Aswini B | 21 April 2020
The little microbe, the SARS-CoV-2, has shaken the whole world and brought it to a standstill. From the greatest nation to the poor nations, everyone has suffered a lot because of this virus. Around 210 countries and territories have been affected by this virus, causing havoc among people. 2,424,634 total cases have been reported worldwide (as of 20th April 12:57 PM). Of which, 166,053 people have been deceased, and 636,187 people have been recovered (1). The statistics for India on the same day is 17,615 total cases, 559 deceased and 2854 recovered cases.
Researchers all over the world are trying to find ways to tackle the disease. Some are working on vaccines, while others are working on drugs that could be efficient against the virus. There are a few others who are working on diagnostics.
FDA has granted emergency use authorization to 'Abbot Laboratories', for COVID-19 tests that could provide the results in 15 mins. The test is a quick molecular test. It can give a positive result in 5 mins, but the negative result needs 13 mins.
'Body Sphere' has submitted an emergency use authorization to the FDA and is waiting for approval for a 2-minute testing kit for detecting novel coronavirus. The diagnostic uses antibodies in blood to test past and current infection. They claim that the test has 99 % sensitivity.
On 2nd April 2020 FDA has approved a rapid antibody-based diagnostic testing for emergency use. This is the first coronavirus antibody test to receive FDA authorization. The test detects IgG and IgM in the blood of suspected patients. However, IgG and IgM titer can be high in an individual due to any infections.
On the same run, CSIR, India has developed a diagnostic technique using the cutting edge CRISPR-Cas9 technology. They call it the paper strip-based testing assay. The team led by Dr Souvik Maiti and Dr Debojyoti Chakraborty from CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) have designed this kit which can detect the viral RNA within an hour. Dr Chakraborty says that any lab with a thermal cycler would be capable of performing this test.
The test works by converting the RNA into DNA, amplifying it and detecting the viral genetic material by deploying the Cas9 complex. Dr Chakraborty says that the kit can work very less viral RNA copy and would cost less than 500.
The director of CSIR-IGIB, Dr Anurag Agarwal said that the institute is developing a ‘sample to sequence’ strategy where the test samples can be diagnosed by next-generation sequencing (NGS). But why and how does sequencing of the virus during this pandemic help us? Sequencing of this viral genome will give us the information regarding its origin, different strains circulating in India (if any), and its efficiency to mutate.
Now that CSIR Labs are allowed do perform testing for COVID-19, they have access to the virus, which will aid them to sequence more of it. The DG CSIR Dr Shekhar C. Mande said that CSIR-CCMB Hyderabad and CSIR-IGIB, New Delhi have started sequencing the viral genome. Dr Rakesh K. Mishra, Director of CSIR-CCMB, has said that CSIR-CCMB and CSIR-IGIB, together are planning to sequence around 200 isolates. However, getting a sufficient quantity of the virus in the sample is still a challenge.
Dr Rajesh Pandey is leading the genomics force in CSIR-IGIB and his team is using a sequencing strategy which has multiple elements or aspects ink it. This strategy, along with the epidemiological data, will help in managing the outbreak and to design potential region for screening. He says that to target the scale and sensitivity for any India-specific strain, his team is using a combination of sequencing platforms. He further says that comparison of the genomic sequences of the strain(s) prevalent in India vs other countries will help to correlate the strain and its aggressive nature. Hence, as Dr Mishra says, we should start sequencing the virus from across the country to get an idea about the diversity of the virus if any.
Dr Mishra also said that CSIR-CCMB is planning to culture the virus, which might be helpful to gain an understanding about it. Also, it would be useful for testing vaccines and drugs.
Recently, students at CSIR-IGIB, with the guidance of Dr Sridhar Sivasubbu, Dr Vinod Scaria, Dr Sheetal Gandotra, Dr Vivek Rao have standardized and prepared a compendium as educational material for CSIR laboratories for performing RT PCR testing of 2019-nCoV samples for research purpose. This provides a standard detailed protocol for identification and confirmation of the viral genome.
With all the initiatives that are being taken, let us hope to ward off the COVID-19 pandemic soon.
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