health

How virus detectives trace the origins of an outbreak – and why it's so tricky

20 Comments
By Marilyn J Roossinck

The requested article has expired, and is no longer available. Any related articles, and user comments are shown below.

© The Conversation

©2021 GPlusMedia Inc.

20 Comments
Login to comment

This article poses only two options for Covid-19:

--natural origin

--lab engineered and escape/release

It tries, somewhat convincingly, to claim it must be natural and could not have been not be "engineered in a lab" through direct alteration of the genetic sequence.

But like everywhere else reporting about these options, including the lips of Dr Fauci himself, they fail to allow a third more viable option:

--a virus that was naturally acquired, which through repeated natural replication in a lab under a variety of stimuli and pressures it developed natural mutations that did not originally exist in nature... and then this somehow got out from the lab.

5 ( +6 / -1 )

But like everywhere else reporting about these options, including the lips of Dr Fauci himself, they fail to allow a third more viable option:

This is because it contradicts available evidence and it just puts extra steps of lower probability. Exaggerating it it would be like expecting specialists to consider the virus was isolated from the wild, mutated in space and leaked while the samples came back to earth without proper control.

The virus shows strong similarities with other strains isolated from the wild, so the mutations are present in nature already. This means there are two possibilities, SARS-CoV-2 came from a common ancestor to those other natural viruses so it shared those mutations, or by coincidence developed exactly the same sequences in the lab as an example of parallel evolution. The natural explanation is much more likely to be the cause since it is what is routinely expected.

Together with other data (some human cases outside of the city of Wuhan long before the market outbreak, evidence of constant, repeated introduction of other coronavirus infections on human samples of the region, etc.) The lab origin at the time is understood as an overly complicated and unnecessary explanation, which makes it much less likely to be true.

The artificial construction would not have that problem (if there was evidence of human manipulation) because it leaves evidence that is not found in natural strains, that is why the first thing it was done was to examine the genome and search for proof of the manipulation, if found that automatically makes the lab origin the most likely answer.

-3 ( +3 / -6 )

The virus shows strong similarities with other strains isolated from the wild, so the mutations are present in nature already. This means there are two possibilities...

In detailing how viruses are studied you've provided case in point support for a third option.

Where would those "other strains" be located in order to be "isolated from the wild"? Perhaps a lab? And to study those viruses, they would need a host... perhaps that mystery missing link species between bat and human?

And once "isolated from the wild" in the lab, the virus will continue to naturally mutate but now in artificial conditions which can be manipulated (so not just "engineered" with direct "human manipulation")

So again, this continually ignored third possibility is not "artificial construction", so stop suggesting that it is.

Even without any sort of lab-based natural mutation, it still could have been found in nature just as it is, brought back to the lab, and then leaked from there. As stated in the article, the closest relative to Covid-19 is RaTG13, which occurs in bats that inhabit an area (Yunnan) well over 1000km from Wuhan in a climate that is completely different. Sure, biology may want to say "natural origin" but physics and geography simply don't agree.

some human cases outside of the city of Wuhan long before the market outbreak

Please cite this claim. It is absolute speculation based on some people who displayed similar symptoms in Hubei province (home to Wuhan), but no solid evidence exists it was Covid-19. And unless it is proven, then please stop suggesting it is a fact.

3 ( +5 / -2 )

Where would those "other strains" be located in order to be "isolated from the wild"? Perhaps a lab? And to study those viruses, they would need a host... perhaps that mystery missing link species between bat and human?

That is again resorting to extra unnecessary steps each lowering the probability of this explanation being correct. If the other strains are isolated from the wild that already puts the sequences in nature, so it would not matter where those strains are kept, the point is that for the same sequences to be exactly replicated in a laboratory setting you need extraordinary coincidences.

And once "isolated from the wild" in the lab, the virus will continue to naturally mutate but now in artificial conditions which can be manipulated (so not just "engineered" with direct "human manipulation")

Why would it "continue to mutate"? virology labs work is based on number of passages, the with the lower the better, the normal procedure is to amplify a sample importantly on one single passage and freeze hundreds of aliquots so the work can continue for many years with the "same" strain that was isolated. Passage of the virus cause adaptation to exactly the medium being used, so it is not uncommon for isolates to be completely freed of their ability to resist immunity when passaged on cell cultures. (They become much better at infecting one specific kind of immortalized cells, and much worse at infecting everything else).

As stated in the article, the closest relative to Covid-19 is RaTG13, which occurs in bats that inhabit an area (Yunnan) well over 1000km from Wuhan in a climate that is completely different.

And as the same article says, this is in no way indication this is the only place where it can be isolated, nor that this is the closes relative there is, only the closest found yet. The main problem is that huge lots of other samples need to be collected in order to actually have a good idea of the whole process. The samples obtained until now are offer just a pinhole view. Thinking samples "must" have come from this precise location is not rational.

Please cite this claim

https://www.sciencedaily.com/releases/2021/03/210318185328.htm

(https://science.sciencemag.org/content/372/6540/412)

https://www.scmp.com/news/china/science/article/3083211/coronavirus-may-have-jumped-humans-early-october-study-says

https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back

This is in no way based on symptoms of some people but on well validated genetic analysis tools that can determine how long time a virus has been in a community based on the differences in the sequence of the isolates on patients, as well as serological evidence that demonstrate people were infected before Wuhan. It is as proven as it can scientifically be, meaning that if better evidence appear this can be demonstrated as wrong (lets say another coronavirus producing extremely specific cross neutralization, but not COVID). Without evidence of the contrary there is no valid reason to doubt it.

Once again, one of the explanations is simpler, corresponds with all the evidence collected and examined by experts around the world and has been observed countless times. The other explanation is overly complicated and fails to explain several things already recorded.

-6 ( +1 / -7 )

At the beginning of the pandemic experts suspected everything, that is not contradictory to finding out much more evidence towards one explanation. This has not changed until now, the sequences examined are open to the analysis of every expert in the world and in general the same conclusions have been made. There is no molecular evidence of tampering, and this includes the sequences that seemed suspicious to some people at the beginning. It may be surprising but not every expert in virology is well versed in all the different viruses.

The scientific consensus is that the natural origin is simply the best explanation until now, not only because it has happened before but because it makes all the evidence collected until now coalesce without problems and without contradictions.

People used to conspiracy theories and dogmatic beliefs keep thinking who says something is the important part, in science the only importance come from the evidence.

-5 ( +1 / -6 )

--a virus that was naturally acquired, which through repeated natural replication in a lab under a variety of stimuli and pressures it developed natural mutations that did not originally exist in nature... and then this somehow got out from the lab.

I believe this is the most likely. They had different cell lines and humanized mice. But they might have also done a combination of this together with direct genetic manipulation. For example, genetically introduce an new engineered spike protein and then do several passages through various cell lines and or animals to optimize the virus.

As stated in the article, the closest relative to Covid-19 is RaTG13, which occurs in bats that inhabit an area (Yunnan) well over 1000km from Wuhan in a climate that is completely different.

And as the same article says, this is in no way indication this is the only place where it can be isolated, nor that this is the closes relative there is, only the closest found yet.

Or better yet, it is the closest one reported. The CCP military is involved in obtaining new bat coronaviruses from nature. There is no reason to assume that they would submit all new sequences.

1 ( +4 / -3 )

The scientific consensus is that the natural origin is simply the best explanation until now, not only because it has happened before but because it makes all the evidence collected until now coalesce without problems and without contradictions.

The thing is that the experts that were publicly explaining that "scientific consensus" were simultaneously privately saying (Emails) it looked like a lab leak of an engineered virus.

The lab leak hypothesis equally makes all the evidence collected until now coalesce without problems and without contradictions. Perhaps even more so since it also explains the fact that none of the intermediates have been isolated from nature, unlike SARS-CoV-1.

0 ( +3 / -3 )

I believe this is the most likely. They had different cell lines and humanized mice. But they might have also done a combination of this together with direct genetic manipulation.

The experts agree in exactly the contrary, this is a overly complicated and unnecessary explanation that makes no sense and contradicts plenty of evidence. In general terms the less a person knows about the topic the more the lab theory seems "likely" to them.

Or better yet, it is the closest one reported. The CCP military is involved in obtaining new bat coronaviruses from nature. There is no reason to assume that they would submit all new sequences.

That is irrelevant for the argument that similar sequences have been already found in nature, having even one reported already proves this point, having 5 or 20 would not make a difference in this.

The thing is that the experts that were publicly explaining that "scientific consensus" were simultaneously privately saying (Emails) it looked like a lab leak of an engineered virus.

That is false, in the email some people said there were some sequences that looked suspicious but ended up being explained perfectly well with phylogenetic analysis of other coronaviruses, that is something completely different from concluding they were a lab leak and much less an engineered virus. Again, those sequences are still there and have been analyzed countless times and found without problem.

The lab leak contradicts plenty of evidence, for example the already cited work that demonstrates the first human infection were not even in Wuhan and that began several weeks (at least) before the first identifed outbreak, a leak do not explain this and would require a magical strain able to escape a populous city without causing outbreaks only to come back after some cases in rural areas to now behave completely differently, that is a lousy explanation that contradicts the data. Intermediates are not expected to be found easily, the article explicitly explains this, you should read it.

-5 ( +1 / -6 )

Or better yet, it is the closest one reported. The CCP military is involved in obtaining new bat coronaviruses from nature

You are referring to a US sponsored program called Project Predict. It was initiated by Congress in 2009 as a result of the SARS, MERS and H1N1 pandemics that swept the world between 2003 and 2009. It was part of the Emerging Pandemic Threats program. The concept was to search areas of the world with high likelihood of finding zoonotic diseases that can jump to humans and become the next pandemic. So you had researchers in places like Brazil and much of Asia combing bat caves and other places capturing creatures and taking samples for analysis in labs all over the world. The US was not the only participant. I believe 33 nations, their labs and universities were involved. China was among them. There is nothing sinister in this effort. In six years the world had experienced three major pandemics. There was a determined effort to find the likely source of the next one. The effort was unsuccessful but there is no shame in trying.

-2 ( +2 / -4 )

Just me but I am not convinced the pandemic started in Wuhan. I am pretty sure I had it in early November 2019 but nobody knew there was a pandemic afoot. In hindsight I had all the symptoms but of course none of the tests came back positive. No one was testing for Covid-19. None existed. The PA who treated me now looks back at her November to December 2019 case load and has come to believe Covid-19 swept our small high desert town during the 2019 holiday season. It was well into summer of 2020 before I could take a deep breath without having a coughing fit and have never been 100% since. I hope there are researchers looking for evidence the disease was circulating earlier than late 2019 because I believe it was.

-1 ( +3 / -4 )

Btw, here is the flyer USAID published for Predict.

https://www.usaid.gov/sites/default/files/documents/1864/predict-global-flyer-508.pdf

-2 ( +2 / -4 )

Nicholas Wade, an ex-NYT writer, is quite sure that SARS-COV-2 leaked accidentally from a lab.

https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/

The problem with him is that he has already been denounced by the scientific community for an earlier book. However, if one focuses on the message, not the messenger, one would find some points worth a second look in his assertion.

0 ( +2 / -2 )

desert tortoise:

Just me but I am not convinced the pandemic started in Wuhan.

There is evidence that the virus existed in the sewers of Barcelona in early 2019. Of course, that doesn't mean it started there or Wuhan or anywhere else. This just goes to show that finding the origin really isn't as easy as coming up with conspiracy stories. I just want the truth - whether it was from a lab, or a wet market or wherever. But I would never say anything based on gossip or listen to people with ulterior motives or listen to stupid people. I'd like the truth from honest scientists and doctors with credibility, not from people like Ronny 'Good genes - he'll live up to 200 years old' Jackson - an absolute disgrace to his profession.

The other day on the news, we had irate American women telling us they became magnetic after taking the vaccines. A key stuck to a woman's chest but she struggled to stick one to her neck - it kept falling off as she angrily told everyone she's magnetic. As someone unvaccinated, I tried it too, and my key instantly stuck to my neck, vertically. However, I admit, I desperately needed a shower.

-2 ( +1 / -3 )

I personally think that most people around the world have lost faith in scientists and researchers. There are so many contradictory statements and theories. The WHO mission which was sent to Wuhan was a BIG JOKE. Its members were under Chinese pressure. Mr Daszak and Embarak should have been sacked for conflict of interest. Please check out this link - drasticresearch.org.

2 ( +4 / -2 )

@VirusRex 

Right, the sources you cite confirm... what? That the virus existed for a few weeks or months before being first discovered. Yeah, bravo, no kidding.

Do any of your sources suggest it was present somewhere "outside of the city of Wuhan", as you claimed? No, none do that. They do not know where those initial cases were.

Actually, what about those lab workers in Wuhan who has Covid symptoms a few weeks/months before the virus being discovered? Seems to match the data you gave...

Again, unless you can cite an example of a proven case of Covid-19 "outside of the city of Wuhan long before the market outbreak" then stop suggesting it as fact.

1 ( +3 / -2 )

Do any of your sources suggest it was present somewhere "outside of the city of Wuhan", as you claimed? No, none do that. They do not know where those initial cases were.

I am telling you from first hand experience that Covid -19 or something very darn close to it was circulating the high desert of California in earyl Novermber 2019. That is a long darn way from China. People are focused on China and I understand the reasons why, but I really want some researchers to consider the possibility it was circulating in North America earlier in 2019. No conspiracy here, just what I and some others out here experienced and the reflection of one of the most experienced PAs you will ever meet. No she is not a scientist but in our own experience she has sussed out medical problems that MDs missed. Old woman who started out as a Navy Corpsman many decades ago and is a bit of an institution here. She saw a lot of cases like me around the end of 2019 that looking back would very likely have been diagnosed as Covid-19 but nobody then was aware of the disease or the coming pandemic.

-3 ( +1 / -4 )

Right, the sources you cite confirm... what? That the virus existed for a few weeks or months before being first discovered. Yeah, bravo, no kidding.

Of course they do, you should try to read the references before trying to discuss them, specifically they say that serological samples show patients infected with the virus in the Hubei province, obviously they did not just took serum samples from thin air but from people from which the information is available.

Actually, what about those lab workers in Wuhan who has Covid symptoms a few weeks/months before the virus being discovered? Seems to match the data you gave...

No, they would be the opposite, any organization with more than 10 people working had some with cold-like symptoms in November, because that is the peak of the infectious respiratory disease in the region. If the workers had COVID then they are hopelessly too early to cause the outbreak on the market, and most importantly being several of them it would mean the virus at that point would have been completely adapted to be transmitted between humans, this means you would have observed not a single outbreak in december (as expected if the disease was introduced from outside of the city) but several big outbreaks around the city in November, each of the workers could have originated many of them.

Once again, since the reference provide proof of infection outside of Wuhan at a time long before the market outbreak the laboratory escape still depends on a magical virus that can escape the whole city without causing outbreaks but only once, the second time behaving normally.

-3 ( +0 / -3 )

they say that serological samples show patients infected with the virus in the Hubei province

Do you not realize that Wuhan is located in Hubei province? That people in Hubei travel and commute to/from Wuhan, being that its the provincial capital? Saying there were people "outside Wuhan" in Hubei infected before the market cases does not mean they are somehow excluded from Wuhan. It's like saying people "in the Tama area" are somehow not in the city of Tokyo.

And again, the closest know related virus, RaTG13, occurs in bats that inhabit an area (Yunnan) well over 1000km from Hubei in a climate that is completely different. Are you suggesting the mysterious intermediate host animal somehow caught this virus in the bat's habitat, then somehow scurried its way across the vast Chinese interior, over rivers, mountains, and urban landscapes, and in the process allowed the virus to mutate itself to be perfectly adaptable to not only human infection but to also become specifically apt for human-to-human transmission, and then this host animal sneezed or whatever on a human in Hubei to infect patient zero... and you say the lab leak is the ridiculous hypothesis?

If the workers had COVID then they are hopelessly too early to cause the outbreak on the market,

The month prior was "too early", when the research you cite specifically stated the virus was present a month before the market cases?

and most importantly being several of them it would mean the virus at that point would have been completely adapted to be transmitted between humans,

Yeah, thats what gain of function research in labs does. It looks to make a virus human-to-human transmissible in order to pre-empt it. And its also what nature usually does not do in an intermediate host animal (unless by nearly unfathomable chance).

this means you would have observed not a single outbreak in december (as expected if the disease was introduced from outside of the city) but several big outbreaks around the city in November,

By your own logic, it would mean seeing several big outbreaks around all of Hubei in November

1 ( +3 / -2 )

the closest know related virus, RaTG13, occurs in bats that inhabit an area (Yunnan) well over 1000km from Hubei

Oh wait, my mistake. Very sorry.

The RaTG13 virus does exist outside of Yunnan.

Samples of it are located in the Wuhan Institute of Virology, where they have studied and analyzed it (hence why they know its so similar to Covid-19) and presumable did gain-of-function research on it (though any record on that are probably long since destroyed).

1 ( +3 / -2 )

Do you not realize that Wuhan is located in Hubei province?

Part of the discussion that you keep skipping is that cases found in rural areas explain the lack of big outbreaks for the first few weeks until the infection entered big cities, once an easily transmitted disease enters an area well populated it causes big obvious outbreaks such as the one that was identified first. This is again in concordance with the genetic modeling of the spread of the disease, a slow extremely difficult to see progression at the beginning (because of people living and working much more isolated) causing limited cases and then an exponential growth in a short time, when it entered the city. It is not difficult to see how a laboratory escape can't fit these two pieces of information, specially if several people were infected from the beginning. Again the natural origin fits perfectly with both pieces of information and do not need any extra unusual situations to fit as the lab escape.

And again, the closest know related virus, RaTG13, occurs in bats that inhabit an area (Yunnan) well over 1000km from Hubei in a climate that is completely different.

Read the article you are commenting in, RaTG13 is the closest known virus, since the sampling is extremely limited this do not mean they are going to be the closest that will ever be found, nor that this is the only location where this virus will ever be located, this is making invalid conclusions from too limited samples. It would be like you getting a genetic test in Tokyo and the results saying that the closest relative they found in their database for you is a guy in Hokkaido.

The month prior was "too early", when the research you cite specifically stated the virus was present a month before the market cases?

Yes, now you are understanding better. There is a huge difference in the epidemiology of a disease that begins in rural areas and a disease that begins in a big crowded city. The contact between people is completely different, a spreading to a dozen cases in a month for a small town is expected, in a big city is unthinkable for COVID-19.

By your own logic, it would mean seeing several big outbreaks around all of Hubei in November

That is wrong, it would mean seeing several small outbreaks, because they were happening in small cities with much lower population density, this is the whole point of the evidence, the disease spread as expected from an introduction from nature, first on few isolated cases in areas of low population and then a rapid spread in big cities (several) where the disease produce much more obvious clusters of many people.

Samples of it are located in the Wuhan Institute of Virology, where they have studied and analyzed it (hence why they know its so similar to Covid-19) and presumable did gain-of-function research on it (though any record on that are probably long since destroyed).

So now the theory is not that SARS-CoV-2 gained the small changes necessary to make it more similar to RaTG13 but that RaTG13 gained the huge amount of changes necessary to make it closer to the SARS virus? that does not make it easier, on the contrary it makes it even less likely to happen. And no, it is trivially easy to find evidence of the kind of gain of function work done in the WIV for all the strains that they used because this is work that takes years and its published continuously all over the world, thinking that they only refrained to publish when working from one strain is not logical, the much more likely explanation is that this was not included in the work they did since the only importance of this specific strain began the moment it was found simmilar to the SARS-C0V-2.

-3 ( +0 / -3 )

Login to leave a comment

Facebook users

Use your Facebook account to login or register with JapanToday. By doing so, you will also receive an email inviting you to receive our news alerts.

Facebook Connect

Login with your JapanToday account

User registration

Articles, Offers & Useful Resources

A mix of what's trending on our other sites