The Origins of The Covid-19 Virus

Submit to Yahoo the search phrase “origins of Covid-19” and the following comes back:

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It’s a list of the various conspiracy theories emerging on the origins of the Covid-19 virus. This is what the algorithms return as most likely to “match” for what I need to know. To find the informed, logical and scientific explanations on the origins takes some digging. Among that list is a chat board where commentators argue vociferously that Covid-19 was created at CERN in Switzerland. Another, in a blog written by a guy with zero scientific training whatsoever, argues at length that the virus originated in US bio-weapons laboratories. And was deliberately released into China. The mind boggles. In these times of uncertainty and fear, these paranoid tin hat wearing conspiracy nuts should be taken down from the web. Google, Yahoo, et al., should not be presenting this nonsense as options when Covid-19 is searched on their browsers. It will achieve nothing positive, but only lead people to be severely misinformed and ill equipped to deal with the psychological toll that this worldwide crisis is going to create.

Lets look at the legitimate factual based theories as to the origins of the virus.

Firstly, it is member of a family of viruses called corona viruses; specifically known as Coronaviridae in taxonomic classification. They are named thus due to the crown of club shaped protein spikes surrounding the viron particle that resemble a solar halo (link). Members infect mammalian and avian hosts, largely infecting either the upper or lower respiratory tracts, though the SARS corona virus that emerged in 2003 infects both upper and lower respiratory tracts in humans. In pigs they cause gatro-intestinal disorders, in humans rarely. So far viral taxonomists have described over 40 species, and they utilise a wide range of hosts.

Structurally they are enveloped viruses. This means they are surrounded by a capsid layer and a coating of phosolipids and proteins derived from their hosts. Non-enveloped viruses are enclosed by the capsid only. It is believed that the viral envelope plays a role in avoiding or overcoming the advances of host immune systems (link). However, enveloped viruses are more prone to degradation outside host cells and are easily deactivated by UV light, heat, desiccation and chemicals (detergents) among other conditions. They therefore usually require direct host to host transmission. As in all things, variations are manifest and some enveloped viruses are more resilient outside host cells than others for longer – such as seemingly, the 2019 corona virus Covid-19. The longer they survive outside host cells, the greater the infectivity of the virus. And if it causes a serious disease, then this renders the virus much more dangerous.

Finally, those interested in the molecular biology of the corona virus may be pleased to learn that it is a positive-sense single-stranded RNA genome virus. Positive sense (refers to the polarity of the RNA), single stranded (refers to the structure of the viral RNA. There are also double stranded RNA viruses and DNA viruses). Among the RNA viruses, corona viruses are considered among the largest.

Most species of corona virus naturally circulate in populations of bat, bird and swine species.

Corona viruses appeared to share a most recent common ancestor (MRCA) some 300 million years ago (link). The evolutionary lineage of corona viruses is controversial, but it seems likely that they co-evolved with their natural animal host species which began to diversify around the same time, according to fossil records. However, once again, as in all things science, there is conflicting evidence on the occurrence of the MRCA, with other studies suggesting corona viruses began to diverge into different species specific pathogens as recently as 3000 BC (link).

There are four genera of corona virus: alpha-corona virus, beta-corona  virus, gamma-conorana virus and delta-corona virus. The first two, alpha and beta circulate largely in the bat gene pool, while the gamma and delta genres circulate in the swine and bird species gene pools (link). Scientists have described far more corona viruses from bats species than bird species. However, birds most likely harbour a comparable range and quantity of corona viruses as bats, but remain largely undiscovered as yet (link). Both birds and bats are highly efficient reservoirs and disseminators of viruses (and corona viruses) and other pathogens due to their high mobility, sociability and being a widespread prey animal (link). It is unclear whether corona viruses appeared in bats or birds first, but it seems likely they appeared first in one and then somehow crossed into the other later, rather than co-evolving in birds and bats simultaneously. Though, it’s possible.

So, to recap, corona viruses began in birds and bats. Where did they go from there?

Well, current theory holds that corona viruses, once established in bats, jumped between bat species to diverge into alpha and beta corona-viruses. The same for the emergence of gamma and delta corona virus in birds. The key question is, when did they begin to jump the more formidable taxonomical barriers of families, orders and even classes?

With the development of agriculture and the domestication of wild animals some 10,000 years ago, human populations began to abandon a nomadic lifestyle and settle in one place. Their numbers exploded exponentially. More people required more food, which led to an intensification of agriculture and animal domestication, which in turn led to many different types of animals living closely together on farms, in animal markets, and even in human homes, for the first time in natural history. It is believed this created the perfect conditions to encourage inter species jumping for a wide range of pathogens and parasites, not just viruses.

Analyses has suggested that corona viruses first jumped from birds to mammals around 500 years ago (link). This seems recent, and it may be likely that they jumped many times through the evolution of life. But this is all we know right now. And it’s an ongoing thing. For example, in 2003, the emergence of severe acute respiratory syndrome (SARS) was attributed to a corona virus reservoir  in bats, from which some viruses most likely mutated and jumped to humans after some kind of human/bat interaction – involving hunting, cooking, capture etc. There was initial suggestions that they came to human via civet cats, which were hunted and farmed for food. This led to widespread culling of wild civets in Asia, a pointless exercise if ever there was one. They could have been just left alone. Nevertheless, it turned out the virus went to humans first, and then we infected the civets (link). SARS infected over 8000 people worldwide, killing about 700, before before it appeared to burn out.

In 2012 another corona virus jumping event occurred in the Middle East, which was subsequently named MERS (Middle Eastern Respiratory Syndrome). Again, it appeared to originate in bat populations (link). It is unclear in this case how the virus jumped, or what the intermediary species might be if any. There was no evidence of contact with bats with any human cases that were presented. There is suspicion that the intermediate species in this case could be camels, as multiple cases of MERS-Cov antibodies present in camels were reported (link). The human death rate with MERS was between 40% and 65%, extremely high. But it did not transmit between hosts so well, so currently this disease is uncommon.

Over all, viral evolution (like all evolution) is messy and and difficult to untangle. The exact evolutionary path of corona virus is unclear, and when  a new human corona virus emerges, when they made the jump to humans is also extremely difficult to work out. Its entirely possible that new corona viruses may have been circulating in human populations long before they were first detected by medics. SARS emerged in a region of China, Yunnan, that has the countries greatest concentration of horseshoe bat species, a species of bat with documented reservoirs  of corona viruses (link). We know little about corona virus diversity, and after the SARS and MERS epidemics burned out, research into corona viruses apparently became less of a priority. This despite the concerns of many scientists who warned that new viruses will jump to humans again in the future, and we might not be able to contain them. And they specifically focused on the same regions of China that produced SARS in 2003  (link).

And indeed, this is exactly what happened. Humans in China yet again, came into contact with a corona virus that emerged from a vast natural viral reservoir that is forever in molecular flux, which had then switched to an intermediary animal, probably pangolins in this case (link), within which it then bid its time, probably mutated some more, perfected its skills of contagion and infectivity, and then jumped to humans. Humans, a massively ubiquitous species, highly mobile globally, and with no natural existing immunity, were this time fair game. Humans called it SARS-Covid -02 or Covid -19. And this one is extremely contagious and extremely dangerous. And has spread all around the world.

So, that is where it came from, most likely.  If the truth is different from what I wrote about above, it will only be a variation of it, or an update on its natural source path as we learn more. Its emergence is the product of evolution and natural selection in practice. Please don’t listen to the tin-hat wearing amateur modern day Nostradamus’s of the internet proclaiming that one source or another ( be it supernatural, religious, military, science fiction novels etc) predicted the rise of this virus and the resulting health and economic crisis. Maybe they did. Who cares, ignore them. The people who really knew about it, scientists, had actually been warning us all along. And their warnings were informed, based on solid experience and facts. Please listen to them now as we try and beat it.

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