Dr. Sujan Sigdel
Bioinformatics is an interdisciplinary science that integrates computer science, mathematics, statistics, and molecular biology to generate, interrelate, and interpret biological data. The use of biological data has been increasing globally in all fields of biology research and education including medicine, agriculture, pharmaceutical, molecular biology, biodiversity conservation, phylogenetics studies etc. Focusing on the application of Bioinformatics on infectious diseases, it has contributed immensely to our understanding of these diseases, its mechanism and the spread of antimicrobial resistance, host immune responses, identification of potential diagnostic markers and vaccine targets. Genomics data generated from pathogens and animal models can be combined to give advice on treatment options as well as potential drug and vaccine development. Despite its immense importance Nepal has lowest research output on infectious disease genomics including coronaviruses, and bioinformatics application.
Coronaviruses didn’t just pop up recently. They’re a large family of viruses that have been around for a long time. Coronaviruses are of both veterinary and medical importance. It includes porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and the human coronaviruses; severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome coronavirus (MERS-CoV). Recent years, many new strains have been identified which infects a wide range of hosts from mammals to birds and closely related coronaviruses have been identified in distantly related animals suggesting interspecies jumps. The new or “novel” coronavirus is one of several known to infect humans. This virus isn’t new to the world, but it is new to humans. When scientists found out that it was making people sick in 2019, they named it as a novel coronavirus. The COVID-19 disease outbreak caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading at a high rate globally. As of 15 April 2020, there have been 1,918,138 confirmed cases of COVID-19, including 123,126 deaths, reported to WHO. New cases spiked outside of China, especially USA, Italy and other European countries, where the number of new cases is larger than in China.
In this global crisis, bioinformatician’s, are trying their best to win the scientific battle against this deadly pathogen. Although most of the time they are working behind closed and confined doors, they have provided critical information to assist scientists throughout the world. The most crucial bioinformatic breakthrough in this outbreak was detailing of the new coronavirus sequence, the genome of COVID-19 and the crystal structure of its protease enzyme which is a starting point in developing drugs, diagnostic tools and a vaccine for this deadly virus. The effort to find the genes that are responsible for viral replication and the protein responsible for the host cell attachment have benefitted from this sequencing. Based on this information, scientists have developed diagnostic tools with reverse transcription polymerase chain reaction (RT-PCR) which has been endorsed by the WHO. Crucial part of primer designing of the PCR protocol was designed with tools that were based upon the bioinformatics sequence alignment method. This demonstrates that bioinformatics played a role in the very early efforts to develop the lab protocol for diagnosing COVID-19.
Furthermore Bioinformatics will have crucial role in developing drugs and especially vaccines by utilizing information from different databases (eg. Pubchem, drug bank, PDB, NCBI etc) and using computational chemistry tools. The next step will be conducting massive molecular simulations using supercomputers to obtain the best lead compounds to be extrapolated as new drug candidates in the wet laboratory setting. Modern supercomputers and software’s can simulate the complexity of the biochemical reaction in the cell, so they will have a high resemblance to the wet lab environment. Another beauty of bioinformatics in the present emergency situation is quicker alternatives to peer-reviewed scientific journals. Life sciences preprint server’s bioRxiv and medRxiv, may have important role to hasten the dissemination of research results in a time of emergency.
Another important application would be the use of artificial intelligence (AI) and natural language processing to analyse the data about the spread and impact of the pandemic to enable the fight against the coronavirus. The aim can be on the analysis of the socioeconomic impact of the virus locally and globally. The goal can be on finding impact indicators, patterns and statistics that can serve local authorities to take better and faster measurements.
Based on the global experiences; in case of any dangerous infectious disease, Nepal needs to work on disseminating biological sequences as soon as possible so the WHO and the rest of the world can help us quickly. However there are some challenges, Nepal is a young and prospective country on biological research spatially on bioinformatics. Till now no university in Nepal has well developed core bioinformatics course that incorporates many of the public-domain databases, research tools, peer review journals and research organizations. Especially three major challenges are there; Inadequate infrastructure, lack of training opportunities and well-structured bioinformatics courses and limited research funding. There are some research groups and institution doing well as per need but no collaborative and integrative activity is shown on bioinformatics research.
Thus, there is a need to strengthen training and capacity building in bioinformatics in Nepal which can be achieved through the establishment of well-structured courses, mentorship for trainee bioinformatician’s and better career prospects to maintain trained bioinformatician’s inside the country. COVID-19 has now emerged as a new global threat and as a developing country Nepal can benefit on research and development work by using Bioinformatics tools.
- Dr. Sujan Sigdel, Bioinformatician
Research Director,
Pokhara Pharmaceuticals Pvt. Ltd.