Reversing the genetic flow: how scientists diagnose COVID-19

Biologists often refer to DNA as the almighty code of life. However, this is not true for all organisms on Earth. Disease-causing organisms, or pathogens, such as viruses contain a slightly different code known as RNA which stores the virus’ genetic information. Therefore, scientists can detect the novel coronavirus, SARS-CoV-2, through the presence of viral RNA in patient samples. 

SARS-CoV-2 belongs to the family, Coronaviridae, which are large RNA viruses comprised of approximately 26,000 to 32,000 RNA “letters” in length. That’s a lot of information for an organism that has been documented to be 0.06 microns in diameter – or 0.00006 millimeters! Like all other viruses, coronavirus relies on a host cell for replication and survival. This is because the viruses need to borrow machinery from another organism in order to replicate their own genetic information. Fortunately, viral RNA (v-RNA) has unique sequences that do not correspond to genetic sequences, or genes, found in human cells. Therefore, scientists can detect v-RNA by a process known as RT-qPCR. This process works as follows.

Firstly, both coding systems (DNA and RNA) have a known role within the “Central Dogma of Biology” (Figure 1). However, human cells only contain the correct machinery, or enzymes to convert DNA to RNA – they cannot convert RNA back to DNA naturally.

Figure 1 The Central Dogma of Biology. Every cell in our body contains an identical genetic code. However, all our cells are different due to which sections of DNA, or genes, are expressed, or transcribed into RNA. RNA is a second ‘code’ that is then translated to produce protein. Cell function is dictated by which proteins are in the cell and, therefore, tight regulation of gene expression is required throughout our lifetime (Khan Academy).

Secondly, RNA is highly unstable, making it difficult to amplify and, therefore, detect in a lab. In addition, scientists are unable to directly detect viral RNA particularly in early stages of infection. This is because the number of viral particles, or viral load, is initially very small as only a few rounds of viral replication have occurred in the host. Therefore, after extracting RNA from a patient, scientists must artificially convert RNA to DNA by a process known as reverse transcription. DNA is much more stable than RNA and can withstand several cycles of hot-cold temperature change. Temperatures of up 96 °C (205 °F) are required to amplify, or copy, the virus’ genetic sequence enabling it to be detectable by even the most sensitive technologies in a lab. These hot-cold cycles are vital for a successful polymerase chain reaction (PCR) to occur which detects whether the virus is present in a sample by specific binding of matching sequences (Figure 2). In particular, scientists are looking for the presence of a viral-specific sequence that encodes the viral nucleocapsid (N) protein (Figure 3).

Figure 2 Diagnostic pathway for COVID-19 using RT-qPCR. RNA is isolated from cells present in the upper respiratory tract of a patient. RNA is converted to DNA before amplification of genetic sequence by performing a polymerase chain reaction (PCR). In order to replicate the DNA, chemical bonds between the two strands need to be broken, a ‘mini-gene’ (or primer) needs to bind and ‘free’ DNA units need to be added to the sequence one by one. The primer is required to allow the cell’s machinery to recognise the DNA.

Figure 3 Structure of Coronavirus. The nucleocapsid (N) holds the RNA sequence, whilst the membrane (M), envelope (E) and spike (S) proteins form the capsule. 

Although this way of testing offers a robust, routinely-performed method to detect SARS-CoV-2, scientists are trying to update this approach to enable faster, but equally sensitive, testing for COVID-19. One of the few downsides to performing RT-qPCR is the length of time it takes to get from sample to result as each stage can take between 2-3 hours (ie. 9-10 hours for 10 samples/per machine). Considering the inevitable influx of samples within the next few months, routine RT-qPCR may become less practical for population testing.

Ongoing research aims to establish a blood test which would allow scientists to gain insight into whether someone has developed an immune response against the virus. This would be particularly advantageous as such testing would identify patients who have caught and then recovered from the virus, allowing epidemiologists – experts in global health and disease distribution – to accurately model the pandemic and provide invaluable information to the government regarding spread and location of disease on a global time-scale.

Such tests will be vital in future research regarding the biology of the virus as scientists hope to determine whether herd immunity for COVID-19 is feasible or how best to develop a vaccination regime for future generations. Researchers at the Centre of Disease Control and Prevention (CDC) are currently working to develop the basic parameters for this test however more samples are required before the method can be fully refined.

Current approaches are based on a routine biochemical test, known as enzyme-linked immunosorbent assay (or ELISA) which detects viral-specific antibodies. Antibodies are produced by our advanced, or adaptive, immune system in order to directly destroy or ‘neutralise’ an infection. However, scientists still need to validate this test in order to confirm that it only detects SARS-CoV-2 – and no other strains of coronavirus such as NL63. Scientists also hope that blood transfusion – from patients who show a powerful immune response to elderly patients who have a weakened immune system – may become an option for treatment of this disease.

COVID-19 has been described by world leaders as “biggest challenge of our lifetimes” with nearly 450,000 cases currently documented worldwide. However, scientists are working endlessly to develop a vaccine which has already begun early stage clinical trials in the US. Several UK-based projects aim to repurpose existing drugs such as research led by Professor Horby at the University of Oxford. This work aims to evaluate the use of antiviral drugs and low-dose steroids as treatments for COVID-19, in an adaptable clinical trial known as RECOVERY. These drugs are currently used to treat HIV and, therefore, have already passed rigorous safety testing unlike novel treatments. Whilst the team at Oxford hopes their trial will inform current patient treatment within the next three months, researchers at Queen’s University Belfast hope a high-throughput drug testing approach, on over 1,000 known compounds, may provide additional future treatments for management of this devastating disease.

I wanted to finish this article by wishing everyone to stay safe and to remind you to check in on family/friends, be respective of others and to look for vulnerable neighbours even if all you do is writing a short note to ask how they’re doing. To those who know me personally, I’m always happy to have a chat – otherwise, please get in contact with any general/science questions and I’ll do my best to respond!

References and further reading:

Featured Image by Republica from Pixabay 

Introduction to COVID-19 by New Scientist

Bedford, J. et al COVID-19: towards controlling of a pandemic (2020) The Lancet DOI: 10.1016/S0140-6736(20)30673-5

Vogel, G New blood tests for antibodies could show true scale of coronavirus pandemic (2020) Science doi:10.1126/science.abb8028

Sheridan, C Fast, portable tests come online to curb coronavirus pandemic (2020) Nature Biotechnology

Other articles:

Blood tests for COVID-19

Ongoing research for COVID-19 treatments (UK)

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