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Discussion: Comparing 2 GenBank coronavirus submittals QHD43418.1 and AVP78033.1 - 100% genome match for 78 sequences on the envelope protein? 2019-nCov
Discussion: Comparing 2 GenBank coronavirus submittals QHD43418.1 and AVP78033.1 - 100% genome match for 78 sequences on the envelope protein? 2019-nCov
from a friend of FluTrackers -
GenBank version QHD43418.1 is the submittal number from the envelope protein from the current 2019-nCov entered January 17, 2020.
GenBank version AVP78033.1 is the submittal number from the envelope protein for Bat SARS-like coronavirus January 5, 2018
"Using the BLAST tool from US National Library of Medicine, running multigenetic genome matches on these two genetic sequences, for 78 sequences, a 100% match on the envelope protein occurs."
I copied this post from another thread we have on the site. This is the research paper related to AVP78033.1. We have been looking at this interesting study.
The China scientific community has the genetic material. In this 2018 study they used mammals, and proposed further such studies.
SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause diseasein suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.
ZXC21 and ZC45 were the 2 closest to nCoV , until we saw RaTG13, which is much closer.
The envelope Protein is pretty short, is a match common in coronaviruses ? I'll check ,
but wouldn't be surprised. But how many nucleotide-differences ?
MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVS LVKPSFYVYSRVKNLNSSRVPDLLV
mysfvseetg tlivnsvllf lafvvfllvt lailtalrlc ayccnivnvs lvkpsfyvys rvknlnssrv pdllv
for the envelope protein these 3 viruses are clearly separated from the others at genbank
and they are much more similar than in total (recombination ?)
I copied this post from another thread we have on the site. This is the research paper related to AVP78033.1. We have been looking at this interesting study.
The China scientific community has the genetic material. In this 2018 study they used mammals, and proposed further such studies.
SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause diseasein suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.
From paper:
"Briefly, each intestinal sample (approximately 0.1 g) was homogenized in a glass grinder with ten volumes of SM buffer (50 mM Tris, 10 mM MgSO4, 0.1 M NaCl, pH 7.5). The homogenate was centrifuged at 12,000 g for 10 min at 4 ?C, but only the supernatant was used"
Paper said this was done at safety level BL-3. USDA standards say:
These devices release considerable aerosols during operation. For maximum protection to the operator during blending or mixing of infectious materials, the following practices should be observed."
...
"5. Glass blender bowls are undesirable for use with infectious materials because of potential breakage. If used, they should be covered with a polypropylene jar to prevent dispersal of glass in case of breakage."
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
I am not sure what they are calling a grinder and what is a blender. a grinder I would expect to be two ground glass surfaces, as you might find on a reagent bottle or drinks decanter's stopper. a blender would be rotating blades as in a liquidiser. In either event nothing would get into a BSL3 lab to perform that function that was not designed to perform it to a BSL3 safety level.
Chinese virologist claims coronavirus derived from 'Zhoushan bat virus'
...
By Keoni Everington, Taiwan News, Staff Writer
2020/08/06 15:02
...
Yan then claimed that she and her team have produced a scientific report that shows the origin of COVID-19 is the "PLA-owned Zhoushan bat coronavirus." She plans to release the report in the near future...
The virologist said Wuhan Institute of Virology (WIV) scientist Shi Zhengli, also known as "Bat Woman," deliberately posted a paper on Feb. 3 to draw attention to a coronavirus strain identified as RaTG13...Yan claims this was an orchestrated attempt to throw investigators off the Zhoushan bat virus strains...
When asked if the Zhoushan strain is in the PLA's catalog of viruses and if COVID-19 resulted from gain-of-function or other manipulations in the WIV, Yan said the virus could have come from any one of the PLA's numerous labs, such as in Hong Kong, Shanghai, or Harbin.
...
Yan said that when she worked on vaccines and virus function testing in Chinese labs and carried out virus replication, "We never made just one type of virus we make a lot of strains of virus and stocked them and then later we would test their function, test their characteristics."
Yan emphasized that COVID-19 is not from nature, but rather it is "lab-modified."
...
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
The E protein is the smallest of the structural proteins (about 75aa) and seems to perform multiple function in various configurations. It can form monomers, dimers, trimers and pentamers which must put considerable biological constraints on its ability to change sequence without impacting fitness. In addition the central section is hydrophobic with hydrophilic terminal domains. Its terminal domains are involved in anchoring it to the ER-Golgi complex and it is critical in correct viral assembly. It also seems to have a roll in aligning and curving the M protein, which makes the viral capsid, to give the virus its spherical shape. When knocked out viruses can not escape the host cell as they are held in phospholipid bi-layer by an umbilical that E is assumed to cut. The homopentameric form is an ion pump analogous the that created by the M2 protein in influenza.
Kuru experiments triggered the emergence of pathogenic SIVmac
"In this context, several questions remain to be addressed to understand the mechanism(s) of emergence of pathogenic viruses following cross-species transmission: Why is SIVmac239 highly pathogenic in Rh? What were the circumstances of the emergence of this pathogenic virus? What are the requirements for a cross-transmitted virus to become pathogenic in a new host?
The answers to these questions are not easy to obtain because the emergence of pathogenic SIVmac occurred in the 1970s and it was not until the mid 1980s that the virus was discovered, by which point it had already reached its full pathogenic potential. However, we have collected and reassembled data that strongly suggest that highly invasive experimental manipulations, rather than casual contact, inadvertently gave rise to the highly pathogenic SIVmacisolate, used in AIDS research from the 1980s to the present time."
Why did they adapt a SARS-like bat virus to rats and in such a way to train it to infect so many different tissue types?
Intracerebral Inoculation of Mice: Fate of the Inoculum
"IT has long been known that a virus may become widely disseminated following intracerebral inoculation into an experimental animal."
I think that somehow this adapted virus spread among lab animals, evolving silently until ultimately infecting a human.
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
A new coronavirus associated with human respiratory disease in China
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei, Ming-Li Yuan, Yu-Ling Zhang, Fa-Hui Dai, Yi Liu, Qi-Min Wang, Jiao-Jiao Zheng, Lin Xu, Edward C. Holmes & Yong-Zhen Zhang
...
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)
...
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
Emily
I had a quick read through the SL-CoV paper you linked to and in answer to you question
"Why did they adapt a SARS-like bat virus to rats and in such a way to train it to infect so many different tissue types?"
I do not think they did. They found they could infect a Vero E6 cell which can be made to express a human ACE2 receptor but there are many other steps beyond cell entry before the host cell can start shedding infectious virions and the Vero cells lacked the ability to perform one or more of them so no infectious virus was produced. They then moved to rats as their animal model and the rats did produce infectious virus. However rats, and mice do not make very good models of human infection as the virus behaves quite differently, in terms of its pathology, and causes death by infecting the brain, also they have reduced (not increased) body temperature and do not sneeze or cough so make poor subjects for respiratory transmission. The virus was not modified get it to display these tissue tropisms it is just the effect it has on rats. In us the SARS-Cov-2 transmission route is currently thought to be first URT followed by movement to the LRT and that in most patients it is mainly localised here without systemic spread. There is some evidence that in some cases it does get into other areas if this is the case then it may be the cause of some of the late stage sequelae and/or apparent reinfection/recurrences.
I do not know enough about retroviruses to comment on SIV but it was a long time ago so lab procedures and safety protocols are entirely different.
The link is to lab suppliers range of homogenisers, with pictures, so you can see what they are. https://www.thomassci.com/scientific...ue-Homogenizer
This is a detailed look inside a BSL4 facility showing the level of containment required.
Daniel Griffin provides a clinical report on COVID-19 and the convalescent plasma trial, then we answer listener questions about the Russian vaccine, choir practice, face masks (wear them!), Mina testing, transmission, and much more.
Edit -Afterthought
Your earlier question made me think about what effect a blender - in the kitchen blender sense - would have on a virus. If you put water on the blender it just flows around the blades unharmed, if you put peas in it homogenises them but what about the virions? Would they flow around the blades and if so how could you redesign the blender.
Grain of salt - 3x10-4 meters
Human eye resolution - 5x10-5 HeLa cell - 5x10-7
Virion - 1x10-7
H2O - 2x10-10
Last edited by JJackson; August 30, 2020, 08:00 AM.
This is a well written paper but it covers a lot of ground with some historical studies described so I want to clear up a couple of things.
The research was done at BSL 3, not BSL 4. BSL 4 would have been better, but the BSL 4 lab was not completed when this work was done.
"They found they could infect a Vero E6 cell which can be made to express a human ACE2 receptor”
They could not infect Vero cells in this study with the two new SL-CoVs from Zhoushan (ZXC21 and ZC45). You were reading the historical section about work done in 2013: “Notably, during longitudinal surveillance of the Rhinolophus sinicus colony in the Yunnan Province of China over the past few years, a Chinese research team successfully isolated a live SL-CoV sample from Vero E6 cells that were incubated in the bat feces in 2013” The bats in this paper’s research were collected in 2015-2017.
The adaptation of the virus to rats was done by forcing the liquefied bat intestines into the rat pups brains. Totally unnatural and just as dangerous as in Gajuseck’s day in terms of the biology.
I don’t buy the paper’s justification for doing this work considering the endangering of the human population and the animal suffering involved. I think the contrived, invasive brain inoculation was done for the purpose of job security: “These findings strongly suggest the need for continued surveillance of viruses originating from wild animals and promote further research to study the possibility of cross-species transmission of these viruses.”
Interesting, too, that there was only one American researcher involved in this study and he did another study as the sole American with the PLA while affiliated with UNC Chapel Hill, (where gain-function research was done in the past and where a researcher was just bitten by a SARS-Cov-2 infected mouse). Seems the same old publicly-funded, self-justifying, crowd reassuring us that all is well.
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
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