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Genome sequencing for all international patients if tested Covid-19 positive: Why it is needed?

Specially, mutations in the spike protein of the coronavirus has fuelled concerns.

To detect the new coronavirus strain, the centre has identified 10 regional laboratories where states will send five per cent of their Covid-19 positive samples for genome sequencing.

Written by Longjam Dineshwori |Updated : December 30, 2020 9:19 AM IST

As fear over the new coronavirus strain grips India, the centre has issued fresh guidelines for COVID-19 surveillance that will remain in force till January 31. It noted that while there has been a continuous decline in the active and new COVID-19 cases, there is a need to maintain surveillance, containment and caution, keeping in view the surge in cases globally, and the emergence of a new variant of the virus in the UK. Meanwhile, the Union Health Ministry has announced that all international passengers who arrived in India during the last fortnight before the travel ban to UK (i.e. between December 9 and December 22) will be subjected to genome sequencing if symptomatic and tested positive for Covid-19.

A week ago, the health ministry had announced genome sequencing of all passengers arriving from the United Kingdom.

India had imposed a temporary suspension on flights coming from UK following reports of the emergence of a new and highly infectious coronavirus strain in Britain. The suspension of flights that came into effect from December 22 midnight will continue till 31 December. The ban could be extended further in view of the prevailing situation, Union Minister of Civil Aviation said today. Passengers arriving from UK were also subjected to mandatory RT-PCR test on arrival at the airports concerned.

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What is genome sequencing?

Genome sequencing is the process of determining the complete DNA sequence of an organism's genome. It involves figuring out the order of DNA nucleotides, or bases, in a genome the order of As, Cs, Gs, and Ts that make up an organism's DNA. For example, the human genome is made up of over 3 billion of these genetic letters.

Knowing the entire genome sequence may help scientists understand how genes work together to direct the growth, development and maintenance of an entire organism.

Researchers believe that genetic sequencing can help monitor mutations in COVID-19, which in turn can help improve diagnostic testing and transmission tracking.

Most of the testing developed for COVID-19 looks for one portion of the gene sequence that causes the virus, but if that one sequence mutates the test is no longer accurate - noted a study published in Cell Reports.

"It is inherent in a virus' nature to mutate. Changes in other areas of the genetic sequence can not only disrupt testing, but hinder the effectiveness of vaccines," said Dirk Dittmer, PhD, professor of microbiology and immunology at the UNC School of Medicine, and senior author of the study.

The study suggested that next generation sequencing can help enhance diagnostic testing accuracy.

17 mutations found in latest COVID-19 strain

Scientists in the UK have found 17 changes or mutations in the latest variant, named VUI 202012/01 (the first Variant Under Investigation in December 2020). One of the most significant mutations, according to them, is the `N501Y` mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of the spike protein is thought to be responsible for the virus becoming more infectious and spreading easily and rapidly amongst people. The UK government had said that the new variant is up to 70 per cent more infectious than the previous strains.

To detect the new coronavirus strain in India, the centre has identified 10 regional laboratories where states will send five per cent of their Covid-19 positive samples for genome sequencing.

The health ministry has also established the Indian SARS-CoV-2 Genomics Consortium (INSACOG) for laboratory and epidemiological surveillance and expand whole genome sequencing of the coronavirus in the country.

The viral genome sequencing data generated will be analysed by the respective centres and sent to the National Centre for Disease Control (NCDC), Delhi, for collation and integration, according to the health ministry's guidance on genomic sequencing released on Monday.

This will help in understanding super-spreader events and outbreaks and strengthen public health interventions across the country to help in breaking the chains of transmission, the ministry said.

Meanwhile, India on Tuesday reported six cases of the new strain of Covid-19. As per a government statement, three samples in NIMHANS of Bengaluru, two in CCMB, Hyderabad and one in NIV, Pune have tested positive for the mutant strain of Covid-19 virus. All patients had recently returned from Britain.

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