The remarkable diversity of bat coronaviruses

All human viruses, including SARS-CoV-2, arose from spillovers from other animals. Results of a recent study of bat samples collected in a small region of Yunnan Province, China revealed additional close relatives of SARS-CoV-2 and SARS-CoV.

After the identification of SARS-CoV-2 in early 2020, wildlife sampling and retrospective genome sequencing revealed highly related viruses in animals. The virus RaTG13, from Rhinolophus affinis, shares the highest overall genome identity with SARS-CoV-2, 96.10%. The virus RmYN02 from the bat R. malayanus is the closest relative of SARS-CoV-2 in the ORF1ab open reading frame. Pangolin viruses from Guangdong have identical amino acids at six key residues in the receptor binding domain (RBD) needed for binding to human ACE2. A more distantly related coronavirus was isolated from a bat in Japan, and two viruses from Cambodia have 92.6% genome identity with SARS-CoV-2 and share five of six critical amino acids in the RBD. Finally a bat coronavirus from Thailand is closely related to RmYN02. These observations demonstrate that bats from a broad part of Asia harbor close relatives of SARS-CoV-2.

Fecal samples, oral swabs, and urine samples collected from mainly horseshoe bats in a small area of Yunnan Province between May 2019 – November 2020 were analyzed by RNA sequencing. The results revealed 9 novel betacoronaviruses and 17 alphacoronaviruses. Four of the betacoronaviruses were related to SARS-CoV-2 and three were related to SARS-CoV. Rhinolophus pusillus virus RpYN06 was the closest relative of SARS-CoV-2 in most of the genome with the exception of the spike gene. The other three SARS-CoV-2 related coronaviruses encode a spike gene that could weakly bind to the hACE2 receptor in vitro. Patches of high sequence identity in different regions of the genome illustrate the work of extensive recombination events.

While all the viruses identified in this study, as well as the previously discovered RmYN01 and RmYN02, were identified in a 1100 hectare part of Yunnan province, the results of ecological modeling show that many species of rhinolophid bats are present in much of Southeast Asia and southern China. Numerous other bat species and other wildlife inhabit this area, many of which can be infected by SARS-CoV-2. Hence much more wildlife sampling is needed to track potential spillovers of viruses into humans.

These findings also demonstrate that a very large part of Asia might harbor the direct ancestor of SARS-CoV-2. Remember that HIV/AIDS was first detected in Los Angeles in 1981 but the virus spilled over from a chimpanzee to a human in Africa in ~1920.

5 thoughts on “The remarkable diversity of bat coronaviruses”

  1. The discoveries so far, by “amateur sleuths”, are very interesting.

    I too am an amateur, and have been posting about Covid on for more than a year, and have had early insights proven right. The below is things that I have been saying long since.

    The “experts” in the west, and transnationally, have been horrifically incompetent over the whole crisis (unless they are guilty of even worse: criminal conspiracy). I think it entirely possible that the virus is of natural origins, AND some Chinese scientists have known the “how” and “why” all along – but they have reasons to withhold what they know even if it exonerates them from any “bioweapon” accusations, or of carelessness in GOF research.

    The “orthodoxies” about this virus in the west (and from the transnational agencies) is wrong on more than one crucial detail. The orthodoxy on “how it spreads” has been catastrophically wrong – it spreads by aerosol buildup indoors, not by contact, droplets and surfaces. It is NOT spreading by means of “highly contagious” one-to-one spreading; actually under a wide range of environmental conditions it does not spread at all, at least not causing serious illness or death. I have said all along that the buildup of aerosols indoors to the level that people will get seriously ill, requires several coincident conditions, and when these conditions are not present frequently enough, spread of this virus can fizzle out, or at least be mild enough to be unnoticed (just another “flu like illness”).

    For whatever reason (surely not explicit collaboration with CCP strategic objectives!) the West has made several “mistakes” that have all been in the direction of creating hysteria and fear, and making people compliant with tyranny. By mid March, we knew from antibodies testing from sample cohorts (eg cruise ship passengers, populations of whole towns) that many times as many people had Covid antibodies as what had been known to have become ill, let alone died. The IFR was calculated then, to be 0.15%. I read about this in the Wall Street Journal, and assumed that the panic would calm down. Also material, was that death was concentrated very much in older people who were clustered around the normal age of death. Even then, many people seem to have assumed that Covid was a death sentence for any elderly person who contracts it – when in fact survival rates even in the over 75’s was around 70%.

    Before long, I suspected that there was a considerable difference between the outcomes for the elderly “in care” versus the independently-living elderly. And this was explained not just by the relative strength of immune systems, but by the aerosol risk level of the living environment. Rest homes are the highest-risk environment! Duration spent in an aerosol-laden environment is most critical – it is one thing to be infected in a 20 minute visit to a supermarket, or a 3 hour function in a restaurant – but living 24/7 in an aerosol laden environment is what is deadly.

    The “natural environment” affects the indoor environment simply by the extent to which people seal the indoor environment against the outdoor conditions. This is why temperate climates with high humidity and strong winds are far more mildly impacted. More ventilation and less internal air recirculation means low pandemic vulnerability. Humidity affects how long aerosols float in the air. In fact overloaded hospitals tend to occur only for a very short period in a few locations where several conditions aligned for indoors superspreading, with spread reaching rest homes in the process. Everywhere else, and for most of the time, Covid would not be any more than a “flu like illness” that did not arouse alarm. The knowing, inner-circle Chinese scientists probably had this worked out very early on. I say that “infection crossing from bats to humans” has probably occurred more than once without being noticed – if it could occur on past occasions that the Chinese have studied, there is no reason that the same conditions might not occur elsewhere in the world. However, these “outbreaks” have fizzled out every time, contrary to false orthodoxies about the high contagiousness one-on-one under all conditions.

    Far too little attention is being given to the virus being found in sewage samples too early for the narrative of spread from Wuhan in late 2019. Barcelona in March 2019 seems to be the earliest, but it has also been found “too early” in Bergamo, France, and Brazil. It seems to me that correlations are likely with resurgent urban populations of bats in recent years. Bat droppings and urine in the human built environment could be a vector similar to the cave and mine incidents observed by Chinese scientists, only not as severe. The virus has also been found in sewerage in Queensland rural towns where there have been no illness in the community or known exposure to the virus – these towns do have significant bat populations, however. Cavers and miners who tolerate bat-related stinks can relate frequent experience of illness afterwards; however it is true that Covid is not the only respiratory disease for which bat droppings are a known vector. Histoplasmosis, a fungal disease, is already well-known as a consequence of spores becoming airborne from accumulations of bat droppings in human built environments. Furthermore, Histoplasmosis has been noted as one of the co-infections present in the lungs in some serious Covid patients. Histoplasmosis itself causes symptoms “similar to Covid”.

    Seeing Covid spreads predominantly by aerosols, and the orthodoxy has ignored this, I say it is quite likely that “our” scientists are missing a pathway between bats and humans that involves aerosols. An interim host species has been sought and not found, but the assumption has been that transfer is via bites and carnivorous action. What if something happens in “waste”, whether in caves, mines, sewers, or smelly built environments? Viral recombination can occur anywhere there is organic matter, it does not have to be somewhere within the physical biology of a mammal. It can even occur in a respiratory tract; perhaps a bat virus and one other virus recombine in conditions we are missing, to create the chimerical SARS CoV-2 without decades of evolution being required.

    The smoking gun for CCP guilt is the absurd propaganda footage from Wuhan in the early days, and the thousands of China-based bots who leveraged hysteria on social media, including attacks on politicians who originally called for calm, for reason, and context. This was not a bioweapon, nor was it even deliberate hiding of the escape of a “deadly virus” to do the rest of the world harm. It was PSY-OPS — including the creation of the impression that it was a deadly virus and that they tried to cover it up, and were scared of it! Plus, the idea that tough lockdowns are a successful strategy that the rest of the world could spend forever destroying themselves trying to replicate.

    I agree with the email to Fauci from Dr Erik A. Nilsen back in February 2020; the Chinese are lying about their death toll. But I take this the opposite way to Dr Nilsen at that time (but he agrees with me now) — I say the inner-circle Chinese knew all along that this was not a particularly deadly virus, and the CCP very easily pivoted to suppressing hysteria rather than “suppressing the virus”. All that is necessary, is truthful reporting of cause of death in the case of co-morbidities, reasonably accurate determination of what are Covid “cases” rather than hyper-sensitized PCR testing, and reasonable context of average age of death. Very few Chinese will argue that “Covid killed grandma and the officials are covering it up” — seeing grandma had a heart attack, or a stroke, or advanced cancer, and was 88 years old anyway. And probably didn’t have a ridiculously sensitive test that claimed she “had Covid”.

    The CCP will be very astute students of Sun Tzu — one of his most famous maxims was that the best way of waging war, is to get your enemy to destroy himself.

    A note about India. I was making lonely arguments for months that the reason for the India and other poor, hot countries, not experiencing early outbreaks is “unsealed” and ventilated buildings due to the heat, and a lack of airconditioning, so that aerosols cannot build up indoors. The rainy season tends to upset this hypothesis in some such countries, it certainly correlates with South American outbreaks – this keeps people indoors and buildings are sealed as best possible.

    But in India, Covid-19 arrived at the wrong time for all such theories – both too late from one point of view, and too early from another. I say that because the air in Indian urban areas STINKS, it is plausibly possible for sewage aerosols to build up to potentially infectious concentrations even in outdoors air. Sewage as a source of aerosols is exponentially greater than aerosols from people’s exhalation, much higher concentrations of the virus have consistently been found in toilet rooms, compared to the main parts of buildings. SARS CoV-2 in human excretions and sewage is proven science. I hypothesized months ago that the reason for dementia units being the most deadly places of all in this pandemic, is the incontinence of many of the the residents, which causes these places to stink notoriously. Of course the virus is present in the excretions of infected people, but it takes a lot longer to reach the critical mass in sewage so as to be infectious even in well ventilated environments, or maybe even outdoors. The smell of Indian urban areas can be noticed inside airliners as they are descending to land. It should be obvious that lack of public infrastructure for sanitation must be the cause of India still suffering a high level of deaths from the aerosol-borne diseases Measles and TB.

    Even in some wealthier nations, leakage of aerosols from sewage may be a factor in Covid spread, especially in locations where there are prolonged periods of lack of wind.

    One question that I am not satisfied has been studied enough, is whether very high inoculum doses of virus aerosol can overwhelm even an immune system that has some prior natural exposure, or has been prepped by vaccination. I say it has been obvious all along that the level of inoculum dose strongly correlates to the deadliness of infection. I do wonder whether the few people “catching Covid a second time” or catching it post-vaccination, have been hit by a very high inoculum dose. Maybe even TB and Measles vaccines are insufficient in India, against very high inoculum doses from aerosols from sewage.

  2. From James’ link:

    “…Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives…”

    Question that occurs to my mind: why would the NIH have deleted these important sequences? And if someone could recover the deleted sequences from the Google cloud, what was the point? Seeing that the deletion itself looks VERY bad for the NIH’s “impartiality” or even its trustworthiness to actually be working in the interests, of, say, American taxpayers, or of “humanity”? No doubt Julius and Ethel Rosenberg had lofty ethics under which they regarded themselves as “working for humanity” in their day.

  3. I real don’t know how we can fight this, as time goes new emerging jumping viruses are on the rise. Some of them become more deadly, I hope that we get a solution for what accelerate the jumping more than waiting for solution after the outbreake.

  4. Steve Hawkins

    If only people would regulary listen to TWiV, and subscribe to ‘Q & A with Vincent and Amy’, we might be spared the effort of writing or reading already tested speculations like those above.

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