COVID-19 Outbreak: India Must Focus On Sequencing Coronavirus Strain Present In The Country

Sars-Cov2, which causes the COVID-19 infection is an RNA virus, which means that the genome of the virus is composed of Ribonucleic Acid. A mutation occurs when there is a change in the sequence of the nucleic acid.

The RNA genome of the virus arms it with two very interesting features, RNA is unstable due to its chemical nature, therefore, it is susceptible to mutations. The other feature is that unlike genomes made of DNA, RNA genomes are incapable of correcting such mutations.

Being an RNA virus, Sars-Cov2 usually undergo much faster genomic changes once they enter their host.

What Is RNA?

Ribonucleic acid (RNA) is one of the three major biological macromolecules that are essential for all known forms of life (along with DNA and proteins). DNA makes RNA which makes protein. When the cell needs to produce a certain protein, it activates the protein's gene–the portion of DNA that codes for that protein–and produces multiple copies of that piece of DNA in the form of messenger RNA, or mRNA. The multiple copies of mRNA are then used to translate the genetic code into protein through the action of the cell's protein manufacturing machinery, the ribosomes. Thus, RNA expands the quantity of a given protein that can be made at one time from one given gene, and it provides an important control point for regulating when and how much protein gets made.

A typical RNA virus can, on an average, undergo more than half-a-dozen mutations in each human it infects. And that, precisely, is the danger, Dr Koustubh Panda told The Logical Indian.

Dr Panda is the Head of The Departement of Biotechnology at the University of Calcutta.

The Sars-Cov2 has evolved into two different genetic strains: 'S' and 'L' apparently within two months. According to scientists, the L type is more aggressively virulent than the S type. This information was obtained from the genome analysis of just 103 Chinese patients at the end of January this year.

Genome data is essential to build tests, manufacture drugs and vaccines. It is also necessary to figure out if there has been a mutation of the virus and how that will affect different populations. It is also key to finding measures to contain its spread.

What Is Genome Sequencing?

Genome sequencing involves revealing the order of bases present in the entire genome of an organism. Genome sequencing is often compared to "decoding," but a sequence is still very much in code. In a sense, a genome sequence is simply a very long string of letters in a mysterious language. Sequencing the genome is an important step towards understanding it.

How Is Genome Sequencing Done?

The entire genome can't be sequenced all at once because available methods of DNA sequencing can only handle short stretches of DNA at a time. There are two approaches to the task of cutting up the genome and putting it back together again. One strategy, known as the "clone-by-clone" approach, involves first breaking the genome up into relatively large chunks, called clones, about 150,000 base pairs (bp) long. Scientists use genome mapping techniques to figure out where in the genome each clone belongs. They then cut each clone into smaller, overlapping pieces the right size for sequencing—about 500 BP each. Finally, they sequence the pieces and use the overlaps to reconstruct the sequence of the whole clone.

The other strategy, called "whole-genome shotgun" method, involves breaking the genome up into small pieces, sequencing the pieces, and reassembling the pieces into the full genome sequence.

Prioritize Genome Sequencing

Sequencing the viral genome in the earliest phases of an outbreak is valuable because it helps in faster decision making on how to contain its spread.

"Sequencing will tell us the existing stairs which are causing the infection in India," Dr Panda said.

Availability of the sequences of the strains infecting Indians will help in understanding the diversity of the viral sequences circulating in the country and its similarities with global strains.

"Two full genome sequencing was done, one matched the strain which originated in Wuhan the other resembled the strain which is infecting in America. This means the virus is continuously mutating. We must trace all the people who entered the country. Especially the last ones who entered in March. Sequencing the virus from their sample will tell us the range of strains that are currently doing the rounds in India," Dr Panda said.

"This will also allow us to formulate specific testing methods," he added.

India Must Mobilize All Of Its Scientific Resources

According to Dr Panda, despite having sufficient scientific resources and manpower to support exercises needed to manage the COVID-19 outbreak, India only utilised institutes affiliated to the Indian Council of Medical Research (ICMR).

"There are lots of institutes in the country, such as those affiliated to DST, DBT, CSIR, IKAR. All you need is a lab with real-time PCR machines. Considering the huge demand for community screening, all the available resources must be mobilized," Dr Panda said.

"A lot of private labs are backing out from providing free tests under the Supreme Court order. The government must step up and use all its institutes to cater to the need of the country," he added.

"The tests are not simples. Trained personnel are required to perform the tests and avoid false negatives. These labs are equipped with such personnel. They should be used. The ICMR is only 5-10% of the scientific resources we have in our country," he further said.

India has around 40 labs, including the Indian Institute of Science and Manipal University, that have the required bio-safety limits (BSL-3) for sequencing the virus, yet it has not opened up the samples to labs outside of the ICMR network.

If more places are roped into studying the strains, the deadly virus can be better understood.

Reportedly, ICMR is cautious about opening up more labs for genome sequencing because of the stringent standards required to extract the strains.

Where Can Sequencing Be Done In India?

According to a report by All India Radio News, the Hyderabad based Centre for Cellular and Molecular Biology (CCMB) has undertaken the Genome Sequencing of Coronavirus jointly with the Institute of Genomics and Integrative Biology (IGIB).

CCMB Director Dr Rakesh K Mishra expressed hope that in next 3-4 weeks the CCMB will be completing several hundreds of isolates and able to reach at some conclusions which will be relevant in practical applications to tackle Coronavirus. According to Dr Rakesh, over hundred isolates of Coronavirus have been sequenced so far and several hundred isolates will be sequenced in the next few weeks. He said genome sequencing will give major understanding about Coronavirus and to know how successful a vaccine or medicine is.

Second Time Testing Positive

On being asked the reason behind testing positive a second time after being cured, Dr Panda said that the test involves using a swab which has to be fully inserted into the nasopharyngeal orifice. When the test is being done the first time, the tester does it without knowing whether the patient is carrying the virus or not. The second time, however, the tester knows that the patient is positive. This could potentially lead to some hesitation and the tester may not be as aggressive with the swab as is required due to the fear that the patient might cough and release droplets containing the virus into the vicinity. Therefore, there is a fair chance that the test results in a false negative.

Patients must be closely monitored before confirming that they are actually negative for the virus.

Also read: China Imposes Restrictions On Publication Of Research On Origin Of COVID-19