Bioinformatics and Its Contribution to the Fight against COVID-19

The number of confirmed COVID-19 cases in Indonesia per Friday (as of 04/17/2020) had reached 5,516 people: 4,472 in treatment, 548 recovered and 496 deaths. The government itself has since continued to work on various ways to break the chain of the coronavirus spread.

The COVID-19 pandemic has been considered a contemporary global issue. World health experts say that Indonesia is facing a surge in the number of patients: the most recent reports on positive cases have shown that the spread has reached 34 provinces. DKI Jakarta becomes the number one most infected province; other four provinces included in the top 5 list are West Java, Banten, East Java and Central Java.

With the increase in new confirmed cases, people become more anxious and without a clear understanding of the coronavirus. In regards to this, it is considered important to provide a Bioinfromatics take on the virus. How is coronavirus analyzed from the perspective of Bioinformatics?

The novel coronavirus or SARS-CoV-2, which is the cause of COVID-19, can be analyzed through Bioinformatics perspective in order to find new solutions for diagnostics, treatments and prevention blueprints in the form of vaccines. In the diagnostic context, what should be done is to navigate the SARS-CoV-2 genome database in order to look for conserved regions that can be developed as markers for molecular diagnosis.

In the context of treatments, there are two strategies developed by bioinformaticians. The first strategy is to use an existing drug database or drug repurposing. The second strategy is to use an herbal database, which has also been widely developed in China. Finally, in the context of vaccine development, bioinformaticians use the immunoinformatics method to design a new generation of safer vaccines which does not use genetic materials.

The development of diagnosis, treatments and prevention with Bioinformatics is made possible by the availability of the SARS-CoV-2 genome and proteome sequence database in the genbank database. Meanwhile, the 3D protein structure is available in the RCSB/PDB (Protein Data Bank) database.

What should be done with the current situation? In general, we need to follow the guidelines from the government which is in line with the WHO procedure, such as practicing physical distancing, maintaining diligent hand washing and wearing masks. Do not go to the hospital if you are not seriously ill and follow the instructions from the RT/RW in relation to securing residential areas.

Dissenting opinions on government regulations or policies should be submitted to experts, such as epidemiology/public health experts, specialists in internal and pulmonary diseases, as well as scientists working in fields related to virology such as molecular pharmacology, biomedicine and bioinformatics. The government and private organizations have opened vacancies for volunteers to help with the development of COVID-19 diagnostic kits, which would be very good if all relevant parties could participate in.

There already is a Bioinformatics science consortium called MABBI (Indonesian Bioinformatics and Biodiversity Society). This consortium is currently working collaboratively with different institutions on finding the best diagnostic kits, treatments and prevention methods for SARS-CoV-2 / COVID-19, and i3L is fully involved in the consortium.

Is there really a vaccine that is being tested to ward off coronavirus? Indeed there are already several countries trying to develop vaccines, the Indonesian government has even formed a task force to develop the COVID-19 vaccine. However, based on the latest phylogeny tree data on SARS-CoV-2, this virus apparently has several clusters, which may develop into several subtypes.

This phenomenon also occurs with other viruses, such as HIV, flu and dengue/DENV. Consequently, future vaccine designs are very likely to have to create a backbone that can cover all clusters, which is not impossible to be further developed into different subtypes.

The biggest challenge of all of this is that SARS-CoV-2 genetic material in the form of RNA can easily mutate. This is why vaccine development is very challenging, even when using the latest Bioinformatics science and molecular-biomedical instruments, success cannot always be guaranteed.

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