Coronavirus

Crowned viruses

Coronaviruses are RNA viruses enveloped with a helical¹ capsid². The genome is in the order of 20,000 base pairs and the virion³ is around 120nm in size. Under electron microscopy Coronaviruses exhibit a protein called “Spike” on their envelope, which gives them the appearance of a crown, explaining their name “coronavirus”.

There are different species of coronavirus. Seasonal human coronaviruses (HCoV) are the second leading cause of colds in Europe after rhinovirus⁴. Although frequent, they are not very dangerous. Conversely, the SARS virus (SARS-CoV-1), the disease agent Covid-19 (SARS-CoV-2) and the virus causing Middle East acute respiratory syndrome (MERS-CoV) may be dangerous to humans, since all three can lead to respiratory distress secondary to viral pneumonia.

The SARS-CoV-2 pandemic

SARS-CoV-2 was discovered in the Wuhan region of China in December 2019. It most often causes asymptomatic infection or flu-like illness characterized by fever, myalgia, arthralgia, severe fatigue and sometimes disturbances in taste (dysgeusia⁵) or smell (anosmia⁶). Unfortunately, it too often causes major respiratory damage with bilateral viral pneumonia requiring administration of oxygen and sometimes assisted ventilation in intensive care. It can also cause a hyperinflammatory and hypercoagulable condition causing venous thrombosis⁷ or pulmonary embolism⁸. The disease is also characterized by late complications (cutaneous vasculitis, cardiac involvement, meningoencephalitis, etc.).

Due to its high contagiousness (effective reproduction rate “Re” of around 3 initially and even 10 with the Omicron variant), it was the source of a global pandemic in 2020, which required the confinement of the population in order to limit the overload observed in hospitals of the whole world.

Diagnostic tests

The disease can be diagnosed by RT-PCR⁹ detecting RNA in different types of samples (mouth swab, nasopharyngeal, oropharyngeal, respiratory secretions, etc.). Diagnosis by immunochromatographic¹⁰ tests (detection of antigens) is also possible, but with a sensitivity of around 1,000 times lower. Indeed, while the detection limit of PCR is of the order of 100 copies per ml, that of antigen tests is only of the order of 100,000 copies per ml.

The serology¹¹ makes it possible to detect antibodies directed against various proteins of the virus including the nucleocapsid (anti-N) and the Spike (anti-S). Infected people develop anti-S and anti-N antibodies about 10 to 15 days after infection. Vaccinated people usually only show antibodies against protein S, as this protein is the key for the entry for this virus. Vaccines are designed to induce the production of antibodies neutralizing¹² the entry of the virus into cells thanks to anti-S antibodies.

The sequencing of the virus genomes makes it possible to precisely characterize which variant has infected a given patient and makes it possible

to confirm transmissions between 2 individuals,
to confirm prolonged infections by the same virus (sometimes for more than 2 months in immunosuppressed individuals) and
to verify whether a patient who is reinfected or infected despite a vaccine has a particular variant¹³.

Zoonotic in origin

Like many other infectious diseases, the coronavirus is of zoonotic origin and several animals have been implicated as possible reservoirs or vectors (pangolins, mink, bats, etc.).

Very contagious

The epidemic spreads particularly quickly when someone has a particularly high viral load (superspreader¹⁴). About 30% of people are asymptomatic and although the viral load is on average 100 times lower in asymptomatic people, large gatherings were the cause of extremely rapid epidemic outbreaks in the first months of 2020. Thus, for example, wide dissemination can occur during large gatherings and especially when people sing and shout at the top of their lungs such as in football stadiums or around hockey rinks or when people sing in a choir. Note that the transmission of the virus can also be facilitated by overcrowding in trains, subways or other public transport. Transmission depends not only on the viral load in the upper airways but also in the lungs. Thus, a symptomatic coughing patient should be considered possibly contagious even if upper airway RT-PCRs show relatively low viral loads.

Vaccines

By the end of 2020, vaccines were available that allowed a significant number of people to be vaccinated in just a few months, gradually bringing the epidemic under control and reducing preventive measures. These vaccines will likely need to be adjusted in future years depending on the emergence of variants¹³, as is the case with other RNA viruses.

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