perjantai 16. huhtikuuta 2021

The origin of SARS-CoV-2 is a riddle - meet the Twitter detectives who aim to solve it


The origin of SARS-CoV-2 is a riddle: meet the Twitter detectives who aim to solve it

If you have read my previous article, you probably know already most of the mysteries that surround the origins of SARS-CoV-2. If you haven’t read it, then I strongly recommend to do so before reading on. In fact, the present article is a tribute to the people who helped unravelling those mysteries. You may have already heard about Alina Chan, but there are many other people, out of the spotlight, who deserve credit. They have been working tirelessly this year: reading academic papers, exploring barely known databases, sifting through Chinese media outlets. Their work place is Twitter. Some of them are professional scientists, others have different backgrounds, many use pseudonyms. They have a tendency to ask uncomfortable questions, and probably for this reason they are often blocked by other scientists and accused of promoting conspiracy theories. You may disagree with their unconvential approach, but the truth is that these people behave, to all intents and purposes, like a small scientific community: they search and analyze data, they share and discuss their findings and, more importantly, they make discoveries.

Guess who?

The first mystery that the Twitter detectives had to solve was the identification of RaTG13. This name appeared in the scientific literature for the first time in January, in a preprint by scientists from Wuhan Institute of Virology, to indicate the bat coronavirus most similar to SARS-CoV-2. Later on, on 3rd February, the same article (with some not-so-minor modifications) was published on Nature (Zhou et al., 2020). At that time we knew almost nothing about RaTG13, although this virus might have once been present in Chinese databases which were taken down, as later discovered by Yuri Deigin and @BillyBockstinson. Anyway, two days later another paper was published by scientists from Wuhan University in the Emerging Microbes and Infections journal (Chen et al., 2020). The authors write:

Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21.
Chen et al., 2020 Emerging Microbes and Infections

When they wrote the manuscript, the most similar bat viruses were in fact ZC45 and ZXC21. They didn’t mention RaTG13 because that name was unknown back then, however they did notice a very strong similarity (99% identity) with a partial RdRp gene of coronavirus BtCoV/4991, which was present in Genbank and linked to a publication from 2016 (Ge et al., 2016).

Emerging Microbes and Infections is a minor journal and this paper was somehow eclipsed by the Nature article, in fact I guess that few people noticed it. One of them was for sure Rossana Segreto (Twitter account @Rossana38510044), biologist at the University of Inssbruck, who wrote a comment on Virology Blog on 16th March. Probably other people had read both papers and tried to align the BtCoV/4991 sequence from Chen et al. with RaTG13 from Zhou et al., but Rossana’s comment is the first public statement that I found suggesting the connection between the two names:

Comment by Rossana Segreto on Virology blog, 16th March 2020

The “same-virus theory” was confirmed on 9th May by Peter Daszak, close collaborator of Wuhan scientist Shi Zhengli. Daszak replied this way to a Twitter user who had asked him about this connection:

Tweet by Peter Daszak, 9th May 2020

That Twitter user was @schnufi666, who had just discovered that in a Chinese database specialized in bat viruses, the entry of BtCoV/4991 had been modified on 7th March, to include a reference to RaTG13. Later on, it was Shi Zhengli herself who confirmed the link between those names in an interview to Science published in July. Finally, after tweets, interviews and editing of little known Chinese databases, WIV scientists updated the RaTG13 entry on Genbank, adding the sentence “former lab designation: Bat coronavirus Ra4991”. They have done this on 24th November, but hey, better late than never.

Treasure hunt

Back in April, almost everybody in this small Twitter community was convinced that RaTG13 was in fact BtCoV/4991, although the connection was not stated explicitely in any paper. People began to wonder then, why the authors of the Nature paper didn’t cite their own paper from 2016, where RaTG13 was first described with a different name. Were they hiding something? To answer this question, the Twitter detectives started exploring the internet to find any relevant information about a mineshaft in Mojiang county (Yunnan), that is the place where RaTG13 was sampled in 2013, as noticed by Yuri Deigin (Twitter account @ydeigin). At that time, the discussions were often led by @luigi_warren, who used to summarize the main discoveries in clear threads such as this one.

The first clue for the investigation was in the 2016 paper itself. On 15th May, @_coltseavers noticed a sentence citing an earlier paper (Wu et al., 2014): apparently, the same mineshaft had been sampled in 2012, in search of henipaviruses (another genus of viruses that includes Nipah and Hendra). Reading the 2014 paper, it was immediately clear why that mineshaft was so interesting for the Chinese virus hunters.

In June 2012, in Mojiang Hani Autonomous County, Yunnan Province, China, severe pneumonia without a known cause was diagnosed in 3 persons who had been working in an abandoned mine; all 3 patients died. Half a year later, we investigated the presence of novel zoonotic pathogens in natural hosts in this cave. For the investigation, we collected anal swab samples from 20 bats (Rhinolophus ferrumequinum), 9 rats (R. flavipectus), and 5 musk shrews (Crocidura dracula) from the mine for virome analysis.
Wu et al., 2014 Emerging Infectious Diseases

So, the bat virus most similar to SARS-CoV-2 had been sampled in 2013 in a mineshaft where three people had died of severe pneumonia with unknown cause, the year before. Quite interesting, no? In fact, the news was reported in other websites. Roland Baker (Twitter account @RolandBakerIII) found an article in Chinese, describing the incident (“In June 2012, three men removing slag from a derelict copper mine in southwestern China fell ill with severe pneumonia and died.”). He also found a news in Science, where scientists explained that the cause of those deaths was yet to be discovered. Interestingly, Scientific American also mentions those events in a recent interview to Shi Zhengli, as noted by @luigi_warren. Oddly enough, this article blames a fungus for the pneumonia, which was quite surprising because, according to the papers, the Chinese scientists were searching for a virus.

Excerpt from “How China’s ‘Bat Woman’ Hunted Down Viruses from SARS to the New Coronavirus”, Scientific American 2020

At that point, the exact location of the mineshaft was still unknown, although Antonio Duarte (Twitter account @AntGDuarte) had noticed on 11th May that the red dot in a blind map included in Ge et al. 2016, was very close to Tongguanzhen, which is the administrative town of Tongguan township: maybe that’s where RaTG13 got its “TG” from!

Tweet by Antonio Duarte, 11th May 2020

Interestingly, while all these things were happening on Twitter, an Indian microbiologist reached independently the same conclusion: her name was Monali Rahalkar (Twitter account @MonaRahalkar), and her preprint was the first attempt to share the mineshaft story to a broader audience. Then, on 18th May, the plot twist. @TheSeeker268 found a Master thesis dealing with the pneumonia outbreak: “The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown Viruses” (by Li Xu, supervisor Prof. Qian Chuan Yun, published in 2014). And a few days later, on 29th May, the same Twitter user posted a PhD thesis on the same topic: “Novel Virus Discovery in Bat and the Exploration of Receptor of Bat Coronavirus HKU9” (by Canping Huang, supervisor Gao Fu, published in 2018). The two documents, mentioned in a preprint posted by Segreto and Deigin, held a bonanza of information about the Tongguan mineshaft and the pneumonia cases. For instance, the two theses precisely describe the six patients as well as their symptoms, which were impressively similar to those of COVID-19, as reported by Monali Rahalkar in a paper published in Frontiers in Public Health (Rahalkar and Bahulikar, 2020).

Summary of the six pneuomina patients (Rahalkar and Bahulikar, 2020)
Common features observed in the six pneumonia patients and COVID-19 (Rahalkar and Bahulikar, 2020)

An important part of the work was carried out by @franciscodeasis, who did the first good translation of parts of the Master and PhD theses. The PhD thesis was particularly important because it revealed the GPS coordinates of the mineshaft, as noted by its discoverer The Seeker: 23°10'36.00'’N, 101°21'28.00'’E. Actually, those were the coordinates of a village named Danaoshan. The mineshaft itself may be quite close: according to Franscico De Asis, it is located at about 1.4km, in an area accessible by dirt road from Danaoshan.

Probable location of the Mojiang mineshaft where six people fell sick in 2012, according to Francisco De Asis (snapshot from Google Earh, 2011)

Our Twitter detectives got it right. On 17th November, Zhou et al. published an addendum to their original paper, that confirmed the mineshaft story: in 2012 the Wuhan Institute of Virology had analyzed serum samples from 4 patients with pneumonia, who fell sick after visiting a mine cave in Tongguan town. For that reason, the Chinese scientists made 1–2 trips each year to the mine, looking for SARS-related viruses that might explain the disease. Some of the details in the addendum do not fully match with the Master and PhD theses, but it’s still impressive how a group of Twitter users managed to bring to surface facts and events that otherwise would have remained probably hidden to the scientific community. In this regard, Rossana Segreto must be credited in particular, for her relentless pressing with the Nature editors, but likely several other scientists asked explanations to the journal.

The final riddle

Consider the information available in January: the closest relative of SARS-CoV-2 was a bat coronavirus, sampled in Yunnan in 2013, that we knew nothing about. Thanks to the research of tireless Twitter users, we now know that SARS-CoV-2 may be linked to an old story of unexplained pneumonia, a story that scientists in Wuhan, apparently, were not eager to share with the world. We also know that RaTG13 was sequenced in 2018, not after the COVID outbreak, as is stated in the Nature paper. It was Francisco De Asis who first noticed the dates in the names of sequences uploaded to NCBI in May, a finding later confirmed by Shi Zhengli in her answers to Science. But the quest is not over!

The addendum recently published on Nature revealed, in fact, that WIV had found other 8 SARS-related coronaviruses in the Tongguan mine, besides RaTG13. What do we know about those viruses? Basically nothing: the article doesn’t even mention their names, let alone their genomic sequences. But they may be somewhere, buried in minor papers or less known databases: this is the final riddle that the Twitter detectives have to solve. For months, Francisco De Asis has been tracking all the information available on this topic: in his huge Excel files he annotates publications, sequence entries, even time and location of the sampling expeditions. He believes the 8 viruses might belong to the so-called “7896 clade”, a group of novel viruses that recently appeared in a paper published on Nature (Latinne et al., 2020).

Tweet by Francisco De Asis, 18th November 2020

Actually, these viruses are never mentioned in the paper, but the Genbank IDs are reported in the Supplementary PDF, and their RdRp sequence (which is the only public sequence currently available) looks quite similar to those of SARS-CoV-2 and its closest cousins RaTG13 and RmYN02 (see this tree by @babarlelephant). Moreover, some of the RaTG13 sequences uploaded in May have a mysterious “7896” label. Will the detectives get it right also this time, like they did before? To find out, just follow them on Twitter: here’s a list with the most active users. You will probably come across tons of tweets by @billybostickson, who has been the aggregator and motivator of this group since the very beginning of this pandemic: just to get an idea of his amazing work, have a look at his “260 questions for scientists and the WHO on the origin of SARS-CoV-2” (Part 1, 2, 3).

If social media is not your thing and you prefer traditional scientific articles, no worries. Below there’s a list of works authored by people mentioned above, as well as others that I didn’t mention: for instance, you will find the first peer-reviewed paper speculating on the lab origin of SARS-CoV-2, by Dan Sirotkin (Twitter account @Harvard2H) and his father Karl, who designed dbSNP; the fascinating Bayesian analysis by Gilles Demaneuf and Rodolphe de Maistre; the preprint by Daoyu Zhang (Twitter account @flavinkins), who first questioned the data on pangolin coronaviruses; the lab leak hypothesis proposed by Anon, which perfectly fits with this detective saga; last but not least, the memorable Medium article by Yuri Deigin on the gain-of-function experiments that were carried out in Wuhan. So many people were involved, as you may see, but this should not come as a surprise: science is a collective enterprise, even when you do it on Twitter.

Peer-reviewed papers


Medium articles and blog posts


perjantai 9. huhtikuuta 2021

Masks … A Ticking Time Bomb!

  • Microbes from your mouth, known as oral commensals, frequently enter your lungs, where they’ve been linked to advanced stage lung cancer; wearing a mask could potentially accelerate this process.
  • Masks Entering Marine Environments Pose Additional Risks.
  • Mask Use May Pose a Risk for Advanced Stage Lung Cancer.
  • Masks Are Harming Children and Adults.

Masks … A Ticking Time Bomb!


Masks Are a Ticking Time Bomb

Story at-a-glance

  • It’s estimated that 129 billion face masks are used worldwide each month, which works out to about 3 million masks a minute

  • Not only are masks not being recycled, but their materials make them likely to persist and accumulate in the environment

  • Because masks may be directly made from microsized plastic fibers with a thickness of 1 mm to 10 mm, they may release microsized particles into the environment more readily — and faster — than larger plastic items, like plastic bags

  • Microbes from your mouth, known as oral commensals, frequently enter your lungs, where they’ve been linked to advanced stage lung cancer; wearing a mask could potentially accelerate this process

  • The “new normal” of widespread masking is affecting not only the environment but also the mental and physical health of humans


Analysis by Dr. Joseph Mercola

The planet may be facing a new plastic crisis, similar to the one brought on by bottled water, but this time involving discarded face masks. “Mass masking” continues to be recommended by most public health groups during the COVID-19 pandemic, despite research showing masks do not significantly reduce the incidence of infection.1

As a result, it’s estimated that 129 billion face masks are used worldwide each month, which works out to about 3 million masks a minute. Most of these are the disposable variety, made from plastic microfibers.2

Ranging in size from five millimeters (mm) to microscopic lengths, microplastics, which include microfibers, are being ingested by fish, plankton and other marine life, as well as the creatures on land that consume them (including humans3).

More than 300 million tons of plastic are produced globally annually — and that was before mask-wearing became a daily habit. Most of it ends up as waste in the environment, leading researchers from the University of Southern Denmark and Princeton University to warn that masks could quickly become “the next plastic problem.”4

Why Disposable Masks May Be Even Worse Than Plastic Bottles

The bottled water crisis is now well-known as a leading source of environmental plastic pollution, but it’s slated to be outpaced by a new mask crisis. While about 25% of plastic bottles are recycled, “there is no official guidance on mask recycle, making it more likely to be disposed of as solid waste,” the researchers stated. “With increasing reports on inappropriate disposal of masks, it is urgent to recognize this potential environmental threat.”5

Not only are masks not being recycled, but their materials make them likely to persist and accumulate in the environment. Most disposable face masks contain three layers — a polyester outer layer, a polypropylene or polystyrene middle layer and an inner layer made of absorbent material such as cotton.

Polypropylene is already one of the most problematic plastics, as it’s widely produced and responsible for large waste accumulation in the environment, as well as being a known asthma trigger.6 Further, the researchers noted:7

Once in the environment, the mask is subjected to solar radiation and heat, but the degradation of polypropylene is retarded due to its high hydrophobicity, high molecular weight, lacking an active functional group, and continuous chain of repetitive methylene units. These recalcitrant properties lead to the persistence and accumulation in the environment.”

They also stated that when the masks become weathered in the environment, they can generate a large number of microsized polypropylene particles in a matter of weeks, then break down further into nanoplastics that are less than 1 mm in size.

Because masks may be directly made from microsized plastic fibers with a thickness of 1 mm to 10 mm, they may release microsized particles into the environment more readily — and faster — than larger plastic items, like plastic bags.

Further, “Such impacts can be worsened by a new-generation mask, nanomasks, which directly use nanosized plastic fibers (e.g., diameter <1 mm) and add a new source of nanoplastic pollution.”8 A report by OceansAsia further estimated that 1.56 billion face masks may have entered the world’s oceans in 2020, based on a global production estimate of 52 billion masks manufactured that year, and a loss rate of 3%, which is conservative.

Based on this data, and an average weight of 3 to 4 grams for a single-use polypropylene surgical mask, the masks would add 4,680 to 6,240 additional metric tons of plastic pollution to the marine environment, which, they note, “will take as long as 450 years to break down, slowly turning into microplastics while negatively impacting marine wildlife and ecosystems.”9

Masks Entering Marine Environments Pose Additional Risks

Plastic particles are known to travel great distances, posing immense risks to virtually every part of the globe. Small, weathered pieces of plastic — suggesting they’d been on a long journey — have been found at the top of the Pyrénées mountains in southern France10 and “in the northernmost and easternmost areas of the Greenland and Barents seas.”11

Calling the Greenland and Barents seas area a “dead end” for the plastic debris, researchers hypothesized that the seafloor below would be a catch-all for accumulating plastic debris.12 In separate research, it was also revealed that plastic pollution has reached the Southern Ocean surrounding Antarctica — an area believed to be mostly free of contamination.13 According to the featured study:14

When not properly collected and managed, masks can be transported from land into freshwater and marine environments by surface run-off, river flows, oceanic currents, wind, and animals (via entanglement or ingestion). The occurrence of waste masks has been increasingly reported in different environments and social media have shared of wildlife tangled in elastic straps of masks.”

Such plastics also contain contaminants, such as polycyclic hydrocarbons (PAHs), which may be genotoxic (i.e., causing DNA damage that could lead to cancer), along with dyes, plasticizers and other additives linked to additional toxic effects, including reproductive toxicity, carcinogenicity and mutagenicity.15

Aside from the chemical toxicity, ingestion of microplastics from degraded masks and other plastic waste is also toxic due to the particles themselves as well as the potential that they could carry pathogenic microorganisms.

Another issue that’s rarely talked about is the fact that when you wear a mask, tiny microfibers are released, which can cause health problems when inhaled. The risk is increased when masks are reused. This hazard was highlighted in a performance study to be published in the June 2021 issue of Journal of Hazardous Materials.16

Researchers from Xi’an Jiaotong University also said scientists, manufacturers and regulators need to assess the inhalation of microplastic and nanoplastic debris shed from masks — both disposable and cloth — noting:17

“… [C]omplaints of throat irritation or discomfort in the respiratory tract by children, the elderly, or other sensitive individuals after wearing these may be alerting signs of excessive amounts of respirable debris inhaled from self-made masks and respirators.”

In the featured study researchers also called on the environmental research community to “move fast to understand and mitigate these risks,” suggesting that reusable cloth masks be promoted in lieu of disposable options and that mask-only trash cans be set up to assist in proper disposal.18 However, another option would be to loosen or eliminate mask mandates, which may turn out to cause more harm than good.

Mask Use May Pose a Risk for Advanced Stage Lung Cancer

While it’s well-known that gut microbiota affect your immune system and risk of chronic diseases, it was long thought that lungs were sterile. Now it’s known that microbes from your mouth, known as oral commensals, frequently enter your lungs.19 Not only that, but researchers from New York University (NYU) Grossman School of Medicine revealed that when these oral commensals are “enriched” in the lungs, it’s associated with cancer.20

Specifically, in a study of 83 adults with lung cancer, those with advanced-stage cancer had more oral commensals in their lungs than those with early-stage cancer. Those with an enrichment of oral commensals in their lungs also had decreased survival and worsened tumor progression.

While the study didn’t look into how mask usage could affect oral commensals in your lungs, they did note, “The lower airway microbiota, whether in health or disease state, are mostly affected by aspiration of oral secretions, and the lower airway microbial products are in constant interaction with the host immune system.”21

It seems highly likely that wearing a mask would accelerate the accumulation of oral microbes in your lungs, thereby raising the question of whether mask usage could be linked to advanced stage lung cancer. The National Institutes of Health even conducted a study22 that confirmed when you wear a mask most of the water vapor you would normally exhale remains in the mask, becomes condensed and is re-inhaled.23

They went so far as to suggest that wearing a moist mask and inhaling the humid air of your own breath was a good thing, because it would hydrate your respiratory tract. But given the finding that inhaling the microbes from your mouth may increase advanced cancer risk, this hardly sounds like a benefit.

Not to mention, the humidity inside the mask will allow pathogenic bacteria to rapidly grow and multiply and, since the mask makes it more difficult to breathe, you’re likely to breathe heavier, thereby risking inhaling the microbes even deeper inside your lungs.

Masks Are Harming Children and Adults

The “new normal” of widespread masking is affecting not only the environment but also the mental and physical health of humans, including children. It’s largely assumed that face masks are “safe” for children to wear for long periods, such as during school, but no risk assessment has been carried out.24 Further, as evidenced by Germany’s first registry recording the experience children are having wearing masks.25

Using data on 25,930 children, 24 health issues were reported that were associated with wearing masks that fell into the categories of physical, psychological and behavioral issues.26 They recorded symptoms that:27

“… included irritability (60%), headache (53%), difficulty concentrating (50%), less happiness (49%), reluctance to go to school/kindergarten (44%), malaise (42%), impaired learning (38%) and drowsiness or fatigue (37%).”

They also found 29.7% reported feeling short of breath, 26.4% being dizzy and 17.9% were unwilling to move or play.28 Hundreds more experienced “accelerated respiration, tightness in chest, weakness and short-term impairment of consciousness.”

It’s also known that microplastics exist in human placentas,29 and animal studies show that inhaled plastic particles pass through the placenta and into the heart and brains of fetuses.30 The fetuses exposed to the microplastics also gained less weight in the later part of the pregnancy.31

We found the plastic nanoparticles everywhere we looked — in the maternal tissues, in the placenta and in the fetal tissues. We found them in the fetal heart, brain, lungs, liver and kidney,” lead research Phoebe Stapleton of Rutgers University told The Guardian.32

Dr. Jim Meehan, an ophthalmologist and preventive medicine specialist who has performed more than 10,000 surgical procedures and is also a former editor of the medical journal Ocular Immunology and Inflammation, also conducted an evidence-based scientific analysis on masks, which shows that not only should healthy people not be wearing masks but they could be harmed as a result.33

Meehan suggests that the notion of mask-wearing defies common sense and reason, considering that most of the population is at very low or almost no risk of becoming severely ill from COVID-19. He also compiled 17 ways that masks can cause harm:34

Medical masks adversely affect respiratory physiology and functionMedical masks lower oxygen levels in the blood
Medical masks raise carbon dioxide levels in the bloodSAR-CoV-2 has a “furin cleavage” site that makes it more pathogenic, and the virus enters cells more easily when arterial oxygen levels decline, which means wearing a mask could increase COVID-19 severity
Medical masks trap exhaled virus in the mouth/mask, increasing viral/infectious load and increasing disease severitySARS-CoV-2 becomes more dangerous when blood oxygen levels decline
The furin cleavage site of SARS-CoV-2 increases cellular invasion, especially during low blood oxygen levelsCloth masks may increase the risk of contracting COVID-19 and other respiratory infections
Wearing a face mask may give a false sense of securityMasks compromise communications and reduce social distancing
Untrained and inappropriate management of face masks is commonMasks worn imperfectly are dangerous
Masks collect and colonize viruses, bacteria and moldWearing a face mask makes the exhaled air go into the eyes
Contact tracing studies show that asymptomatic carrier transmission is very rareFace masks and stay at home orders prevent the development of herd immunity
Face masks are dangerous and contraindicated for a large number of people with pre-existing medical conditions and disabilities

Adding insult to injury, the first randomized controlled trial of more than 6,000 individuals to assess the effectiveness of surgical face masks against SARS-CoV-2 infection found masks did not statistically significantly reduce the incidence of infection.35

Considering the lack of evidence for their use, and the potential harms to human health and the environment, it’s no wonder that calls for peaceful civil disobedience against mandatory masking are growing. The U.S. nonprofit Stand for Health Freedom has a widget you can use to contact your government representatives to let them know wearing a mask must be a personal choice

Sources and References: