COVID-19’s Biological Politics

[badger2]

It’s difficult to say that California is the state to watch for the Delta variant. Even though it contains the California mutation, L452R, moister Missouri is coming up from behind:

5 Jul 2021 Missouri Requests Federal COVID Aid

https://www.yahoo.com/news/missouri-requests-federal-covid-19-aid-143914640.html

’....Missouri reported 4, 271 new COVID-19 cases in the past week....265 are in intensive care....’

 

[badger2]

Missouri requests federal COVID aid as cases surge; Fourth of July travel raises concerns: Latest COVID-19 Updates

Americans enjoying newfound liberty are expected to travel and gather over the Fourth of July weekend in numbers not seen since pre-pandemic days.

www.yahoo.com

 

[badger2]

A statistic of note is for those who either received the chimpanzee adenovirus-vectored vaccine, or the BNT 162b2 vaccine. Also, “Fauci’s mutation” (D614G) is implicated:

Home - ProMED - ProMED-mail

ProMED is the largest publicly-available surveillance system conducting global reporting of infectious diseases outbreaks. Subscribe today.

promedmail.org

’....In vitro, Delta variant shows approximately an 8-fold decrease in sensitivity to vaccine-elicited antibodies compared to wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against the SARS-CoV-2 Delta variant were significantly lower in participants vaccinated with ChadOx-1 as compared to BNT 162b2 (GMT 3372 vs. 654, p under 0001). These combined epidemiological and in vitro data indicate that the dominance of the Delta variant in India has been most likely driven by a combination of evasion of neutralizing antibodies in previously infected individuals and increased virus infectivity. Whilst severe disease in fully vaccinated HCW was rare, breakthrough transmission clusters in hospitals associated with Delta are concerning and indicate that infection control measures need continue in the post-vaccination era.’

 

[badger2]

Promedmail, above, continues, with further explanations of Delta:

’Our work shows that the Delta variant virus had a fitness advantage compared to the Alpha variant in a validated 3D respiratory organoid system....In the absence of published data on the transmissibility of the Delta variant, we predict that this variant will have a transmission advantage relative to Wuhan-1 with D614G in individuals with pre-existing immunity from vaccination/natural infection as well as in settings where there is low vaccine coverage and low prior exposure. At population scale, extensive vaccinations will likely protect against moderate to severe disease and will decrease transmission of the Delta variant. However, vaccine breakthrough clusters among HCW is of concern given that hospitals frequently treat individuals who may have suboptimal immune responses to vaccination due to comorbidity. Such patients could be at risk for severe disease following infection from HCW or other staff within hospital environments. Therefore, strategies to boost vaccine responses against variants are warranted in HCW and attention to infection control procedures should be continued even in the post-vaccination era.’

 

[badger2]

Already mentioned is the Delta variant mutation L452R (California). The new variant is called Lambda, where glutamine replaces the arginine.

Lambda Variant / Peru

Lambda — the new coronavirus variant puzzling scientists due to its 'unusual mutations'

The strain was first detected in Peru and has since spread to 27 countries including the UK

www.geo.tv

’....L452Q....’

 

[badger2]

This Lambda variant is using a glutamine, and there is at least one example for the coronavirus genome where mutation to glutamine links both a porcine coronavirus and human coronavirus. This mutagenesis links to the N/T mutations of the mu-opioid receptor for fentanyl (Johnson & Johnson vaccine, previously mentioned):

‘Reversion of this site by mutagenesis of p6-hAPN to change asparagine 291 (N291) to glutamic acid (N291E) or threonine 293 to glutamine (T293Q, generated pg-hAPN/N291E and p6-hAPN/T293Q, respectively.....Transfection of BHK-21 cells....resulted in expression of hAPN in all of the cells except those transfected by empty vector....inoculation of these transfected cells resulted in infection of cells expressing....p6hAPN/T293Q....feline APN also has amino acid differences....Q293....resulted in a protein that serves as receptor for both TGEV and HCov-229E.’
(Wentworth DE, Holmes KV, Addition of a Single Glycosylation Site to hAPN Blocks Human Coronavirus-229E Receptor Activity, in Nidoviruses: Coronaviruses and Arteriviruses)

 

[badger2]

Thus returning to the Wakaleo marsupial lion connection in Australia and the COVID-infected Bronx tiger, the new Peruvian Lambda variant links to humans via the mutation to glutamine:

Uniprot Human APN, Q293
(scroll down to sequences)

UniProt

www.uniprot.org

’....Q293....’

 

[badger2]

Avian Flu Talk, 2 Jul 2021:

Mexico and Peru thread: ‘Of all the COVID variants, Mexican and Peru variants frightens me the most. Why? 10% death rate. Whatever the reason, 10% is extreme....No, it’s the new Lambda variant — hell on wheels — I spotted it....UK, US, Germany and Australia.

The case fatality rates are

USA 1.80%

Brazil 2.79 %

India 1.32%

Mexico 9.20%

Peru 9.36%....’

 

[badger2]

More statistics on the Lambda variant are found at Avian Flu Talk, Lambda thread:

COVID-19 / South Africa Omicron Variant Forum

COVID-19 South Africa Omicron Variant - Discussion Forum

www.avianflutalk.com

’Lambda Cases

U.S. 623

Germany 99

Spain 55

Israel 25

France 14

Italy 11

UK 7

Netherlands 1

 

[badger2]

The Sydney lockdown has been extended until 16 Jul 2021.

More on Lambda:

The Lambda coronavirus variant has arrived in Australia. Here's what we know so far

Some reports suggest the new Lambda variant could be fast spreading and difficult to tackle with vaccines. What is this strain and should we be worried?

www.abc.net.au

’....What this should emphasize to everyone is that we need global effort in the vaccination campaign.’

 

[badger2]

In deadly Appalachia, they don’t believe it’s real:

ICU Nurses: Their Neighbors Called COVID-19 A Hoax

Their neighbors called covid-19 a hoax. Can these ICU nurses forgive them?

ABINGDON, Va. - The hospital executives at the lectern called her a hero, and the struggle that had earned Emily Boucher that distinction showed on her face: in the pallor acquired over 12-hour shifts in the intensive care unit, the rings beneath eyes that watched almost every day as covid-19...

www.yahoo.com

’....You leave the hospital and you come out into a community that doesn’t believe that it’s real and in what it can do....’

 

[badger2]

Japan’s new Delta variant declaration extends to 22 Aug 2021. Further Lambda variant studies are warranted, because it differs from Delta by one amino acid.

8 Jul 2021 Japan Olympics

https://www.yahoo.com/news/japan-declare-state-of-emergency-tokyo-045948435.html

 

[badger2]

Yahoo | Mail, Weather, Search, Politics, News, Finance, Sports & Videos

Latest news coverage, email, free stock quotes, live scores and video are just the beginning. Discover more every day at Yahoo!

www.yahoo.com

 

[badger2]

The C-19 Lambda variant arose in Peru, which sports the highest case fatality rate in the world, approaching 10%. Here we link the SARS-CoV-2 Lambda variant back to Nadia and Azul, the Bronx Zoo tigers, via feline infectious peritonitis virus and by default, the Alice Springs marsupial lion, Wakaleo.

The Wuhan Institute of Virology is no doubt implicated in the uniqueness of glutamine, the amino acid that COVID-19 mutated to in Peruvian infections, the L452Q mutation, that sets Lambda apart from the Delta variant, which mutation is L452R.

We’ve already mentioned FIPV in Australian marsupials in this thread (Trichosurus opposum), though this report fails to give important details about how a feline virus (changes [italics]) in virulence due to mutations, and they don’t give the name of the virus they are talking about:

12 Ap 2020 The Real Reason Veterinarians Gave A Tiger A COVID-19 Test

The Real Reason Veterinarians Gave a Tiger a Covid-19 Test

It’s hard for humans in New York City to get a test for the coronavirus. So when a Bronx Zoo tiger tested positive for Covid-19, it invited some questions.

www.wired.com

‘....Cats are extremely susceptible to a type of coronavirus that impacts the GI tract, for instance. Ann Hohenhaus, a staff doctor at New York’s Animal Medical Center, estimates that as many as 80% of cats get this “extremely common” strain. It causes mild diarrhea; it doesn’t make them very sick,” Hohenhaus says.’

Whether this virus of Hohenhaus is named or not, FIPV links to the GI tract, and is a disease that is 100% fatal in cats.

 

[badger2]

As will be shown, a GI tract coronavirus, due to mutations, changes to a 100% fatal coronavirus, FIPV. First, the Wuhan lab link:

Jun 2020 Mpro / Wuhan Institute of Virology; Taussig Cancer Center, Cleveland, Ohio; Utah State University; University of Queensland, Brisbane, Australia; Shanghai; Tianjin; Academy of Military Medical Sciences, Beijing.

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors - PubMed

A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19)^1-4. Currently, there are no targeted therapeutic agents for the treatment...

pubmed.ncbi.nlm.nih.gov

From the extremely common coronavirus of Hohenhaus to the rare glutamine of SARS-CoV-2:

Dec 2020 Arizona; Greece / Mpro Non-Specific Promiscuous SARS-CoV-2 Protease Inhibitors

Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors - PubMed

Among the drug targets being investigated for SARS-CoV-2, the viral main protease (M^pro) is one of the most extensively studied. M^pro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites. It is highly conserved and has a unique substrate...

pubmed.ncbi.nlm.nih.gov

’....Mpro is a cysteine protease that cleaves the viral polyprotein at more than 11 sites. It has a unique substrate preference of glutamine at the P1 position, while no host protease is known to have such a preference. As such, the most potent Mpro inhibitors such as GC376 and N3 all contain a 2-pyrrolidone substitution at the P1 position as a mimetic of the glutamine in the substrate. Several crystal structures of Mpro in complex with inhibitors have been solved, showing that the pyrrolidone forms multiple hydrogen bonds with the His163 and Glu166 side chains and the main chain of Phe140. In addition to the classic pyrrolidone-containing Mpro inhibitors, seeral noncanonical Mpro inhibitors have also been reported with both enzymic inhibition and cellular antiviral activity. (ref. 11).’

 

[badger2]

Continuing with reference # 11 of the above study, we link the peritoneal macrophages of Australian bursh-tailed opposum, Tricholurus, recalling that rabies series of vaccines that target the powerful macrophages of the peritoneum, is given in the stomach:

It’s obvious Hohenhaus’s tiger report is referring to FECV, though leaves the most important thing, mutations, out:

Reversal of Feline Infectious Peritonitis / 3CLpro

Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor - PubMed

Coronaviruses infect animals and humans causing a wide range of diseases. The diversity of coronaviruses in many mammalian species is contributed by relatively high mutation and recombination rates during replication. This dynamic nature of coronaviruses may facilitate cross-species transmission...

pubmed.ncbi.nlm.nih.gov

’....Feline enteric coronavirus (FECV) causes inapparent or mild enteritis in cats, but a highly fatal disease, called feline infectious peritonitis (FIP), can arise through mutations of FECV to FIP virus (FIPV)....Here we evaluated therapeutic efficacy of our 3CLpro inhibitor in laboratory cats with FIP. FIP is 100% fatal once certain clinical and laboratory signs become apparent. We found that antiviral treatment led to full recovery of cats when treatment was started at a stage of disease that would be otherwise fatal if left untreated.
....
Shifts in tissue or cell tropism and resulting changes in virulence have also been reported for coronaviruses; porcine respiratory coronavirus causes mild respiratory infection in pigs and presumably arose from transmissible gastroenteritis virus (TGEV), the etiologic agent of gastroenteritis in young pigs with a high fatality, by spontaneous mutations and/or deletions in its genome.

Seemingly innocuous coronavirus infection can also be turned deadly by changing its tropism, exemplified by mutation of feline enteric coronavirus (FECV) to feline infectious peritonitis virus (FIPV). Feline infectious peritonitis virus (FIP) has intrigued researchers for half a century since its first description in the 1960s.’

 

[badger2]

The report, above, continues:
’....GC376, a dipeptidyl compound, consists of a warhead, a Gln surrogate structure in a position that corresponds to the P1 position, Leu in position 2, and a cap structure....resistant viruses against GC376 have not been selected at up to 20 passages....It may be speculated that the small size of GC376, compared to that of anbother 3CLpro inhibitor, NP152, makes it difficult for the virus to evade drug binding while retaining substrate cleavage capability....Our dipeptidyl 3CLpro inhibitor series was shown to be safe by the dosage regimen used in cats and effective at reversing the progression of FIP, even when the treatment was started at advanced clinical stages.’

 

[badger2]

Almost 12,000 Indonesian children have been infected in one week:

8 Jul 2021 Indonesia

'It's our failure': Half of Indonesia's COVID deaths in children are under the age of five

Almost 13 per cent of Indonesia's new COVID infections are being detected in children and the president of the Indonesian Pediatric Society says it is due to a failure to properly care for the country's young.

www.abc.net.au

 

[badger2]

Pfizer is on it with a booster for the Delta variant. Since the booster is designed to take care of the California mutation in Delta (L452R), it should hold against the Lambda variant (L452Q).

Pfizer and BioNTech plan to file for emergency use authorization for COVID vaccine booster as Delta variant spreads

Pfizer and BioNTech plan to share their booster data with the FDA in August and file for emergency use authorization shortly thereafter.

www.cbsnews.com

 

[badger2]

The Delta variant shows high numbers of cases in Vermont, Washington State, and New Mexico:

Fauci urges people to put politics aside to get vaccinated as 'nasty' delta variant rages

Unvaccinated individuals should put politics aside and get vaccinated to protect themselves from the highly transmissible and "nasty" delta variant Dr. Anthony Fauci said Sunday. This is a public health issue and viruses, and public health don't know the difference between a Democrat and...

www.yahoo.com