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As we enter 14th day of lock-down (April 7, 2020) in India, global death toll has reached more than 74,000, while as total Corona positive confirmed cases stands more than 13 lakh across the world, which is growing only, when you are reading this column. In India the tally stands at 4,281 people infected while as 111 deaths have been reported so far (April 7, 13:40).

The question is, how to deal with the new unseen villain. Is Science of Genomics helping us out? Let’s dive a bit into what Genomics is and how it is helping us know this new actor in the epidemic world, SARS-Cov-2 virus, responsible for Covid-19 disease?

What is a Genome?

Genomes or genetic material of any organism are our guides to understanding how life works. Genomics (field which deals with study of Genomes) has revolutionized our understanding of human and pathogen (disease causing microbes) biology and also how the two interact.

Genome is an entire genetic material, containing hereditary information and present inside an organism such as human or bacteria or even virus. Genome consists of Genes. Genes themselves are small parts of larger molecules called DNA molecules (Deoxyribo Nucleic Acid) or RNA molecules (Ribo Nucleic Acid). DNA is a long molecule made up of a repeating string of just four different chemicals.  (In scientific terminology these chemicals are also known as bases or nucelotides). Most genes are codes describing how to make different types of proteins. The information in genes is stored in order of these bases or chemicals only.

This digital like storage of information was one of the first big discoveries of modern science. Human genome is made of DNA. Same is the case with animals and plants or even bacteria or while as genome in some viruses is made of RNA only. Humans have an average of about 25,000 genes which control our various characteristic features and if there is some defect in our genes, they might result in diseases such as Haemophilia, Sickle Cell disease, Downs’s syndrome etc.

Similarly, bacteria have around 4000 genes. In the same way Viruses, which are much smaller than bacteria have genomes which contain information about their body biology and also the information required to make the virus and how they would work as well as interact with other organisms or hosts such as humans.

They also decide how a virus would respond if there is any change in its environment. How a virus would control the host cell (cells which they infect), is all coded in their genomes only. Some mutation or changes in genome of a virus renders him pathogenic or disease causing, which otherwise is non-toxic. Living organisms are mostly made of proteins and fats. Thus, to understand genes is to understand the organism itself.

Now why are viral or bacterial genomes important here?

Genome variations in bacteria and viruses give us a lot of information. For example, how they cause diseases, how they originate, how they interact with the host (organisms they cause diseases) and their pathogenicity or how toxic they are. By sequencing the genome of a bacteria or virus one can, not only determine which genes of bacteria and virus play a role in causing disease but through better understanding can help in creating possible solutions of how to stop them.

Thus, Genomic data is essential not only to build tests for identifying the villain (virus) but also to create drugs and vaccines against them. Whole genome sequencing (WGS) or complete genome sequencing is actually the process of determining the complete DNA sequence of an organism’s genome at a single time.

Modern scientific methods such as WGS, enable us better examination of diversity and the analysis of virus populations, their origins as well as mutations they undergo during any epidemic. Genome sequencing has emerged as major and vital diagnostic tool for disease outbreak as well as identification of the disease-causing microbes.

What Novel Corona Virus (SARS-Cov-2) genome analysis has revealed so far?

Bacteria & Viruses differ from each other in two main aspects. One, bacteria are single celled organisms that are found throughout our body and in our environment while as viruses are much smaller than bacteria and live as long as they are inside a host organisms.

Second is antibiotics usually kill most of the bacteria but they aren’t effective against viruses. A virus has either a DNA or RNA genome. But vast majority of viruses have RNA genome. A virion is an entire virus particle consisting of an outer protein shell called a capsid or capsule and an inner core of nucleic acid (RNA or DNA). Thus, a genome in viruses is often packed within a protein capsule.

Now let us come to Novel Coronavirus, also known as SARS-Cov-2. Despite its similarity to other viruses in the coronavirus family, the virus is relatively unknown. It is thought to spread more easily and has higher mortality rates than some of its better-known counterparts, adding to the existing challenges of any public health crisis of this scale.

Scientific attempts to know the Novel Coronavirus, which causes Covid-19 disease, started with the study of its genetic material by using gene sequencing techniques. One amongst the first attempts of whole genome sequencing of SARS-Cov-2 virus outside China, was made by a group of scientists from Nepal, Colombia, Saudi Arabia, United Kingdom and Japan, from a strain which was taken from a Covid-19 patient in Nepal.

The patient was a Nepalese student of Wuhan University of Technology in Wuhan, China who had returned to Nepal and was showing symptoms such as mild fever, cough and throat congestion. The specimen was collected at the National Influenza Centre, National Public Health Lab-oratory in Kathmandu, Nepal and subsequently its genome was studied at WHO laboratory in University of Hong Kong, Hong Kong. This was done in February 2020 and then subsequently it got published in Microbiology Resource Announcements on 12th March 2020.

Similar attempts of isolation and sequencing of whole genome of the virus were done at many different laboratories of the world. For example genome sequencing was also carried out in African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer University, Nigeria. This was a preliminary attempt to reveal the sequence. Around 20th March 2020, the study of SARS-Cov-2 genome was carried out by ICGEB-Trieste, Italy, by a group of scientists, led by Alessandro Marcello.

Likewise, genome analysis was also carried out by a group of scientists from USA, UK and Australia. This particular study was led by Kristian G. Andersen of Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA and got published in Nature Medicine on 17th March 2020. These genome detailing procedures have revealed some important features about the virus such as it’s outer coating also known as ‘Spike protein’.

The analysis has shown the high affinity of the outer coating of the virus with humans and that this affinity is a result of natural selection process or evolution of this virus. This study done by Kristian G. Andersen and his colleagues, has revealed that the virus is not a product of any human manipulation, thus debunking many theories about its possible laboratory origins.

The study has also revealed that there have been some mutations in the virus which have changed its outer protein shell and thus facilitated it’s easy binding with with the human cells (e.g. Lung Cells). The virus has acquired few other mutations which make it so contagious as well as deadly for humans. The study has suggested two possibilities by which it could have evolved and acquired such features and traits which make it so deadly and resistant to all known vaccines & drugs. One is by natural selection in an animal host before it could jump into humans and second is natural selection in humans itself after it got transferred from animals.

More such studies are in progress across many different laboratories just to precisely determine how this animal virus sidestepped the species boundaries to infect humans to such an extent that it soon became a pandemic. The genomic studies would also help us reveal partly the spread and infectiousness in human population.

Genome sequencing of the virus (SARS-Cov-2), causing Covid-19 disease is currently going on in different research laboratories around the world to effectively understand the various strains, their biology and the mutations they undergo, which are causing the epidemic. Genome sequencing is also important in every country which is facing the epidemic to know the course of the disease and thus to explore effective ways which are needed to tackle it.

The war against Covid-19 is not over yet and there are still many unknowns regarding SARS-Cov-2 virus as well as Covid-19 disease, which need to be uncovered. It is just a matter of time before an effective vaccine is developed against the virus, and the villain, which has snatched many souls from their loved ones, is finally defeated by us. I don’t know what better way to conclude than with this beautiful line from a play by Shakespeare, ‘Health Shall Live Free and Sickness Freely Die’.

Rayies Altaf is a science & technology writer and is currently consultant at Centre for Community Knowledge, Ambedkar University, New Delhi.

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