4-11-20 We compared the codon usages of three coronaviruses (SARS-CoV-2, SARS-CoV and MERS-CoV) to those of more than 10,000 different kinds of animals…..
Our follow-up study also found that the genetic sequence of a coronavirus, discovered in lung samples of Malayan pangolins, was highly similar to SARS-CoV-2. The two viruses shared 91 percent of their genetic sequence. There is a particularly strong similarity between the spike proteins of these two viruses. The spike protein, which is on the surface of a coronavirus, is used by the virus to get into an animal cell.
The bat coronavirus, which was the ancestor of SARS-CoV-2, has 19 amino acids on the spike protein that are different from SARS-CoV-2; the pangolin coronavirus only has five amino acids that are different from SARS-CoV-2. -Yang Zhang, Professor of Computational Medicine & Bioinformatics, University of Michigan; Chengxin Zhang, PhD Candidate in Bioinformatics, University of Michigan, and Wei Zheng, Postdoctoral Fellow of Computational Medicine and Bioinformatics, University of Michigan. https://www.sciencealert.com/more-evidence-suggests-pangolins-may-have-passed-coronavirus-from-bats-to-humans
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If you go into a live market, you see cages containing bats stacked upon cages containing porcupines, stacked upon cages containing palm civets, stacked upon cages containing chickens. And hygiene is not great, and the animals are defecating on one another. It's just a natural mixing-bowl situation for viruses. It's a very, very dangerous situation. And one of the things that it allows is ... the occurrence of "amplifying hosts" [a species that rapidly replicates copies of the virus and spreads them]….
a couple of Chinese scientists did further work and they established that, in fact, the virus was not living permanently in the civet population in the wild or in captivity. It [had] a different reservoir host. It was living in bats and had passed, presumably, at a market somewhere. It had passed from a bat into one or more civets, and they became the amplifier host. https://www.npr.org/sections/goatsandsoda/2020/02/05/802938289/new-coronavirus-wont-be-the-last-outbreak-to-move-from-animal-to-human
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Dr. Daszak said that South China “has an abundance of mixed wildlife-livestock farms that house chickens, ducks, civets, porcupines, pigs, bamboo rats, altogether all in conditions that would be conducive to viral spillover and spread. These farms are often open, rustic, with access to bats which are abundant in the region,” he said. A spillover could have occurred at one of the farms and an infected human could have infected others at the Wuhan market….
Sars-cov-2 could have circulated in humans in a less efficient form, from the virus’s point of view. Then it evolved its pandemic equipment in humans.
In any case, Dr. Andersen said, although the current pandemic is the war we are now fighting, there is no question that another one could come. This one was no surprise, he pointed out. He said, “We hear that nobody could have predicted a pandemic,” he paused, “except for everyone who works in infectious diseases.” As to finding the animal that was the intermediate host, it may happen. But without viral genetic material from the very first human cases or from animals with highly similar viruses, including animals that might have been present at the Wuhan seafood market, that search is very difficult. https://www.nytimes.com/2020/03/26/science/pangolin-coronavirus.html
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4-9 The role of pangolins in the spread of Sars-CoV-2, the virus that causes Covid-19, remains unclear. A closer look at more of the Sars-CoV-2 genome, published last week by Maciej Boni at Penn State University and David Robertson at Glasgow University, together with Chinese and European colleagues, finds that human versions of the virus are more closely related to the RaTG13 horseshoe bat sample from the cave than they are to the known pangolin versions.
Rather, it is probable that somewhere much closer to Wuhan, there is another colony of bats carrying the same kind of virus. …The significance of the Yunnan cave sample is that it shows the bat virus didn’t need to recombine with viruses in other species in a market to be infectious to people. The role of the wet markets may be that other animals get infected there and produce much higher loads of virus than the bats would, amplifying the infection….
In the United Kingdom, the Health and Safety Executive “held formal investigations into more than 40 mishaps at specialist laboratories between June 2015 and July 2017, amounting to one every two to three weeks.”…I do not understand why so many people insist that an accident at either Wuhan Institute of Virology or Wuhan Center for Disease Control is so unthinkable. https://www.nationalreview.com/corner/new-study-the-human-version-of-sars-cov-2-is-closer-to-the-one-in-bats-than-the-one-in-pangolins/
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