The need for SARS-CoV-2 genome sequencing

Professor Sharif Akhteruzzaman, PhD, Department of Genetic Engineering and Biotechnology, University of Dhaka

The ongoing coronavirus pandemic has suddenly and drastically changed the way we lived in the world, only a few months ago. We have not seen such devastation in recent history since World War II. The virus has already killed more than 170,000 people worldwide and billions are at risk of getting infected. There is no drug yet with convincing scientific evidence that can cure the illness, neither is there any effective vaccine in sight. We really don’t know how the crisis is going to end. But we know for sure that the post-pandemic world is never going to be the same as before. Therefore, envisioning a comprehensive strategy to cope with post-pandemic challenges by exploring all scientific means and ways of the 21st century is crucial.

We all know by now that the causative agent of Covid-19 is a novel coronavirus called SARS-CoV-2. Biologically speaking, viruses are not true biological entities and therefore require a host to survive. All viruses carry their genetic information as either DNA or RNA. The SARS-CoV-2 genome is an RNA molecule of about 30,000 bases containing only 15 genes. The human genome, on the other hand, is a double helix DNA—about three billion bases in size and containing about 30,000 genes. RNA is less stable and more prone to mutation than DNA, so RNA viruses generally change and evolve faster. This sometimes allows RNA viruses to jump from one species to another.

Coronavirus did not just pop up very recently. There are hundreds of coronaviruses belonging to a large family of viruses called coronaviridae. They have been around us for a long time in many avian and mammal reservoirs including bats, migratory birds, camels, civets, pangolins, mice, dog and cats. The current trail of death and disease around the world is believed to have been created by at least eight strains of the novel coronavirus.

Since novel coronavirus is a new virus, mining its genome sequence is of crucial importance. Genome sequencing has now become a powerful tool for tracking diseases—this is called “genomic prediction”. Whole genome sequencing will help researchers identify genetic changes that occur in a virus when it spreads through the population. The changes in the genetic sequence of the viral genomes collected from several patients will allow the monitoring of the spread of the disease within the country and between populations over time. It will also provide us with answers to the following questions, which are not known to us at this moment with certainty.

These are—why are some countries suffering more from the virus when compared to other countries? Why do children seem to be less vulnerable than adults? Can the virus evolve into a more virulent strain, and what will happen then? How fast is the coronavirus mutating? How can a vaccine be developed, targeting a particular population? Where did the virus actually originate?

From the perspective of any specific country, including ours, the most important information from the viral genome sequence at this moment will be—identification of particular viral strain/s that are prevalent, identification of infection hotspots or super-spreaders (individuals who spread the infection to more than the expected number of people), and formulation of strategies for public health intervention. This will also help develop a vaccine targeting our own population.

Many countries have already started sequencing the viral genomes collected from patients. In India, three institutes (CSRI, CCMB and IGIB) have started working together on the whole genome sequencing of the novel coronavirus. The government of UK has announced a GBP 20 million investment for mapping the Covid-19 spread in UK through whole genome sequencing. The study will be conducted through a consortium comprised of several research organisations and numerous academic institutes. According to the National Centre for Biotechnology Information (NCBI), there are 818 entries of SARS-CoV-2 complete genome sequence from various countries around the world. Countries that have submitted complete genome sequence include USA, China, Spain, Tunisia, Turkey, Iran, South Africa, Taiwan, Thailand, Vietnam, Nepal and Nigeria, with the highest number of submissions from the US.

From our country, we need to take the initiative to sequence the whole genome of the virus samples collected from infected patients in order to understand more about the virus type, its origin, rate of mutation, what type of vaccine would suit our population and most importantly, how we could face the next wave of infection in case of its re-emergence. In Bangladesh, we have several universities and institutes capable of doing genome sequencing with the necessary expertise. What is important is that we act quickly, before it is too late.