> Historically, there have been far, far more documented lab leaks of SARS-CoV than there have been animal-human jumps
No. First of all, there were many jumps of SARS from animals into humans, over a period of months in which the markets containing infected animals were open. Second, while there were a few leaks of SARS-CoV after it had been discovered and was being grown in large quantities (these leaks were recognized immediately, too), there is no precedent for a previously unknown coronavirus leaking.
> It is very possible that the virus was both zoonotic in origin, and leaked from the lab.
Not really. If the virus is natural in origin (which is a certainty now) and completely unknown before the initial outbreak (also a virtual certainty now), the chance that it somehow entered a lab, unknown, and then exited again are basically zero, compared to the chance that it spilled over in any one of the many millions of daily interactions between humans and wild or farmed animals.
They were selling farmed wild animals that we know can carry SARS-CoV-2 at the Huanan market, and that's where the initial outbreak was centered. In contrast, there's zero evidence for a lab leak, and not for lack of searching. There's simply no evidence that anyone at the Wuhan Institute of Virology had or knew about this virus before the outbreak, and we have a very good idea of what the WIV was researching.
> First of all, there were many jumps of SARS from animals into humans, over a period of months in which the markets containing infected animals were open.
Can you point me to one or two cases you are talking about, please?
They may be referring to the study below [0]. This showed that several genetic variants (lineages) of SARS-CoV2 were identified in infected people associated with the market, indicating 1) that the virus was already circulating among people before the epidemic took off, and 2) that there was more than one transmission event.
Note that no comparable data associates SARS-CoV2 with the lab in Wuhan.
>we inferred separate introductions of SARS-CoV-2 lineages A and B into humans from likely infected animals at the Huanan market (38). We estimated the first COVID-19 case to have occurred in November 2019, with few human cases and hospitalizations occurring through mid-December. [...] the evidence presented here that lineage A, like lineage B, may have originated at the Huanan market and then spread from this epicenter into the neighborhoods surrounding the market and beyond.
>We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted “A” and “B.” Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event.
For the rec, comment I'm replying to highlights two simultaneously released papers that both include 4 of the 5 authors of the 2020 paper, Proximal Origins, that is in question by the Nate Silver piece that headlines this HN post. (The 5th author, Lipkin's "view has changed":
"The revelation that the WIV was working with SARS-like viruses in subpar safety conditions has led some people to reassess the chance that SARS-CoV-2 could have emerged from some type of laboratory incident. “That’s screwed up,” the Columbia University virologist Ian Lipkin, who coauthored the seminal paper arguing that covid must have had a natural origin, told the journalist Donald McNeil Jr. “It shouldn’t have happened. People should not be looking at bat viruses in BSL-2 labs. My view has changed.”
SARS repeatedly spilled over into humans during 2002-2003, until the markets were shut down and the infected animal populations were culled. A review on SARS [0] describes how many independent clusters of SARS popped up over a period of months, spread across different markets in the Pearl River Delta:
> Between November 2002 and February 2003, the first cases or clusters of SARS appeared in several independent geographic locations in the Pearl River Delta region in southern Guangdong, and suggested multiple introductions of a virus or similar viruses from a common source. Several of the early cases were reportedly associated with occupations that involved contact with wildlife, including handling, killing and selling wild animals as well as preparing and serving wildlife animal meat in restaurants (Xu et al. 2004). Moreover, a study of early SARS cases (i.e. those with disease onset prior to January 2003) compared to those identified later in the outbreak found that 39% of early-onset cases were food handlers, whereas only 2%–10% of cases between February and April 2003 were associated with this occupation.
The review goes on:
> It was observed that early cases of SARS occurred independently in at least five different well-separated municipalities in Guangdong Province. The study also found that early patients were more likely than later patients to report living near a produce market, but not near a farm, and nine of 23 (or 39%) early patients were food handlers with probable animal contact.
The review also discusses how many SARS spillover events were not recognized at the time:
> Several studies revealed a higher than normal seroprevalence of SARS-CoV antibodies among wild animal traders. Guan et al. (2003) found that eight of 20 (40%) wild animal traders sampled from a market in Shenzhen, Guandong, in 2004 had anti-SARS-CoV antibodies in comparison to 1 from 20 (5%) vegetable traders from the same market. Yu et al. (2003) analysed serum samples taken on May 4, 2003 from animal traders in three different live animal markets in Guangzhou. Out of 508 animal traders surveyed, 13% had antibodies to SARSCoV; 72% of traders of masked palm civets ( Paguma larvata ) were seropositive. Interestingly, none of the animal traders had SARS or atypical pneumonia diagnosed during the SARS outbreak in Guangdong, suggesting asymptomatic infection by SARS-CoV or a closely related SARS-like coronavirus.
SARS probably spilled over countless times into humans during 2002-2003, because there was a large population of farmed animals that had it, and very little was done to cut off the spillover source for months.
This is a key difference from SARS-CoV-2. This outbreak was detected much more quickly (because of China's experience with SARS), and the very first thing the authorities did was to close the Huanan market and crack down on farms that raise the types of animals that are most likely to be involved in the spillover.
There were countless spillover events for the original SARS. To this day, it's not known precisely how many SARS spillover events there were, because they were so numerous and tracing was so poor back then. In a different comment in this thread, I cited a review article that goes over the evidence for widespread spillover events of SARS in 2002-2003.[0]
The gist of it is that SARS popped up independently at numerous markets, dotted across the Pearl River Delta. SARS infection was very common among palm civet traders in the region (it's even possible that most of them became infected).
The lab leaks came later, after huge interest emerged in the new virus and it started to be cultured in large quantities in many labs. Those leaks were extremely rare compared to the spillover events, they were immediately detected, and they led to much stricter lab security practices. But the relative probability of a novel virus that nobody even knows they have initially leaking from a lab vs. spilling over from large animal populations that host the virus is basically nil.
You're mixing up animal > human transmission, and zoonotic events. They are not equivalent. Human SARS spike protein RBD could bind palm civet ACE2, but not vice versa. Palm civets (and other animals) could act as reservoirs for human SARS, (as well as non-human SARS, which contributed to the zoonotic event), but that's not the same as a new virus jumping species. It's more like getting rabies from a raccoon.
It's possible that the original SARS jumped 3 times total, based on the genetic evidence, but the later two we don't really know because of the hinam -> animal route. Still, with the number of laboratory acquired infections of SARS-CoV-2, it doesn't really tip the scales.
If rabies were a novel virus that had never infected humans before, you could make the comparison. SARS was a novel virus, which spilled over into humans in a very similar manner to SARS-CoV-2 (wild animal markets in a major Chinese city).
> It's possible that the original SARS jumped 3 times total, based on the genetic evidence
As the review I cited explains, the epidemiological and serological evidence makes clear that SARS independently jumped over to humans at many different locations, over the course of months.
> It's possible that the original SARS jumped 3 times total, based on the genetic evidence
You're saying animal -> human transmission of a human virus is equivalent to animal -> human transmission of a new virus. Those are two *extremely* different things. The palm civet SARS spike protein RBD did not gain the ability to bind human ACE2 many times. In fact, the evidence for that seems to only be a single time. The remaining two suggested origin events show mutation of the existing virus, followed be retransmission across species barriers.
Those are two completely different types of events.
> You're saying animal -> human transmission of a human virus is equivalent to animal -> human transmission of a new virus.
You're making up an entirely arbitrary distinction.
> The palm civet SARS spike protein RBD did not gain the ability to bind human ACE2 many times.
You have no idea if this is the case. Most of these small outbreaks were not analyzed in detail (or even known about until well after the fact). The evidence shows that the virus was able to jump from animals to humans numerous times, and possibly spread in small clusters.
No, they're two very different things, because one involves an adaptation. Once adapted, the rules of the game for cross-species transmission events are completely different.
Or do you maintain that a combination cross-species transmission and adaptation to the new host is as common as cross-species transmission of already-adapted viruses?
I see that you're trying to imply that SARS-CoV-2 was pre-adapted to humans, while SARS wasn't, so this is going in a conspiracy-theory direction.
I guess the Wuhan Institute of Virology also produced a special deer-adapted version which they released into the wilds of North America, and a mink-adapted version they released on farms in Denmark, and a hamster-adapted version, and a cat-adapted version, and on and on. Both SARS and SARS-CoV-2 have shown an ability to infect a range of different species.
You haven't made a coherent point yet. You're trying to draw a distinction between zoonosis and animal-to-human transmission. The former literally means the latter.
And then claiming that the numerous independent clusters of SARS that popped up in wild animal markets across the Pearl River Delta aren't examples of zoonosis?
No. First of all, there were many jumps of SARS from animals into humans, over a period of months in which the markets containing infected animals were open. Second, while there were a few leaks of SARS-CoV after it had been discovered and was being grown in large quantities (these leaks were recognized immediately, too), there is no precedent for a previously unknown coronavirus leaking.
> It is very possible that the virus was both zoonotic in origin, and leaked from the lab.
Not really. If the virus is natural in origin (which is a certainty now) and completely unknown before the initial outbreak (also a virtual certainty now), the chance that it somehow entered a lab, unknown, and then exited again are basically zero, compared to the chance that it spilled over in any one of the many millions of daily interactions between humans and wild or farmed animals.
They were selling farmed wild animals that we know can carry SARS-CoV-2 at the Huanan market, and that's where the initial outbreak was centered. In contrast, there's zero evidence for a lab leak, and not for lack of searching. There's simply no evidence that anyone at the Wuhan Institute of Virology had or knew about this virus before the outbreak, and we have a very good idea of what the WIV was researching.