This Is My 69th Post, Here Is Everything I Know About The Coronavirus


According to ls -l _posts/ | wc -l this is my 69th post and I thought it would be fun to finally talk about Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or COVID-19 or just “Coronavirus”). In doing so, I’ve tried to read up on a bunch of research papers much like a certain relevant xkcd.

But be warned: I’m not a virologist, the last time I tried to read a paper not about computer science/lingusitics was with “Urban herring gulls use human behavioural cues to locate food”, and I had to look up what a word meant almost every paragraph. It was brutal.(1) Because of this I’m not going to talk about structural biology at all. There are parts of each paper that talk about but since I don't understand it, I'm going to ignore it.

(1) It wasn’t actually that bad. Once you learnt what the words meant, it was easy to understand.

But anyway, what’s up with the Coronavirus?

In late December 2019, a cluster of unexplained pneumonia cases has been reported in Wuhan, China. A few days later, the causative agent of this mysterious pneumonia was identified as a novel coronavirus. This causative virus has been temporarily named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the relevant infected disease has been named as coronavirus disease 2019 (COVID-19) by the World Health Organization respectively.

SARS-CoV-2 is a novel member of coronaviruses, which are a large group of highly diverse, enveloped, positive-sense, single-stranded RNA viruses. The analysis of samples from seven SARS-CoV-2 infected patients suggested that SARS-CoV-2 shares 79.5% sequence identity to SARS-CoV.[1]

The 2002 SARS-CoV (SARS) outbreak in southern China has only limited value for predictions, even if both are coronaviruses. SARS largely died out during the Northern Hemisphere summer of 2003 when the virus became significantly less infectious. However, while SARS-CoV-2 appears to be considerably less lethal than SARS, which had a fatality rate of 9.6%, killing 774 of the 8,098 reported patients, it is more infectious.[2] However, COVID-19 mortality rates are preliminary, and the values may change as more individuals will be confirmed retrospectively with mild respiratory illnesses that were attributed at the time to the common cold, or to have died from COVID-19 that was believed to be influenza.

Recent research reported that SARS-CoV-2 likely originated in bats, based on the similarity of its genetic sequence to that of other coronaviruses. Simplot analysis showed that SARS-CoV-2 share 96.2% overall genome sequence identity to RaTG13, which is a short RdRp region from a bat coronavirus.[3]

Briefly, cases tend to be in clusters which arrive in waves, and develop into larger outbreaks all over the world. Mode of transport is known to be human-human and occurs primarily via respiratory droplets from coughs and sneezes within a range of about 6 feet (1.8 m). Whether infection can occur through the oral or conjunctival routes is unknown, but SARS-CoV-2 has been detected in tears.[4]

Population genetic analyses of 103 sequenced genomes of SARS-CoV-2 indicate that there are two strains, L, more prevalent (70%) in the early stages of the outbreak and more aggressive, and S, which less prevalent (30%) and less aggressive.[5]

Reproductive number (R0) was estimated by some studies. Based on the clinical data of patients in COVID-19 early outbreak, the mean R0 was ranging from 2.20 to 3.58, meaning that each patient has been spreading infection to 2 or 3 other people.[6] But it still too early to develop an accurate R0 estimate or to assess the dynamics of transmission and more research is needed in the future.

Some aspects about the outbreak were anticipated. Its rapid worldwide spread within and across countries was predictable, and so was the increased mortality among certain population groups. The magnitude of the outbreak in various countries, however, came somewhat as a surprise. The first two cases in Italy were detected on January 29, 2020. As of March 13, 2020, the country experienced 12,462 infections and 827 deaths, becoming to date the largest one and the one that claimed most fatalities outside of Asia.

Several scenarios may explain the large outbreak and the high COVID-19 mortality rate in Italy. Prior to the first COVID-19 diagnoses in Italy, it was reported that an unusually high number of people with pneumonia were diagnosed at a hospital in the Northern part of the country, opening the possibility that they were the first cases but they had been treated as if they had the flu. It is also conceivable that by the time the outbreak in Italy was noticed, several transmission chains were already becoming established in the country.

Additionally, Italy has one of the world’s oldest populations. In 2015 and 2016, 21-22% of its residents were aged 65 and over, and the average life expectancy at birth, 82.7 years, is one of the highest in the world. The high COVID-19 mortality in Italy may at least in part reflect the disproportionately high mortality that it causes in elderly individuals.[7]

Until the diagnosis is confirmed, SARS-CoV-2 infected patients are treated in single rooms. As SARS-CoV-2 is an emerging virus, an effective antiviral treatment has not been identified. The main treatment of COVID-19 is symptomatic treatment. The antiviral drugs, including oseltamivir, ribavirin, ganciclovir, lopinavir, and ritonavir have been used in attempts to reduce viral load and to prevent the likelihood of respiratory complications in several studies[8][9]. However, the efficacy of these antiviral drugs for COVID-19 need to be verified by randomised, controlled clinical trials.

The WHO issued a public health emergency of international concern on January 30, 2020. SARS-CoV-2 epidemic is becoming a global concern. The best strategy to deal with SARS-CoV-2 epidemic includes controlling the sources of infection, protecting the susceptible people, and cutting off the transmission.

That’s all. Turns out we don’t actually know very much. I’d also like to talk about the opinion paper “Global health crises are also information crises: A call to action”[10], which “argue(s) that global health crises are also information crises. Using as an example the coronavirus disease 2019 (COVID-19) epidemic, we (a) examine challenges associated with what we term “global information crises”; (b) recommend changes needed for the field of information science to play a leading role in such crises; and (c) propose actionable items for short- and long-term research, education, and practice in information science.“

I think the paper brings up very important points such as calling for “information scientists to examine: (a) how information science might assist the use of trustworthy social media information while avoiding misinformation/ disinformation, (b) systematic ways to automatically detect and stop the spread of misinformation/disinformation on mass media and social media, and (c) strategies to help authoritative organizations in using social media to communicate with individuals and intervene when health misinformation/disinformation spreads.”

I’ve seen a lot of misinformation on social media cough Reddit cough, so this is certainly an issue that needs more research.

Now with all that boring stuff over, it is time to talk about etymology! YAY!

“Corona” is a Latin term meaning “a crown, a garland”[11], and has been extended into “coronavirus” which refers to the characteristic appearance of virions (the infective form of the virus) by electron microscopy, which have a fringe of large, bulbous surface projections creating an image reminiscent of a crown or of a solar corona. Remember that coronaviruses are a group of related viruses, and not one single virus.

Ok bye bye! Remember to wash your hands!

[1]: He, Feng, et al. “Coronavirus Disease 2019 (COVID‐19): What We Know?” J Med Virol. Wiley, doi:10.1002/jmv.25766.

[2]: Hunter, Philip. “The Spread of the COVID ‐19 Coronavirus.” EMBO Rep. EMBO, doi:10.15252/embr.202050334.

[3]: Zhou, Peng, et al. “A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin.” Nature, vol. 579, no. 7798, 2020, pp. 270–73. Springer Science and Business Media LLC, doi:10.1038/s41586-020-2012-7.

[4]: Xia, Jianhua, et al. “Evaluation of Coronavirus in Tears and Conjunctival Secretions of Patients with SARS‐CoV‐2 Infection.” J Med Virol. Wiley, doi:10.1002/jmv.25725.

[5]: Tang, Xiaolu, et al. On the Origin and Continuing Evolution of SARS-CoV-2. Oxford University Press (OUP), doi:10.1093/nsr/nwaa036.

[6]: Li, Qun, et al. “Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia.” N Engl J Med. Massachusetts Medical Society, doi:10.1056/NEJMoa2001316.

[7]: Stein, Richard. “COVID‐19 and Rationally Layered Social Distancing.” Int J Clin Pract. Wiley, doi:10.1111/ijcp.13501.

[8]: Wang, Dawei, et al. “Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China.” JAMA, vol. 323, no. 11, 2020, p. 1061. American Medical Association (AMA), doi:10.1001/jama.2020.1585.

[9]: Chen, Nanshan, et al. “Epidemiological and Clinical Characteristics of 99 Cases of 2019 Novel Coronavirus Pneumonia in Wuhan, China: A Descriptive Study.” The Lancet, vol. 395, no. 10223, 2020, pp. 507–13. Elsevier BV, doi:10.1016/s0140-6736(20)30211-7.

[10]: Xie, Bo, et al. “Global Health Crises Are Also Information Crises: A Call to Action.” J Assoc Inf Sci Technol. Wiley, doi:10.1002/asi.24357.