states, variants are dominant and that too different in different parts," Agrawal said.

GISAID is a global science initiative and primary source that provides open access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pandemic.

On Friday, India added a record 2,17,353 new coronavirus infections in a day, taking the total tally to 1,42,91,917 (14.2 million/1.42 crore), the Union Health Ministry said.

This is the second consecutive day that the country has reported over two lakh cases.

The death toll also increased to 1,74,308 with 1,185 new fatalities, the highest since September 19, 2020.

(With PTI Inputs)



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