The current Coronavirus epidemic (COVID-19) has been causing widespread panic and has been a major health concern in the past months. Efforts from both governments, pharmaceutical companies and the scientific community have been focused on developing a vaccine and identifying therapies to contain its spread and treat patients. Beside the lack of a vaccine or an effective therapy, another major concern of the COVID-19 epidemic is also the presence of asymptomatic patients that cannot be easily detected and can thus hamper efforts to contain the epidemics, leading to the draconian measures imposed in China and the quarantine of entire boats or planes, as seen, for example, in Japan.
Scientists and companies are racing against time to find a cure and there has been a flurry of articles and announcements on repurposed drugs that show promise as a potential treatment. A recent review indicated several candidates for repurposing based on their mode of action. These includes various nucleoside agonists (such as ribavirin or favipiravir) , protease inhibitors (such as disulfiram, lopinavir and ritonavir), spike inhibitors (griffithsin), interferons and immune modulators (such as the antimalarial drug chloroquine). A report from Thailand indicated that a combination of three antiviral drugs (ritonavir, lopinavir and oseltamivir) improved the condition of several patients. The broad-spectrum antiviral drug remdesivir, in combination with chloroquine, has shown high efficacy in the inhibition of COVID-19 in vitro in a recently published article. Finally, using an AI approach based on chemical structures and medical literature, researchers identified baricitinib, an inhibitor of endocytosis, as a potential treatment.
The latter study indicates the power of accessing currently available databases to extrapolate to gain insights. In fact, there is now a large public collection of gene expression datasets on a multitude of drugs and health-related conditions (such as viral infections, tumours and autoimmune diseases) that can be mined for information. Even larger databases are held privately by pharmaceutical and biotech companies. Unfortunately, access to such information is restricted to busy researchers with adequate computing skills and statistical knowledge and as such progress and discoveries hit a bottleneck that depends on the priorities of this small number of scientists.
In order to address this bottleneck, we have developed a user-friendly platform (Omics Playground) to make this type of sophisticated analysis accessible to researchers without requiring programming knowledge. Another advantage is also the rapid access to databases and generation of results. With the current explosion of single cell sequencing, data on a multitude of diseases and conditions are likely to be both rapidly and abundantly generated. Our platform is perfectly poised to allow the rapid, accurate and efficient analysis of these enormous datasets and immediately cross-reference any findings against various databases, including viral, immune and drug-related gene expression datasets. This should further reduce the time required to gain novel insights and lead to the rapid development of early detection biomarkers, the identification of protective immune mechanisms or the repurposing of known drugs for tackling emerging infections such as COVID-19.
As our contribution to help the community in tackling the current Coronavirus emergency, we decided to offer a special open access online edition of our platform, pre-loaded with various viral infection datasets (including publicly available SARS and MERS Coronavirus studies). Users can either load and analyses these datasets or upload their own samples. We will not store or use any of the uploaded data. The data will remain exclusive property of the users, unless they decide to make it publicly available by contacting us. The main purpose is to make our tool available to the scientific community and speed up the discovery of treatments against the COVID-19 epidemic.