Lack of collaboration slacking India’s coronavirus fight

Deepak Nair and Neel Sarovar Bhavesh are part of a growing breed of frontline structural biologists in India. As far as interesting work on a pandemic virus goes, their labs – Nair’s Laboratory of Genomic Integrity and Evolution at the Regional Centre for Biotechnology, Faridabad and Bhavesh’s Transcription Regulation Group at the International Centre for Genetic Engineering and Biotechnology (ICGEB) in New Delhi – are not the first to come to mind. However, both these groups have uploaded interesting unpublished work on preprint servers on 23 March 2020.

India appears to be in an early phase of the pandemic, but positive cases are adding up faster now than even last week. The virus causing Coronavirus Infectious Disease-2019 (COVID-19) that emerged in China in December 2019 and has travelled the world with over 380,000 confirmed cases and over16,500 deaths¹, is gathering steam in India.

The COVID-19 virus has a positive-sense RNA genome, which means that the genetic material of the virus released in the infected cells gets directly converted into proteins. One of these proteins is the nonstructural protein 12 (nsp12), an enzyme also called the viral replicase or RNA-dependent RNA polymerase (RdRp). Its function is to amplify each molecule of the genomic positive RNA (+RNA) into hundreds of new (+)RNA molecules via (-)RNA intermediates. But this enzyme, which uses RNA as a template to make more RNA, has a fidelity problem compared to replicases that use DNA as a template to make either more DNA or RNA. And that is why RNA viruses show much more variation in their sequences and evolve faster than DNA viruses. This variation can be used to trace their lineage.

The RdRp is a good target of antivirals because this enzyme is missing from human and animal cells, which don’t have to replicate their RNA. Though the virus hijacks the cellular machinery for its replication, it must make its own RdRp. The COVID-19 virus is no exception. Deepak Nair and his student Naveen Narayan used a high-resolution structure of the RdRp from SARS virus, which is 97 per cent identical in sequence to the RdRp from the COVID-19 virus. They then virtually screened the various databases of FDA approved drugs, natural, antiviral and drug repurposing compounds. Their best hit for a compound turned out to be methylcobalamine, commonly known as Vitamin B12.

Using energy minimisation protocols, they found that Vitamin B12 sits tightly in the RdRp nucleotide-binding pocket. Since the RdRp adds nucleotides (nucleic acid building blocks) to a growing RNA chain, its inability to bind them in the presence of Vitamin B12 would inhibit the enzyme and limit viral replication².

Neel Bhavesh and his student Anupam Patra carried out virtual screening of a library containing 1.2 million small molecules to show that Valproic Acid Coenzyme-A, a metabolite from prodrug valproic acid, binds stably to the COVID-19 virus RdRp³. On 22 March 2020, scientists at the University of California at San Francisco, USA, also added supporting data for valproic acid in another preprint server⁴.

The need for rapid collaboration

The next logical step would be to test if Vitamin B12 or valproic acid inhibit the growth of the COVID-19 virus in a cell culture. It would quickly validate in silico (virtual) results and could point to a simple preventive solution to the COVID-19 threat. The Nair paper has already been viewed over 360 times and downloaded about 70 times; the Bhavesh paper shows over 400 views and 120 downloads (as on 24 March 2020). Bhavesh also confirmed in a social media message that within hours of his paper going online, the multinational pharmaceutical company GlaxoSmithKline contacted him.

For laboratories with a COVID-19 culture system, it would be fairly simple to test these leads. It would happen in another part of the world and India would lose out once again. This would not be due to lack of trained people or Biosafety Level 3 (BSL3) containment facilities, but for the lack of sharing. Currently, no one in India outside of the National Institute of Virology (NIV), Pune and the Indian Council of Medical Research (ICMR) has access to the COVID-19 virus. For these agencies, opening up to share resources would be in national interest now.

A recent communication from the India government’s Empowered Committee for COVID-19 Response allows all national laboratories with the required manpower, equipment and containment facilities to test for COVID-19 and to be able to culture the virus⁵. It also directs the central and state governments, and private hospitals to co-operate with national laboratories. Clearly, unless these laboratories and facilities work together, India cannot move quickly towards finding solutions.

Next frontiers

What are the other COVID-19 research questions that can be quickly explored by Indian scientists? Researchers at NIV, Pune have published the first transmission electron micrographs of the virus from an Indian patient⁶. In the past few years, India has invested heavily in structural biology, with a state-of-the-art cryo-electron microscope available in the Bengaluru Biocluster, and smaller machines available at a few other locations including Pune.

With virus grown in culture, it should be possible to get its high-resolution structure. At least two laboratories in India – the ICGEB/Emory Vaccine Centre and the Department of Biochemistry at AIIMS, New Delhi, have used blood from recovered patients to develop clonal B-cell derived human monoclonal antibodies against dengue virus and HIV-1, respectively. Given access to recovered patients, such antibodies against the COVID-19 virus can be developed within 3-4 months by these laboratories. The antibodies are likely to have therapeutic value.

Since the outbreak began in December 2019, over 1100 strains of the COVID-19 virus have been sequenced from around the globe. This provides us insights into how the virus is evolving as it jumps continents. How are selective variants seeding localised outbreaks in different parts of the world? Does it have any bearing on the morbidity and mortality observed in those regions? Is the virus evolving into a more virulent or a more benign human-adapted form? Unfortunately, none of these questions can be answered for the virus circulating in India. Though we now have around 500 confirmed positive cases in India, only two viral sequences from Indian patients are publicly available. These sequences are different from each other, and cluster with two different clades, each of which have sequences from China. This is yet another opportunity to get cracking on.

Public investment in R&D becomes most useful when it can be mobilised to serve national interests when needed. India stands to lose valuable time not due to lack of capability, but because of the lost chances of working together.

[Nature India's latest coverage on the novel coronavirus and COVID-19 pandemic here. More updates on the global crisis here.]

References

1. Covidindia.org

2. Narayanan, N. & Nair, D. T. Vitamin B12 may inhibit RNA-dependent-RNA polymerase activity of nsp12 from the COVID-19 virus. Preprints.org. (2020) doi: 10.20944/preprints202003.0347.v1

3. Patra, A. & Bhavesh, N. S. Virtual screening and molecular dynamics simulation suggest Valproic acid Co-A could bind to SARS-CoV2 RNA depended RNA polymerase. OSF. (2020) doi: 10.17605/OSF.IO/Y8UAC

4. Gordon, D. E. et al. A SARS-CoV-2-Human protein-protein interaction map reveals drug targets and potential drug-repurposing. bioRxiv (2020) doi: 10.1101/2020.03.22.002386

5. http://psa.gov.in/

6. Prasad, S. et al. Transmission electron microscopy imaging of SARS-CoV-2. Ind. J. Med. Res. (2020) doi: 10.4103/ijmr.IJMR_577_20