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COVID-19: Virology and Epidemiology

The Basics

Virology is the study of viruses and virus-like agents. Virologists often study the taxonomy, disease-producing properties, cultivation, genetics, as well as any other factors that may be required, to draw important conclusions in correlation to their study. Epidemiology is the study of the distribution and determinants of health-related states and events in populations. Epidemiologists are often referred as “Disease Detectives” because they are on a constant lookout for the cause behind the disease, identify people who are at risk, and suggest prevention and outbreak control techniques.

Doctors and healthcare experts also count as epidemiologists(Image courtesy of Wix)

The Virus in Itself

You might have heard of the COVID-19 virus being referred to as “SARS-CoV-2”. The Coronavirus Study Group of the International Committee on Taxonomy of Viruses has decided on this name because the Coronavirus is linked to the Severe Acute Respiratory Syndrome(SARS) in many ways. In fact, the COVID-19 virus falls in the same subgenus and has the same receptor as the SARS coronavirus: Angiotensin-Converting Enzyme 2(ACE2). The only difference is the clade in which SARS-CoV-2 falls in. The COVID-19 virus has also been found that related to another betacoronavirus: The Middle East respiratory syndrome(MERS).

The closest similar RNA sequence found in the COVID-19 relates to the bat coronaviruses. Upon phylogenetic analysis, researchers have come to discover that there are two types of strains found in cases: L(70%) and S(30%). In most cases, the symptom onset took multiple days to develop in the individual affected. A study conducted among 77 transmission pairs in China showed that the mean serial interval between the onset of symptoms was 5.8 days.

Strain L and Strain S explained(Image courtesy of Daily Mail)

Moreover, coronavirus’ genome is 3X larger than the influenza virus’. It has other packages to interfere with interferon function, allowing it to spread faster. It takes 7-10 days for the T cell responses to be initiated(patients get better or worse). This mostly depends on an individual’s genetic factors, magnitude, and type of immune response. The timing of antivirals is considered important since medications like Remdesivir have shown efficacy after approximately 12 hours of infection. While T cell immunity has been found to be protective in animals, more data can help us understand wherever IL-1 and IL-6 based therapies can increase efficacy in patients who experience cytokine storm syndrome.

Virus Transmission

SARS-CoV-2 has expanded to all continents but Antartica. The primary mode of transmission remains person-to-person as this virus can be caught from up to 6 feet of distance. The likelihood of blood borne transmission remains low but is still possible.

A video explaining the transmission of COVID-19 through respiratory droplets.

As of June 7, 2020, statistics reported over 94,450 reported cases in Canada. Cases were slowly starting to develop as travellers returned from parts of the world from January to late February. There was a sharp spike in the epidemic curve in March. Commonly reported symptoms among reported cases include cough (73%), headaches (47%), and fever and chills (36%). Based on case reports received to date, 9,056 cases have been hospitalized, including 1,828 in intensive care. The majority (85%) of COVID-19 cases are related to domestic acquisition(exposure that occurred within Canada).

A quantitative reverse-transcription polymerase chain reaction(qRT-PCR) is a test used to detect whether a person is infected or not by detecting the presence and relative quantity of viral RNA. Viral genes with mistakes are indistinguishable from the ones that aren’t. Virions are the RNA inside the packages of the functional/non-functional RNA, which are also what we’re looking for. Virologists use plaque or TCID50 assays to assess how much potentially transmissible virus would shed from recovered patients or the environment. Unfortunately, these tests are time-consuming, require a specialized biocontainment, and are not very practical for clinical diagnosis or broad surveillance. Generally, no virus remains infectious on surfaces for anywhere around 17 days and by cleaning objects as well as surfaces in the environment, the risk of the virus spreading can be greatly minimized.

Common Concerns

  1. There were initially concerns about COVID-19 escaping from a lab as there were safety concerns regarding the high containment Wuhan Institute for Virology. This was the case with Influenza and SARS-CoV.

  2. Other theories that have come up include one that proposes that the virus escaped from Malayan pangolins. These small, scaly mammals are native to Asia and have anywhere from a 85.5% to 92.4% similarity to the COVID-19 sequence.

None of these are true, however, because COVID-19 strains have been traced back to Wuhan’s animals market. Fruits bats are unique because they serve as hosts for viruses and are able to break the barrier, passing it on.  For example, filoviruses can lead to hemorrhagic Ebola-like fevers and have caused small deadly outbreaks in Australia/Asia. Additionally, deforestation and climate change have minimized the ecological niches of wildlife, including the migratory range of bats, forcing animals to come into closer and closer contact with humans.

According to Shi, the Wuhan Institute’s Deputy Director, also referred to as “bat woman” for tracking down dozens of SARS-like diseases in bats: "If we want to prevent human beings from suffering from the next infectious-disease outbreak, we must go in advance to learn of these unknown viruses carried by wild animals in nature and give early warnings.”

Next Steps

The term “herd immunity” refers to when a sufficiently high proportion of the population is immune to a contagious disease. According to Dr. Nair, we haven’t reached anywhere near herd immunity. More importantly, the new spread must be kept under control is because the coronavirus can spread before the individual displays any symptoms, like mentioned earlier.

By now you’re probably wondering how we can avoid the second wave of COVID-19. Well, logically, the second wave cannot be avoided without a vaccine but the good news is that we can control the impact of the second wave with our habits i.e. by maintaining good hygiene, keeping a safe distance of at least 2 metres from others, and wearing protective gear such as masks. The curve will only flatten if we continue to social distance like we have been for the past few months.


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Featured Image courtesy of Unsplash

Article Author: Palak Agarwal