Wednesday, April 1, 2020

SARS-CoV-2, recombinant in nature or by man, or what?

2-26-20  It is more likely that SARS-CoV-2 is a recombinant CoV generated in nature between a bat CoV and another coronavirus in an intermediate animal host.  https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1733440
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1-29-19  Frequent interspecies recombination may result in another human infectious coronavirus from these SARSr-CoVs. Furthermore, there are still unanswered questions about SARS, e.g., ‘Why did the first SARS case occur in Guangdong Province, but all the human-ACE2-using SARSr-CoVs were found in Yunnan Province?’ and ’Why does R. sinicus in certain areas carry human-ACE2-using SARSr-CoVs but no other Rhinolophus species carry the same viruses?’   https://www.mdpi.com/1999-4915/11/3/210/htm
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John Schloendorn    2-2-20
Gene And Cell Technologies
  In brief, one cannot rule out genetic engineering by a skilled group taking appropriate measures to cover its tracks.  Methods such as scarless assembly, deliberate codon matching, and random mutagenesis would not necessarily leave tracks that can be identified at the sequence level alone.  It is possible nowadays to synthesize a sequence that would look indistinguishable from a naturally evolved sequence.

Heather Young  2-2-20
recent study on using CRISPR in a pig CoV and the resulting change in virulence:  https://osf.io/6vd54/
It is significant to note that this paper claims to represent the first instance of CRISPR editing of a coronavirus in the literature (published 2019).

Further, Is it possible to create coronations like SARS-Co-2 by genetic engineering?
David Escors  3-3-20
Navarra biomed
Yes, but not only for coronaviruses.  I remember that a whole picornavirus infectious cDNA was generated by chemical synthesis, basically from scratch.  But this is nothing new.... Retroviral and lentiviral vectors were generated from infectious cDNA clones in the early 80s, and now they are used in gene therapy, for example. It does not mean that this particular lentivector was engineered by any means. Any virologist from the CDC could tell you that every year there are dozens of unknown viruses that jump to the human population, some of them belonging to families such as poxviridae, very similar to small pox. In several places in Africa this is not uncommon (monkey pox, ebola, many unknown viruses), in America (Zika virus, Hataviruses). Here in Europe we worked with an unkown virus associated to Balkan Nephropathy. It was not a coronavirus, and we could only identify it by electron microscopy. But we do not have its sequence yet. You only need a combination of good spreading capacities and some incubation time to get the "perfect storm". For example pandemic flu (not the same as common human flu).  This corona is a natural virus, we are just suitable hosts.

Cardinal Stefan Wyszynski University in Warsaw
Theoretically, this is possible with the involvement of large funds.  But who would care to take such a high risk of causing a global epidemic.  Considering the estimation of potential profits and losses, the rational analysis shows that the risk is too great.

Rachel L Roper  4-4-20
East Carolina University
The truth is we don't know enough about all the genes to design one that is more virulent or transmissible. There are over 380 point mutations - we don't know what they do.  Any one could alter virulence or transmissibility. if you look at all the amino acid changes in the receptor binding domain, you see no one could have predicted that!  It's a natural virus.  Evolution is better than our genetic engineering.

Torsten Wurm  4-4-20
East Carolina University
One hypothesis is actually that a bat CoV infected Malayan Pangolins which not only acted as an amplifier host but where both bat and pangoline CoV also recombined. Alternatively, pangoline CoV might have crossed the species barrier in wet markets. However the authors pointed out that the current data cannot rule out either scenario. (Lam et al., 2020 Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins)
https://www.researchgate.net/post/Ability_of_conversion_of_genes_of_Coronavirus_group_to_novel_Coronavirus_2019-nCoV_named_as_COVID-19_by_WHO_by_genetic_engineering
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Oct. 5, 2001 -- The same advances in technology that may save millions of lives could also be used to take them.
  Experts fear that the genetic revolution, which helped map the Human Genome, may provide terrorists with far more deadly weapons, that could bring about diseases that would be even more difficult to treat than anthrax or smallpox.
  "Advances in genomics have greatly increased the possibilities of mixing and matching traits from different microorganisms," says Dr. Ketan Desai, bioterrorism expert and author of Germs of War.
  This mixing and matching, also known as recombinant technology, can be used, for example, to take a gene that makes a deadly toxin from one strain of bacteria and introduce it into other bacterial strains.
  Dangerous pathogens or infectious agents can be made more deadly, and relatively benign agents can become major public health problems.  Bacteria that cause diseases such as anthrax could be altered in such a way that would make current vaccines against them ineffective.
  "In my opinion, this is not fanciful and there is good reason for concern," says Dr. David Yandell, Director of the Vermont Comprehensive Cancer Center.  The expertise and technology to create lethal new strains of viruses and bacteria are available at almost any university in the United States and abroad.
  Essentially all that is required are a few people with solid molecular biology skills and the state of the art facilities that can be found in many university settings. The work itself would be relatively easy to conceal.
  While experts agree that it is less likely that terrorists will be able to mass produce such weapons without detection, the chances are very high that someone could "create a crude engineered weapon with a moderate probability of success," adds Yandell.
  Additionally slightly altering a common virus such as the flu virus to make it deadlier may be an easier feat than tracking down much rarer viruses, such as smallpox.  https://abcnews.go.com/Health/story?id=117204&page=1
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9-21-2001   The Guardian     Unfortunately to date the politicians, military experts and media have skirted a far more troubling reality about bio-terrorism.  The fact is, the new genomic information being discovered and used for commercial genetic engineering in the fields of agriculture, animal husbandry and medicine is potentially convertible to the development of a wide range of novel pathogens that can attack plant, animal and human populations.
Moreover, unlike nuclear bombs, the materials and tools required to create biological warfare agents are easily accessible and cheap, which is why this kind of weapon is often referred to as the "poor man's nuclear bomb". A state-of-the-art biological laboratory could be built and made operational with as little as $10,000-worth of off-the-shelf equipment and could be housed in a room as small as 15ft by 15ft.  All you really need is a beer fermenter, a protein-based culture, plastic clothing and a gas mask.

Equally frightening, thousands of graduate students in laboratories around the world are knowledgeable enough in the rudimentary uses of recombinant DNA and cloning technology to design and mass-produce such weapons.  -Jeremy Rifkin is the author of The Biotech Century (Penguin, 1998) http://online.sfsu.edu/rone/GEessays/NowGMweapons.htm

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