Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA

The Society for Molecular Biology and Evolution (SMBE) is a pretigious society of workers in the field of molecular evolution. I am a member and I have attended many of their conferences. SMBE sponsors several journals incucluding Genome Biology and Evolution (GBE), which is published by Oxford Academic Press.

The latest issue of GBE has a paper by Stitz et al. (2021) that describes some repetitive elements in the platyhelminth Schistosoma mansoni. The authors conlcude that some of these elements might have a function and this prompts them to begin their discussion with the following sentences.

The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.

It is unfortunate that the senior authors didn't receive a good undergraduate education but one might think that they would rectify that problem by learning about genomes and junk DNA before publishing in a good journal devoted to genomes and evolution. Alas, they didn't and, even worse, the journal published their paper with those sentences intact.

As you might imagine, these statements were seized upon by Intelligent Design Creationists who wasted no time in posting on their creationist blog [Oxford Journal: “The Days of ‘Junk DNA’ Are Over ”].

But that's not the worst of it. The same issue contains an editorial written by Casey McGrath who self identifies as a employee of the Society for Molecular Biology and Evolution in Lawrence Kansus (USA). She is the Social Media Editor for Genome Biology and Evolution. The title of her editorial is "Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation" (McGrath, 2021). She starts off by repeating and expanding upon the words of the senior authors of the study that I referred to above.

“The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution. Their study provides an in-depth look at an enigmatic superfamily of repetitive DNA sequences known as W elements in the genome of the human parasite Schistosoma mansoni (Stitz et al. 2021). Titled “Satellite-like W elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni,” the analysis reveals structural, functional, and evolutionary aspects of these elements and shows that, far from being “junk,” they may exert an enduring influence on the biology of S. mansoni.

“When we studied genetics at university in the 1980s, the common doctrine was that the non-protein coding parts of eukaryotic genomes consisted of interspersed, ‘useless’ sequences, often organized in repetitive elements like satellite DNA,” note Grunau and Grevelding. Since then, however, the common understanding of such sequences has fundamentally changed, revealing a plethora of regulatory sequences, noncoding RNAs, and sequences that play a role in chromosomal and nuclear structure. With their article, Grunau and Grevelding, along with their coauthors from Justus Liebig University Giessen, University of Montpellier, and Leipzig University, contribute further evidence to a growing consensus that such sequences play critical roles in evolution.

There's no rational excuse for publishing the Stitz et al. paper with those ridiculous statements and there's no rational excuse for compounding the error by highlighting them in an editorial comment. The Society for Molecular Biology and Evolution should be ashamed and embarrassed and they should issue a retraction and a clarification. They should state clearly that junk DNA is alive and well and supported by so much evidence that it would be perverse to deny it.

---

McGrath,C. (2012) Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation. Genome Biology and Evolution 13: evab217 [doi: 10.1093/gbe/evab217]

Stitz, M., Chaparro, C., Lu, Z., Olzog, V.J., Weinberg, C.E., Blom, J., Goesmann, A., Grunau, C. and Grevelding, C.G. (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biology and Evolution 13:evab204. [doi: 10.1093/gbe/evab204]

The biggest mistake in the history of molecular biology (not!)

The creationists are committed to proving that most of our genome is functional because otherwise the idea of an intelligent designer doesn't make a lot of sense. They reject all of the evidence that supports junk DNA and they vehemently reject the notion that 90% of our genome is junk.

I was recently alerted to a video on junk DNA produced by Creation Ministries International in which they quote John Mattick.

A leading figure in genetics, Prof. John Mattick said ...'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology'.

The creationists are making the common mistake of equating noncoding DNA and junk DNA but the quotation sounded accurate to me since John Mattick makes similar mistakes in his publications. I decided to try and find the exact quotation and reference and the closest I could come to a direct quote was in a paper by Mattick from 2007 (Mattick, 2007). He's referring to introns—here's the exact quotation.

It should be noted that the power and precision of digital communication and control systems has only been broadly established in the human intellectual and technological experience during the past 20–30 years, well after the central tenets of molecular biology were developed and after introns had been discovered. The latter was undoubtedly the biggest surprise (Williamson, 1977), and its misinterpretation possibly the biggest mistake, in the history of molecular biology. Although introns are transcribed, since they did not encode proteins and it was inconceivable that so much non-coding RNA could be functional, especially in an unexpected way, it was immediately and almost universally assumed that introns are non-functional and that the intronic RNA is degraded (rather than further processed) after splicing. The presence of introns in eukaryotic genomes was then rationalized as the residue of the early assembly of genes that had not yet been removed and that had utility in the evolution of proteins by facilitating domain shuffling and alternative splicing (Crick, 1979; Gilbert, 1978; Padgett et al., 1986). Interestingly, while it has been widely appreciated for many years that DNA itself is a digital storage medium, it was not generally considered that some of its outputs may themselves be digital signals, communicated viaRNA.

However, the idea of the biggest mistake in molecular biology predates that reference. Mattick is quoted in a Scientific American article by W. Wayt Gibbs where Gibbs is discssing the "suprising" fact that regulatory sequences are conserved and that some genes are noncoding genes (Gibbs, 2003).

“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.”

The discovery of introns in the mid-1970s was definitely a surprise but it's not true, as Mattick implies, that they were immediately assumed to be junk. In fact, as he points out, there was a lot of debate over the possible role of introns in the evolution of protein-coding genes where they could stimulate exon shuffling. Later on, the presence of introns was recognized to be an essential component of alternative splicing.

Once more and more sequences were published it became apparent that neither their size nor their sequences were conserved except for the spliceosome recognition sequences. It soon became obvious that their sequences were evolving at the neutral rate demonstrating that they were mostly junk. Mattick assumes that this conclusion—that introns are mostly junk—is one of the biggest mistakes in molecular biology. I think the opposite is true. I think that the failure of most molecular biologists to understand junk DNA is a huge mistake.

The creationists are misquoting Mattick when they say that the classification of all noncoding as junk is the biggest mistake in molecular biology. In the quotations above, Mattick is specifically referrring to introns but I'm sure he won't be upset to be misquoted in that manner since he firmly believes that most noncoding DNA is functional.

There's a bit of an ironic twist here. If it were true that knowledgeable scientists in the 1970s actually believed that all noncoding DNA was junk then I'd have to agree that this would have been a big (biggest?) mistake. But they didn't and it wasn't a big mistake. As I've said many times, no knowledgeable scientist ever said that all noncoding DNA was junk since they (we) all knew about noncoding genes, regulatory sequences, centromeres, and origins of replication, all of which are functional noncoding DNA. We now know that about 1% of our genome is coding sequences and about 9% is functional noncoding DNA. The other 90% is junk.

[Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]

---

Mattick, J.S. (2007) A new paradigm for developmental biology. Journal of Experimental Biology 210:1526-1547. [doi: 10.1242/jeb.005017]

Gibbs, W.W. (2003) The unseen genome: gems among the junk. Scientific American 289:46-53.

Most scientists dismiss the lab leak conspiracy theory

A recent review in Science has the following subtitle, "Why most scientists say it's unlikely that SARS-CoV-2 originated from a lab leak." The title of that article was Call of the Wild but on the Science website it's The hunt for SARS-CoV-2’s ancestors heats up. The website article is behind a paywall but the original magazine article is open access.

21 experts support a natural origin for SARS-CoV-2

Here's a link to a recent review on the origins of SARS-CoV-2 written by 21 scientists from seven different countries. They are all recognized experts on the subject.

Holmes, E.C., Goldstein, S.A., Rasmussen, A.L., Robertson, D.L., Crits-Christoph, A., Wertheim, J.O., Anthony, S.J., Barclay, W.S., Boni, M.F., Doherty, P.C., Farrar, J., Geoghegan, J.L., Jiang, X., Leibowitz, J.L., Neil, S.J.D., Skern, T., Weiss, S., R, Worobey, M., Anderson, K.G., Garry, R.F. and Rambaut, A. (2021) The origins of SARS-CoV-2: A critical review. Cell. (published online Aug. 19, 2021) [doi: 10.1016/j.cell.2021.08.017]

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a “laboratory escape” scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

If you are interested in the origin of this virus then you must read this paper, especially if you are a supporter of the lab leak conspiracy theory. The review attempts to put the issues into the proper perspective by looking at the big picture instead of focusing on the kinds of trivia promoted by conspiracy theorists. For example, the review notes that SARS-CoV-2 is the ninth documented coronavirus that has spread to humans and all of the previous ones have zoonotic origins as do the vast majority of human viruses. Four of these viruses are endemic (HCoV-OC43, HCoV-HkU1, HCoV-229E, and HCoV-NL63). They cause minor respiratory illnesses that we classify as common colds. Its interesting to learn about HCoV-HKU1 ...

"These [endogenous] viruses have zoonotic origins, and the circumstances of their emergence are unclear. In direct parallel to SARS-CoV-2, HCoV-HKU1, which was first described in a large Chinese city (Shenzhen, Guangdong) in the winter of 2004, has an unknown animal origin, contains a furin cleavage site in its spike protein and was originally identified in a case of human pneumonia (Woo et al., 2005)."

The authors look at the bat coronaviruses that have been isolated and sequenced before and after the pandemic began. In particular, they examine RaTG13, a bat virus that was identified at the Wuhan Institute of Virology (WIV). They note that this virus is not particularly closely related to SARS-CoV-2 and that three other bat viruses that were identified only last year are more closely related to SARS-CoV-2. The sequences of all these viruses were examined because there has been unfounded speculation that scientists at the WIV created SARS-CoV-2 from RaTG13.

"Collectively, these data demonstrate beyond reasonable doubt that RaTG13 is not the progenitor of SARS-CoV-2, with or without laboratory manipulation or experimental mutagenesis."

Furthermore, the authors note that the RaTG13 virus didn't actually exist. It was just a bunch of sequences assembled in silico from short sequence reads.

The lab leak conspiracy theorists imagine that the WIV was working on SARS-CoV-2 prior to the beginning of the pandemic and they somehow allowed to virus to escape and infect the citizens of Wuhan. The experts examined this speculation and conclude ...

"... there is no data to suggest that the WIV—or any other laboratory—was working on SARS-CoV-2, or any virus close enough to be the progenitor, prior to the COVID-19 pandemic."

This is a very important point. There is no evidence to support the most important part of the lab leak claim. It's just unfounded speculation.

What about the claim that some workers at the WIV were hospitalized with COVID-19 in November 2019? This claim was spread on Reddit and made it's way into some US intelligence briefings in Januray 2020.

"Despite extensive contact tracing of early cases during the COVID-19 pandemic, there have been no reported cases related to any laboratory staff at the WIV, and all staff in the laboratory of Dr. Shi Zhengli were said to be seronegative for SARS-CoV-2 when tested in March 2020 (World Health Organization, 2021), with the laboratory reportedly following the appropriate biosafety protocols during their coronavirus work (Cohen, 2020)."

This is another important point because if it were true that workers had been infected with SARS-CoV-2 then it would support the lab leak theory. But the scientists at the WIV deny that any such infections occurred and reported to WHO that nobody tested positive for the virus. Furthermore, the public version of the American review of intelligence reports on the origin of SARS-CoV-2 published last month failed to mention the speculation that WIV workers were infected [Intelligence Community: Unclassified Report]. The most logical explanation is that the intelligence agencies could not back up the claim. If they had evidence to support the Reddit rumour then you can bet they would have made it public.

What this means is that, in the absence of evidence, the lab leak supporters have to add an additional layer to their accusation. They have to assume that the scientists at the WIV are lying and covering up the fact that they were secretly working with SARS-CoV-2 and allowed it to escape. The speculation becomes a conspiracy theory.

There's another aspect to this false claim that's very interesting. The 21 experts note that in order for there to have been multiple hospitalizations of lab workers in November 2019 there would have to have been widespread circulation of the virus since not all infections result in hospitalizations. However, a close examination of the known cases coupled with extensive modeling indicates that the virus probably started with a single individual around November 1st.

Epidemiological modeling suggests that the number of hypothetical cases needed to result in multiple hospitalized COVID-19 patients prior to December 2019 is incompatible with observed clinical, genomic, and epidemiological data (Pekar et al., 2021).

The conspiracy fans will no doubt claim that this is just part of a massive coverup by the Chinese government. This coverup involves hundreds of patients who were sick with COVID-19 in October and November 2019 and many who were hospitalized. They have all been silenced along with dozens and dozens of health care workers. Not only that, the Chinese government has been clever enough to release just enough information to make it look like the pandemic stated with a few individuals in November and spread slowly until late December as shown in the figure accompanying the review paper.

The available evidence doesn't rule out a lab leak but it's inconsistent with the Reddit rumour that three or four WIV workers were hospitalized with COVID-19 in November.

Nobody can definatively rule out a conspiracy theory—that's why they are so popular. But you can address false claims that presumably support the conspiracy theory. That's why the experts considered whether the scientists at WIV had been working on gain-of-function research or had previously worked with infectious human viruses. They could find no such evidence.

"There is no rational experimental reason why a new genetic system would be developed using an unknown and unpublished virus, with no evidence nor mention of a SARS-CoV-2-like virus in any prior publication or study from the WIV (Ge et al., 2012; Hu et al., 2017; Menachery et al., 2015), no evidence that the WIV sequenced a virus that is closer to SARS-CoV-2 than RaTG13, and no reason to hide research on a SARS-CoV-2-like virus prior to the COVID-19 pandemic. Under any laboratory escape scenario, SARS-CoV-2 would have to have been present in a laboratory prior to the pandemic, yet no evidence exists to support such a notion and no sequence has been identified that could have served as a precursor."

Sandwalk readers will recognize the issue here. You can't prove a negative so the lab leak conspiracy theorists will always be able to say that their conspiracy theory hasn't been disproven. If that's all you have to go on then I feel sorry for you. You are in the same group as those who believe in all other conspiracy theories.

The 21 experts then go on to address the claim that the virus was "pre-adapted" to humans suggesting that scientists at the WIV had selected the virus for its ability to infect human cells. This speculation includes the ridiculous claim that the furin cleavage site had been deliberately engineered. That particular claim has been debunked but so has the general claim of pre-adaption. In fact, the data shows that the virus was a generalist virus that has gradually become more adapted to humans during the pandemic. This fact, that it was a generalist virus, has been known for more than a year but that hasn't squelched the conspiracy theorists.

"SARS-CoV-2 is also notable for being a host generalist virus (Conceicao et al., 2020), capable of efficient transmission in multiple mammalian species (including mink, tigers, cats, gorillas, dogs, raccoon dogs, and ferrets), and large outbreaks have been documented in mink with spill-back to humans (Oude Munnink et al., 2021) and to other animals (van Aart et al., 2021). Combined, these findings show that no specific human “pre” adaptation was required for the emergence or early spread of SARS-CoV-2, and the claim that the virus was already highly adapted to the human host (Zhan et al., 2020), or somehow optimized for binding to human ACE2, is without validity."

The authors conclude that the lab leak conspiracy theory has no merit because there's no evidence to support it. Thus, the only reasonable hypothesis is a natural origin and there's plenty of evidence to support that hypothesis.

"There is currently no evidence that SARS-CoV-2 has a laboratory origin. There is no evidence that any early cases had any connection to the WIV, in contrast to the clear epidemiological links to animal markets in Wuhan, nor evidence that the WIV possessed or worked on a progenitor of SARS-CoV-2 prior to the pandemic. The suspicion that SARS-CoV-2 might have a laboratory origin stems from the coincidence that it was first detected in a city that houses a major virological laboratory that studies coronaviruses. Wuhan is the largest city in central China with multiple animal markets and is a major hub for travel and commerce, well connected to other areas both within China and internationally. The link to Wuhan therefore more likely reflects the fact that pathogens often require heavily populated areas to become established (Pekar et al., 2021).

We contend that although the animal reservoir for SARS-CoV-2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Although the possibility of a laboratory accident cannot be entirely dismissed, and may be near impossible to falsify, this conduit for emergence is highly unlikely relative to the numerous and repeated human-animal contacts that occur routinely in the wildlife trade. Failure to comprehensively investigate the zoonotic origin through collaborative and carefully coordinated studies would leave the world vulnerable to future pandemics arising from the same human activities that have repeatedly put us on a collision course with novel viruses."

---

Image credits: The first figure is from the Holmes et al. paper and the second one is from a Scientific American article [A Visual Guide to the SARS-CoV-2 Coronavirus]

Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?

I would like to think that the media will eventually wake up and recognize the science behind the origin of SARS-CoV-2. It overhelmingly supports a natural origin and does not support the lab leak conspiracy theory. I was encourgaged by a Los Angeles Times article published a few weeks ago [Column: The lab leak theory for the origin of COVID-19 is fading.]. It was written by Michael Hiltzik who took the time to read some of the scientific papers that have recently been published. He has written an excellent summary of the issues.

Here's the bottom line ....

It would be inaccurate to say that evidence for the lab leak theory is fading. That’s because there never was any evidence for the theory, just conjecture.

Virtually from the outset, the lab leak theory was driven by ideology, not science. It employed the vocabulary of science, but that’s a familiar technique for bamboozling a susceptible public.

"The only evidence for a lab leak, period, is just that the virus emerged in Wuhan, where the Wuhan Institute of Virology is,” Rasmussen told me. “That’s it. Since day one, that has been the only piece of evidence.”

The assertions supporting the lab leak theory are not only conjectures, but in many cases provably wrong conjectures. They’re often based on misinformation, scientific ignorance, or even bad translations from Chinese documents.

Unfortunately, journalists like Michael Hiltzik are rare. Furthemore, there's no evidence that the talking heads on TV are even close to realizing that they have been duped.

---

Conversation with Massimo Pigliucci

This is really worth one hour of your time. You will learn about knowledge and abduction and lots of other things.

---

Mutation, Randomness, & Evolution

I just received my copy of a book by Arlin Stoltzfus on mutation. I haven't finished reading it but I thought Sandwalk readers should know about it so they can order their own copy.

This is not light reading since the topics are complicated and there's a lot of misinformation about evolutionary theory floating around. In order to make his points, Arlin has to explain what's wrong with orthodox thinking and why it needs to change and this isn't an easy task. But it's worth the effort ... buy this book!

Here's a short synopsis from page 13.

The following represents a brief guide to the book, which has three parts that correspond roughly to the three combinations of terms.

• mutation and randomness—how does the biological process of mutation seem random, or not?
• randomness and evolution—what role does the concept of "random variation" play in evolutionary thinking?
• mutation and evolution—what is the role of mutation in evolution, and particularly, the role of mutational tendencies?

---

Richard Dawkins talks about the genetic code and information

This is a video published a few weeks ago where Jon Perry interviews Richard Dawkins. Jon Perry is the author of animations posted on his website Stated Clearly. He (Perry) has a very adaptaionist view of evolution—a view that he got from Richard Dawkins.

The main topic of the interview concerns DNA as information and the genetic code. Both Dawkins and Perry give the impression that the only kind of information in the genome is the genetic code (sensu stricto); in other words, the code that specifies a sequence of amino acids using the sequence of nucleotides in a coding region [The Real Genetic Code]. Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.

Perry points out that most people don't understand this, including many atheists who argue that the "code" is merely an analogy and not to be taken literally. Atheists, and others, also argue that the information content of DNA includes lots of other things such as genes that specify functional RNAs and sites that bind proteins. It's hard to argue that a gene for tRNA functions as any kind of a code and it's hard to argue that the DNA binding sites in origins of replication are codes even though you could argue that they carry information.

I don't get excited about arguments over whether DNA carries "information" because there's not much to be gained by such arguments. Who cares whether the genetic code falls under the definition of "information theory"? However, I do get annoyed when people say that the ONLY information in DNA is in the form of the genetic code.

Watch the video and let me know what you think. Jerry Coyne watched it and he wasn't the least bit bothered by the things that bothered me [A discussion on genetics, evolution, and information with Richard Dawkins].

---

Is the Modern Synthesis effectively dead?

The Modern Synthesis is the version of evolutionary theory popularized by Julian Huxley and supported by the leading evolutionary biologists of the 1930s, 40s, and 50s.

The general idea was to merge Dawrin's view of natural selection with the relatively new field of population genetics. Evolution was now defined as a change in allele frequencies in a population and the emphasis was on natural selection as the most important mechanism although, in the original version by Huxley, the fixation of alleles by random genetic drift can occur in small populations. By the early 1960s the most popular vesion of the Modern Synthesis focused almost exclusively on natural selection—an emphasis that's referred to as the hardening of the synthesis. It was this excessively adaptationist view of evolution that led to Gould and Lewontin's paper on "The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme" (Gould and Lewontin, 1979).

Let's analyze the Newsweek lab leak conspiracy theory article

Lots of people have been sucked in to the lab leak conspiracy theory based on reporting in newspapers and magazines. One of the widely-cited sources is an article published in Newsweek on June 2, 2021. The focus of the article is on How Amateur Sleuths Broke the Wuhan Lab Story and Embarrassed the Media. Those "amateur sleuths" go by the name "Decentralized Radical Autonomous Search Team Investigating COVID-19" or DRASTIC. I'm not interested in them; I'm interested in scientific facts so let's look at all of the so-called "facts" in the Newsweek article. I'll leave it up to you, dear reader, to judge whether the media should be embarrassed by this story.

Newsweek statment #1: Thanks to DRASTIC, we now know that the Wuhan Institute of Virology had an extensive collection of coronaviruses gathered over many years of foraging in the bat caves, and that many of them—including the closest known relative to the pandemic virus, SARS-CoV-2—came from a mineshaft where three men died from a suspected SARS-like disease in 2012.

Some of this is correct. The WIV scientists and their collaborators have been collecting samples from bats all over China and Indochina for several years and many of them have been examined for the presence of coronaviruses. WIV scientists routinely sampled bats from the Yunnan mine cave from 2012 to 2015 after they were informed that four people had been admitted to hospital with severe respiratory disease in 2012 (one of them died). The workers tested negative for Ebola, Nipah virus, and coronavirus so the scientists were looking for a likely unknown virus that caused the infection. (The serum samples were subsequently tested for SARS-CoV-2 and they were negative.)

Several coronaviruses were detected in the bat samples based on short PCR sequences (370 bp) from the RdRp gene and they were classified as either alphacoronaviruses or betacoronaviruses. The data was published in 2016 (Ge et al., 2016) and the sequences were deposited in GenBank in 2016. Improvements in sequencing technology in 2018 prompted a re-examination of those bat samples and an almost full-length sequence of a betacoronavirus was obtained (missing the 5′ and 3′ ends). This virus was named RaTG13 and one of the short GenBank sequences identified as BtCoV/4491 (Accession #KP876546) comes from that virus (Zhou et al., 2020 Addendum).

The bat virus is RaTG13 and it is 96% similar in sequence to SARS-CoV-2—that means that they probably shared a common ancestor about 50 years ago (Zhou et al. 2020). The sequence was deposited in GenBank as Accession #Mn996532. There are parts of SARS-CoV-2 that are not closely related to RaTG13 and this includes the spike protein gene, which is essential for infecting humans. The spike gene sequence is most closely related to a coronavirus from pangolins, Pangolin-Cov.

The data is consistent with a recombination event between different strains of coronaviruses giving rise to SARS-CoV-2 or its immediate ancestors. Such recombinations are a common feature of coronavirus propagation in various animals, including bats. What's clear is that none of the currently known coronavirus sequences could possibly be the ancestors of SARS-CoV-2 so the hunt is on to locate those viruses.

Recently, the scientists at WIV and their collaboratore at the University of Chinese Academy of Sciences in Beijing looked at some of the other samples from bat anal swabs collected in Yunnan in 2015. This in depth analysis was prompted by the discovery of SARS-CoV-2 and the pandemic. They found a number of other bat coronavisus sequences and some of them were more closely related to SARS-CoV-2 in the ORF1b regions but not in other parts of the genome. Again, this is consistent with frequent recombination events that have been documented over the past few decades. Surprisingly, some of these new bat coronavisuses were able to use the bat angiotensin-converting enzyme 2 (ACE2) as a receptor, but they did not bind to human ACE2. (These assays take a lot of time and effort.) This and other data show that the evolution of ACE2 binding can occur in bats giving rise to a generalist virsus, SARS-CoV-2, than can bind to ACE2 from many different species. (MacLean et al., 2021; Guo et al., 2021).

A group of scientists from France, United States, Vietnam, and Cambodia looked at bat samples that were collected in Cambodia in 2010 and found coronaviruses from another species of bats that were cloesly related to SARS-CoV-2 across most of the genome except for a small region of the spike protein gene. In some parts of the genome (ORF1a and ORF8) these viruses were more closely related to SARS-CoV-2 than RATG13 (Hu et al. 2021). The evolutionary history of the Cambodian viruses indicate that they are mosaic viruses due to recombination events. This data indicates that SARS-CoV-2 related viruses are found in Southeast Asia as well as China—that's signficant since pangolins are only found in Southeast Asia and not in China.

SARS-CoV-2-like viruses have also been found in Thailand (Wacharapluesadee et al., 2021).

A group centered in Taian, China, has recently examined coronaviruses from bats at the botanical garden in Mengal county in Yunnan. They have identified four additional SARS-CoV-2 related viruses including one, RpYN06, that is the closest relative to SARS-CoV-2 outside of the spike gene. This is now the leading candidate for the "backbone" that might have given rise to the pandemic virus (Zhou et al., 2021).

CONCLUSION: The Newsweek statement is not wrong but it is highly misleading. The WIV labs had bat samples that contained coronaviruses but so did lots of labs all over the world. In that sense, these labs have an "extensive collection of coronaviruses" but they are stored in bat poop at -80° C! They identified two coronavirus, RaTG13 and RmYN02, by sequencing PCR fragments but the sequences were not complete. It's misleading for Newsweek to imply that the WIV labs had an RaTG13 coronavirus in their labs because that implies that they were working with active viruses. It's true that the RaTG13 virus came from a place where several workers had gotten sick with respiratory disease a few years before the sample was collected. One of these men died (not three) but none of the patients tested positive for coronavirus.

Newsweek statement #2: We know that the WIV was actively working with these viruses, using inadequate safety protocols, in ways that could have triggered the pandemic, and that the lab and Chinese authorities have gone to great lengths to conceal these activities.

CONCLUSION: This is misleading. As far as I know, the scientists are WIV were not actively working with the RaTG13 virus because they had never isolated that virus. Furthermore, it's almost impossible to create SARS-CoV-2 from RaTG13 [Could scientists use the bat coronavirus RaTG13 to engineer SARS-CoV-2, the virus that causes COVID-19, in a lab?]. They were working with other bat coronaviruses but none of them were closely related to SARS-CoV-2 so it's extremely misleading to imply that the escape of these viruses could have triggered the pandemic. They were not using inadequate safety protocols because all of the work with bat coronaviruses was carried out in level 2 labs, exactly as required. There's no evidence that the scientists at the WIV labs have concealed anything. You can only accuse someone of concealing something if you have strong evidence that they did something that they deny doing.

Newsweek statement #3: We know that the first cases appeared weeks before the outbreak at the Huanan wet market that was once thought to be ground zero.

CONCLUSION: This is correct. Chinese scientists and health workers identified a number of earlier cases that appear to be unrelated to the seafood market and they published their results in scientific journals over a year ago. They now conclude that the virus was circulating in the Wuhan population for more than a month before the superspreader event at the market ignited the pandemic. This appears to be a case where Newsweek trusts the work of Chinese scientists.

Newsweek statement #4: The Newsweek article talks a lot about the DRASTIC group as though they have uncovered a huge conspriacy theory. One of their "discoveries" relates to the bat coronavirus RaTG13 that's first mentioned in the paper where the SARS-CoV-2 sequence was published. Here's what Newsweek wrote: "The paper was vague about where RaTG13 had come from. It didn't say exactly where or when RaTG13 had been found, just that it had previously been detected in a bat in Yunnan Province, in southern China.

The paper aroused Deigin's suspicions. He wondered if SARS-CoV-2 might have emerged through some genetic mixing and matching from a lab working with RaTG13 or related viruses. His post was cogent and comprehensive. The Seeker posted Deigin's theory on Reddit, which promptly suspended his account permanently."

CONCLUSION: This is written like it's a big mystery that was uncovered by some clever sleuthing. It's true that the origin of RaTG13 was not discussed in the SARS-CoV-2 paper in January 2020 other than to say that it was found in a bat in Yunnan. I assume that the authors didn't think it was important (and still don't). The origin was explained in November 2020 in an Addendum to the Nature article (Zhou et al., 2020, Addendum). It was one of the viruses discoverd in the bats from the Yunnan mine cave and a partial sequence had been published earlier (Ge et al., 2016). It's not particulary close to SARS-CoV-2 and there's no reason to speculate that it was artificially created unless you are trying to create a conspiracy.

Newsweek statement #5: The key facts quickly came together. The genetic sequence for RaTG13 perfectly matched a small piece of genetic code posted as part of a paper written by Shi Zhengli years earlier, but never mentioned again. The code came from a virus the WIV had found in a Yunnan bat. Connecting key details in the two papers with old news stories, the DRASTIC team determined that RaTG13 had come from a mineshaft in Mojiang County, in Yunnan Province, where six men shoveling bat guano in 2012 had developed pneumonia. Three of them died. DRASTIC wondered if that event marked the first cases of human beings being infected with a precursor of SARS-CoV-2—perhaps RaTG13 or something like it.

In a profile in Scientific American, Shi Zhengli acknowledged working in a mineshaft in Mojiang County where miners had died. But she avoided connecting it to RaTG13 (an omission she had made in her scientific papers as well), claiming that a fungus in the cave had killed the miners.

This reads just like a typical conspiracy theory where "clever" sleuths (i.e. internet anateurs) uncover information that was hidden or covered up by those they are accusing. The origin of RaTG13 was explained in an addendum to the publication of the SARS-CoV-2 sequence in February 2020. The addendum was added in November 2020 in reponse to questions about the origin of RaTG13 but that information was widely known. The sequence of a short fragment of this virus was obtained earlier as explained above.

The WIV scientists were very concerned about the Yunnan mine workers because they had symptoms that were similar to those of SARS patients and that's why they tested serum from the patients. They were negative for all the viruses, including the original SARS-CoV-1. (The serum is also negative for SARS-CoV-2.) The WIV scientists were worried that the infections were due to an unknown virus that could cause a pandemic so they went back to the mine every year to collect samples from the bats. The RaTG13 sequence came from one of those samples but by then the scientists knew that there was no connection between the bat coronaviruses and the sick mine workers. (They were probably disappointed at the lack of connection because they were looking for the cause of the 2002 SARS outbreak.)

The WIV scientists now believe that the Yunnan mine workers had contracted a fungal infection from the fungus growing on the bat guano. There is no reason to connect RaTG13 to the mine workers because it's been known for many years that the workers were not infected with any coronavirus.

The RaTG13 virus is from the bat species Rhinolophus affinis (hence the designation "Ra") but up until the beginning of the pandemic the WIV scientists were much more interested in another cave in Yunnan populated by a number of different species. They reported that this cave represents the most diverse collection of bat coronaviruses in the world. Most of the ones that are SARS-like were from a different species of bat, Rhinolophus sinicus and many of these bound the same ACE2 receptor that SARS-CoV-1 used—the same one used by the more recent SARS-CoV-2 (Hu et al. 2017; Cui et al., 2019).

CONCLUSION: The Newsweek article is repeating innuendos and conspiracies that have been discredited in the past. The DRASTIC team is deliberately making up connections between coroanvirus and the mine workers but all of the data shows that there's no direct connection. It just happened that one of the bat coronaviruses collected in that mine happened to be the one closest to SARS-CoV-2, in part because that was a pretty extensive collection. The RaTG13 sequence is not similar enough to SAS-CoV-2 to be the direct ancestor and, besides, there are now known to be other virus sequences from as far away as Cambodia that are just as similar to SARS-CoV-2.

Newsweek statement #6: That explanation didn't sit well with the DRASTIC group. They suspected a SARS-like virus, not a fungus, had killed the miners and that, for whatever reason, the WIV was trying to hide that fact. It was a hunch, and they had no way of proving it.

At this point, The Seeker revealed his research powers to the group. In his online explorations, he'd recently discovered a massive Chinese database of academic journals and theses called CNKI. Now he wondered if somewhere in its vast circuitry might be information on the sickened miners.

Working through the night at his bedside table on phone and laptop, fueled by chai and using Chinese characters with the help of Google Translate, he plugged in "Mojiang"—the county where the mine was located—in combination with every other word he could think of that might be relevant, instantly translating each new flush of results back to English. "Mojiang + pneumonia"; "Mojiang + WIV"; "Mojiang + bats"; "Mojiang + SARS." Each search brought back thousands of results and half a dozen different databases for journals, books, newspapers, master's theses, doctoral dissertations. He combed through these results, night after night, but never found anything useful. When he ran out of energy, he broke for arcade games and more chai.

He was on the verge of calling it quits, he says, when he struck gold: a 60-page master's thesis written by a student at Kunming Medical University in 2013 titled "The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown Viruses." In exhaustive detail, it described the conditions and step-by-step treatment of the miners. It named the suspected culprit: "Caused by SARS-like [coronavirus] from the Chinese horseshoe bat or other bats."

CONCLUSION: Move along folks; there's nothing to see here. The WIV scientists suspected that the miners were infected with an unknown virus and that's why they were concerned in 2012. They knew that coronavirus wasn't responsible and neither was any other known virus. This is why they went back every year to test the bats in the mine shaft. The know that the stored serum from these workers is negative for SARS-CoV-2, which is not a surprise. They now suspect that the mine workers had contracted a fungl infection and not a viral infection. It's not particulary surprising that a student reported the suspected cause of the symptoms back in the beginning of the investigation.

Newsweek statement #7: Ribera was responsible for solving another piece of the RaTG13 puzzle. Had the WIV been actively working on RaTG13 during the seven years since they discovered it? Peter Daszak said no: they had never used the virus because it wasn't similar enough to the original SARS. "We thought it's interesting, but not high-risk," he told Wired. "So we didn't do anything about it and put it in the freezer."

Ribera disproved that account. When a new science paper on genetics is published, the authors must upload the accompanying genetic sequences to an international database. By examining some metadata tags that had been accidentally uploaded by the WIV along with its genetic sequences for RaTG13, Ribera discovered that scientists at the lab had indeed been actively studying the virus in 2017 and 2018—they hadn't stuck it in a freezer and forgotten about it, after all.

I don't know what this means. The WIV scientists sequenced a bit of what turned out to be the RaTG13 virus when they catagorized all the other viruses back in 2012-2015 (Ge et al. 2016). They then completed an almost whole genome sequence later on in 2018 when their sequencing techniques improved. It's important keep in mind that the WIV never worked with the RaTG13 virus as emphasized by Frutos et al. (2021): "One must remember that SARS-CoV-2 was never found in the wild and that RaTG13 does not exist as a real virus but instead only as a sequence in a computer. It is a virtual virus which thus cannot leak from a laboratory." ¹

CONCLUSION: The scientists at WIV were "working with" the RaTG13 PCR fragments in 2017 and 2018 as they assembled the whole genome sequence. They also assembled the sequences of seveal other viruses at the same time. To say that they were "actively studying" the virus is very misleading and to accuse Peter Daszek of lying is irresponsible.

Newsweek statement #8: In fact, the WIV had been intensely interested in RaTG13 and everything else that had come from the Mojiang mineshaft. From his giant Sudoku puzzle, Ribera determined that they made at least seven different trips to the mine, over many years, collecting thousands of samples. Ribera's guess is that their technology had not been good enough in 2012 and 2013 to find the virus that had killed the miners, so they kept going back as the techniques improved.

He also made a bold prediction. Cross-referencing snippets of information from multiple sources, Ribera guessed, in a Twitter thread dated August 1, 2020, that a cluster of eight SARS-related viruses mentioned briefly in an obscure section of one WIV paper had actually also come from the Mojiang mine. In other words, they hadn't found one relative of SARS-CoV-2 in that mineshaft; they'd found nine. In November 2020, Shi Zhengli confirmed many of DRASTIC's suspicions about the Mojiang cave in an addendum to her original paper on RaTG13 and in a talk in February 2021.

The mine shaft is located in Mojiang county, Yunnan—a map of the location was published in Ge et al. (2016). It contains six different bat species and many of them were infected with coronaviruses. The WIV scientists collected many samples over a number of years in order to determine the phylogeny of the viruses and which species were infected. They also did longitudinal studies to see if the different virus variants changed over time and to see if the infection rates of the various bat species were different from year to year. They also wanted to see if they could detect recombinations between different virus groups.

They obtained 152 partial sequences and then picked 12 of them for more detailed analysis in order to construct a phylogenetic tree from 816 bp of the RNA-dependent RNA polymerase (RdRp) gene. Anyone can read the Ge et al. (2016) paper to see why they were doing these experiments. There's nothing mysterious or unusual about their approach. It's the same one they took with the viruses from the other site (cave) in Yunnan where they identified the two bat coronaviruses that are most closely related to the original SARS virus (Ge et al., 2013) (see: SARS ouotbreak linked to Chinese bat cave)

CONCLUSION: The Newsweek article is making a huge mountain out of a molehill and it's misrepresenting the work of the "amateur sleuths." It's not a secret or a mystery that the WIV scientists were studying the coronaviruses from the mine shaft. That's what they do and they publish in journals that are easy to access.

Newsweek statement #9: "Other databases yielded other clues. In the WIV's grant applications and awards, The Seeker found detailed descriptions of the Institute's research plans, and they were damning: Projects were underway to test the infectivity of novel SARS-like viruses they'd discovered in human cells and in lab animals, to see how they might mutate as they crossed species, and to genetically recombine pieces of different viruses—all being done at woefully inadequate biosecurity levels. All the elements for a disaster were on hand."

CONCLUSION: It's true that the WIV scientists were looking at SARS-like coronavisuses and they were testing for infectivity in humanized mouse cells. The goal was to look for new coronaviruses that could bind ACE2 and they found quite a few of them. In many cases, they expressed the spike protein in recombinant viruses and plasmids just as you would expect them to do if they were looking for the source of the original SARS virus (SARS-CoV-1). All this is described in their grant applications and in their publications. Looks like they didn't make much of an attempt to hide this research. All the experiments were done under the appropriate biosafety measures as specified by international inspectors who visited the lab on several occasions. None of this has anything to do with the pandemic because they were not working with SARS-CoV-2 or any close relative.

The rest of the Newsweek article consists mostly of praise for the DRASTIC heros and the excellent work they have done in uncovering a huge conspiracy to cover up the fact that the WIV scientists started a pandemic. However, one embarrassing fact remains: there is not a shred of evidence that the lab was working with SARS-CoV-2 before the pandemic started. In the absence of such evidence it is irresponsible to accuse these reputable scientists of lying.

---

1. One could quibble slightly about the accuracy of this statment since there might be RaTG13 virus particles in the bat fecal samples that are stored in the -80°C freezer.

Cui, J., Li, F. and Shi, Z.-L. (2019) Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology 17:181-192. doi: [doi: 10.1038/s41579-018-0118-9]

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.

Hu, V., Delaune, D., Karlsson, E.A., Hassanin, A., Tey, P.O., Baidaliuk, A., Gámbaro, F., Tu, V.T., Keatts, L. and Mazet, J. (2021) A novel SARS-CoV-2 related coronavirus in bats from Cambodia. bioRxiv. [doi: 10.1101/2021.01.26.428212]

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.

Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A.A., Zhu, G., Epstein, J.H., Mazet, J.K., Hu, B., Zhang, W. and Peng, C. (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503:535-538. [doi: 10.1038/nature12711]

The 2002–3 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV) was one of the most significant public health events in recent history1. An ongoing outbreak of Middle East respiratory syndrome coronavirus2 suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses3,4,5, attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa5,6,7,8, but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2)9,10. Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness.

Ge, X.-Y., Wang, N., Zhang, W., Hu, B., Li, B., Zhang, Y.-Z., Zhou, J.-H., Luo, C.-M., Yang, X.-L. and Wu, L.-J. (2016) Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virologica Sinica 31:31-40. [doi: 10.1007/s12250-016-3713-9]

Since the 2002–2003 severe acute respiratory syndrome (SARS) outbreak prompted a search for the natural reservoir of the SARS coronavirus, numerous alpha- and betacoronaviruses have been discovered in bats around the world. Bats are likely the natural reservoir of alpha- and beta-coronaviruses, and due to the rich diversity and global distribution of bats, the number of bat coronaviruses will likely increase. We conducted a surveillance of coronaviruses in bats in an abandoned mineshaft in Mojiang County, Yunnan Province, China, from 2012–2013. Six bat species were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus fuliginosus, and Miniopterus fuscus. By sequencing PCR products of the coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high frequency of infection by a diverse group of coronaviruses in different bat species in the mineshaft. Sequenced partial RdRp fragments had 80%–99% nucleic acid sequence identity with well-characterized Alphacoronavirus species, including BtCoV HKU2, BtCoV HKU8, and BtCoV1,and unassigned species BtCoV HKU7 and BtCoV HKU10. Additionally, the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species. Furthermore, coronavirus co-infection was detected in all six batspecies, a phenomenon that fosters recombination and promotes the emergence of novel virus strains. Our findings highlight the importance of bats as natural reservoirs of coronaviruses and the potentially zoonotic source of viral pathogens.

Guo, H., Hu, B., Si, H.-r., Zhu, Y., Zhang, W., Li, B., Li, A., Geng, R., Lin, H.-F. and Yang, X.-L. (2021) Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. bioRxiv. [doi: 10.1101/2021.05.21.445091]

Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.

MacLean, O.A., Lytras, S., Weaver, S., Singer, J.B., Boni, M.F., Lemey, P., Pond, S.L.K. and Robertson, D.L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology 19:e3001115. [doi: 10.1371/journal.pbio.3001115]

Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.

Wacharapluesadee, S., Tan, C.W., Maneeorn, P., Duengkae, P., Zhu, F., Joyjinda, Y., Kaewpom, T., Chia, W.N., Ampoot, W. and Lim, B.L. (2021) Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nature communications 12:1-9. doi: [doi: 10.1038/s41467-021-21240-1]

Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.

Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B. and Huang, C.-L. (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270-273. [doi: 10.1038/s41586-020-2012-7]

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1,2,3,4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5,6,7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

Zhou, P. et al. (2020) Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 588:E6-E6. [doi: 10.1038/s41586-020-2951-z]

Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Hu, T., Song, H., Chen, Y., Cui, M. and Zhang, Y. (2021) Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv. doi: [doi: 10.1101/2021.03.08.434390]

Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

Real scientists discuss the lab leak conspiracy theory

Here's an interesting video where the hosts of "This Week in Virology" (Vincent Racaniello, Rich Condit, and Kathy Spindler) discuss the origin of COVID-19 with three scientists who were on the WHO investigation committee that visited the Wuhan Institute of Virology a few months ago (Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans). If you've fallen for the lab leak conspiracy theory then you need to watch the entire video. The rest of you might want to skip to 50 minutes where they discuss the lab leak accusation and relate how they interviewed the scientists at WIV.

The WHO scientists want to emphasize three things: (1) it is extremely unlikely that SARS-CoV-2 was being studied at WIV so it couldn't have escaped from there; (2) there is no evidence to support the lab leak conspiracy theory but if any evidence shows up they are perfectly willing to investigate; (3) it's very likely that SARS-CoV-2 originated naturally in the wild and all efforts should be focused on the most likely scenario and not on an extremely unlikely scenario.

After the interview is over, the three hosts talk about the lab leak conspiracy theory. You should hear what they have to say about Nicholas Wade and his failure to understand the furin cleavage site (1:10 minutes)! And they have lots to say about everything else in the Wade article. Everyone needs to watch that discussion if you are really interested in science and not half-baked conspriacy theories.

The next video is an interview with Robert Garry, a virologist at Tulane University in New Orleans. His area of expertise is emerging infectious viruses. Listen to Garry and the hosts discuss the possibility that SARS-CoV-2 was present in the Wuhan Institure of Virology and released acidentally to start the pandemic (starting at 15 mins). It's good to hear real experts debunk the conspiracy theory.

---

Nessa Carey talks about epigenetics

Nessa Carey wrote a horribe book about junk DNA where she completely misunderstood the science. It's one of many examples of bad science journalism [Nessa Carey doesn't understand junk DNA].

I recently became aware of a talk given in 2015 by Nessa Carey on epigenetics so I'm posting it here. (She also wrote a book about epigenetics.) She is an entertaining speaker and gives a very good presentation but that's a problem if the science is misleading. Judge for yourselves.

---

Telomere-to-telomere sequencing of a complete human genome

Here's a paper that has recently been posted on the preprint server bioRxiv.

Nurk et al. (2021) The complete sequence of a human genome. [doi: 10.1101/2021.05.26.445798]

I usually don't like to comment on preprints but this one is surely going to be published somewhere and it's important.

The authors have sequenced the entire chromosomes (telomere-to-telomere) of the 22 autosomes and the X chromosome of the cell line CHM13. The cell line is a complete hydatiform mole, which means it is derived from a molar pregnancy where a sperm combines with an egg cell that has lost its nucleus. The sperm DNA duplicates giving rise to cells that have two identical copies of each chromosome. The karyotype of the CHM13 cell line is 46,XX. The advantage of sequencing the DNA from such cell lines is that the interpretation of the sequencing results is not complicated by the heterogeneity of normal diploid cell lines. This was important because the focus of this study was on sequencing repetitive regions of the chromosomes and most chromosome pairs have different numbers of repeats.

The SARS-CoV-2 reference genome

Chinese scientists isolated virus particles from a patient admitted to hospital on December 26, 2019 in Wuhan, China. The RNA genome was sequenced and the sequence was immediately distributed to interested scientists around the world. It was submitted to GenBank on January 5, 2020 and appeared as entry NC_045512 on January 13, 2020 [Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome].

The original GenBank record was annotated and updated by NIH staff on January 17, 2020 and now appears as updated locus NC_045512 last modified on July 18, 2020 now called SARS-CoV-2 [Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome].

The sequence was extensively mapped and analyzed by Chinese scientists in Shanghai, Wuhan, and Beijing, and Ed Holmes in Sydney, Australia and the results were submitted to Nature on January 7, 2020 and published on February 3, 2020.

Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E.C. and Zhang, Y.-Z. (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265-269. [doi: 10.1038/s41586-020-2008-3]

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.

The Nature paper notes that this is a novel coronavirus related to known bat coronaviruses but it's exact origin remains unclear. The authors also mention that the origin of other disease-causing coronavirus-like viruses is also unknown.

Coronaviruses are associated with a number of infectious disease outbreaks in humans, including SARS in 2002–2003 and Middle East respiratory syndrome (MERS) in 2012. Four other coronaviruses—human coronaviruses HKU1, OC43, NL63 and 229E—are also associated with respiratory disease. Although SARS-like coronaviruses have been widely identified in mammals including bats since 2005 in China, the exact origin of human-infected coronaviruses remains unclear. Here we describe a new coronavirus—WHCV—in the BALF from a patient who experienced severe respiratory disease in Wuhan, China. Phylogenetic analysis suggests that WHCV is a member of the genus Betacoronavirus (subgenus Sarbecovirus) that has some genomic and phylogenetic similarities to SARS-CoV1, particularly in the RBD of the spike protein. These genomic and clinical similarities to SARS, as well as its high abundance in clinical samples, provides evidence for an association between WHCV and the ongoing outbreak of respiratory disease in Wuhan and across the world. Although the isolation of the virus from only a single patient is not sufficient to conclude that it caused these respiratory symptoms, our findings have been independently corroborated in further patients in a separate study.

The identification of multiple SARS-like CoVs in bats have led to the idea that these animals act as hosts of a natural reservoir of these viruses. Although SARS-like viruses have been identified widely in bats in China, viruses identical to SARS-CoV have not yet been documented. Notably, WHCV is most closely related to bat coronaviruses, and shows 100% amino acid similarity to bat SL-CoVZC45 in the nsp7 and E proteins (Supplementary Table 3). Thus, these data suggest that bats are a possible host for the viral reservoir of WHCV. However, as a variety of animal species were for sale in the market when the disease was first reported, further studies are needed to determine the natural reservoir and any intermediate hosts of WHCV.

Subsequent work suggests that the virus did not originate in the Wuhan market but was circulating in Wuhan in November 2019 among a small number of people who were not associated with the market. It looks like market workers were the source of superspreader event.

It's important to keep in mind that the exact origin of several other viral diseases has never been determined. This is quite normal so don't be fooled by people who think that the mysterious origin of SARS-CoV-2 demands an immediate explanation. That's likely not going to happen no matter how many outside investigators go snooping around Wuhan looking for clues to support their favorite conspiracy theory.

---

MIT Professor Rick Young doesn't understand junk DNA

Richard ("Rick") Young is a Professor of Biology at the Massachusetts Institute of Technology and a member of the Whitehead Institute. His area of expertise is the regulation of gene expression in eukaryotes.

He was interviewed by Jorge Conde and Hanne Winarsky on a recent podcast (Feb. 1, 2021) where the main topic was "From Junk DNA to an RNA Revolution." They get just about everything wrong when they talk about junk DNA including the Central Dogma, historical estimates of the number of genes, confusing noncoding DNA with junk, alternative splicing, the number of functional RNAs, the amount of regulatory DNA, and assuming that scientists in the 1970s were idiots.

In this episode, a16z General Partner Jorge Conde and Bio Eats World host Hanne Winarsky talk to Professor Rick Young, Professor of Biology and head of the Young Lab at MIT—all about “junk” DNA, or non-coding DNA.

Which, it turns out—spoiler alert—isn’t junk at all. Much of this so-called junk DNA actually encodes RNA—which we now know has all sorts of incredibly important roles in the cell, many of which were previously thought of as only the domain of proteins. This conversation is all about what we know about what that non-coding genome actually does: how RNA works to regulate all kinds of different gene expression, cell types, and functions; how this has dramatically changed our understanding of how disease arises; and most importantly, what this means we can now do—programming cells, tuning functions up or down, or on or off. What we once thought of as “junk” is now giving us a powerful new tool in intervening in and treating disease—bringing in a whole new category of therapies.

Here's what I don't understand. How could a prominent scientist at one of the best universities in the world be so ignorant of a topic he chooses to discuss on a podcast? Perhaps you could excuse a busy scientist who doesn't have the time to research the topic but what excuse can you offer to explain why the entire culture at MIT and the Whitehead must also be ignorant? Does nobody there ever question their own ideas? Do they only read the papers that support their views and ignore all those that challenge those views?

This is a very serious question. It's the most difficult question I discuss in my book. Why has the false narrative about junk DNA, and many other things, dominated the scientific literature and become accepted dogma among leading scientists? Soemething is seriously wrong with science.

---