CoVid/CCP Virus Phylogeny: 01/24/2021

This week’s update.

Let’s also note the preprint released by Wells et al. regarding the evolutionary history of ACE2 usage.

As evident in the Nexstrain phyologeny, CoVid-2/CCP (CoV-2) is a rather stable virus – unlike other zoonotics that have jumped species.

Wells examines possible genealogical histories for CoV-2 sequences. They demonstrate the lineage containing CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. They propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous.

This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

Importantly, genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines.

This finding of overlapping Lineage 1 and Lineage 5 viruses in geographic space is inconsistent with the previously observed pattern of biogeography for sarbecoviruses. SARS-CoV-2 was isolated first frompeople in Hubei Province and one of the pangolin viruses was isolated from an animal sampled in Guangdong, neither of which are Lineage 1 provinces. However, the true geographic origins of these viruses are unknown as it is possible they were anthropogenically transported to the regions in which they were detected. For example, the Malayan pangolin (Manis javanica) has a natural range that reaches southwestern China (Yunnan Province) at its northernmost edge and extends further south into Myanmar, Lao PDR, Thailand, and Vietnam. So, if they were naturally infected (as opposed to infection via wildlife trade), the infection was potentially not acquired from Guangdong Province. Similarly, SARS117 CoV-2 cannot be guaranteed to have emerged from bats in Hubei Province, as humans are highly mobile and the exact spillover event was not observed. If the clade containing SARS-CoV-2 and its close relatives is indeed endemic in animals in Yunnan and the nearby Southeast Asian regions as suggested by the presence of RaTG13, RmYN02, and the natural range of the Malayan pangolin, whatever mechanism is facilitating the biogeographical concordance of Lineages 1, 2 and 3 within China appears to no longer apply for the biogeography of Lineage 5, since they all appear to overlap in and around Yunnan Province.

Further, investigations into determinants of pathogenicity and transmission for CoVs and the genomic signatures of such features will be an important step towards the prediction of viruses with spillover potential, and distinguishing those with pandemic potential.

Finally, these findings reiterate the importance of recombination as a driver of spillover and emergence, particularly in the spike gene. If SARS-CoV-1 gained the ability to use hACE2 through recombination, other non-ACE2-using viruses could become human health threats through recombination as well. We know that recombination occurs much more frequently than just this single event with SARS-CoV-1, as the RdRp phylogeny does not mirror host phylogeny and the RBD tree has significantly different topology across all geographic lineages. In addition the bat virus RmYN02 appears to be recombinant in the opposite direction (Lineage 5 backbone with Lineage 1 RBD) [36], again supporting the hypothesis that recombination occurs between these lineages. Our analyses support two hypotheses: first, that sarbecoviruses frequently undergo recombination in this region of the genome, resulting in this pattern, and second, that sarbecoviruses are commonly shared amongst multiple host species, resulting in a lack of concordance with host species phylogeny and a reasonable opportunity for coinfection and recombination. Bats within the family Rhinolophidae have also repeatedly shown evidence of introgression between species [67–72], supporting the hypothesis that many species in this family have close contact with one another which may facilitate viral host switching. Given that we have shown that ACE2-using viruses are co-occurring with a large diversity of non-ACE2 using viruses in Yunnan available under aCC-BY-NC-ND 4.0 International license. Province and in a similar host landscape, recombination poses a significant threat to the emergence of novel sarbecoviruses.

Reference

Wells, H. L., Letko, M., Lasso, G., Ssebide, B., Nziza, J., Byarugaba, D. K., … Anthony, S. J. (2020). The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. BioRxiv.Org: The Preprint Server for Biology. doi:10.1101/2020.07.07.190546

Corrupt Joe’s Adviser Concedes CoVid Was a Containment Breach

From ZeroHedge:

“There’s no irrefutable evidence,” said the Kansas-born Metzl, a senior Atlantic Council fellow who was appointed to the WHO expert advisory committee on human genome editing in 2019. “There’s just more evidence and as more evidence arrives, the case for accidental lab leak, in my view, increases.”

More from Metzl’s interview with the Sun (emphasis ours):

What about the original theory that this all started in a wet market in Wuhan?

That was a lie. And the Chinese government knew very early on that that was a lie. And so in the face of overwhelming evidence in May of last year, the Chinese government shifted its position.

Do you get the idea of scary viruses being created in a lab may seem a little sci-fi?

It may feel like sci-fi to people but what’s happening is sci. There is a field of study called “gain of function” research, which is highly controversial in which some scientists amplify the virility of viruses. We know that the Wuhan Institute of Virology was involved in gain of function research on bat coronaviruses.

Is it because this specifically started in China that we still don’t know how COVID-19 started?

If there had been an outbreak in Congo or some country in Africa and that country, in the earliest days of the pandemic, prevented World Health Organization investigators from going onto the scene of the outbreak, for nearly a month, the world would have gone berserk.

Will a change of the U.S. administration help find an answer?

Biden will be tougher on China than President Trump because President Biden is very smart and strategic and he understands that American power and American strength doesn’t rest on bluster, it rests on principles, it rests on partnerships, and alliances and accountability. And the Trump administration unfortunately gave China a pass by over politicizing the question of the origin of the virus by alienating America’s partners and allies.

*  *  *

All of this begs a simple question; if a senior Atlantic Council fellow who operated at high levels of government under Democratic presidents is suddenly ‘coming out’ with the Wuhan lab leak theory, three days after Biden’s inauguration, is the official narrative about to change?

Reference:

https://www.zerohedge.com/covid-19/it-was-all-lie-biden-linked-who-adviser-says-covid-19-likely-leaked-wuhan-lab

WTI Inventory Up

USEIA (January 22, 2021):

U.S. crude oil refinery inputs averaged 14.8 million barrels per day during the week ending January 15, 2021 which was 110,000 barrels per day more than the previous week’s average. Refineries operated at 82.5% of their operable capacity last week. Gasoline production increased last week, averaging 8.9 million barrels per day. Distillate fuel production decreased last week, averaging 4.5 million barrels per day.

U.S. crude oil imports averaged 6.0 million barrels per day last week, down by 194,000 barrels per day from the previous week. Over the past four weeks, crude oil imports averaged about 5.7 million barrels per day, 11.8% less than the same four-week period last year. Total motor gasoline imports (including both finished gasoline and gasoline blending components) last week averaged 504,000 barrels per day, and distillate fuel imports averaged 460,000 barrels per day.

U.S. commercial crude oil inventories (excluding those in the Strategic Petroleum Reserve) increased by 4.4 million barrels from the previous week. At 486.6 million barrels, U.S. crude oil inventories are about 9% above the five year average for this time of year. Total motor gasoline inventories decreased by 0.3 million barrels last week and are about 3% below the five year average for this time of year. Finished gasoline inventories increased while blending components inventories decreased last week. Distillate fuel inventories increased by 0.5 million barrels last week and are about 8% above the five year average for this time of year. Propane/propylene inventories decreased by 6.2 million barrels last week and are about 11% below the five year average for this time of year. Total commercial petroleum inventories decreased by 0.7 million barrels last week.

Click to access wpsrsummary.pdf

“We know that no one ever seizes power with the intention of relinquishing it.” George Orwell, “1984”

Franke Miele, Real Clear Politics:

In Nancy Pelosi’s “Twenty Twenty-One,” members of the Democratic Party engage in the Two Hours Hate against Donald Trump, who is supposed to be the enemy of the people, but may actually just be a fabricated symbol to distract the people from their real enemy — Big Tech.

Two hours of hate — er, debate — was held in the House of Representatives last Wednesday for the avowed purpose of removing a president of the United States. That’s all it took. Two hours. That should tell you everything you need to know about the state of democracy in our country.

More time is routinely spent on picking wallpaper. But let’s face it, most families wouldn’t trust Congress to pick out wallpaper for their living room, so why should we trust these self-appointed moral arbiters to pick our president?

Well, we don’t. Not all of us.

And for those with a taste for irony, consider this one: Jeff Bezos challenges mail-in ballots in a union election. You know, the high likely of election fraud from mail-in ballots.

OK for presidential elections.

But “unfair” for a union election.

Some things are just too funny.

https://www.realclearpolitics.com/articles/2021/01/18/big_tech_big_brother_and_the_end_of_free_speech__145050.html

https://www.wsj.com/articles/amazon-seeks-to-postpone-alabama-unionization-vote-11611339250

CoVid Vaccination Status

A medical worker vaccinates a man against the coronavirus disease in Israel

Nature published a status report covering the in-flight vaccination programs (Mallapaty, 2021)), focusing on Israel and the United Arab Emirates programs.

Israel reports preliminary figures suggesting that people vaccinated there were about one-third less likely to test positive for SARS-CoV-2 two weeks after the first injection than people who had not received a shot. More than 75% of older people have been vaccinated and Israel expects to see hospitalization rates fall in this demographic in the weeks to come.

The United Kingdom and Norway targeted their vaccination programmes at high-risk groups. Britain vaccinated more than 4 million people, mostly health-care workers and older people, including those living in care homes; Norway has immunized all residents living in nursing homes, some 40,000 people.

Clinical trials of the Pfizer–BioNTech vaccine show it to be around 90% effective at preventing COVID-19, and the preliminary data suggest it can also provide some protection from infection.

Reference:

Mallapaty, S. (2021). Are COVID vaccination programmes working? Scientists seek first clues. Nature. doi:10.1038/d41586-021-00140-w

4th Anniversary of Democrat Inauguration Riots

Witnesses describe destruction during Inauguration Day riots | WTOP

Four years ago, the violent Democrat assault on Washington was met by force.

The Democrat assaults were joined by an FBI assault on the then-newly elected president and the persecution of his staff.

Today, the violent and corrupt Democrat assault of 4 years ago is joined by tech oligarchs. This time, the target isn’t an elected president.

This time, the target American liberty.

Christopher Bedford in The Federalist:

The decision by the most powerful companies in history to conspire against social media competitor Parler — without even an attempt to provide evidence of wrongdoing — was a step beyond any previously taken. By denying the No. 1-downloaded app in the country access to Amazon Web Services, the host it had built its existence on, the rulers of Silicon Valley destroyed the upstart.

In addition, with companies like online credit-card processor Stripe joining in, the ability of other “unacceptable” businesses and causes to so much as accept payments and donations is now on notice.

This isn’t surface level: This is the guts of capitalism, and it’s just begun. Credit card companies, banks — they’re moving into the innards of our freedoms and it will impact your business, newspaper, and yes, eventually even your church group if you believe the wrong Christian tenet.

In a free society, if you see an opportunity or don’t like what’s already out there, you can try to make your own. You can accept payments for services, turn a profit, hire, expand. These are both fundamental aspects of the American dream. In the span of one week they were shattered, not by government, but by private and unelected businessmen.

It’s a moment in Big Business’s campaign unlike any before: It’s the sacking of the American Dream. 

https://thefederalist.com/2021/01/22/the-fracturing-of-america-a-weak-government-complicit-media-and-radical-silicon-valley-might-have-finally-set-it-all-off/

Cooler Canada

The anthropogenic hypothesis holds the rising concentration of greenhouse gases is due to human activities alone with no contribution from natural sources. Natural sources can be the result of temperature change from non-greenhouse gas drivers and from natural sources (e.g., ocean, landmass).

Atmospheric GHG has been growing steadily with no material change in slope for more than 60 years. Over that period, climate temperature has varied – cooling in the late 1970s, rising in the 1990s, and then slowly as the solar Modern Minimum approached its end.

Satellite radiometers are the most consistent and most reliable temperature record and data only goes back some 40 years. Here is the satellite record as reported by the University of Alabama.

Simulations generated by IPCC’s CMIP5 is the basis for the UN agency’s claims of a climate crisis. CMIP5 tends to run hotter than actual data.

In the top image of this post, Dr. Roy Spencer (University of Alabama, Hunstville) compares 108 CMIP5 simulations against surface temperatures in Canada recorded over 30 years over latitudes encompassing 51N to 70N.

For observations, Spencer used the same lat/lon bounds and the CRUTem5 dataset, which is heavily relied upon by the UN IPCC and world governments. All data were downloaded from the KNMI Climate Explorer.

Spencer:

We see that Canada has been warming at only 50% the rate of the average of the CMIP5 models; the linear trends are +0.23 C/decade and +0.49 C/decade, respectively. Note that in 7 of the last 8 years, the observations have been below the average of the models.

This finding is consistent with other backtests reported in the peer-reviewed literature.

Simply put, IPCC forecast models “run hot”.

I suspect one of the reasons is that IPCC models assume a much higher ECS than consistent with the current literature. This is not a recent problem:

In the 25 years of IPCC’s First to Fifth Assessment Reports [1–5], the atmosphere has warmed at half the rate predicted in FAR. (Moncton, 2015)

Several researchers observe natural variation (i.e., not caused by GHG) to explain the CMIP model problem, resulting in the poor model performance evident in this 2017 analysis and presentation to Congress:

Modsvsobs

Christy explains the problem as due to unduly sensitive estimates of climate sensitivity to GHG.

References

Canada is warming at only 1/2 the rate of climate model simulations « Roy Spencer, PhD. (n.d.). Retrieved January 22, 2021, from Drroyspencer.com website: http://www.drroyspencer.com/2021/01/canada-is-warming-at-only-1-2-the-rate-of-climate-model-simulations/

Christy (2017) https://science.house.gov/imo/media/doc/Christy%20Testimony_1.pdf?1

Monckton, C., Soon, W. W.-H., Legates, D. R., & Briggs, W. M. (2015). Why models run hot: results from an irreducibly simple climate model. Science Bulletin, 60(1), 122–135.