Coronavirus 2019

The Basics:
What is a virus? 
A virus is a non-living pathogen that utilizes the host body’s cellular machinery to replicate and infect other nearby cells. Antibiotics are ineffective to treat viruses because they are not living organisms with cell walls. Most viruses are little particles that inject their DNA/RNA into the host’s cells. Many different viruses have been known to spread disease throughout history such as Rabies, Smallpox, HIV/AIDS, Measles, etc…
Viruses are seen every day in every home, school, and workplace. Many viruses cause common colds, while others can cause severe and acute symptoms which can be fatal. Scientists estimate that there are several million different viruses in the world, with only ~5,000 that have been identified.
What is a coronavirus
Coronaviruses are a family of viruses named Coronaviridae based on the Latin word corona which means “crown” and “wreath” due to the way the virons look when viewed by electron microscopy (see below). They are an enveloped virus, with a helical nucleocapsid. These viruses carry a positive-sense single-stranded RNA genome approximately 27-34 kb. There have been three main coronaviruses that have caused outbreaks in the last 20 years: Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS) and now, Noval Coronavirus 19 which has recently been named Severe Acute Respiratory Syndrome 2 (SARS-2).
Coronaviruses have been known to infect multiple species such as chicken, cows, and camels. There are seven known human coronaviruses listed below:
– Human coronavirus 229E (HCoV-229E)
– Human coronavirus HKU1
– Human coronavirus OC43 (HCoV-OC43)
– Human coronavirus NL63 (HCoV-NL63, New Haven coronavirus)
– Severe acute respiratory syndrome coronavirus (SARS-CoV)
– Middle East respiratory syndrome-related coronavirus (MERS-CoV), previously known as novel coronavirus 2012 and HCoV-EMC
– Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019-nCoV or “novel coronavirus 2019”
Human coronaviruses are known to cause ~10-30% of all common colds seen annually in the human population. The first four strains 229E, HKU1, OC43, and NL63 are continually seen circulating in the human population yearly, causing people to have respiratory symptoms and are generally classified as “colds”. However, every now and then, there will be an outbreak of a novel coronavirus which has severe symptoms. The first large outbreak in recent history was the 2002-2003 outbreak of Severe acute respiratory syndrome coronavirus (SARS-CoV) and then the second was in 2012 with Middle East Respiratory Syndrome coronavirus (MERS-CoV).
Transmission of coronaviruses has generally been known to be through respiratory droplets. Most respiratory droplets come from coughing and sneezing while infectious.
Situation update on Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 2019-nCoV or “novel coronavirus 2019”
The 2019 Novel coronavirus is through to have begun its spread in the last quarter of 2019 in the Wuhan province of China. Towards the end of January 2020, the WHO and other health organization were notified of a possible outbreak of a respiratory illness which was likely to spread outside of China. Between mid-January and now, over 400,000 cases have been confirmed.
Annotation 2020-03-25 121850
As of 12:11 MST on March 25, 2020, there have been 413,467 confirmed cases throughout the world with 18,433 associated fatalities. Approximately 197 countries have a confirmed case.
MAP 2020-03-25 121850
In 2002 a novel coronavirus was discovered in the Guangdong province of China, with signs and symptoms such as fever, fatigue, headache, dry cough, shortness of breath and diarrhea. This coronavirus has infected 8,098 individuals since 2002 in 26 different countries and there were 774 deaths leading to a 9.6% fatality rate.
Since the end of the epidemic in July 2003, SARS-CoV has resurfaced four times, three of which were laboratory-related incidents and the fourth has since been undetermined transmission, but is thought to be animal-human transmission.
In 2012 a novel coronavirus was discovered in the Arabian Peninsula, with signs and symptoms similar to those of severe acute respiratory syndrome coronavirus (SARS-CoV). This coronavirus was named Middle East respiratory syndrome coronavirus (MERS-CoV) and has infected 2,494 individuals since 2012 in 27 different countries. These two viruses exhibit multiple similarities, such as signs and symptoms, routes of transmission, and prevalence of health-care-related infections.
MERS-CoV causes respiratory illness and may be compounded by acute pneumonia, septic shock, and multiorgan failure. Currently, approximately 37.1% of reported patients with the disease die. The incubation period for MERS-CoV is roughly 2 to 14 days, with a median of 5 days. MERS-CoV is transmitted from human to human and spreads rapidly in hospital and clinic settings.
How do we determine the severity of an outbreak?
Key concepts: Pandemic, epidemic, R0, communicability, lethality, the fatality rate
There are two different concepts I would like to discuss, one is the communicability of an infectious disease versus the potential lethality of that disease. In public health one way we estimate communicability is by calculating the R0 (R naught). The R0 is an estimate of the number of people a confirmed patient is likely to infect. is the number of secondary cases that one case would produce in a completely susceptible population. It depends on the duration of the infectious period, the probability of infecting a susceptible individual during one contact, and the number of new susceptible individuals contacted per unit of time.
For any infectious disease outbreak, the goal is for the R0 to be less than 1. If it is below 1, that means it is able to be contained. This can happen either through biological processes (the virus is weak, the route of transmission isn’t effective, etc.) or it can be through public health interventions such as Personal Protective Equipment (PPE), social distancing, vaccines etc.
R0 of the SARS-CoV is 3; Fatality 9.6%
R0 of the SARS2-CoV is ~2.2; Fatality rate estimates are between 0.2-4.2% for different vulnerable populations.
R0 of the MERS-CoV epidemic in 2012 was approximately 0.85-1.12. There has been great controversy in determining an R0 for MERS-CoV as the virus seems to be outbreak and environment-dependent, with some low estimates starting at 0.5 and high estimate for specific outbreaks being ~8. There is no defined R0 for MERS-CoV
R0 of Ebola 2014: between 1.3 and 1.9 with an outlier in a population for 2.53. Number of cases: 28,616 number of fatalities 11,310. Fatality estimates of ~40%. The historical average of Ebola can be between 50-90% fatality.
What is Social Distancing and why is it important?
Social distancing is a community based public health intervention that is utilized to slow down or eradicate transmission between people. Essentially, by ensuring you are not near others we are able to decrease the R0 I discussed above. If we can get the R0 of SARS2 to below 1, we will be able to contain the pandemic.
Unfortunately, this technique relies on the responsibility and reliability of the community understanding and adhering to social distancing.