Lungs – the largest petri dish in the world?

In the summer of 2020, during a rare lull of COVID-19 pandemic where most people around the world were still free to venture into the streets and interact, an interesting article came out online proposing a curious hypothesis that perhaps COVID-19 actually emerged many years prior in China. This hypothesis was based on the fact that in 2012 six miners became severely ill with a mysterious inflammatory lung disease after clearing bat guano from a Mojiang copper mineshaft. All of them developed symptoms that appear very similar to COVID-19. Four of them needed to go on ventilators and three of them subsequently died.

We already wrote about this in one of the articles dedicated to circulating SARS-CoV-2 conspiracy theories as it was very unusual proposition. The authors of this hypothesis, Drs. Jonathan Latham and Allison Wilson, (a virologist and a geneticist) proposed that SARS-CoV-2 could actually have evolved in the lungs of the miners that became ill, whereby the lung tissues acted as a form of a living organic laboratory that facilitated serial passaging of the virus which caused a bat virus to transform into a SARS-CoV-2. In scientific parlance, virus passaging means exposing a virus to an inhospitable environment but allowing a small amount of it to survive and be cultured repeatedly thus promoting rapid genetic evolution of the virus (that would not be expected to be observed in nature). Furthermore, Drs. Latham and Wilson proposed that because the overall surface area of a lung is so large, different areas in a lung could allow simultaneous, unrelated adaptations of a virus - or even multiple different viruses - all independently of one another - and then further, these viruses could then combine whenever they happen to infect the same cells at the same time! The actual term for this is recombination, a process of swapping some genetic information between viruses.

This occurrence of sick miners in Mojiang, China was not just some obscure, random newspaper-clipping type of event. At the time, it was a big deal due to the prior scare of SARS in Asia from 2002-2004. An entire Master’s thesis was written on the subject of these patients’ treatment (which was subsequently translated and provided by Drs. Latham and Wilson due to the potentially enormous significance of this information to current events) as well as apparently one doctorate dissertation as well. The fate of these miners was also mentioned in a , and even reported by the US Centre of Disease Control and Prevention. Furthermore, samples collected from these patients are known to have been shipped to the Wuhan Institute of Virology (as revealed by the Master’s thesis and the PhD dissertation). What Drs. Latham and Wilson proposed is that perhaps in late 2019 it was these samples that could have been the source of SARS-CoV-2 which leaked out of the lab, causing a global pandemic. In other words, COVID-19 might have already emerged in 2012 but was contained to perhaps only a few individuals. The reason for the lag between the first infection and the current outbreak, Drs. Latham and Wilson propose, could have been due to the fact that in order to further study and work on the virus isolated from miners’ samples, the Wuhan Institute of Virology awaited the BSL-4 lab designation (the highest level needed for work with most dangerous pathogens) which did not occur till late 2018.

By the way, the conclusion of the above mentioned Master’s thesis was that the Mojiang miners were likely infected with some yet unknown at a time coronavirus!

To add to the overall craziness of this story, that same cave where the unfortunate Chinese patients worked was also investigated by the now infamous Dr. Shi Zhengli of the Wuhan Institute of Virology. Her team isolated the Bat-CoV RaTG13 coronavirus from samples from that very cave, which currently is the closest known relative virus to SARS-CoV-2. Seriously, we are not making this stuff up! To make this story even more whack, along the way, the virus was mysteriously renamed Bat-CoV RaTG13 from its previous designated name of BtCoV/4991, without any reference. When Bat-CoV RaTG13 was announced to the world, this connection was lost on many and some say done to purposefully obscure the true provenance of the virus.

All of these seemingly independent events, point to the importance of the outbreak in 2012 that resembled COVID-19. The subsequent isolation of the closest viral relative to SARS-CoV-2 from that same cave in Mojiang, China has also been described in a scientific article published in the late 2020 (with its preprint publication preceding the Drs. Latham and Wilson Mojiang Miners Passage Theory - as they refer to it). Thus, this is not some novel news we are breaching here; it has already been openly discussed in scientific circles, but is still not being investigated. We do not know why that is the case, due to the significance in relation to the current pandemic, but that is a question that seems to be popping up a lot lately.

The lab-leak theory is finally breaking taboo barriers in the American mainstream media. Interestingly, at the start of pandemic (for some strange reason) it was utterly dismissed despite the fact that the natural origins theory had no intermediate species between bat and human yet established that could explain how the pandemic has started. One major problem with the Mojiang miners hypothesis was that there was no prior scientific evidence that human lung tissue could in fact act as an environment that could mimic lab-based serial passaging of a virus to drive the substantial mutational changes that would be required for adaptation of a bat virus to a human-infectious virus.

However, thanks to the current pandemic taking place around the world, it appears that we finally have evidence that this indeed can happen. Multiple such reports have been documented since late 2020!

Decoding the genetics of multiple SARS-CoV-2 samples in the same patient lead to surprise findings

One such reported case comes from a Boston patient who struggled for an astonishing 154 days with SARS-CoV-2 before dying of respiratory failure. This individual was only in his 40s but had prior serious health complications. During this patient’s treatment, entire batteries of tests were performed to try to understand the progression of the disease. The patient’s PCR results were up and down in terms of the Ct value or cycle threshold - which indicates how much/little viral material is present in the sample at the start of the PCR test in order for the amplification of that genetic information to reach statistical certainty thus indicating the sample is positive. Cycle threshold in current PCR testing of SARS-CoV-2 is another source of great controversy, in terms of when (ie. what Ct threshold) should results be considered as positive, as was explained in our past post. At times this patient was testing as negative. But as the cycle threshold number decreased (meaning more virus was present in the sample allowing faster detection, or fewer cycles of duplicating the genetic material in the PCR reaction), the same samples were also used to isolate the virus for genetic sequencing. The last viral isolation was on day 143, which is the longest duration reported to date of an infectious SARS-CoV-2 virus being isolated from a patient. In this way it was shown that the SARS-CoV-2 virus was continuously mutating and evolving inside the patient. 57% of all changes occurred in the SARS-CoV-2 spike protein, the virus surface protein that is used by the virus to bind to our cell receptors and gain entry into our cells. 38% of these changes were specifically in the receptor binding domain of the spike protein, or the area of the protein that makes contact with our human cell receptors, ACE2 receptors. In essence, the patient seemed to have three waves of recurrences, as the virus continuously evolved to be able to evade attempts to get rid of this catastrophic infection. Post mortem analysis of collected biopsy samples allowed measurements of viral load in different tissues, indicating a very high viral presence in the lungs.

Thus, similar to what previously Drs. Latham and Wilson proposed, here we have evidence that human lungs can harbour very high viral loads for prolonged periods of time leading to a proportionately rapid viral evolution. For comparison, one of the Chinese miners battled with infection for 120 days and another for 117 days.

Cancer patients infected with SARS-CoV-2

Another example comes from a scientific publication earlier this month (February 2021).

And this is a bit of a detective story as well.

This tale starts with a man in his 70’s, a cancer patient who had undergone CAR-T-cell therapy. This is where a cancer patient’s own immune cells are isolated and genetically modified to be able to attack the patient’s cancer. Unfortunately, the man also developed COVID-19 disease. The patient ended up being sick for 72 days then sadly dying. Patient samples revealed a large viral load in the blood as tragically, this patient’s immune system did not seem to have produced much of any type of immune response. Pretty much no antibodies against SARS-CoV-2 in the blood despite the duration of infection.

This is where the interesting news comes in – the authors of the article studied the genetics of the SARS-CoV-2 virus that infected this cancer patient. What intrigued them was the SARS-CoV-2 virus had two mutations whereby some of the genetic material was deleted i.e. a portion of the virus’ genetic code disappeared.

This caught their attention because of another published case of an asymptomatic cancer patient (once again, a person with compromised immune system) who was shedding viruses for astounding 70 days and had viral genetic material detected in samples for 105 days! This is a highly unusual occurrence to have such a long persistence of viral infection and be asymptomatic no less! Typically, people shed viral matter for a mere few days and usually only after the onset of symptoms, and hence it was with an abundance of precaution that COVID-19 quarantine protocol was actually set to two weeks to eliminate any chance of people being infectious to others. Importantly, during the time span of that cancer patient’s bout with infection, the SARS-CoV-2 virus continued to mutate within the cancer patient as revealed by the sequencing of the virus genome from multiple consecutive samples. Of the many mutations observed, there was also a deletion mutation.

Other published stories like these are also to be found where cancer patients with weak immune systems end up with long-term infections. And such situations appear to favour promoting viral mutation on a rapid scale. This is because the weak immune response of those people does not clear the infection, leaving enough virus in the system, long enough, to respond to this destructive pressure and produce a mutant that becomes unrecognized by the immune response.

This is how new, dangerous virus strains can emerge!

The researchers who observed these deletions in the virus in such patients wondered how often do they happen? SARS-CoV-2 normally mutates slowly because the viral genome comes with a code for a big robot molecule that proofreads the viral genomic RNA as it is being copied when a virus replicates inside an infected cell. Basically, the virus copying machine is at the same time a spell-checking machine. But this virus spell-checking machine does not work with deletions: it does not correct for that. Thus, deletions are potentially easier mutations to sneak through during virus adaptations due to a hostile environment.

The authors investigated nearly 150K SARS-CoV-2 virus genome sequences that have been detected from patient samples all around the world. This virus is being monitored on enormous scale - constantly being tracked on how its genetics mutate and so everyone’s constantly being vigilant for new strains.

Of these 150k, just over 1000 times the SARS-CoV-2 virus genome was spotted with deletions in the gene coding for the spike protein; the same gene in which they observed the deletion in their cancer patient sample that they were investigating. It turned out that 90% of these deletions in the gene coding for the virus spike protein mapped to just four specific areas in the virus genome. Thus, some very specific adaptation.

One of such deletions has indeed been observed in the newly emergent UK SARS-CoV-2 strain.

The US State Department fires a damning shot at China

In light of these newly presented scientific findings, suddenly the hypothesis advanced by Drs. Latham and Wilson that SARS-CoV-2 might have actually developed in 2012 in Mojiang, China no longer seems so far fetched.

Indeed, the theory of a potential laboratory leak was indirectly supported by the US State Department of the former administration when they published a scathing criticism of the Wuhan Institute of Virology just a few weeks ago in January of 2021. Most notably, they stated that in the autumn of 2019 several workers became ill at the institute with symptoms similar to those of COVID-19. This published document from the US State Department also reiterated that the most closely related bat virus to SARS-CoV-2 was studied by the institute for many years and that it was the virus isolated from caves in 2013 we discussed above. And just to really drive the point home, the document also adds that several laboratory virus leaks have already occurred previously in China, including a leak of the original SARS virus. It is very telling document that for all intents and purposes seems to be trying to spell out that a leak most likely occurred but cannot be proven due to lack of concrete evidence. Although statements of the ill workers in the institute are thus, by far, the most damning evidence so far provided that could link the institute to the possibility of creating the virus outbreak that ended up taking over the world! Of course, in true American fashion, no actual evidence was presented beside the written statement.

Nevertheless, this new observation delivered from the government of the United States itself would also support the hypothesis of Drs. Latham and Wilson, that the SARS-CoV-2 virus itself originated already many years ago, and it was an accidental exposure of workers in the Wuhan Institute of Virology laboratory that lead to the current global pandemic.

The plot surrounding the origin of COVID-19 pandemic is definitely thickening and it is not in favour of the story fed to the world by China thus far. Time will only tell how on or off the mark Drs. Latham and Wilson truly were but they appear to be gaining supporting evidence from very credible sources to back their theory.

So is the world too busy or too afraid to notice?

This article has been produced by Merogenomics Inc. and edited by Jason Chouinard, B.Sc. Reproduction and reuse of any portion of this content requires Merogenomics Inc. permission and source acknowledgment. It is your responsibility to obtain additional permissions from the third party owners that might be cited by Merogenomics Inc. Merogenomics Inc. disclaims any responsibility for any use you make of content owned by third parties without their permission.

Products and Services Promoted by Merogenomics Inc.

Select target group for DNA testing

Healthy screening	Undiagnosed diseases	Cancer	Prenatal

Or select popular DNA test

Pharmaco-genetic gene panel	Non-invasive prenatal screening	Cancer predisposition gene panel	Full genome