Virology

The Coronavirus Disease 2019 (COVID-19) is a respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). By late March 2020, the viral infection, originally detected in China, had expanded into a worldwide pandemic.

Reservoir and strains: The viral strain was first discovered in the city of Wuhan, Hubei province of China in November, 2019. It is believed to be a zoonotic virus, related to coronavirus species found in bats with an intermediate animal reservoir that remains to be determined, although pangolins have been suspected. Features of the SARS-CoV-2 genome, including mutations in the receptor binding sites and subunit spikes, support the view that this is a novel virus that evolved through natural selection during the process of zoonotic transfer and that it is not derived from any previously known virus. Extensive mapping and tracking of the viral strains is currently underway through projects such as Nextstrain.

Viral characteristics: SARS-CoV-2 is a positive-sense, linear, single-stranded RNA virus from the coronaviridae family, specifically the betacoronavirus genus. Other viruses in coronaviridae family were responsible for the SARS-CoV outbreak in 2003 and the MERS-CoV outbreak in 2012. The viral infection commences with the attachment of the viral spike glycoprotein (S) to the receptor, which is suspected to be the angiotensin converting enzyme 2 (ACE2) receptor. Once in the cell, the virus is translated using the host ribosome. The virus also carries its own RNA-dependent RNA polymerase used to replicate the RNA for progeny viruses. The virus also has a number of virulence factors (Nsp1, Nsp3c, ORF7a) that interfere with host immunity. These virulence factors may be potential targets for effective anti-viral therapy.

Transmission: The virus is transmitted via the respiratory route by human-to-human contact, largely via respiratory droplets. These droplets have an effective range for infectivity of about two meters, but the virus may also be aerosolized and may be acquired from fomites (contaminated surfaces), both of which would extend the range of transmissibility beyond that possible by droplets alone. The virus has been found in blood and stool samples, but fecal-oral transmission has not yet been determined to be a major source of spread.

Incubation Period: The incubation period following infection, based on early data from Wuhan, appears to be about 5.2 days (95% confidence interval [CI], 4.1 days to 7.0 days), with the 95th percentile of the distribution at 12.5 days, suggesting that little infection occurs beyond 14 days of exposure.

Infectivity: The period of disease infectivity following infection remains uncertain. The basic reproductive number (R0) of the virus is not entirely clear and likely to vary by population density and other factors. Estimates from Wuhan, China have been from 2.2-2.7, and as high as 5.7, all of which suggest a very highly transmissible virus. Findings regard the role of viral load in determining the severity and prognosis of the disease have been mixed.

Immunity: Following infection with the virus, antibodies are induced in those infected. However, how protective the response is, and how long the immunity lasts, is not securely known. What we know of antibody status in this disease can be found here.