COVID-19’s Biological Politics

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Delta is surging in South Carolina in this hour-old report:

Code Red, Charleston

As COVID delta variant cases surge, MUSC expert says Charleston has ‘code red situation’

“It’s worse than I thought,” the leader of MUSC’s Epidemiology Intelligence Project said this week. “I worry that people aren’t realizing this is happening.”

news.yahoo.com

’ “ I worry that people aren’t realizing this is happening.” ‘

 

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Congress wants to subpoena Daszak, so compilation of military connections to Wuhan lab are up for scrutiny:

2 Aug 2021 COVId Did Leak from Wuhan Lab

Covid did leak from Wuhan lab, say Republicans who want to question British virus hunter

Republicans in Congress want to subpoena a British-born scientist as part of an investigation in which they have concluded Covid-19 leaked from a Wuhan laboratory.

news.yahoo.com

 

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From Flutrackers today, artificial intelligence is being now being used:

AI / ECG

Rapid Exclusion of COVID Infection With the Artificial Intelligence Electrocardiogram - PubMed

Infection with SARS-CoV-2 results in electrocardiographic changes that permit the artificial intelligence-enhanced ECG to be used as a rapid screening test with a high negative predictive value (99.2%). This may permit the development of electrocardiography-based tools to rapidly screen...

pubmed.ncbi.nlm.nih.gov

’....Infection with SARS-CoV-2 results in electrocardiographic changes that permit the artificial intelligence-enhanced ECG to be used as a rapid screening test.’

 

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We will list the ACE2 binding mutations in comparison with other coronavirus genomes. For the HIV dynamics connection, the reader can scroll down to the paragraphs under “Mutant Frequency Under neutral Drift is Liklely to Lead to Escape from Single and Double Antibody Combinations.”

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these...

journals.plos.org

1.) Y453F
2.) Y508H
3.) N440K
4.) E484K
5.) Q493K
6.) R346S
7.) N439K
8.) E484Q
9.) L452R
10.) K444Q
11.) F490S
12.) S494P
13.) R346K
14.) N450D
15.) V483A
16.) K444T
17.) V445A
18.) E484A
19.) Q493R
20.) F490L
21.) K444N
22.) A475V
23.) V445E
24.) L455F
25.) G446V
26.) V445G
27.) E484D
28.) F486V
29.) G485D
30.) F456V
31.) L455R
....
First, what is the evolutionary cost of harboring nAb-evading RBD mutations? Second, given the evolutionary cost, how likely is it that SARS-CoV-2 patients will harbor viruses with pre-existing nAb-evvading RBD mutations as their dominant viral sequence? Third, how rapidly will such nAb-evading RBD mutations become fixed in the population once nAb vaccines and therapies are widely deployed?’

 

[Rigby5]

We will list the ACE2 binding mutations in comparison with other coronavirus genomes. For the HIV dynamics connection, the reader can scroll down to the paragraphs under “Mutant Frequency Under neutral Drift is Liklely to Lead to Escape from Single and Double Antibody Combinations.”

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these...

journals.plos.org

1.) Y453F
2.) Y508H
3.) N440K
4.) E484K
5.) Q493K
6.) R346S
7.) N439K
8.) E484Q
9.) L452R
10.) K444Q
11.) F490S
12.) S494P
13.) R346K
14.) N450D
15.) V483A
16.) K444T
17.) V445A
18.) E484A
19.) Q493R
20.) F490L
21.) K444N
22.) A475V
23.) V445E
24.) L455F
25.) G446V
26.) V445G
27.) E484D
28.) F486V
29.) G485D
30.) F456V
31.) L455R
....
First, what is the evolutionary cost of harboring nAb-evading RBD mutations? Second, given the evolutionary cost, how likely is it that SARS-CoV-2 patients will harbor viruses with pre-existing nAb-evvading RBD mutations as their dominant viral sequence? Third, how rapidly will such nAb-evading RBD mutations become fixed in the population once nAb vaccines and therapies are widely deployed?’

Why would ACE2 receptors want to accept any spike protein except the one used by exosomes?

If ACE2 receptors are so flexible, then how flexible will our immune system be after being sensitized to attack one particular spike protein?

 

[badger2]

We now link the Chinese large spotted civet to Yunnan, and a liver fluke of civets to the first reported case of cholangiocarcinoma in a COVID-19 patient in Illinois. There is also a thrombotic link:

Illinois: COVID-19 / Thrombotic Microangiopathy / Cholangiocarcinoma / Gemcitabine

Thrombotic Microangiopathy in a Patient With COVID-19 Infection and Metastatic Cholangiocarcinoma - PubMed

This is a case report of a 63-year-old African American female with a past medical history most significant for metastatic cholangiocarcinoma that presented for evaluation of persistent shortness of breath. Initial workup was remarkable for refractory anemia, moderate schistocytes on peripheral...

pubmed.ncbi.nlm.nih.gov

Aug 2021 Thailand: Opisthorchis viverrini as Risk Factor for Cholangiocarcinoma

Opisthorchis viverrini Infection Induces Metabolic and Fecal Microbial Disturbances in Association with Liver and Kidney Pathologies in Hamsters - PubMed

<span><i>Opisthorchis viverrini</i> (Ov) infection causes hepatobiliary diseases and is a major risk factor for cholangiocarcinoma. While several omics approaches have been employed to understand the pathogenesis of opisthorchiasis, effects of Ov infection on the host systemic metabolism and...

pubmed.ncbi.nlm.nih.gov

2012: Opisthorchis: Unarguable Cancer Risk Factor

The tumorigenic liver fluke Opisthorchis viverrini--multiple pathways to cancer - PubMed

Liver fluke infection caused by Opisthorchis viverrini is a major public health problem in Thailand and adjacent countries. In addition to infection-associated morbidity, infection with O. viverrini and the related Clonorchis sinensis are unarguable risk factors for cholangiocarcinoma (CAA...

pubmed.ncbi.nlm.nih.gov

Yunnan: Viverra megaspila Large Spotted Civet (Map)

Large-spotted civet - Wikipedia

en.wikipedia.org

Therefore, the COVID-19 cholangiocarcinoma case in Illinois links to a parasite of the Yunnan Large Spotted Civet, Viverra megaspila.

 

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SARS-CoV-2’s closest relative came from the Mojiang copper mine, Yunnan. We have already mentioned in this thread the Mengla filovirus (ebola-Marburg family) from Rousettus fruit bat in Yunnan. The second-most common cancer in this Rousettus bat was cholangiocarcinoma:

Rousettus aegypticus Iron Storage Disease / Cholangiocarcinoma

A RETROSPECTIVE STUDY OF THE LESIONS ASSOCIATED WITH IRON STORAGE DISEASE IN CAPTIVE EGYPTIAN FRUIT BATS (ROUSETTUS AEGYPTIACUS) - PubMed

Egyptian fruit bats (Rousettus aegyptiacus) are one of many species within zoologic collections that frequently develop iron storage disease. The goals of this retrospective multi-institutional study were to determine the tissue distribution of iron storage in captive adult Egyptian fruit bats...

pubmed.ncbi.nlm.nih.gov

 

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Why would ACE2 receptors want to accept any spike protein except the one used by exosomes?

If ACE2 receptors are so flexible, then how flexible will our immune system be after being sensitized to attack one particular spike protein?

There are clues to sensitivity in the cited article.

 

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France is now rebelling against vaccine mandates, as seen in this video:

 

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Because of Delta, chances of achieving herd immunity are few:

Delta Has Wrecked Chances of Herd Immunity

https://www.telegraph.co.uk/news/2021/08/10/delta-variant-has-wrecked-hopes-of-herd-immunity-warn-scientists/

 

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In this report from Iran, a chart shows number of cases per 100,000 population in different countries:

11 Aug 2021 Iran’s Fifth Wave at Muharram

Iranians gather in packed Muharram ceremonies amid fifth wave

Videos of observers disregarding health protocols add to public anger as Delta COVID variant kills hundreds a day.

www.aljazeera.com

 

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In both posts #670 and 671, the URLs are correctly transcribed.

 

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The earliest SARS-CoV-2 was in humans was early November, 2019.

Jul 2020 SARS-CoV-2 ORF8 Deletions

Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 - PubMed

To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence...

pubmed.ncbi.nlm.nih.gov

’....significantly increased replicative fitness....the lack of ORF8 mays assist host immune evasion....The emergence of ORF8 deletion variants may also impact vaccination strategies....The dated tree demonstrates the intra- and intercontinental dissemination of wild-type (WT) viruses, whereas all del.382 viruses from Singapore and Taiwan are closely related (99.9%)....del.382 viruses emerged between the middle of Dec 2019 and early Jan 2020. The introductions of SARS-CoV-2 into humans occurred early Nov 2019, suggesting that the viruses were present in humans approximately one month before the outbreak was detected.’

 

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Post #637 is from an Obama-Biden funded facility, DUKE-NUS. As we compile a list of military connections to Wuhan, it was Bottlecap who first pointed to the funding by these two stupid and arrogant psychopaths:

Post #27

Covid 19 news 9.14.2020. NY Post reports virus made in lab

This Virologist will be on FOX tonight... Looking forward to hear what it is she has to say.. I know MD's on both sides of this fence and I want to hear where the evidence is and what she has. She may be on fox but she has to stay hidden or die

www.usmessageboard.com

 

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Post #673 (rather) is an Obama-Biden funded facility. Singapore linked to Taiwan in the 99.9% identity of the viral strains that were in place in Homo sapiens in Nov 2019, though there is questioning due as to the contribution of each of these variants for their deletions in SARS-CoV-2 ORFs. Delta is not only not the new kid on the block, the Alpha variant B.1.1.7 is just as interresting.

 

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Here is a webpage of current variants to assist the reader in analyzing mutations as they arise, in conjunction with the eight coronavirus spike sequences shown in post #518 of this thread:

SARS-CoV-2 Variants of Concern as of 5 Aug 2021

SARS-CoV-2 variants of concern as of 15 June 2023

ECDC regularly assesses new evidence on variants detected through epidemic intelligence, rules-based genomic variant screening or other scientific sources.

www.ecdc.europa.eu

 

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There is concern by some recipients of thew J&J vaccine as to efficacy. J&J uses human adenovirus, and AstraZeneca uses chimp adenovirus:

Delta Sparks Fear For J&J Recipients

'Naked in the world of COVID': Some J&J vaccine recipients feel unprotected against delta and want mRNA shots

Some who got the Johnson & Johnson COVID-19 vaccine are worried they're not protected against the delta variant and want a Pfizer or Moderna shot.

www.yahoo.com

’....suggested it was less effective against the Delta variant....The AstraZeneca vaccine is a viral vector vaccine, the same technology used by the J&J vaccine.’

Already posted in message #554, this viral-vector technology is the same one funded by the Obama-Biden administration, and links North Carolina To Singapore:

Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted? - PubMed

Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of HAdV 4 and 7 vaccine.

pubmed.ncbi.nlm.nih.gov

’....Nicholas School of the Environment, Durham, North Carolina; Emerging Infectious Disease Programme, Duke-NUS Medical School, Singapore....from 2012 to 2018....’

 

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Linking to J&J and AstraZeneca adenovirus-vectored vaccines in more comprehensively listing military connections, two references from the report in post #677:

Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted? - PubMed

Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of HAdV 4 and 7 vaccine.

pubmed.ncbi.nlm.nih.gov

’....reference #6: Adenovirus 4 and 7 Vaccine: New Body Armor for U.S. Marine Corps Officer Trainees (2019)....Reference #10: Human Adenovirus Type 7 Outbreak in Police Training Center, Malaysia, 2011.’

Earlier in this thread (post #555), we linked 2019 also to the discovery of an ebola-related virus from China: ‘A New Disturbing Ebola Related Virus from Bats in China: ‘ 8 Jan 2019....a professor at the Duke-NUS Medical School in Singapore....George Mason University, Manassas, Virginia....American University, Washington, D.C.’

 

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The first adenovirus ever isolated from a North American bat was the Jan 2017 report from Kentucky:

Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses - PubMed

Although many adenoviruses are host specific and likely codiverged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic diversity of...

pubmed.ncbi.nlm.nih.gov

 

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Speculation is that this report from India is correct: the earliest SARS-CoV-2 ancestor was from a pig rather than a bat.

Dec 2020 India / Zoonotic Evolution

Zoonotic evolution and implications of microbiome in viral transmission and infection - PubMed

The outbreak and spread of new strains of coronavirus (SARS-CoV-2) remain a global threat with increasing cases in affected countries. The evolutionary tree of SARS-CoV-2 revealed that Porcine Reproductive and Respiratory Syndrome virus 2, which belongs to the Beta arterivirus genus from the...

pubmed.ncbi.nlm.nih.gov

’....The evolutionary tree of SARS-CoV-2 revealed that Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2), which belongs to the beta Arterivirus genus from the Arteriviridae family is possibly the most ancient ancestral origin of SARS-CoV-2 and other Coronaviridae.’

Minnesota now being the U.S. hotspot for the Delta variant, links to Minnesota PRRSV:

Ap 1992 University of Minnesota Department of Veterinary Diagnostic Medicine

Isolation of swine infertility and respiratory syndrome virus (isolate ATCC VR-2332) in North America and experimental reproduction of the disease in gnotobiotic pigs - PubMed

A recent epizootic of swine infertility and respiratory syndrome (SIRS) in a Minnesota swine herd was investigated. Examination of a sow, neonatal piglets, and stillborn fetuses obtained during the epizootic from the affected herd revealed interstitial pneumonitis, lymphomononuclear...

pubmed.ncbi.nlm.nih.gov

’A syndrome of reproductive failure and respiratory disease of unknown etiology was first recognized in 1987-1988 in swine herds in North Carolina, Iowa, and Minnesota. A similar syndrome has been recognized in Germany, The Netherlands, England, Belgium, and Spain.’

1989 Indiana: PRRSV Outbreak

SAGE Journals: Your gateway to world-class research journals

Subscription and open access journals from SAGE Publishing, the world's leading independent academic publisher.

journals.sagepub.com

’....An outbreak of Porcine Reproductive and Respiratory Syndrome (PRRS), formerly called swine infertility and reproductive syndrome or mystery swine disease, occurred on 18 farms in Wabash County, Indiana, in spring of 1989. An extensive diagnostic investigation conducted at Purdue Animal Disease Diagnostic Laboratory and diagnostic testing at a number of other laboratories did not result in a conclusive etiologic diagnosis.’

’Retrospective serological studies indicate that PRRSV first appeared in North America in 1979, in Asia in 1985, in Europe in 1987, and the virus was subsequently disseminated to swine populations throughout the world. PRRSV is most similar genetically to LDV (lactate dehydrogenase-elevating virus).’
(MacLachlan NJ, et al, Arterivirus Pathogenesis and Immune Response, Ch. 21, Nidoviruses, ASM Press, Washington, D.C. 2008)