The origin of SARS-Cov-2 is a hot topic these days. As far as I can tell, the consensus view among the experts is that the ancestor is from bats but it evolved in an intermediate host before jumping to humans. However, there's a vocal group who claim that the virus was engineered in a lab in the Wuhan Institute of Virology and accidentally escaped causing a pandemic. A group of scientists from WHO investigated this speculation and decided that it was "extremely unlikely." I posted a summary of their analysis a few days ago [World Health Organization (WHO) report on the lab leak conspiracy theory].
That's not going to put an end to the speculation since proponents of the lab leak hypothesis are now saying that the WHO report, and the opinion of other experts, can't be trusted. They claim that there's a widespread consiracy to lie and cover up the fact that SARS-CoV-2 was created in a lab and leaked to the Wuhan population.
There's not much point in arguing with people once they go down the conspiricy theory path since they will refute every argument by claiming that it's part of the conspriacy. However, it's worth pointing out that there's a perfectly valid alternative explanation; namely, natural origin. For those who still have an open mind I'm posting the explanation of the WHO scientific team who conclude that this is the most likely explanation [WHO-convened global study of origins of SARS-CoV-2: China Part].
Introduction through intermediate host followed by zoonotic transmission
Explanation of hypothesis
SARS-CoV-2 is transmitted from an animal reservoir to an animal host, followed by subsequent spread within that intermediate host (spillover host), and then transmission to humans. The passage through an intermediate host can be without or with virus adaptation.
Arguments in favour
Although the closest related viruses have been found in bats, the evolutionary distance between these bat viruses and SARS-CoV-2 is estimated to be several decades, suggesting a missing link (either a missing progenitor virus, or evolution of a progenitor virus in an intermediate host). Highly similar viruses have also been found in pangolins, suggesting cross-species transmission from bats at least once, but again with considerable genetic distance. Both these putative hosts are infrequently in contact with humans, and an intermediary step involving an amplifying host has been observed for several other emerging viruses (Henipaviruses, influenza viruses, SARS-CoV and MERS-CoV). SARS-CoV-2 infection and intraspecies spread (including further transmission to humans) has been documented in an increasing number of animal species, particularly mustelids and felids. SARS-CoV-2 adapts relatively rapidly in susceptible animals (such as mink). The increasing number of animals shown to be susceptible to SARS-CoV-2 includes animals that are farmed in sufficient densities to allow potential for enzootic circulation. High-density farming is common in many places across the world and includes many livestock species as well as farmed wildlife. There was a large network of domesticated wild animal farms, supplying farmed wildlife. In high-density farms, there often are connections between farms (for instance, through the workforce and food supply), leading to complex transmission pathways that may be difficult to unravel, as was observed in other zoonotic outbreaks involving farmed animals. Optimized conditions for sustained virus transmission chains in large-scale animal farms may also impact on virus seasonality in favour of a year-round endemic transmission pattern, and thereby increasing the zoonotic risk in winter months.
Arguments against
SARS-CoV-2 has been identified in an increasing number of animal species, but genetic and epidemiological studies have suggested that these were infections introduced from humans, rather than enzootic virus circulation. In addition, since the containment of SARS-CoV-2 in China, new outbreaks have occurred for which genomic sequence data was generated. Based on epidemiological analysis and genetic sequencing of viruses from new cases throughout 2020, there is no evidence of repeated introduction of early SARS-CoV-2 strains of potential animal origins into humans in China. There was no genetic or serological evidence for SARS-CoV-2 in a wide range of domestic and wild animals tested to date. The screening of the major livestock species was done across the country and provided no evidence for circulation of a related virus. The scale of testing in these species was such that widespread circulation is extremely unlikely. Screening of farmed wildlife was limited but did not provide conclusive evidence for the existence of circulation.
Assessment of likelihood
Based on the above arguments, the scenario including introduction through an intermediary host was considered to be likely to very likely.
I should note that it's often very difficult to figure out who's right and who's wrong in a scientific controversy but in general there's one group that appears to be thinking critically and one that's not. Critical thinking is also hard to recognize but when I was teaching it we emphasized one important clue. Critical thinkers usually present both sides of an argument and discuss not only their own opinions but also the views of the other side. That's one of the things that impress me about the WHO report. It doesn't mean that they are necessarily correct but they sure look a lot better than proponents of the lab leak conspiracy theory who seem to dismiss out of hand the possibility of a natural origin.
I'd also like to make note of the fact the WHO is not a perfect organization. They have made mistakes during this pandemic as have every single government on the planet (some more than others). I'm not defending everything that WHO has done but I don't see any reason to be overly suspicious of the integrity of the scientists who wrote this report.
