The History of Coronaviruses.

By Alfred Sibanda T.

Where were coronaviruses all along? Why the sudden emergence? How did it all start? In this section we discuss these questions which many may have been pondering about for a while now.

The coronaviruses were discovered in the mid-1960s, later two variants were described, HCoV‐229E and HCoV‐OC43. These were isolated from people with the common cold. They were thus shown to be associated with the common cold, being a cause of the cold. A few if any of these patients suffered from a severe infection, in other words, infection with a coronavirus was not that serious. In-fact, more people have been infected by a coronavirus at some point in their lives than we might think. After the discovery of the coronaviruses in the 1960s, the infections went quiet for close to four decades. In the year 2002, around November, the world experienced the first infectious disease outbreak of the century. An outbreak of a coronavirus called the SARS-CoV (Severe Acute Respiratory Syndrome-coronavirus) which began in Guangdong, China. Here the world was awakened to the realisation that coronaviruses were a potential cause of more than just the common cold. Later in the year 2012, another coronavirus was discovered in Saudi Arabia, the MERS-CoV. Although less troublesome than the SARS-CoV, it further showed us that coronaviruses were more a problem than previously imagined in the 20th century. In October 2016, Guangdong China, yet another coronavirus was classified, the SADS-CoV (Swine Acute Diarrhoeal Syndrome Coronavirus). This coronavirus, unlike the other two, primarily affects the intestinal tract rather than the respiratory. The SADS-CoV was seen to cause up-to 90% mortality in piglets less than five days old. By this time the entire scientific community was well aware of coronaviruses and their effects, as such, swift responses were being made to all situations where they were suspected. The latest outbreak in a coronavirus-related disease is the one the world is currently experiencing, that of COVID-19. This disease (COVID-19) is caused by a virus called the SARS-CoV 2.

But where were these coronaviruses coming from? Well, let us back up a little. When SARS-CoV was discovered, almost all the early patients were found to have had animal exposure before developing symptoms of the disease. With further investigations, anti-SARS-CoV antibodies were detected in masked palm civets. Antibodies are protein molecules produced by the B-cells of the immune system in response to infection. These antibodies are specific to pathogens, what that means is that if someone is infected by, say the HIV, the body produces antibodies that are specific to the HIV (Anti-HIV antibodies), they can only bind and cause destruction of only the HIV. These cannot fight other infections like TB and Gonorrhoea. Now, since researchers found anti-SARS-CoV antibodies in masked palm civets, it meant that at some point these animals had been infected by the same virus and had passed it on to humans who were now suffering from it. Scientists being curious people, when they see such information, do not just then stop investigations with the idea that they have “finally” figured out the source, they dig deeper! The next question on the line is of course “where did the palm civets get the disease themselves? Is it just a zoonosis among them or did they also get it from other animals?” these questions are very important to a researcher as in some cases with zoonosis, the infective agent (in this case coronaviruses) is cycled between different animals. A zoonosis is an infection that affects animals. In 2005, researchers discovered SARS-CoV-related viruses in Horseshoe bats. Analysis of results suggested that these bats could be the actual natural hosts of the virus and that the palm civets were actually intermediate hosts. To further support this point, many other different types of SARS-CoV-related viruses were discovered in bats from different areas in China and also in other countries as well. The level of variation and diversity of the strains of the SARS-CoV- related viruses discovered to date in bats suggests that these viruses may have been in bats for a very long time. Why do we use this as some evidence of that fact? Well, let us go back in time and imagine a time in the past, think of the “first” time that some bats got infected by the coronavirus. Since this was the first generation, it is only realistic to believe that there were only a few different variants of the virus. With time, many strains begin to form and more from those as well till we get to the number we have to date. This is much like going back in time and imagining one of your ancestors, and then travelling through time, getting pictures of all your ancestors and then lining these up for observation. You will observe similarities between perhaps the first two to three generation ancestors but further than that, there begins to be so many differences such that if you were given 4 random ancestor pictures, one of which is of one of your ancestors and you were asked to take a pick which one is your ancestor, there would probably be close to 1 in 4 chances that you pick the right one. This is to illustrate what variation may mean with regards to time in circulation of the coronaviruses in bats. With the magnitude of the number we have today, it is reasonable to believe that the coronaviruses may indeed have been circulating among the bats for a long time. I would add that the fact that the SARS-CoV-related viruses were observed not only in bat species in China but also other continents further supports that hypothesis.

Palm civets were also involved with the discovery of the MERS-CoV but most of the early cases of patients infected with the virus were also found to have had contact with dromedary camels in the Middle East, Africa and Asia. And as one would predict, the camels were found to have anti-MERS-CoV antibodies. Preserved camel samples taken in 1983 were also found to contain the virus, meaning that MERS-CoV was present in the camels for more than 22 years before the discovery of the virus. There is almost a 100% identity between the MERS-CoV strain in camels and the one in humans. To investigate relationships between hosts of viruses, scientists make use of phylogenetic trees. These show the levels of similarity between genes isolated and sequenced from different strains of microorganisms. It is from these that we investigate the possible explanations for the flow of transmission of the microorganism.

After the 2016 SADS crisis, the current pandemic is the next one caused by a coronavirus. This one again emerged from China, Wuhan in 2019. The virus quickly spread to other areas in China and to date is in all the continents, causing drastic effects in all spheres of life. There is strong evidence that the virus originated from bats, but we cannot rule out other possibilities. It is a new strain that has also managed to make a jump from its animal sources to humans. Researchers are still working on finding the links between the organisms suspected to be involved in the transmission circle. Finding out these links will play a crucial role in prevention of future pandemics and even to slow and eventually bring to an end the current pandemic. One still wonders what the future holds for humanity. With this many variants of the coronaviruses, will we have even more of them jumping to humans again in the future? With the current rate of pandemics caused by the coronaviruses, will this become the norm? Will humans have to get used to a new way of living? What will we learn from this pandemic, and how will our lives change after the pandemic? In times like this we turn to science as our hope of saving humanity. Past pandemics have taught us new ways of managing disease and we all hope that we come out of this one a stronger generation, with a story to tell to future generations perhaps with this as a turning point in some regards.

The table below shows the estimated cumulative totals of the number of cases of COVID-19 since January. This is how COVID-19 has progressed over the months.

Date Cumulative total Percentage increase over previous month.
31 January 2020 9 826 –
29 February 2020 85 225 767%
31 March 2020 799674 838%
30 April 2020 3 135 141 292%
31May 2020 6 028 755 92%
30 June 2020 10 273 541 70%
24 July 2020 15 477 472 51%

Raw data from Statistica.

It can be seen from the data that the disease had a very high rate of transmission in the early months, reached a peak in the months February to March. Thereafter it seems there is now a gradual decrease in the rate of infection although the number of cases are still increasing. The end goal is to reach zero new transmissions worldwide and this will take multinational efforts. No contribution is too small on our part as citizens, let us obey the preventative measures that our governments have put in place as this will contribute towards ‘flattening the curve’.

Source: https://www.labmanager.com/lab-health-and-safety/covid-19-a-history-of-coronavirus-22021 (accessed July 26th, 2020)

 

Why so many variants of some viruses?

Our cells have information stored in the nucleus, encoded by DNA. As we grow, the numbers of cells increase, new cells are constantly being formed from old ones and this is essential not only for growth but for repair of damage, occurring in our organs due to usage and other factors. Look at your hand, forearm and arm, what you see is an organ of uniform colour and form isn’t it? Your cells are dividing but they are able to maintain the information they encode and pass it on to next generation cells. Not to say that our cells are without mistakes, in-fact they do make a lot of mistakes in copying information but at least two things are in their favour to maintain a more or less identical pool of information as that passed on to them by parent cells. Firstly, most of these mistakes, called mutations, are inconsequential as they occur in non-coding sequences of our DNA. Yes, a big part of our DNA has useless information and in this part, when mistakes occur, it is inconsequential. Second, our cells have enzymes that try and follow up and check for mistakes when the genetic material is being replicated. Viruses, like us, also have mutations occurring in their DNA sequences and some of these are indeed inconsequential in terms of changing the virus’ pathogenicity. There is a difference among viruses however in terms of the rate at which mutations occur. As you might predict, a DNA virus has a lower rate of mutations as compared to an RNA virus and as such, there is a greater chance of an RNA virus changing over time as compared to a DNA virus. Now, coronaviruses are RNA viruses, and this is bad news in light of the preceding point and the fact that we are now experiencing a pandemic caused by an RNA virus.

As the information in the coronavirus RNA is copied in order to make new virus “children”, mistakes are made, and are mostly not corrected. This introduces antigenic variation in one strain of the virus and new ‘lineages’ of the virus are created. This simply means that there are alternative forms of the virus but these do not really mean that they are now different, in fact they remain the same and are classified under one strain. The kinds of mutations giving rise to new lineages of the virus strain are termed silent mutations.

However, mutations that alter the virus’ immunogenicity, pathogenicity and/or virulence can give rise to new strains. These mutations can lead to an increase or a decrease the extent of the virus’ effects. These mutations can also cause changes in certain protein components leading to the inability of our bodies to detect them effectively. This is perhaps the more common definition of a ‘strain’, however, the word strain can be defined in another way, arising from a somewhat different situation. When there are many variants of a virus in the same population, there can be one individual who is a “super spreader”, who somehow infects a lot of other people. This then creates a situation where there is a prevailing variant or lineage of the virus, in this case, this is now termed as a strain as well since it is the most prevalent of all the other variants in the lineage.

The current pandemic is a result of these changes in the causative agent, the SARS-CoV -2. There are now more than a thousand variants of this virus in the world and perhaps between one and ten strains.

References

https://www.statista.com/statistics/1103040/cumulative-coronavirus-covid19-cases-number-worldwide-by-day/ (accessed 25 July 2020)

Cui, J., Li, F. & Shi, Z. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 17, 181–192 (2019). https://doi.org/10.1038/s41579-018-0118-9 (accessed 25 July 2020).

Zhong NS, Zheng BJ, Li YM, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. Lancet. 2003;362(9393):1353-1358. doi:10.1016/s0140-6736(03)14630-2

Drosten C, Günther S, Preiser W, et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003;348(20):1967-1976. doi:10.1056/NEJMoa030747

https://www.cdc.gov/coronavirus/mers/index.html (accessed 25 July 2020).

Guan Y, Zheng BJ, He YQ, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302(5643):276-278. doi:10.1126/science.1087139

Lau SK, Woo PC, Li KS, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A. 2005;102(39):14040-14045. doi:10.1073/pnas.0506735102

Vince McLeod. COVID-19: A History of Coronavirus.Lab manager.March 16th 2020.

Zhou, P. et al. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 556, 255–258 (2018).

https://www.nature.com/articles/d41586-020-01449-8 (accessed 26 July 2020)

Tu, C. et al. Antibodies to SARS coronavirus in civets. Emerg. Infect. Dis. 10, 2244–2248 (2004).

Song, H. D. et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc. Natl Acad. Sci. USA 102, 2430–2435 (2005).

Tatiane K. Cabeça, Celso Granato, and Nancy Bellei. Epidemiological and clinical features of human coronavirus infections among different subsets of patients. Influenza Other Respir Viruses. 2013 Nov; 7(6): 1040–1047. Published 5 March 2013.

https://medium.com/swlh/variants-lineages-and-strains-of-coronavirus-7a71a0e699d7 (accessed 26 July 2020).

Naming the coronavirus disease (COVID-19) and the virus that causes it, WHO.

Kumar D, Malviya R, Kumar Sharma P. Corona Virus: A Review of COVID-19. EJMO 2020;4(1):8–25.

https://www.ancient.eu/article/939/the-plague-at-athens-430-427-bce/ (accessed 14 August 2020)

 

 

 

 

Alfred Sibanda
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