Wednesday, April 21, 2021

Rejected by The Conversation (again)

In recent years (about 7) The Conversation has rejected every single "pitch" I have made. This is typical:

"Thanks for the pitch. It’s an interesting idea but unfortunately I have to decline. With current resources we’re only able to publish  a small minority of the pitches we receive and while this idea has merit I’ve reluctantly decided there are others with stronger content."

Here are some of the topics they have not thought of sufficient interest. They have a common theme; limits to growth, existential risk to civilization, regional overload, the "fortress world" and philanthrocapitalism and planetary health. 

The most recent rejection concerned existential risk. My paper (Climate change, health and existential risks to civilization: A comprehensive review (1989–2013)) showed that while the risk to civilization, and thus to global public health, from climate change has grown, the willingness to discuss this in the health literature has fallen considerably.

I know that the budget for the Conversation has fallen a lot in recent years.
 
But I also think that their gatekeepers are very conservative.  

PS They didn't just reject my approach suggesting that the origins of COVID-19 could be from a lab even though, again, I had a published paper (the 4th such paper in the world, that I know of, published in 2020); instead they ignored my pitch.

On the other hand, TC has solicited one paper from me (since 2012); the experience (for me) was unsatisfactory; I felt rushed and pressured.




Monday, April 5, 2021

A discrepancy between the WHO-convened report into the origins of SARS-CoV-2 and the Addendum to Nature

On March 30, 2021, the WHO-convened study into the origins of SARS-CoV-2 was released. Annex D3 states that “with regard to the matter of morbidity and mortality in miners in a mine in Mojiang, Yunnan Province, where bats were present, Professor Shi said that the events had been clarified in an addendum to her Nature article.” 

These illnesses had occurred in miners exposed to bat guano in 2012. 

The Annex states “the reported illnesses associated with the miners, according to the WIV experts, were more likely explained by fungal infections”. However, the Nature Addendum referred to (Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin) states that “we suspected that the patients had been infected by an unknown virus”. In addition, the Master’s thesis by Li Xu, which meticulously documents the clinical course of the six miners, hypothesised a viral illness, stressing this in its title (Analysis of Six Patients With Unknown Viruses). This thesis records that Dr. Nanshan Zhong (consulted remotely) reached a similar diagnosis, even noting that he stated there is a “great possibility for virus (sic) infection”. The Master’s thesis makes it clear that the Kunming-based clinical team (and Dr Nanshan Zhong) considered that a secondary (co-existing) fungal infection (secondary aspergillosis) was considered plausible. For this reason the patients were treated with anti-fungal medication, including Caspofungin. However, three of the six patients still died and it is clear that the primary scientific interest in the cases was the possibility of a novel virus. It is inferable that the possibility of novel viruses being found in the Mojiang cave was rapidly communicated to Professor Shi’s team, most probably by Dr Nanshan Zhong or  the Kunming medical team (or both), leading to the first of about seven visits made to the Mojiang cave between 2012-2015, by Professor Shi’s team, as described in Annex D7.   However, Annex D7 does not explain why the theory of a bat (or bat-guano) associated virus infecting the miners, originally considered such a strong possibility as to provoke about seven visits to this remote cave, was discarded, apparently between November 2020 (when the Nature Addendum was published) and February 2021 (when Professor Shi and her colleagues provided this different opinion included in Annex D7). 

 Annex D7 also provides a rudimentary occupational history of the miners’ exposure, stating that the “miners had been to the cave 2-3 times”. This contradicts the details provided by Li Xu (published in 2013, apparently based on clinical records made at the time of the miners’ illnesses, three of which were fatal) which states, for example, that one patient (aged 63) “had been working in the mining well for half of a month. He worked 7 hours a day”. The occupational history for case three (aged 45) is described as: “The patient went into a 150 meter deep cave 24 days ago. He continuously inhaled some unknown gas for 10 days”. The relevant occupational history of case five (age 30) is translated as “he has been to a big cave (about 150 meters deep) to work and was exposed to feces of bat for 4 days.” 

 Annex D7 does not give any detail of the source or “provenance” of information about the miners’ illnesses, other than it was provided by Professor Shi between January 14 and February 10, 2021. Unless one or more of Professor Shi’s team was working in the Kunming hospital in 2012 and was caring for one or more of the Mojiang-exposed miners the Wuhan team’s information about the miners must be secondary. Was it from Dr Nanshan Zhong? Was it obtained directly from one or more doctors at the Kunming hospital? Was additional information obtained from the Master’s thesis, written by Li Xu? In any case, claiming (as Annex D7 does) that “the illnesses of the miners exposed to bat guano in 2012 in Mojiang” were  “clarified” in the Nature addendum is a gross exaggeration. 

 There is a long history of obfuscation about the exposure and illnesses of these miners (three of whom died), as documented, for example by Rahalkar and Rahalkar (2020) "Lethal pneumonia cases in Mojiang miners (2012) and the mineshaft could provide important clues to the origin of SARS-CoV-2" and Butler (2020) "Plagues, pandemics, health security, and the war on nature". Neither of these studies is cited in the WHO-convened Global Study of Origins of SARS-CoV-2 (including the Annexes), further demonstrating the biased and incomplete knowledge and selection of the literature used by the report’s authors.

 

Saturday, February 13, 2021

COVID-19, the WHO investigation, and Gain of Function research

COVID-19 may develop into the worst infectious disease crisis since “Spanish” flu, even worse than HIV/AIDS (if it evolves the capacity to outsmart vaccines, a worrying possibility, given recent South African data). In any case, it is a very unusual and disturbing event, several orders of magnitude worse than SARS or Ebola, if raw numbers of deaths and illnesses are considered.

Ascertaining the origin of COVID-19 is of utmost importance. Unlike almost all other recent “emergent” viral zoonoses, of which there are perhaps a score that are significant (e.g. Ebola, Hendra, Nipah, Lassa fever, Marburg and SARS) SARS-CoV-2 has a strongly developed “stealth capability”, i.e. the ability for significant asymptomatic transmission. MERS (also a coronavirus) also has stealth characteristics, but to date has proven far less contagious. (SARS lacks this capacity, hence it did not become a genuine pandemic, unless one uses a very low barrier for the definition of that term). 

HIV/AIDS, like many sexually transmitted infections, also has stealth characteristics, as it can be transmitted to people who are unaware they are at risk. Sometimes too, the person transmitting HIV is unaware of their illness. HIV/AIDS is a pandemic, using any definition, and its death toll still far exceeds that from COVID-19.

 

Could SARS-CoV-2 have been "engineered"?


The highly developed capacity of SARS-CoV-2 for such significant asymptomatic transmission struck me as extremely unusual, even in early 2020. However, initially, I put my unsettling thoughts (explained following) to the side, thinking that for reasons that I did not understand, nature, by itself (perhaps assisted by farmed or captured and traded species that are exotic in the West, but common in China, eg palm civets, raccoon dogs or pangolins) had evolved a viral "super-pathogen”. 

 

The leading British virologist John Oxford has, for almost two decades, published work postulating that "Spanish” flu was not entirely “natural", but had its characteristics “shaped’ by human factors associated with the Western Front in the Great War, especially the dense crowding together of ill troops, which (he argues) created a natural laboratory allowing a form of "serial passage” of the influenza virus (H1N1) among them. (See also here). Thus, Oxford postulates, evolution favoured the “honing” of a form of H1N1 which was unusually efficient at killing young people. Although Oxford’s theories on this topic are generally regarded as speculative, no one can deny that Spanish flu emerged in the closing period of the Great War; if the two events were not related then the world struck extraordinary bad luck. 

Because I have long been familiar with Oxford’s theory, including the principle of serial passage and other techniques used in “Gain of Function” research, it therefore crossed my mind, quite early, that SARS-CoV-2 might have been “engineered”. When I read the letter, published in The Lancet in February 2020 (Calisher et al), which we now know (thanks to US “Right to Know” which published relevant email correspondence concerning it) was conceived and driven by Dr Peter Daszak, head of the EcoHealth Alliance, I was dismayed with how the laboratory leak hypothesis had been dismissed. The letter even characterised such a view as “conspiracy”. 

 

In early 2020 the United Nations Environment Programme (UNEP) commissioned me to write a 15 page report (plus references) on the origin of SARS-CoV-2 and how future pandemics might be avoided. I thus started to read everything I could about this new virus, including via twitter. I thus gradually became aware of COVID-19 activists, several of whom are anonymous including a team called “D.R.A.S.T.I.C.". I also started to read, with great attention, statements by Professor Shi, director of the Wuhan Institute of Virology. 

 

"Gain of Function": a deadly euphemism? 

 

I soon realised that there were other troubling elements which gave plausibility to a laboratory leak hypothesis. One was that I became aware that Gain of Function (GOF) studies were being undertaken at the WIV, involving not only betacoronaviruses but chimeric creatures such as “humanised mice”. I also learned that these studies were (until suspended by the US administration headed by President Trump) being funded by the US National Institutes of Health, via the EcoHealth Alliance.  (Funding has apparently been restored, from a non-government source.)


GOF studies seek to answer questions such as what genetic sequences of a pathogen (generally a virus) impart characteristics, perhaps such as airborne transmission, or human to human transmission. Serial passage, using living animals, has long been a key technique of GOF, but is now complemented by cell lines, as well as animals with at least some characteristics of other species, eg humanised mice.

 

Two extreme examples of potential GOF experiments that should never be undertaken are: (1) could HIV be made transmissable by coughing? (2) Could a pathogen be engineered to target an ethnic minority? In my opinion, we collectively know far to little to conduct even simple, apparently "safe" GOF experiments. Of course, others differ. (See this debate in Nature Reviews Microbiology, published in 2015). But if GOF is to be conducted, surely we can agree that it needs strict safety protocols, transparent, accessible records (available for decades) and a strong "safety culture".


In fact, I think GOF studies warrant oversight similar to nuclear power, with teams of inspectors from neutral countries. In the film SARS COV2 – Identikit di un killer (Identikit of a killer), by Italian media organisation RAI, Canadian Professor of Public Health Amir Attaran likens GOF work to "playing with nuclear material to build a bomb" (approximately at the 54 minutes mark). Finally, GOF studies, to be safe, need to operate in countires with strong whistleblower protection, a quality clearly lacking not only in China, but many other nations.


In 2012 I co-authored an editorial with the editor and other co-editors of the journal EcoHealth that discussed some of the pros and cons of “dual use” technologies with regard to influenza viruses. The term “dual use” (in relation to virus research) has fallen from use, replaced by “Gain of Function”. I formed the opinion, in 2012, that these studies could be very dangerous. Indeed a moratorium on such studies was applied for several years, but has since been relaxed. For more information on the risks of Gain of Function, see: http://www.cambridgeworkinggroup.org/

 

 

Strange comments by Professor Shi 

 

In mid-2020 I learned, initially via the activists on Twitter, of illnesses of six mine workers, exposed to large quantities of bat guano from their work clearing a mine shaft in Yunnan, China, in 2012. At first, I was incredulous, wondering if the Master's thesis which described the clinical course of these workers (of whom three died, despite aggressive treatment), could be an elaborate hoax. I wondered why these cases had not been brought to international attention far earlier. Why, for example, had the EcoHealth Alliance, whose self-described mission is to alert the world to new viruses, had not known of them? 

 

Although fragmentary evidence of these illnesses was released in 2014 (see http://dx.doi.org/10.3201/eid2006.131022), a more complete story was not confirmed until an Addendum was published in Nature in November 2020, written by Professor Shi and others at the Wuhan Institute of Virology. More recently Professor Shi has also commented on this thesis, to John Sudworth of the BBC. Her comments about this thesis were oddly disparaging.

 

In December 2020 I published an editorial in The Journal of Human Security documenting some of Professor Shi’s inconsistencies and belated, piecemeal, revelations. In that essay, I argued that the laboratory leak was a plausible hypothesis. 


A story from George Orwell?

 

Now I come to the recent WHO-associated investigation into the origins of COVID-19. This involved scientists screened by China. I am unaware of whether members of the team were considered whose selection was later vetoed by China. I certainly was not invited.

 

A report by this team is to follow, and there was a press conference lasting over two hours, to which I have not listened. However, there appears to be an impression, widely circulated, that there was consensus among the team that the virus was not from a laboratory. The evidence stated in favour of this appears to boil down to something like “we spent 3 hours at the Wuhan Institute of Virology, we talked to the people there, and we formed the opinion that they are honest and competent. When they said the virus had not leaked we believed them”. Even if I am over-simplifying the evidence which they found, my opinion is that this conclusion is based on flimsy evidence. For a start, at least one of the participants, (who has, at least in one interview I have seen on Chinese media called Prof Shi a “friend”) has an obvious conflict of interest. The credibility of this team is reduced by including this person in the team, as was pointed out in the recent open letter "Call for a Full and Unrestricted International Forensic Investigation into the Origins of COVID-19" (to which I contributed).

This scientist is also involved in The Lancet, “commission” about the origins of SARS-CoV-2. I will try to write more about that in future; suffice to say, at this point, the attempt that I and others (including some of the authors of the recent open letter) recently made to publish on this topic, in that journal, was rejected.

 

More convincing evidence to refute the laboratory leak hypothesis would require the release of detailed laboratory records, perhaps going back for a decade or more, and answers to many of the questions posed by the “D.R.A.S.T.I.C.” twitter team. Were the Wuhan Institute of Virology (WIV) transparent, such records and answers would not require a visit to China, and they would long ago have been provided. The release of such records would restore some trust and goodwill, in a way that this recent visit has not. Importantly, however, even if the WIV were more forthcoming, evidence of a laboratory leak could still be hidden. That is, while WIV could confirm a leak, they could also hide it, even if one occurred. However, the release of such detailed records (even if screened by WIV) might provide clues which forensic investigation could uncover. From the point of view of China, this is a risk not worth taking, if they have something to hide. And, even if the pandemic did not involved Gain of Function work done in Wuhan, it is virtually certain that other work by the WIV would be scientifically valuable, with potential for good or ill (ie “dual use”) and it would be naive to expect transparency.

 

Alternatively, however, if a virus of 99.9% similarity to SARS-CoV-2 were found in a bat or an intermediary species (eg a ferret-badger), and investigators could be confident that it was authentic, then the laboratory leak hypothesis for SARS-CoV-2 could be confidently excluded. Though it would not exclude the chance of a leak in future.


In summary, the WHO-associated team’s dismissal of the laboratory leak theory could have been provided in a novel by George Orwell. It is absurd to think this reassurance should be taken seriously, and it is depressing that the team appear to think it will be taken seriously. Curiously, however, WHO Director General Tedros Adhanom has since appeared to indicate that the laboratory leak hypothesis should not be dismissed.


Past laboratory leaks

 

I think the tide is turning, in the sense that consideration that the virus may have been a laboratory leak is no longer automatically considered as evidence of conspiracy thinking. There have been many such leaks in the past; here is a partial list: smallpox (1966, 1972, 1978, all in the UK), SARS (2002, Singapore; 2004 Taiwan, 2004, China), anthrax (1979 USSR)Yersinia pestis (2009, USA), Ebola (2004, Russia, 2009 Germany), Marburg, Neisseria meningitis, Venezuelan equine encephalitis, foot and mouth disease (2009, UK), H5N1 influenza (2014, USA) and H1N1 influenza c1976 (China or USSR)

 

In the absence of genuine and complete co-operation from China, getting to the truth is very difficult. But, on the balance of probability, the theory of a lab leak is becomes increasingly plausible. Although supporters claim Gain of Function studies can do great good, such studies can, obviously, do great harm, at least in theory. At a minimum, such studies need to be managed by people with great integrity and scrupulous attention to detail. My opinion of Prof Shi is that she either lacks the qualities needed for this (shown by her own documented inconsistencies), or, more charitably, is working in a milieu, in a totalitarian society, where such qualities are impossible to display. 

 

Trying to explain Professor Shi's inconsistencies 


It is perhaps possible that Prof Shi’s inconsistencies are a result of Chinese security policy and officials, who greatly restrict her freedom of speech. This could explain otherwise inexplicable errors (for such a senior person) such as her attribution of the miners’ deaths to fungal infection, her mis-reporting of the number of sick miners who died (she says two*, to Jane Qiu in Scientific American). Richard Ebright  described some of Prof Shi's responses as "formulaic, almost robotic, reiterations of statements previously made by Chinese authorities and state media”.

 

Her inconsistencies and occasionally facile comments (eg concerning the Master's thesis) might be because Prof Shi is too frightened to speak out (and has long been constrained in what she could write and speak). In a way that would be encouraging, as it could indicate that, in fact, she is a person of great integrity, as Dr Peter Daszak has long argued. It could signify that she is in danger, although it's hard to see how even the Chinese state could risk making her "disappear" at this stage, without raising far even more questions. 

 

The alternative explanation (that Prof Shi is, to put it kindly, rather simple) is perhaps better for Prof Shi's safety, but even more unsettling for the world.


I honestly don't know which explanation is more plausible, but I am confident that Gain of Function research needs strong regulation, and also that independent journalists and analysists need to press on, trying to uncover the truth. I am dismayed that top journals such as Nature and The Lancet are not more penetrating; I wonder to what extent they too are influenced by Chinese censorship and money. Back in 2007 we argued that journals also have conflicts of interest, which journals should periodically declare.

 

Gain of Function studies are probably being undertaken in many countries. Because they are not banned, there is likely to be an "arms race" underway. Banning them might not stop this race, but it would dampen it. WHO should speak out strongly about GOF research, irrespective of the origin of COVID-19, such experiments could go wrong, with devastating consequences. The relationship between the Anthropocene and infectious diseases is far more complicated than deforestation, climate change and landuse change; it also includes medical proceedures and laboratory research, and - yes - the possibility of a laboratory escape.


* It is not only Prof Shi who presents alternative numbers regarding the miners' deaths. The original report, by a different Chinese team, from 2014, incorrectly says that there were three cases, all of whom died (See: http://dx.doi.org/10.3201/eid2006.131022). In fact there were six, of whom half died (that is, if the Master's thesis is correct).


This blog was slightly updated on March 7, 2021


Some key references on laboratory leaks:

Brault, A.C., et al., Potential sources of the 1995 Venezuelan equine encephalitis subtype IC epidemic. Journal of virology, 2001. 75(13): p. 5823-32.

Branswell, H., Bio-unsafety level 3: could the next lab accident result in a pandemic? Scientic American, 2014

Enserink, M., Reports blame lab for foot-and-mouth fiasco. Science, 2007.

Heymann, D.L., R.B. Aylward, and C. Wolff, Dangerous pathogens in the laboratory: from smallpox to today’s SARS setbacks and tomorrow's polio-free world. The Lancet, 2004. 363: p. 1566-68.

Meselson, M., et al., The Sverdlovsk anthrax outbreak of 1979. Science, 1994. 266: p. 1202-1208.

Silver, S., Laboratory-acquired lethal infections by potential bioweapons pathogens including Ebola in 2014. FEMS Microbiology Letters, 2014. 362: p. 1–6.

 

Some key references on medical procedures and epidemics

 

Bookchin, D. and Schumacher, J. (2004) The Virus and the Vaccine, St Martins Griffin, New York.

Jain, S.L. (2020) The WetNet: What the oral polio vaccine hypothesis exposes about globalized interspecies fluid bonds. Medical Anthropology Quarterly, n/a. https://doi.org/10.1111/maq.12587.

P├ępin, J. (2013) The origins of AIDS: from patient zero to ground zero. Journal of Epidemiology and Community Health, 67, 473-475. 10.1136/jech-2012-201423.
 


  

Sunday, December 6, 2020

Plagues, Pandemics, Health Security, and the War on Nature

Now published: see http://www.librelloph.com/journalofhumansecurity/article/view/johs-16.1.53

Journal of Human Security j 2020 j Volume 16 j Issue 1 j Pages 1–5

DOI: 10.12924/johs2020.160100XX

ISSN: 1835–3800

Journal of Human Security

Editorial

Plagues, Pandemics, Health Security, and the War on Nature

Colin D. Butler

The Australian National University, Canberra, Australia

Corresponding author: colin.butler@anu.edu.au

Published: XX XXXXX 2020

 

Abstract: This editorial presents a brief review of pandemics from antiquity to COVID-19. Although all large-scale epidemic diseases (“pandemics”) can be considered ecological “checks” on human population size, and although COVID-19 is the biggest such pandemic since HIV/AIDS emerged it is not likely to approach the deathtoll of earlier pandemics, such as the plague. There are two major hypotheses to explain the origin of COVID-19. One is the “natural origin” hypothesis, the other is that it might have escaped from a laboratory, with its origin subsequently hidden. Although most scientists support the natural origin idea the other cannot yet be dismissed. Evidence for each hypothesis is presented. If the first theory is correct then it is a powerful warning, from nature, that our species is running a great risk. If the second theory is proven then it should be considered an equally powerful, indeed frightening, signal that we are in danger, from hubris as much as from ignorance. More pandemics are inevitable, but their severity can be reduced by greater transparency, international co-operation, and retreat from planetary boundaries.

 

Keywords: bats, China; COVID-19; ecology; health; limits; medical history; pandemics; security.

 

Human health depends on many forms of security, most obviously sufficient quantity and quality of air, water, food and shelter. Less well recognised, humans also need social connectivity [1]. Our species also seeks freedom from devastating infectious diseases, which have periodically plagued civilisations for so long (over 2000 years) that humans may share a collective, usually sub-conscious, apprehension of epidemics [2].

 

The word “plague”, is, today, mostly associated with the disease caused by the bacterium Yersinia pestis, the causal organism (for which antibiotics are today effective) for the Black Death and the Justinian plague. In antiquity, plague was a generic name for any pestilence. The viral disease smallpox (which probably was passed to humans from cattle) may have caused the Antonine plague that infected Romans in the reign of Marcus Aurelius.

From the 6th to the 8th centuries a series of plague outbreaks, generally now named after the emperor Justinian, weakened the Byzantine empire and helped the spread of Islam, as nomadic Arab tribes, moving on desert or semidesert territories, “succeeded in escaping the contagion more easily”. Estimates of its death toll range from 25 to 100 million people, localised to Europe and the Mediterranean region [3].

Civilizations do not decline purely because of disease; climate change, undernutrition and invasions are important co-factors. It is estimated that, almost seven hundred years ago (1348-50), the Black Death killed over one third of the population of Western Europe, and up to 100 million globally, including in Africa and China. Its mortality in Europe appears to have been worsened by preceding decades of undernutrition, as the climate cooled following the end of the Medieval Warm Period. The Great European famine (1315-17) was compounded by a devastating viral disease in cattle, probably rinderpest, which killed over half the cows in England (1319-20), creating in England a scarcity of milk that lasted until at least 1332 [4].

Starting in the 15th century, the violent conquest of the so-called New World was facilitated by a complex of diseases, including measles, malaria, smallpox and yellow fever, introduced to populations with no immunity. Smallpox was repeatedly spread to some American tribes by “gifts” of contaminated blankets. The deathtoll from infections brought to the Americas was lower than from the Black Death, but was far more devastating, killing as many as 80-95% of the Indigenous peoples within 150 years of invasion [5]. Only a century ago, in less than 5 years (1917-1921), “Spanish” influenza killed approximately as many people as the Black Death, though a smaller fraction of what was by then a much larger global population, about two billion.

 

But fear of infectious diseases abated in recent decades, at least for the most privileged fraction of the global population. Positive feedback loops, whose elements include advances in science and technology, public hygiene, improved nutrition and the burning of vast quantities of fossil fuel generated a false sense of security. WH Stewart, appointed US Surgeon General in 1965, is reputed to have stated “it is time to close the book on infectious diseases and declare the war against pestilence won.” It is less wellknown that this qualifies as an urban myth [6]. Nevertheless, this statement was, for over a decade, considered plausible.

 

The spell was fractured by the emergence of HIV/AIDS, a pandemic virus generally thought to have been originally transmitted to humans from contact with “bushmeat” (probably a primate) in the African forest [7]. But, once the causes ongoing of HIV/AIDS transmission were understood, fear of it faded, at least for populations with access to health literacy and effective anti-viral medication.

 

 1. COVID-19 and Other Recently Discovered Zoonoses

 

Zoonoses (defined here as pathogens that have spread from other animal species to humans) recognised in the last 70 years cause diseases including Ebola, Human Immunodeficiency Virus (HIV), Lassa, Marburg, Nipah, Severe Acute Respiratory Syndrome (SARS) and Middle Eastern Respiratory Syndrome (MERS), as well as COVID-19, whose causal agent is the virus named SARSCoV-2. Compared to historic pestilences, the global death toll of COVID-19, though now over a million, is minor. Unlike previous plagues, COVID-19 has emerged in an age of vaccines, antibiotics, and sophisticated epidemiology. But, without a vaccine, COVID-19 seems likely to become endemic, posing a perennial threat, not only to the elderly and people with pre-existing conditions, but to younger people who risk developing chronic manifestations, including cardiac, renal and neurological effects.

 

There is great concern, some of it overstated, that zoonotic pathogens have global pandemic potential. For example, all of the pathogens mentioned above, other than HIV, are listed by the World Health Organization (WHO) as priority diseases, claimed to “pose the greatest public health risk due to their epidemic potential and/or whether there is no or insufficient countermeasures” [8]. However, of this WHO list, only COVID-19 and MERS are known to be transmitted by asymptomatic patients, and of these, only COVID-19 is easily transmitted by aerosols. The other zoonoses in this list are highly contagious and have high mortality but are less problematic from a public health perspective because, with proper barrier nursing and strict infection control, they “burn out” [9]. Note, however, that before SARS was brought under control almost 8,000 people were infected, of whom about 800 died.

 

COVID-19 causes justifiable fear not only because it has no vaccine and no proven treatment (yet), but also because it shares, with influenza, HIV/AIDS and a small number of other pathogens a “stealth” capacity, enabling it to spread from people who are either completely asymptomatic, or whose infections may be hidden to others. This makes it far harder to control than other newly discovered viral zoonoses, including SARS and Nipah virus [9].

 

Apart from HIV/AIDS, historical plagues long precede the contemporary global crisis, which is marked by extreme stratification, plummeting biodiversity and worsening climate change. Two planetary boundaries have already been exceeded. It may thus not be accurate to attribute devastating infectious diseases solely, or even mostly, to the “war on nature”, the plundering of planetary resources for the alleged benefit of one species, humans [10]. On the other hand, zoonoses have only affected humans in significant numbers since plant and animal domestication and other manifestations of human ingenuity that enabled densely inhabited human settlements. While most experts date the beginning of the Anthropocene to the 18th century or later, Ruddiman and his colleagues have long argued for a much earlier date, perhaps 7,000 years ago [11]. All major infectious diseases that have affected humans have not only occurred in this period, in a time when humans have increasingly transformed nature, but also laboratory ingenuity, though not necessarily laboratory wisdom [7,12].

 

2. The Natural Origin Theory for the Emergence of SARS and COVID-19 

 

There are two major hypotheses to explain the origin of COVID-19. One is the “natural origin” hypothesis, the other is that it might have escaped from a laboratory, with its origin subsequently hidden.

 

Most recently recognised zoonoses have been facilitated by factors associated either with falling biodiversity or intensive farming, especially of chickens and pigs. These ecological determinants include deforestation, and the hunting, slaughtering, smuggling, trading and farming of wild animals, from chimpanzees to pangolins and civet cats. Climate change may also be an element, such as via heat waves and other forms of stress, including pregnancy and poor nutrition, that might increase viral “spillover” from bats and rodents to other species [13].

 

Social factors, especially poverty and exploitation, are also relevant. High population density, where many people share a single dwelling, is an important risk factor, as is the common practice of a single shared toilet for many slum dwellers, such as in India. Crowded public transport is a setting for COVID-19 transmission. On the other hand, enormous, densely packed cities may not necessarily be at very high risk, if housing is of sufficient standard and there are alternatives for commuting, such as the internet.

 

The average level of wealth and the degree of stratification are also important. A highly egalitarian population where most people are poor does not provide protection, and is likely at greater threat than a stratified population with high average wealth. However, many cities are highly stratified, with people living in pockets of affluence alongside poverty and human exploitation. Away from the cities, rural poverty not only helps to motivate legal activities such as participating in deforestation, but illegal acts such as participating in wildlife trafficking.

 

Bats are the reservoir species for many recently discovered viral zoonoses, responsible for diseases including SARS, COVID-19, Nipah and Ebola. The coronavirus that causes SARS is widely considered to have crossed into human populations (in 2002) via the farming of civet cats (and possibly other “exotic” species, such as bamboo rats) in southern China. But for 17 years, despite monitoring and anxiety, nothing quite like SARS emerged again, until late 2019 when an unusual cluster of pneumonia cases, now known as COVID-19, was detected in the central Chinese city of Wuhan. A new strain of coronavirus was rapidly identified by staff at the Wuhan Institute of Virology (WIV), one of China’s most prestigious viral research laboratories. It was, soon after, named SARS-CoV-2. 

SARS-CoV-2 is generally thought to have evolved and to have entered the human population in a way similar to the causal organism for SARS. Consistent with this hypothesis, the location of the first cases in Wuhan was identified as associated with a local market, where many live animals, different species, were held in close proximity for sale [14]. 

Several early articles speculated that the bridging species (between bats and humans) was a pangolin, one of the world’s most frequently traded mammals, mostly illegally, used not only for food but for its alleged medicinal value. It initially seemed plausible that viruses in infected pangolins might have had opportunities to exchange genetic material en route to China, in cages transported by smugglers, where the secretions and breath of stressed, frightened animals, perhaps from different origins, and even of different species, may mix. Alternatively, a new strain could have emerged in a farm, where animals such as civet cats are bred in captivity, also in crowded conditions. However, there is an emerging consensus that the coronaviruses to date identified in pangolins are not sufficiently close to SARS-CoV-2 to be the source, despite intensive searching [15]. Despite intense effort, the natural origin hypothesis has not yet been further strengthened.

 

3. An Alternative Hypothesis for COVID-19: Laboratory Escape 

 

Although most scientists support the natural origin hypothesis an alternative theory for the origin of COVID-19 is slowly gaining interest. It has always been striking that a disease like SARS would emerge in Wuhan, a city more than a thousand kilometres north of tropical Yunnan, where there are larger bat populations and identified natural sources of coronaviruses. However, one plausible route could be via infected animals imported into Wuhan, bringing the virus along. WIV researchers originally asserted that COVID-19 entered humans in a market offering seafood and other animals in Wuhan, which was promptly closed for cleaning and investigation.

 

Curiously, however, samples from living animals in the market (such as of faecal material or swabs) were reportedly not taken. Dr Shi Zhengli, who heads a group that studies bat coronaviruses at the WIV, wrote, in a series of responses to the journal Science, that only frozen samples of animals had been taken from the market, and that no coronaviral RNA had been found in them [16]. More recently, the head of the Chinese Centre for Diseases Control (CDC) denied the fish market as the source, adding that “the novel coronavirus had existed long before” [17]. 

 

Many self-published essays on the internet have disputed the natural origin hypothesis. Most such essays suggest that it instead accidentally escaped from the WIV, after either being manipulated in the laboratory, or perhaps because it was already archived there, reaching the wider population after infecting a researcher. The laboratory escape argument is also considered plausible by the U.S. government which, in addition, has suspended its funding of the EcoHealth Alliance [18] which has reportedly undertaken “gain of function” viral research in China [19].

 

Circumstantial evidence gives plausibility to this alternative hypothesis. Suspicion is heightened by the opacity and power of the Chinese Communist Party, its almost complete suppression of free speech, and the increasing sense it conveys of feeling besieged by hostile forces. The mother of Dr. Li-Meng Yan,a scientist currently in hiding after being granted asylum in the U.S. (after alleging that SARS-CoV-2 was derived from a laboratory), is reported to have been detained by Chinese authorities [20]. Such evidence may seem thin, but it is widely known that a deceased Chinese doctor’s attempts to warn of the pandemic were originally suppressed [20]. It also well accepted that Chinese authorities initially attempted to disguise the outbreak.

 

The provenance of the closest known betacoronavirus to SARS-CoV-2 (a variant called RaTG13, which is 96% similar, meaning that the two strains may share a common ancestor that diverged 20 to 50 years ago) is also curious. Evidence for RaTG13 was found in material collected between 2012 and 2015 from a mine cave near Tongguan town, in Mojiang County, Yunnan, and taken from there to the WIV [21]. Six miners, of whom 3 died, had worked in this mine in 2012, removing bat guano. The cause of their respiratory illness was hypothesised by the medical team treating them as a viral and fungal co-infection [22,23]. This information, reported in a thesis, was scarcely known outside China until revealed in 2020 by activists and then in a single (to date) peer reviewed paper [23]. The thesis also revealed that several of these cases of pneumonia had been brought to the attention of Zhong Nanshan, one of the most senior doctors in China.

 

The provenance of RaTG13 is striking for several reasons. Firstly, the link between the mine-associated human illnesses and RaTG13 was not officially disclosed until November 17, 2020, in an addendum written by WIV-associated investigators, published in Nature [21], over nine months after the original report of RaTG13, also published in Nature, on February 3, 2020 [14]. The addendum appeared almost one month after Rahalkar and Bahulikar’s paper, which not only discussed the Masters thesis, but which also speculated that RaTG13 was first found in material sampled from the same cave where the miners had acquired their illness [23]. An earlier paper (published February 2016), also led by WIV researchers, had reported the identification of viruses sourced in material from the mine but had also failed to disclose any human illness [24]. Yet, as reported in the addendum, the WIV researchers had sampled the Mojiang mineshaft specifically because of its association with miners who had sickened, a fact known to the WIV in 2012 [21]. These facts demonstrate a reluctance by WIV researchers, ongoing for almost 5 years, to report (at least in internationally available journals) the association between an infection with a case fatality rate of 50% and viruses that they had isolated. The timing of their addendum, which ends this silence, may be coincidence, but can also be interpreted as an attempt to save face, by publishing additional, highly pertinent information, without apology, but when embarrassed by growing awareness of their previous non-disclosure.

 

Adding to the fog, a profile of the senior WIV investigator Dr Shi Zhengli, published in March 2020 in Scientific American (final author for the 2016 and 2020 reports) reveals knowledge of six mine-associated cases of pneumonia, two (sic) of whom had died [25]. This profile does not precisely reveal the source for this information, but creates the impression that such information was given to the reporter by Dr. Shi herself. The report states that “Shi’s team had been called in to investigate the virus profile of a mineshaft in Yunnan’s mountainous Mojiang County ... where six miners suffered from pneumonia like diseases (two of them died). After sampling the cave for a year the researchers discovered a diverse group of coronaviruses in six bat species.” 

 

The profile also states “although the fungus turned out to be the pathogen that had sickened the miners”. This contradicts not only the Masters thesis (which finds that fungal co-infection may have been possible) but also the addendum for which Shi is again final (senior) author which states “We suspected that the patients had been infected by an unknown virus” [21]. In a longer interview with Shi, conducted by correspondence and published in Science in July 2020, she is asked “What do you think of the theory that infected people who lived near mines were the index cases and that they travelled to Wuhan?” Shi answers “I guess you are referring to the bat cave in Tongguan town in Mojiang county of Yunnan Province. To date, none of nearby residents is infected with coronaviruses” [16]. This answer also seems disingenuous.

 

A high-level panel, initiated by WHO, but stated as acting independently, has been formed to investigate the response to the pandemic. Co-chaired by Nobel Laureate Ellen Johnson-Sirleaf and former New Zealand Prime Minister Helen Clark, an advance party of the panel is reported to have spent three weeks in Beijing, in August 2020, but without visiting Wuhan, where the outbreak started. WHO has stated that this first visit is to prepare for a subsequent, larger mission (13 people including Dr Zhong Nanshan). However, WHO was also reported as being vague in response to being asked if this larger task force would even visit Wuhan [26]. Such procrastination means the trail will be even colder, and casts further doubt on the willingness and capacity of both WHO and the Chinese authorities to uncover the true cause of the outbreak.

4. Conclusions

The proximal origin of COVID-19 is unclear, other than its distal origin in a bat. The natural origin and the laboratory associated theories remain plausible, not only for COVID-19, but even for HIV/AIDS [7]. If the first theory is correct then it is a powerful warning, from nature, that our species is running a great risk. If the second theories are proven (for either or both pandemics) then it or they should be considered an equally powerful, indeed frightening, signal that we are in danger, from hubris as much as from ignorance. In either case, each hypothesis for the origin of COVID-19 is related to our evolving planetary crisis. More pandemics are inevitable, but their severity can be reduced by greater transparency [27], international co-operation, and retreat from planetary boundaries.

 

Acknowledgements

The author wishes to thank A/Prof Ro McFarlane, Dr Alex Lautensach and @BillyBostickson.

 

Apologies: not all of the links work - will slowly fix!

 

References and Notes 

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