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Fearsome Viruses and Where To Find Them

Almost a year has passed since the outbreak of COVID-19. The coronavirus SARS-CoV-2 started its journey in the city of Wuhan, China, and since then it infected over 50 million people worldwide, killing 2.5% of them (Johns Hopkins data). Scientists are largely convinced it has a natural origin, but there are many things we still do not know. Genetic analyses clearly tell us that the ancestor of SARS-CoV-2 was a bat virus, most likely originating in southern China: both its closest relatives (RaTG13 and RmYN02), have been identified in Yunnan province, as well as many other SARS viruses discovered in bats so far. It is still not clear, however, how exactly this virus has traveled the 1000 km that separate Yunnan from the city of Wuhan, home of the famous Institute of Virology that has been studying bat coronaviruses for years. On this specific point, opinions differ, even within the scientific community itself.

Most scientists believe the virus has passed to humans through an intermediate host, for example an animal sold at a wet market, one of those places where humans and wildlife come into closer contact. After all, this had already happened with the first SARS, which had made the “jump” from civets to humans, and with MERS, which had passed through camels. But this time, the intermediate host is yet to be found. Initially, everybody blamed the Huanan fish market, but Chinese scientists found the virus only on surfaces and not in animals for sale. They also sampled farmed animals throughout the Hubei province, but again without success.

With the first SARS virus, things went differently. The first case appeared in Guangdong in November 2002, the pathogen was identified in April 2003 and already in May we had discovered an almost identical virus in palm civets sold in markets (Guan et al., 2003). Somehow, it was the opposite situation compared to the current one: at that time we didn’t know yet the role of bats as animal reservoirs, but it took only six months to find the intermediate host.

Given the difficulties that we are facing this time, scientists are also considering another remote hypothesis, which is quite hard to demonstrate: the virus could have jumped directly from bats, and then evolved slowly among humans, adapting more and more to the new host over time. In this case, one would expect to find traces of the virus also in other regions of China, before last December: sporadic cases of atypical pneumonia caused by a similar virus, for example. But if such pneumonia had occurred, as far as we know the Chinese health authorities have not detected them.

A third, disturbing, possibility remains, one that only a few scientists consider seriously: that SARS-CoV-2 has accidentally leaked from a laboratory, and may even be the result of genetic manipulation. This hypothesis would also be compatible with the fact that the virus seemed already well adapted to humans when it appeared in Wuhan, as suggested by a preprint published in May and now confirmed by the WHO, which anyway supports the natural origin hypothesis. Scientists who deem this a realistic scenario are very few, or at least very few of them have taken this stance publicly: I recall the biologist Richard Ebright, the immunologist Nikolai Petrovskj, the virologist Étienne Decroly, the microbiologist David Relman and, of course, the researcher Alina Chan of Broad Institute, now a star on Twitter, who has always maintained that with current evidence no scenario could be ruled out. The fact is that any discussion on the origins of the virus inevitably clashes with political issues. From the very beginning, Donald Trump accused China of creating SARS-CoV-2 in one of their laboratories, and my feeling is that these political pressures are corrupting the debate within the scientific community. It’s tempting to politically label anyone who even remotely considers the “lab hypothesis”, and these days very few scientists want to look like Trump supporters (by the way, how can you blame them?). In my view, the natural origin scenario has been pushed not only by the evidence, but also (and maybe more) by a feeling of aversion towards the outgoing US president, and the fear of fuelling his narrative.

In these months I have followed this issue very closely, I have read a lot and discovered really surprising things. After a long time, I’ve decided to share with you everything I learned, providing you with all the references and links that you may need to evaluate the correctness of my words. I will not dwell on improbable conspiracy theories like Li-Meng Yan’s (others have already written about them), I will instead focus on data and peer-reviewed scientific papers, and I assure you it will be an interesting story. At the end of this very long article, you will know (almost) everything there is to know about the origins of this virus, but most of all everything we don’t know yet.