COVID-19 - origins, transmission, symptoms and diagnosis

The novel coronavirus pandemic has left the world in shambles, with countries all over the globe placed under lockdown and the economy deteriorating. So far, half a million people have lost their lives to the virus, and the numbers are continuing to rise. It is no wonder that so many people are motivated to find a cure or vaccine in order to return life to normal and remove any traces of the virus which is terrorising so many. To explore possible gateways which can be taken to access a vaccine or cure, it is essential that the science behind the virus is thoroughly understood.

Origins and transmission

The term coronavirus not only describes the specific virus which people are suffering from today, but is rather a blanket term for many types of viruses which all share the same structure. They are spherical in shape and have spike glycoproteins protruding from the viral envelope. This family of RNA viruses often exhibit respiratory illnesses and some of the most notable coronaviruses include SARS (Severe Acute Respiratory Syndrome) and MERS - Middle East Respiratory Syndrome. While there are hundreds of different coronaviruses, only seven of them can occur in humans. Four of them cause common colds, two cause severe respiratory illnesses, and the one we are suffering from today can cause either of these results.

The coronavirus which causes Covid-19 has been labelled ‘SARS-CoV-2’ and can spread through respiratory droplets. It spreads most rapidly in enclosed spaces, where individuals are in close proximity and the respiratory droplets, made up of viral saliva or sputum, can be inhaled before the particle’s weight leads them to fall to the ground. The larger the size of the particles inhaled, the further down the respiratory tract the virus can travel, likely causing more serious symptoms.

Once the virus has gotten within the human body, it uses the glycoprotein spikes of its specialised structure to bind to the membrane of human cells. After initial binding of the receptor to the cell, through the binding of the spike proteins to the ACE2 (Angiotensin-Converting Enzyme 2) receptors, viral particles need to fuse their envelope to the cell membrane to allow for the nucleocapsid (a protein shell which holds the genetic material of a virus) to be delivered inside the cell for replication. The spike proteins both mediate receptor binding and help membrane fusion. When the fusion process occurs, there are two large conformational changes of the spike proteins, allowing for the fusion protein to shift from a place where it is protected to the membrane of the human cell, facilitating the merging process of the two membranes. After the attachment of the viral membrane to the cell membrane, the viral genes enter the human cell through endocytosis and are copied until lysis of infected cells allows for further infection.

Despite the spike glycoproteins being essential for the spread of the virus, they also act as a weakness for the virus, due to them being exposed and hence easily targeted by the immune system. The only way that the virus protects itself is with a sugar coat that hides the conserved parts of its spike proteins from the immune cells. This likely makes it more difficult for the immune system to destroy the virus naturally. SARS-CoV-2 has undergone a few mutations since its introduction in humans. Multiple different strains have been identified in infected individuals. This is because the coronavirus family are the largest RNA viruses, meaning that the likelihood of replication errors occuring is higher. Only enzymes which are a part of the replication process are able to recognize and correct these errors, decreasing the mutation rate.

Symptoms

The SARS-CoV-2 virus has affected over 10 million people globally, and the numbers continue to rise. It is essential to monitor the number of cases and actively diagnose members of society in order to monitor how severe and widespread the virus is at any given point in time. Often, people are asked to keep watch for any of the common symptoms of the virus and isolate themselves for 14 days. This is because symptoms of the virus can begin to show up between 2 to 14 days following exposure to it. The symptoms to look out for are:

• Fever or chills

• Cough

• Shortness of breath

• Breathing difficulties

• Congestion or runny nose

• Headaches

Less common symptoms include:

• Fatigue

• Body aches

• Loss of taste or smell

• Nausea and vomiting.

As there is such a vast array of symptoms, and many of these symptoms are shared with other illnesses, like the common cold, it is very difficult to distinguish whether or not they are a cause for concern. Additionally, infected individuals can be asymptomatic, making the process of diagnosis harder and the threat of spreading the illness higher.

Diagnosis

There are two main types of tests which are used to diagnose the SARS-CoV-2 coronavirus. The first of these is the PCR (polymerase chain reaction) based test, which is used to see if a patient is actively infected with the virus. PCR is a method of replicating DNA under laboratory conditions and is highly useful in genetic research. A standard PCR sequence of 30 cycles can create over 1 billion copies of DNA. The PCR-based test begins with the collection of a sample by inserting a sterile swab into the nostril and moving it forward into the nasal cavity. This swab is rotated for several seconds in order for secretions which could contain viral particles to be absorbed. This swab is then placed into a sterile tube which contains a viral transport medium that allows for the virus to survive until it can be identified by the test.

In order for PCR to be used to replicate SARS-CoV-2, which is an RNA based virus, the RNA from the virus must be converted to DNA using a process called reverse transcription. RT-PCR, which stands for reverse-transcriptase-polymerase chain reaction is the specific type of PCR which is used in coronavirus testing. The enzyme reverse transcriptase is responsible for the conversion of RNA to DNA through the reverse transcription process. A solution called a lysis buffer is used to break the virus particles open. This is followed by the process of centrifugation, where the virus particles are suspended in a liquid and placed in a centrifugation tube. The tube is then placed on a rotor and spun to speed up the process of sedimentation.

After centrifugation, the RNA of the virus is separated from its other contents. The RNA is then combined with a buffer solution containing reverse transcriptase, DNA polymerase enzymes, as well as DNA nucleotides and primers, which are all crucial to the process of reverse transcription. This is thoroughly mixed and placed onto a PCR plate using a pipette. The plate is then placed into the PCR machine, where the reaction takes place. In PCR, the newly formed DNA is first heated to separate the DNA strands. Next, it is cooled slightly so that primers can be bound to their complementary sequences on each single-stranded DNA template. Finally, everything is heated once more, at a slightly lower temperature than in the first step so that DNA polymerase can extend the primers and synthesize new strands of DNA. A fluorescent light signal on a selected target gene in the PCR machine indicates the presence of SARS-CoV-2. The fluorescent light signal is converted into digital data and is input to a computer, where the results can be read and analysed.

The second test used to diagnose SARS-CoV-2 is called a serology, or antibody, test. This test is used to identify whether someone carries antibodies in the blood for the virus, making it likely that they have already come into contact and their body has fought it off before it could cause infection. The serology test takes a sample of blood using a finger prick and places the blood onto a testing kit which uses a technique called ELISA (Enzyme-Linked Immunosorbent Assay) to check for one or both of the antibodies for SARS-CoV-2. These are called IgM antibodies, which occur earlier in an infection, and IgG antibodies, which are more likely to occur later on in the course of an infection. The test is done by adding the specific antigen to the blood. If the person’s blood contains antibodies to the antigen, the two will bind together. In order to determine whether the antigen has been bound to the antibodies, an enzyme is added to the testing kit and it allows for a visible observation of how the blood and the antigen react together. The result of this test occurs in a few minutes, which is a much shorter time span than that of the PCR-based test. Since the coronavirus that causes COVID-19 is relatively new, it is not known how long immunity will last. This means that there is a possibility that an individual’s immune system could respond to the virus without either of these antibodies being detected in their blood, because immunity could be short lived. The accuracy of the serology test is also debated, hence the PCR-based test is much more frequently used.

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References

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