Scouring The Globe For Viral Fragments And Making Them Whole Again (VIRAL ANALYSIS)

Publisher’s Note: We are pleased to publish Putney, Vermont independent researcher Jacqueline Brook’s essay on viruses and synthetic DNA.

This afternoon I received in the post a slim FedEx envelope containing four small vials of DNA. The DNA had been synthesized according to my instructions in under three weeks, at a cost of 39 U.S. cents per base pair (the rungs adenine-thymine or guanine-cytosine in the DNA ladder). The 10 micrograms I ordered are dried, flaky, and barely visible to the naked eye, yet once I have restored them in water and made an RNA copy of this template, they will encode a virus I have designed. —William McEwan (1)

*      *      *      *

On October 25th, 2019, the NY Times reported that a global virus-hunting project called PREDICT, part of the Emerging Pandemic Threats (EPT) program established by the U.S. Agency for International Development (USAID) in partnership with the Department of Defense (DoD) (2), was being shut down by President Trump. 

Just a short time later: PANDEMIC!

According to the Times article: “The initiative has collected over 140,000 biological samples from animals and found over 1,000 new viruses, including a new strain of Ebola (3).”

However, since the reported shutdown of the program, that figure has apparently doubled. In an interview with Kaiser Health News published on March 16th, 2020, Dennis Carroll, who designed and oversaw the PREDICT program, asserted: “Predict discovered more than 2,000 novel viruses from viral families we know have posed a past threat to people. We calculate now there are about a million and a half of which — maybe 500,000 to 600,000 ― could be potential threats to people (4).”

The hunt for novel viruses is all about vaccines, therapeutics, and One Health Security—which “will require the integration of professionals with expertise in security, law enforcement, and intelligence (5)” to help keep us all healthy and safe from dastardly virus designers. This, on a planet where the United States is incessantly fabricating reasons to bomb people and infrastructure. If the DoD is a partner, it’s more believable to highly cynical me that it’s about population reduction. Indeed, a PREDICT project member has cheerily implied as much (6):

Let’s take the lower of Carroll’s numbers above—500,000—and translate it into vaccines: That’s one vaccine per hour, for 24 hours per day, for a little over 57 years.

Although, Dr. Eddy Rubin, former Director of the DoE Joint Genome Institute and current Chief Science Officer of Metabiota, another overseer of PREDICT programs, quoted in the article “The Virus Hunters,” says the goal is to create vaccines against entire viral families. (An aside: Back in 2013, the Department of Energy had a team led by Monica Borucki, partially funded by the Defense Threat Reduction Agency, working on how coronaviruses jump species. That’s right, the Department of Energy.)

The article tells of a guano harvester agreeing to lead a group, working for PREDICT, to a cave in the Democratic Republic of Congo, where they can trap bats and collect saliva, feces, and blood samples. Watching the scientists suited up in full haz-mat gear, the guano harvester is described as being very amused: “We are not concerned,” he says. “We hear that these scientists are looking for microbes that can give diseases. We’ve never seen it, we have no proof, and it’s never been a problem (7).”

According to the same article: “…there are more than a billion viruses in a pinch of soil… Most viruses have no noticeable impact on our health. Some are probably helpful, and only a tiny fraction cause disease.” So, the guano harvester’s disbelief is more or less justified. Perhaps he’s seen Dennis Carroll’s illustration, below, of even more sharply honed estimates of the imagined versus the currently known (8).  

Yet, as a result of this “pandemic,” according to the Philadelphia Inquirer, the budget for USAID’s global health security-related efforts has been increased fivefold, “to more than half a billion dollars,” which could “reboot stalled efforts to have the U.S. help lead a global quest to corral an estimated 1.6 million animal-borne viruses that threaten to leap to human hosts (9).”

1.6 million animal-borne viruses threaten to leap…! But, really, just how threatening are these “viruses”?

From the abstract of a Metabiota paper entitled “Uncovering Earth’s Virome”:

“Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes… Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses (10).”

Partial viral genomes, almost half, unrelated to those in known viruses. In other words—fragments. Decayed? Degraded? Handled elegantly and tossed out by healthy immune systems? Possibly from exosomes—those vesicles that are shed by most cell types and that are found in all biological fluids, including blood, urine, saliva, breast milk, lymph fluid, etc.? 

Exosomes can carry proteins, lipids, and DNA. Or messenger RNAs or microRNAs, with profiles that “differ from those of the parent cells (11);” long-coding, short-coding, and non-coding RNAs (12). Environmental toxins can alter the cargo of exosomes (13). “Diseased, unhealthy cells have been noted to secrete more exosomes than healthier cells,” and treatment with one antibacterial drug, Ciprofloxacin, has been shown to induce exosome release (12). They can also express self-antigens (12), meaning that your exosomes and my exosomes may not play well together. Antibodies have been found to develop against exosomes that express self-antigens, released from transplanted organs following lung, heart, and kidney transplants. It is thought that “stress to the transplanted organs can release exosomes, and that persistence of these exosomes in the circulation can lead to immune activation” and increase the risk of rejection of the transplanted organ (12). Because, again, donor and recipient exosomes may not play well together. They may be xenophobic. Same as a lot of us. Same as your blood type and my blood type.

Can virologists really have any idea what they’re gathering from blood and urine and feces? I don’t see how, after learning about exosomes and other extracellular vesicles and DNA. But, they’ll bring all those bits of RNA and DNA back to laboratories and begin the work of trying to figure out how they can kill us all—which is called gain-of-function (GOF) research. There was a moratorium on funding it for awhile in the U.S. But, oddly, some gain-of-function research on SARS-CoV was allowed to go ahead during that time in Ralph Baric’s lab at Chapel Hill, North Carolina. A scientist from Wuhan, China—Zheng-Li Shi—was involved in that work which created a chimeric coronavirus—“expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone (14).” The abstract alone makes for pretty chilling reading: Notable pathogenesis, along with failure of antibody and vaccine approaches to neutralize and protect from infection…

That’s not the only GOF research that has been done on SARS-CoV. There was some interesting work done in Tokyo in 2008 in which a “furin-like cleavage sequence” was introduced to the spike (S) protein (15). This seems quite relevant to SARS-C0V-2, in which a peculiar furin-like cleavage site in the spike protein has been found, “that is lacking in the other SARS-like CoVs (16).”

Getting back to virus hunting: The March 2018 “USAID Emerging Pandemic Threats 2 [EPT2] Program Evaluation” recommends that: “USAID should investigate if there are linkages between the viral pathogens it identifies and risks posed to human health, especially risks from wildlife.” Also: “One question the evaluation team heard repeated during headquarters and field interviews concerned the discovery of more than 1,000 novel virus sequences by PREDICT 2: ‘So what does it mean?’ ” Especially since the EPT2 program had not successfully predicted anything. The program was not active in the geographic areas where the “emergence [had occurred] of the four major zoonotic viruses that had been EPTs since the 2008 Jones et al. ‘hot spots’ paper was published.” Severe epidemic disease of one sort or another had emerged from Mexico, Jordan, Saudi Arabia, Zaire, French Polynesia, Brazil, and elsewhere in the Americas. According to the map on page 66 of the document and the accompanying text, of those countries, EPT2 was active only in Jordan. On top of this, there seemed to be tremendous confusion on the part of many program partners as to the actual objectives of the EPT2 program. To some, the objectives were “unknown (2).”

Even renowned infectious disease expert Michael Osterholm has allegedly wondered about the value of such virus hunting and how one would “hear the signal through the static” that so much data would create (17). 

Jon Cohen tells the story of a faint signal teased from 3 years’ worth of static in order to piece together and name the dubious bas-Congo virus, implicated in 3—that’s right, three—possible cases of hemorrhagic fever, in two children, at least one of whom reportedly did not suffer fever, and a nurse who treated them:

The researchers did not actually isolate a rhabdovirus, but instead plucked out RNA sequences from the surviving man’s blood sample and reconstructed what they contend is the genome of the pathogen that caused the disease. “It looks fairly solid,” says Thomas Ksiazek, an epidemiologist and virologist who specializes in hemorrhagic disease at the University of Texas Medical Branch in Galveston. “Clearly, they have identified a virus in one of the three patients they describe. But trying to make more out of this is speculative. Is the disease due to the agent? You can speculate all you want, but until you have a virus in hand it’s hard to answer that.”

The PLoS Pathogens paper has 22 authors, a reflection of the long and winding journey from Mangala to the discovery of what they called the Bas-Congo virus, a reference to name of the Congolese province that includes Mangala village. First, the nurse’s sample went to the Institut National de Recherche Biomédicale in Kinshasa, the capital of the Congo. When researchers there couldn’t find any evidence of a pathogen, they sent the sample to Eric Leroy, a renowned authority on hemorrhagic fever at the Centre International de Recherches Médicales de Franceville (CIRMF) in Gabon. Leroy expanded the analysis and could not find any virus known to cause hemorrhagic fever in Africa. Global Viral Forecasting Inc., a for-profit company now called Metabiota and started by Nathan Wolfe of Stanford University, obtained a sample from CIRMF and gave it to Eric Delwart at Blood Systems Research Institute in San Francisco, California.

Delwart’s group randomly amplified genetic material with the polymerase chain reaction, sequenced the products, and then checked what they created against databases of known genomes. “We got one very intriguing read,” Delwart says. “It was clearly a rhabdovirus.” But his team couldn’t amplify any more meaningful sequence, so they passed the sample on to Charles Chiu, head of a viral discovery center at the University of California, San Francisco. Chiu sequenced 140 million fragments of genetic material and then merged related fragments to assemble the genome of the Bas-Congo virus (18).

After all that time, transportation, and effort, I hope they ruled out contamination of the samples.

With regards to the much-maligned bat species from which most terrible viruses are thought to originate, a 2018 paper on the discovery of a ‘new ebolavirus’ reports: “Despite more than 40 years of research and continued outbreaks, the reservoirs of EBOV and the other ebolaviruses remain unknown. Current evidence points to bats, though failure to isolate a virus or recover a complete genome means that no ebolavirus has been conclusively linked to any particular bat species (19).” And: “further studies are required to test whether exposure has actually occurred or if BOMV [the alleged new ‘Bombali’ ebolavirus] is pathogenic in humans (19).” I wonder how they’ll carry out those further studies. The Bombali ebolavirus story reminds me of the bas-Congo virus story above. It’s a story that begins with viral fragments, collected by a Metabiota/PREDICT team (20).

And from a 2008 paper: “Although several complete Bat CoV [coronavirus] genome sequences are available, no Bat CoV has been successfully cultivated in cell culture or in animals… (21)”

Scientists had been looking for the bat coronavirus from which SARS-CoV had likely leapt to humans, but, since “none had been recovered in culture, the infectivity of the reported viral genomic RNA sequences was hypothetical, having been derived from RT-PCR sequencing of bat fecal or rectal swab samples. Sequence databases have error frequencies from 1/500 to 1/10,000, making viable genome reconstruction problematic with increasing size (21).” 

No problem. A group, including Ralph Baric, decided to create the ‘consensus’ virus:

“The ability to design and recover pathogens reconstituted from synthesized cDNAs … [allows] studies of replication and pathogenesis without identification of reservoir species or cultivation of primary isolates. Here, we report the design, synthesis, and recovery of the largest synthetic replicating life form, a 29.7-kb bat severe acute respiratory syndrome (SARS)-like coronavirus (Bat-SCoV), a likely progenitor to the SARS-CoV epidemic (21).”

__________________________________________________________________________________________

“Here, we report the design, 

synthesis, and recovery 

of the largest synthetic 

replicating life form…”

________________________________________________________________________________________

There was evidently no real need for Zheng-Li Shi’s team to spend a year, later on, collecting samples from bats out in Kunming, China (22).

Jump ahead to the current pandemic and SARS-CoV-2, and Ralph Baric’s lab is racing to synthesize this new virus! From the Technology Review article: “The ability to make a lethal virus from mail-order DNA was first demonstrated 20 years ago (23).” Back before we fabricated endless, global war. Seems almost like a lifetime ago. Ten years before the first iPad was released. But, this is why no pathogenic disease can be eliminated anymore. It doesn’t matter how many people are forcibly vaccinated. We can think we’ve beat it, but like the reconstructed polio virus, somebody can always look up the genetic code and order the required bits from a catalog again. Although, in 2017, there were 3 and a half times more cases of vaccine-derived polio than ‘wild-type’ polio (24). So, choose your poison. Synthetic biology guarantees that any vaccine that makes it onto the schedule is unlikely to be removed. Any company that can make a vaccine can just as easily make the thing for which the vaccine has been created. And vice versa.

Reassuringly, in 2012, Nathan Wolfe acknowledged: “Whatever we’re doing that’s cutting-edge in the lab now is going to be do-it-yourself biology within the next ten years (25).” Like following a recipe! Or, the assembly instructions for a piece of Ikea furniture. 

Baric wrote a 49-page paper on synthetic biology and biowarfare back in 2006, laying out just how incredibly easy biowarfare would become, as a result of synthetic genes, synthetic genomes, synthetic biology, synthetic DNA, catalogs from which you can order any bits of DNA you want… But, Baric offers these incredibly soothing words: “counterterrorism think-tanks anticipate that these particular threats will ameliorate [i.e., improve, not go away] over the next decade because of medical countermeasures (e.g., drugs, vaccines, diagnostics)… (26).” 

In other words, lucky for us that maybe we can be vaccinated and cared for by the same people, who have been working on making biowarfare so easy, for decades. Hey, look how that’s worked out these past few months! 

In case you’re still a little bit in doubt as to the headline of this article, I refer you finally to the 2010 paper “Virus recovery by deep sequencing and assembly of virus-derived small silencing RNAs.” It describes how invertebrates process viral RNA genomes by chopping them up into smaller discreet units for clearance by the immune system, and how the researchers have hit upon an “approach for virus discovery in invertebrates by assembling viral genomes directly from host immune response products without prior virus enrichment or amplification (27).” In other words, they assert that they can put the cleared and/or silenced viral fragments back together again. Ahhh…fixing the things that aren’t broken. 

So, encourage your kids to be virologists and microbiologists. Wouldn’t you just love to shelter in place forever?! 

By the way, for whatever it’s worth: I’ve been healthy thus far (except for one day). I’ve been relying on an ionizer, a bottle of elderberry syrup, and I’ve been putting my head over a simmering pan of water on the stove, breathing in the steam for maybe 30 seconds to a minute, every time I’ve felt a tickle in my nose, throat, or lungs. (The virus is enveloped, and, as such, heat-sensitive.) I have also been rubbing my fingertips over my jeans in a rather OCD fashion, whenever I’ve been out and about. I have not been wearing a mask or gloves. I have not been cleaning my house more than usual or anything I bring back from any store, or washing my clothes more than usual, or using any disinfectants. I’ve been doing a fair amount of hiking and yard work, getting outside and getting fresh air into my lungs. On the one day that I felt somewhat sick, I had some wild ginger root in that saucepan on the stove (which unexpectedly turned the water oily and black after it sat for some time). But, I breathed in its vapors at least 3 times. I also drank and gargled with some hot tea that afternoon, sat in my bedroom with the ionizer on a couple of times, got outside and got some fresh air twice, ate a light dinner and got a good night’s sleep. And woke up feeling great the next day! 

None of which, unfortunately, I paid anyone a dime for—except for the not inexpensive bottle of locally-produced elderberry syrup. The little NeoTec ionizer, I’ve had for years.

—————-

References:

1. https://www.edge.org/conversation/william_mcewan-molecular-cut-and-paste

“Molecular Cut and Paste: The New Generation of Molecular Tools,” Introduction by Nathan Wolfe, 7/22/11. Emphasis added.

2. https://pdf.usaid.gov/pdf_docs/PA00SW1M.pdf

USAID Emerging Pandemic Threats 2 Program Evaluation, March 2018, pps. 12, 19, 45, 49, 66, & 89.

3. https://www.nytimes.com/2019/10/25/health/predict-usaid-viruses.html

“Scientists Were Hunting for the Next Ebola…,” Donald G. McNeil Jr., 10/25/19.

4. https://khn.org/news/former-federal-virus-hunter-says-u-s-cant-wait-for-new-germs-to-kick-your-door-in/

“Former Federal Virus Hunter Says U.S. Needs To Act Before New Germs ‘Kick Your Door In,’ ” Carmen Heredia Rodriguez, 3/16/20.

5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171112/

“One Health Security: An Important Component of the Global Health Security Agenda,” Gronvall et al, 9/1/14.

6. https://twitter.com/i/web/status/1049338581624311808

7. https://undark.org/2017/05/25/virus-hunters-ebola-usaid-predict/

“The Virus Hunters,” Jeffrey Marlow, 5/25/17.

8. https://www.irinsider.org/science-technology-1/2018/2/26/global-virome-project-set-to-launch-in-2018, Fei Zhao.

9. https://www.inquirer.com/health/coronavirus/coronavirus-covid-usaid-global-health-bureau-pandemic-response-funding-20200412.html

“Trump, Congress scramble to revive virus-hunting agency that was marked for cuts,” Rainey & Baumgaertner, Los Angeles Times, 4/12/20.

10. https://www.metabiota.com/publications#!uncovering-earth-s-virome-83

“Uncovering Earth’s Virome,” Espino et al, 8/19/16.

11. https://www.sciencedirect.com/science/article/pii/S167202291500011X

“Exosome and Exosomal MicroRNA: Trafficking, Sorting, and Function,” Zhang et al, Genomics, Proteomics & Bioinformatics, Feb. 2015.

12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092208/

The Role of Exosomes in Allograft Immunity, Bansal et al, Sept. 2018.

13. https://academic.oup.com/toxsci/article/158/1/3/3827743

“Exosomes in Toxicology: Relevance to Chemical Exposure and Pathogenesis of Environmentally Linked Diseases,” Harischandra et al, 5/15/17.

14. https://www.nature.com/articles/nm.3985

“A SARS-like cluster of bat coronaviruses shows potential for human emergence,” Menachery et al, 11/9/15.

15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583654/

“Entry from the Cell Surface of Severe Acute Respiratory Syndrome Coronavirus with Cleaved S Protein as Revealed by Pseudotype Virus Bearing Cleaved S Protein,” Watanabe et al, 9/10/08.

16. https://www.sciencedirect.com/science/article/pii/S0166354220300528

“The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade,” Coutard et al, April 2020.

17. https://theweek.com/articles/667704/there-are-more-than-1-million-viruses-that-know-absolutely-nothing-about

“There are more than 1 million viruses that we know absolutely nothing about, from Stat, Helen Branswell, 12/27/16.

18. https://www.sciencemag.org/news/2012/09/3-year-search-uncovers-novel-hemorrhagic-fever-virus

Jon Cohen, 9/27/12.

19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557442

“Discovery of a new ebolavirus (Bombali virus) in molossid bats in Sierra Leone,” Goldstein et al, 10/3/18.

20. http://www.floridahealth.gov/programs-and-services/public-health-laboratories/forms-publications/_documents/LLV16I4.pdf

“Scientists Discover New Species of Ebola in Sierra Leone,’ Darryl Pronty, Florida Health, Vol. 16, Issue 4, Oct.-Dec. 2018.

21. https://www.pnas.org/content/pnas/105/50/19944.full.pdf

“Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice,” Becker et al, 10/14/08. Emphasis added.

22. https://www.universityofcalifornia.edu/news/sars-virus-discovered-chinese-horseshoe-bats

“SARS-like virus discovered in Chinese horseshoe bats,” Kat Kerlin, UC Davis, 10/30/13.

23. https://www.technologyreview.com/2020/02/15/844752/biologists-rush-to-re-create-the-china-coronavirus-from-its-dna-code/

“Biologists rush to re-create the China coronavirus from its DNA code,” Antonio Regalado, 2/15/2020.

24. https://www.npr.org/sections/goatsandsoda/2017/06/28/534403083/mutant-strains-of-polio-vaccine-now-cause-more-paralysis-than-wild-polio

“Mutant Strains Of Polio Vaccine Now Cause More Paralysis Than Wild Polio,” Jason Beaubien, 6/28/17.

25. https://www.hsph.harvard.edu/news/features/nathan-wolfe-viruses-microbes/

“Virus hunter Nathan Wolfe tells of ‘the good, the bad, and the ugly’ of microbes,” Karen Feldscher, 10/22/12.

26. https://dspace.mit.edu/bitstream/handle/1721.1/39652/Baric%20Synthetic%20Viral%20Genomics.pdf;sequence=1

“Synthetic Viral Genomics: Risks and Benefits for Science and Society,” Ralph S. Baric, University of North Carolina at Chapel Hill, 2006, PDF p.5 (37).

27. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824396/

“Virus recovery by deep sequencing and assembly of virus-derived small silencing RNAs,” Qingfa Wu et al, 1/4/10.