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House votes to repeal Iraq War authorization
The House voted Thursday to repeal the 2002 legal authorization for the war in Iraq, marking what the bill's backers hope is a first step to curbing the President's expansive war powers enacted after the September 11, 2001, terrorist attacks.
The House voted 268-161 to repeal the authorization, with 49 Republicans joining Democrats to back the measure authorized by Rep. Barbara Lee, a California Democrat. One Democrat voted against the bill.
The vote occurred after the White House said this week that it supported repealing the 2002 war authorization -- the first time the Executive Branch has explicitly backed the effort -- saying that the legal authority in Iraq was no longer necessary.The Senate is taking up similar legislation in the Senate Foreign Relations Committee next week, and Senate Majority Leader Chuck Schumer said he planned to put that legislation on the Senate floor this year. It's still not clear whether the measure would be able to gain enough support from Senate Republicans to reach the 60 votes needed to pass, however, as Senate Minority Leader Mitch McConnell expressed his opposition on Thursday.
counterrevolution
Xi Van Fleet was six when Chairman Mao launched his Cultural Revolution. The lady lived through the revolution. She doesn't go into great depth to describe what she went through, or what she had to do to survive. But, she does warn America that we are on the brink of the same thing in the USA.
Yes, of course she's on Fox. Did you think CNN would give her a soapbox to stand on? The liberal mainstream media would rather cut her off at the knees.
Click the link, watch the video.
A Virginia parent, whose remarks at a Loudoun County school board meeting against critical race theory and cultural Marxism went viral this week, described on "Hannity" how the tenets public schools are using regarding CRT are similar to how Chinese Communist revolutionary Mao Zedong successfully divided the society she lived in as a young child in the 1960s.
Earlier this week, Xi Van Fleet spoke during a school board meeting in Leesburg condemning the school board for the critical race theory curriculum it is imposing on young students.
"We are teaching our children to be social justice warriors and to loathe our country and our history. Growing up in China, all of this sounds very familiar. The Communist regime use the same critical theory is to divide people. The only difference is that used class instead of race. This is indeed the American version of the Chinese cultural revolution," she said at the time.
On "Hannity," Van Fleet expanded on her warning to America as a onetime victim of mandated Maoist indoctrination:
"I just want to let the American people know that what is going on in our schools and in our country is really a replay of the cultural revolution in China," she said, calling the similarities "terrifying."
"[Critical race theorists] use the same ideology, the same methodology, even the same vocabulary. The ideology is cultural Marxism."
At school in Maoist China, Van Fleet recalled being divided into groups of "oppressor" and "oppressed' based on what social class the student came from.
The same is happening today in schools and other institutions, except it is based on White and non-White races, she noted.
Chinese dissenters from the Maoist doctrine were labeled "counterrevolutionary", as dissenters in America are labeled "racist" – a moniker that in both regards is "like a hat that fits all" that can ruin one's life and livelihood.
Van Fleet added that the left's intent on "cancel culture" and "canceling" everything from public statuary to references to uncomfortable historic events, to historic figures they deem flawed is the same thing that Mao sought when he essentially erased thousands of years of Chinese cultural history.
"We basically canceled the whole Chinese civilization pre-Communism and we changed our school names, street names, store names, even our personal names," she said.
"Wokeness – to be specific – we used class wokeness in China," she also recalled.
"Your level of wokeness determines your chance to get a promotion or to get benefits and who decides your level of wokeness? The party leaders," she said, implying the same can be said in the United States for people and workers who do not ascribe to their moral superiors' intended ideologies.
Van Fleet added that she knows from experience that "freedom is fragile" and that many other Chinese-Americans also know the struggle and see the parallels between the left's cultural Marxism and the Maoist revolution of the 1960s.
"[C]ritical race theory is not antiracism. It itself is racist. It is divisive, destructive and it is dangerous."
Those of you who haven't read of the Cultural Revolution might want to brush up. Here are some starting points:
https://aaww.org/surviving-chinas-cultural-revolution/
https://www.csmonitor.com/World/Asia-Pacific/2016/0531/How-an-ancient-Chinese-town-survived-the-tumultuous-Cultural-Revolution
https://spectator.org/china-cultural-revolution-world-turned-upside-down/
https://www.ydr.com/story/opinion/columnists/2016/05/11/survived-chinas-horrific-cultural-revolution-column/84192734/
For they have sown the wind
For they have sown the wind, and they shall reap the whirlwind Hosea 8:7
I don't rely on scripture to make my point very often, but couldn't resist that one.
'People are scared' as gang activity fuels Portland violence
PORTLAND: When Oregon's most populous city had a rampant gang problem 30 years ago, Portland detectives were stunned if they found more than a few dozen bullet casings after a shooting. Now, police are recording multiple shootings a week with 50 to 70 shots fired, and in one case more than 150, as gang attacks and retaliatory shootings again spiral into a vicious cycle.
With more bullets comes more bloodshed. There have been 37 homicides in Oregon's largest city so far this year, more than six times the number recorded in the same period last year. If nothing changes, Portland will surpass its all-time record for homicides of 70 set in 1987, when the city was in the midst of a gang siege.The violence has deeply affected Portland, a liberal city that continues to grapple with the role of its police force more than a year after thousands of Black Lives Matter protesters demanded change following the murder of George Floyd.
The surge in gang-related shootings, which has disproportionately impacted people of color, puts the spotlight on a sensitive and polarizing topic - felt in major cities across the country - where violence is increasing as people continue to call for defunding police.
“This touches all of us,” said Portland Pastor Matt Hennessee, a longtime anti-gun violence activist whose 33-year-old stepson was shot and killed in a parking lot in May. “I have lived here for 32 years and I have always seen this city as a safe place. This is not the Portland that we know.”Police estimate half of Portland's 470 shootings this year, which have injured more than 140 people, are gang-related. Mayor Ted Wheeler warned last month that perpetrators are being told by gangs to shoot someone within 30 days or be shot and that people are traveling from other states to engage in violence in the Rose City.
https://news.yahoo.com/people-scared-gang-activity-fuels-050223817.html
Another liberal city, another out-of-control crime problem. More than a year of rioting in the streets was supposed to have consequences, right? Oh, DAMN, we forgot about that pesky law of unintended consequences!!
Biden Administration Aims To Close Guantanamo Bay Prison
The White House announced Friday that President Biden hopes to shut down the prison at the Naval Station Guantanamo Bay in Cuba, a tall task that the Obama administration failed to do nearly a decade ago.
"We are undertaking an NSC process to assess the current state of play that the Biden administration has inherited from the previous administration, in line with our broader goal of closing Guantanamo," she said. "There will be a robust interagency process to move forward on this, but we need to have the right people seated to do this important work."
Former President Barack Obama said the detention center went against American values and was a "stain on our broader record" when he argued for the prison's closure in 2016, NPR reported.
Later that same year, then-President-elect Donald Trump vowed to keep the installation open.
"We're gonna load it up with some bad dudes, believe me," Trump said in 2016.
Biden pushes Belt and Road rival 'Blue Dot'
NEW YORK -- U.S. President Joe Biden's administration, along with the governments of Japan and Australia, is reviving an infrastructure initiative that would provide emerging markets an alternative to China's Belt and Road initiative.
After a prolonged period of inactivity, the Blue Dot Network -- first announced during President Donald Trump's administration -- kicked off talks among stakeholders in Paris on Monday. The meeting and the launch of an executive consultation group was convened by the Organization for Economic Cooperation and Development and funded by Washington and Canberra.
We'll just ignore that Biden is dusting off a Trump initiative, because Biden has no initiatives of his own.
Which is better, Belt and Road, or Blue Dot?
Well, China's idea seems pretty "inclusive", if I may use that term in a non-racist manner. Build a million miles of roads, that cut through jungles and coastlines, cross mountains and deserts, pulling a myriad of small towns, villages, and fogotten backwaters into that Big Globalist Economic Network.
Blue Dot? Huh - established players on the economic scene get to expand their own economic stranglehold on the world, pushing into undeveloped countries, and setting the rules as they go.
Are the neocons and the New American Century running this from behind the scenes? It is their goal that every man, woman, and child on earth work to enrich Wall Street, after all. With Blue Dot, you can join the America-centric global market. With Belt and Road, you can join in a China-centric global market.
If I were a third world resident, the Chinese option would look more attractive.
Here, in the US, the Interstate and US Highway systems have done more to develop our country, than all the development of ocean ports. A similar highways system spanning Asia and Africa could bring many third world countries out of limbo.
Odd that Establishment Joe aims to enrich three already wealthy countries, while opposing a Chinese idea that will benefit billions of not-so-wealthy people.
EDIT: Forgot to post my link:
U.S. forces are halfway through withdrawal from Afghanistan
The Pentagon on Tuesday reached the midpoint in its herculean task of withdrawing troops and equipment out of Afghanistan.
The U.S. military has removed the equivalent of approximately 500 loads of material flown out of the country by large cargo aircraft, according to an update from U.S. Central Command.
Approximately 13,000 pieces of equipment that will not be left to the Afghan military have also been handed over to the Defense Logistics Agency for destruction. The U.S. has officially handed over six facilities to the Afghan military.
In April, Biden announced a full withdrawal of U.S. troops from Afghanistan by Sept. 11, which would end America’s longest war.
Biden’s withdrawal timeline breaks with a proposed deadline brokered last year by the Trump administration with the Taliban. According to that deal, all foreign forces would have had to leave Afghanistan by May 1.
U.S. forces are halfway through their withdrawal from Afghanistan
California assault weapon ban
First, if you can't read, or if you won't read, you have no valid opinion on the subject. I took the time to read the opinion, in it's entirety. (I didn't time myself, and I got up to do things a couple times. I think it took about 1 1/2 hours to read.)
Judge Roger Benitez takes the time to cover pretty much all evidence introduced, point by point.
Starting with "experts" whose presumed expertise has nothing to do with guns, or with law enforcement, or with statistical research. Going on through "experts" who simply make shit up as they go, who failed to use any scientific method in their "research", and whose "work" is impossible to verify or falsify.
I repeat: Read, or STFU. I'm sick to death of people repeating talking points that no one understands.
Those talking points begin with the word "assault weapon", which Judge Benitez methodically tears to shreds as a meaningless term. Then there is the "common sense" nonsense, which he shreds as well. How can uninformed people create a "common sense" law regarding something they have no understanding of?
Then, there are the outright lies. You are about 5 times more likely to be stabbed to death, than to be shot with a rifle - of any kind in the United States. You are 3 times more likely to be beaten to death with fists and feet, than to be shot with a rifle of any kind.
Ohhh, but mass shoootttiiiinnnnggsss!
Judge Benitez addresses that. Most mass shootings are carried out with PISTOLS not rifles. Shotguns figure into mass shootings as well. And, when rifles are used, more traditional "hunting" rifles are often used.
Once again, read or STFU!
Judge rules California’s ban on assault weapons unconstitutional
A federal judge on Friday struck down California’s ban on assault weapons as unconstitutional but left plenty of time for the state to file an appeal.
The state’s definition of illegal military-style rifles unlawfully deprives law-abiding Californians of weapons commonly allowed in most other states and by the U.S. Supreme Court, the judge wrote.
Judge Roger T. Benitez, who has favored pro-gun groups in past rulings, described the AR-15 rifle, used in many of the nation’s deadliest mass shootings, as an ideal weapon.
“Like the Swiss Army Knife, the popular AR-15 rifle is a perfect combination of home defense weapon and homeland defense equipment,” he wrote in Friday’s decision.
“Yet, the State of California makes it a crime to have an AR15 type rifle,” Benitez continued. “Therefore, this Court declares the California statutes to be unconstitutional.”
He praised the AR-15 as a rifle that should be formally protected by the law for its “militia readiness.”
Gov. Gavin Newsom was indignant in a statement late Friday.
“The fact that this judge compared the AR-15 — a weapon of war that’s used on the battlefield — to a Swiss Army Knife completely undermines the credibility of this decision and is a slap in the face to the families who’ve lost loved ones to this weapon,” he said.
The office of Attorney General Rob Bonta said it would appeal.
“Today’s decision is fundamentally flawed, and we will be appealing it,” Bonta said in a statement Friday night. “There is no sound basis in law, fact, or common sense for equating assault rifles with swiss army knives.”
The Firearms Policy Coalition, which backed the suit, celebrated the decision. “We look forward to continuing this challenge at the Ninth Circuit and, should it be necessary, the Supreme Court,” the group’s president, Brandon Combs, said in a statement.
Police amazed as four customers thwart armed bank robber
Police 'amazed' as four customers thwart armed bank robbery in Abbotsford
The four customers tackled, disarmed and held the suspect until officers arrived.Police say a suspect is in custody after customers in a B.C. bank refused to obey orders from a shotgun-brandishing robber and tackled her instead.
A statement from Abbotsford police says the suspect entered the Scotiabank branch just before noon Wednesday and ordered customers to the floor.
As she threw bags onto a counter and demanded money, police say one customer confronted her and three more stepped up.
The four tackled and disarmed the woman and held her until officers arrived minutes later.
No one was hurt and Sgt. Judy Bird says a 46-year-old is facing robbery and firearms-related charges.
Bird says police are thankful for the community support and “amazed” at the willingness of the four customers to protect others in the bank.
“As grateful as we are for this outcome, we remind the public to be aware of how volatile and dangerous these situations can be, especially with armed suspects,” Bird said in a statement Thursday.
Moral of the story: A gun doesn't make you invincible. It's the hoplophobe's fear of that gun that makes a shooter seem to be invincible.
Further coverage reveals that the failed robber is a transvestite/gender bender who was looking for some easy money.
https://www.langleyadvancetimes.com/news/4-customers-tackle-armed-bank-robber-in-abbotsford/
Interview of the good citizen here, https://www.langleyadvancetimes.com/news/im-not-going-to-die-today-abbotsford-bank-robbery-hero-speaks-out/
‘I’m not going to die today’: B.C. man 1 of 4 to stop bank robber
68-year-old Garry Amyot shares story of how he and others prevented potential tragedy in bankGarry Amyot went to Scotiabank in Abbotsford on Wednesday (June 2) to check on the status of a new bank card, but instead he helped thwart an armed robbery.
Amyot, 68, was one of four customers inside the bank on Gladwin Road and South Fraser Way who tackled the gun-wielding culprit before the suspect could leave the premises.
Amyot said he was in a line to inquire about his new card at about 11:30 a.m. when another customer walked past the line, and Amyot noticed the person was acting unusual.
“All of a sudden, the guy walks in past us, pulls out a 12-gauge shotgun and yells out, ‘Everybody! This is a bank robbery, nobody move!’ ” Amyot said.
“So I’m looking from a little distance and I see the shotgun, and I own and know firearms so I’m thinking this is pretty serious, but I’m also thinking, ‘I’m not going to die today.’ “
The suspect threw a bag to Amyot, who then passed it to a teller. As the tellers began filling the bag with money, Amyot shared a glance with another customer behind the suspect and the wheels began turning in his head.
“When I looked at that guy I just knew he was going to do something no matter what,” Amyot said, noting he could tell the fellow customer looked irritated. “I wasn’t going to let him do this by himself. I winked at him and that was the green light – we were comrades in this situation.”
Suddenly, the other man in line grabbed the suspect’s gun and pointed it straight up to avoid anyone getting hurt. Amyot quickly followed and tackled the suspect.
“It all happened so freaking fast,” Amyot said. “The other guy grabbed the barrel of the shotgun and then milliseconds later – bang! – we’re all on the ground. I’ve got my arms around his back and my elbow in his face and we have him pinned down. The gun was on the floor and I remember telling someone, ‘Kick that gun out of the way!’ “
Two other customers assisted in restraining the suspect until the police arrived a few minutes later.
“It was so surreal; it all happened so fast,” Amyot said.
Amyot, who has about 15 years of martial arts training, said the situation was intense but he felt confident.
“It was all instinct,” he said. “But my adrenaline was pumping so fast after that.”
Amyot, who works at Ashley Furniture HomeStore in Abbotsford, said Tuesdays and Wednesdays are his days off but after the incident at the bank he decided to engage in some liquid counselling.
“I went and had something to eat because I hadn’t ate anything all day but the next thing I did was go to the liquor store. I bought a case of beer, came home, had a shot of tequila and a beer or two,” he said.
When Amyot arrived home after the incident, he discovered that the bank card he had gone to the bank to check on had arrived in the mail.
He said he doesn’t consider himself a hero and just wanted everyone in the bank to be safe.
Amyot has lived in Abbotsford on and off for the past two decades and said he thinks it would be nice for the man who stopped the suspect and himself to receive some sort of recognition from the city.
“I’d be OK with getting some sort of commendation or a placard or a medal from the city of Abbotsford,” he said. “We just happened to be in the right place at the right time.”
He also said he’d be OK with getting some sort of acknowledgement or tip of the hat from Scotiabank itself.
“It’s good that it all came out the way it came out, but I’d be fine if Scotiabank decided to take care of whatever is left on my credit card for me,” he joked.
The 46-year-old suspect remains in police custody facing numerous charges, including robbery and weapons offences. Police are continuing to investigate.
The FBI wants to know who read UPDATED
Strange, when government spooks want to know who reads the news. Maybe the spooks should explain why they need that info? Maybe, at the least, the spooks should explain, in detail, to a judge, why they need that info?
USA Today fights subpoena aimed at readers of Florida FBI shooting story
Gannett, the publisher, contends that demand for details on who accessed article violates the First Amendment.Newspaper publisher Gannett is fighting an effort by the FBI to try to determine who read a specific USA Today story about a deadly shooting in February near Fort Lauderdale, Fla., that left two FBI agents dead and three wounded.
The subpoena, served on Gannett in April, seeks information about who accessed the news article online during a 35-minute window starting just after 8 p.m. on the day of the shootings. The demand — signed by a senior FBI agent in Maryland — does not appear to ask for the names of those who read the story, if the news outlet has such information. Instead, the subpoena seeks internet addresses and mobile phone information that could lead to the identities of the readers.
The nature of the ongoing criminal investigation is unclear. Authorities said David Lee Huber, 55, watched the FBI agents arrive via a doorbell camera, then opened fire on them. The agents were serving a search warrant in a child pornography investigation, the FBI said.
Huber died during the exchange of gunfire, officials said. That would be hours before the article was written and half a day before the window of time the FBI appears to be zeroing in on. It’s unclear whether the FBI might suspect someone else of involvement with Huber’s activities or whether someone drew suspicion by the way they reacted to the shooting.
https://www.politico.com/news/2021/06/03/usa-today-subpeona-florida-shooting-491847
The article in question is https://www.usatoday.com/story/news/nation/2021/02/02/sunrise-florida-shooting-fbi-agents-injured/4352344001/
As noted above, the guy who did the shooting couldn't have read the article - he was already assuming room temperature when the article was published. I don't see a comments section, in which the FBI might be interested. The subpoena doesn't even mention comments, they are looking for people who read the story.
Maybe the FBI got a threatening email that starts with, "I just read the USAToday article about you assassinating Huber . . . . "???
UPDATE:
US Justice Dept says it will no longer seize reporters' records in leak investigations
The Department of Justice said on Saturday that it would no longer seek source information from reporters in leak investigations after recent revelations that former President Donald Trump's administration had secretly obtained phone and email records from a number of journalists.
CNN and the Washington Post have said the Trump administration had secretly tried to obtain the phone records of some of their reporters over work they did in 2017.
The New York Times reported that the Justice Department under presidents Trump and Joe Biden waged "a secret legal battle to obtain the email logs of four New York Times reporters," including a gag order on executives.
Last month, Biden said he would not allow his Justice Department to seize the phone or email records of reporters, saying any such move would be "simply wrong."
"DOJ has now completed a review to determine all instances in which the Department had pending compulsory requests from reporters in leak investigations," Justice Department spokesman Anthony Coley said in a statement.
"Going forward, consistent with the President’s direction, this Department of Justice - in a change to its longstanding practice - will not seek compulsory legal process in leak investigations to obtain source information from members of the news media doing their jobs," Coley added.
Trump had a contentious relationship with the press, often publicly lambasting reporters and their outlets as "fake news."
Lab-Made? SARS-CoV-2 Genealogy
Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research
Yuri Deigin
Yuri Deigin
Apr 22, 2020· . . . 64 min read (bolded by Runaway)
How I Learned to Start Worrying
Oh, come on. Lab-made? Nonsense! Back in January, that was my knee-jerk reaction when ideas that Covid-19 is caused by a laboratory leak had just surfaced. Bioweapon? Well, that is just Flat Earth crazies territory. Thus, whenever I kept hearing anything about non-natural origins of SARS-CoV-2, I brushed it aside under similar sentiments. So what if there is a virology institute in Wuhan? Who knows how many of those are sprinkled throughout China.
At some point, it became necessary to brush such theories aside in a substantiated manner, as their proponents began to back up their theses about the possible artificial nature of the virus with arguments from molecular biology, and when engaging them in debate, I wanted to smash their conspiracy theories with cold, hard scientific facts. Just like that Nature paper (or so I thought).So it was then, in pursuit of arguments against the virus’s lab-madeness, that I got infected by the virus of doubt. What was the source of my doubts? The fact that the deeper you dive into the research activities of coronavirologists over the past 15–20 years, the more you realize that creating chimeras like CoV2 was commonplace in their labs. And CoV2 is an obvious chimera (though not nesessarily a lab-made one), which is based on the ancestral bat strain RaTG13, in which the receptor binding motif (RBM) in its spike protein is replaced by the RBM from a pangolin strain, and in addition, a small but very special stretch of 4 amino acids is inserted, which creates a furin cleavage site that, as virologists have previously established, significantly expands the “repertoire” of the virus in terms of whose cells it can penetrate. Most likely, it was thanks to this new furin site that the new mutant managed to jump species from its original host to humans.
IMPORTANT NOTE by Runaway: The miners who originally got sick from the COVID-like SARS virus were obviously infected by a wild variant of SARS. For that reason, we can't actually rule out the same, or a closely related wild virus being the cause of the pandemic. We can, however, weigh the odds.
As noted by the bolded text above, this is an hour long read. I'm not going to c/p it all into a journal. Maybe a spoiler tag? Click the link - and then click some or all of the reference links on that page.
(Note that the text is sprinkled with images, graphs, charts, etc - click the link to see all of them.)
Indeed, virologists, including the leader of coronavirus research at the Wuhan Institute of Virology, Shi Zhengli, have done many similar things in the past — both replacing the RBM in one type of virus by an RBM from another, or adding a new furin site that can provide a species-specific coronavirus with an ability to start using the same receptor (e.g. ACE2) in other species. In fact, Shi Zhengli’s group was creating chimeric constructs as far back as 2007 and as recently as 2017, when they created a whole of 8 new chimeric coronaviruses with various RBMs. In 2019 such work was in full swing, as WIV was part of a $3.7 million NIH grant titled Understanding the Risk of Bat Coronavirus Emergence. Under its auspices, Shi Zhengli co-authored a 2019 paper that called for continued research into synthetic viruses and testing them in vitro and in vivo:
Currently, no clinical treatments or prevention strategies are available for any human coronavirus. Given the conserved RBDs of SARS-CoV and bat SARSr-CoVs, some anti-SARS-CoV strategies in development, such as anti-RBD antibodies or RBD-based vaccines, should be tested against bat SARSr-CoVs. Recent studies demonstrated that anti-SARS-CoV strategies worked against only WIV1 and not SHC014. In addition, little information is available on HKU3-related strains that have much wider geographical distribution and bear truncations in their RBD. Similarly, anti-S antibodies against MERS-CoV could not protect from infection with a pseudovirus bearing the bat MERSr-CoV S. Furthermore, little is known about the replication and pathogenesis of these bat viruses. Thus, future work should be focused on the biological properties of these viruses using virus isolation, reverse genetics and in vitro and in vivo infection assays. The resulting data would help the prevention and control of emerging SARS-like or MERS-like diseases in the future.
If the above quote might seem vague as to what exactly “using reverse genetics” might mean, the NIH grant itself spells it out:
Aim 3. In vitro and in vivo characterization of SARSr-CoV spillover risk, coupled with spatial and phylogenetic analyses to identify the regions and viruses of public health concern. We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.
“Infectious clone technology” stands for creating live synthetic viral clones. Considering the heights of user friendliness and automation that genetic engineering tools have attained, creating a synthetic CoV2 via the above methodology would be in reach of even a grad student.
But before delving into CoV2 origins, let’s first take a quick dive into its biology.
Biology
Ok, let’s start from the basics. What’s a furin site, an RBM, or a spike protein? Bear with me: once you wade through the jungle of terminology, conceptually, everything is pretty straightforward. For example, spike proteins are those red things sticking out of a virus particle — the very reason for which these viruses got “crowned”:
It is with the help of these proteins that the virion clings to the receptor of the victim cell (ACE2 in our case) to then penetrate inside. So it is a vitally important part of the virus, as without getting into a cell viruses cannot replicate. The spike protein also determines which animals the virus can or cannot infect, as ACE2 receptors (or other targets for other viruses) in different species can differ in structure. At the same time, out of the entire 30 kilobase genome (quite huge by viral standards), the gene of this protein makes up only 12–13%. So the spike protein is only about 1300 amino acids long. Below is how the spike (S) protein is structured in CoV2 and close relatives:
As can be seen from the figure above, the S protein consists of two subunits: S1 and S2. It is S1 that interacts with the ACE2 receptor, and the place where S1 does so is called Receptor Binding Domain (RBD), while the area of direct contact, the holy of holies, is called Receptor Binding Motif (RBM). Here is a beautiful illustration from an equally beautiful work:
When the CoV2 genome was just sequenced and made publicly available on January 10, 2020, it was a riddle, as no closely related strains were known. But quite quickly, on January 23, Shi Zhengli released a paper indicating that CoV2 is 96% identical to RaTG13, a strain which her laboratory had previously isolated from Yunnan bats in 2013. However, outside of her lab, no one knew about that strain until January 2020.
It was immediately clear that RaTG13 is special. Take a look at the figure below:
This is a genome similarity graph between CoV2 and other known strains. The higher the curve, the higher the percentage of matching nucleotides. As you can see, in the spike protein (S) gene region (between nucleotides 22k and 25k), only RaTG13 is more or less close to CoV2, while all other strains take a deep dive around this spot — both strains from other bats and the first SARS-CoV (red curve). This in itself is far from suspicious — who knows how many unknown SARS-like strains lurk in the bat caves of Yunnan? Ok, maybe it is not very clear how exactly the virus could get from there to Wuhan, but hey, with those wet markets you never know.
Pangolins
Next, pangolins appeared on the scene: in February, another group of Chinese scientists discovered a peculiar strain of pangolin coronavirus in their possession, which, while generally being only 90% similar to CoV2, in the RBM region was almost identical to it, with only a single amino acid difference (see the upper two sequences, dots indicate a match with the top sequence):
Surprisingly, in the first quarter of the S protein, the pangolin strain is highly dissimilar from CoV2, but after the RBM all three strains (CoV2, Pangolin, RaTG13) exhibit a shared high degree of similarity. Most strikingly, RaTG13’s RBM itself is quite different than that of CoV2, which can be seen from the steep dive of the green RaTG13 graph compared to the red CoV2 graph in the RBM region (pink strip) in the following graph:
areas highlighted in the graph above — in the RBM, the pangolin strain is closer to CoV2 than is RaTG13, but it is RaTG13 that is closer to CoV2 to the left and right of RBM. So there is obvious recombination, as the authors (and other papers) conclude.
How did the researchers obtain those pangolins? This is how:
They were confiscated from smugglers by Chinese customs and transferred to an animal rehab center in Guangdong, where they died while exhibiting severe coronavirus symptoms. This, of course, must have gotten the attention of local virologists, who took several samples:
Pangolins used in the study were confiscated by Customs and Department of Forestry of Guangdong Province in March-December 2019. They include four Chinese pangolins (Manis pentadactyla) and 25 Malayan pangolins (Manis javanica). These animals were sent to the wildlife rescue center, and were mostly inactive and sobbing, and eventually died in custody despite exhausting rescue efforts. Tissue samples were taken from the lung, lymph nodes, liver, spleen, muscle, kidney, and other tissues from pangolins that had just died for histopathological and virological examinations.
Those pangolins attracted the attention of other virologists too. For example, a team in Hong Kong also received samples of confiscated pangolins and in February 2020 they also released a paper that noted clear signs of recombination in the CoV2 spike protein:
We received frozen tissue (lungs, intestine, blood) samples that were collected from 18 Malayan pangolins (Manis javanica) during August 2017-January 2018. These pangolins were obtained during the anti-smuggling operations by Guangxi Customs. Strikingly, high-throughput sequencing of their RNA revealed the presence of coronaviruses in six (two lung, two intestine, one lung-intestine mix, one blood) of 43 samples. With the sequence read data, and by filling gaps with amplicon sequencing, we were able to obtain six full or nearly full genome sequences — denoted GX/P1E, GX/P2V, GX/P3B, GX/P4L, GX/P5E and GX/P5L — that fall into the 2019-CoV2 lineage (within the genus Betacoronavirus) in a phylogenetic analysis (Figure 1a).
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More notable, however, was the observation of putative recombination signals between the pangolins coronaviruses, bat coronaviruses RaTG13, and human 2019-CoV2 (Figure 1c, d). In particular, 2019-CoV2 exhibits very high sequence similarity to the Guangdong pangolin coronaviruses in the receptor-binding domain (RBD; 97.4% amino acid similarity; indicated by red arrow in Figure 1c and Figure 2a), even though it is most closely related to bat coronavirus RaTG13 in the remainder of the viral genome. Bat CoV RaTG and the human 2019-CoV2 have only 89.2% amino acid similarity in RBD. Indeed, the Guangdong pangolin coronaviruses and 2019-CoV2 possess identical amino acids at the five critical residues of the RBD, whereas RaTG13 only shares one amino acid with 2019-CoV2 (residue 442, human SARS-CoV numbering).
By the way, the authors of this article also highlighted the high phylogenetic mosaicity of the CoV2 spike protein:
Interestingly, a phylogenetic analysis of synonymous sites alone in the RBD revealed that the phylogenetic position of the Guangdong pangolin is consistent with that in the remainder of the viral genome, rather than being the closest relative of 2019-CoV2 (Figure 2b). Hence, it is possible that the amino acid similarity between the RBD of the Guangdong pangolin coronaviruses and 2019-CoV2 is due to selectively-mediated convergent evolution rather than recombination, although it is difficult to choose between these scenarios on current data.
Translated from science-speak, what this means is that if we analyze the entire RBD of the three strains, ignoring the obvious differences (i.e. non-synonymous substitutions) among them, which are mainly found in the RBM (which, recall, is identical between CoV2 and Pangolin), and construct a phylogenetic tree for synonymous substitutions, CoV2 is still closer to RaTG13 than to the pangolin strain. Which is rather strange in light of the fact that the pangolin strain and CoV2 have identical RBMs (which are segments inside RBD).
The authors go on to put forth a conjecture that this may be the result of convergent evolution, in other words, that CoV2 and the pangolin strain came to possess identical RBMs each in their own way, rather than through recombination between common ancestors. Because it would have required a rather unique recombination event — as if someone cut out a precise RBM segment from a pangolin strain and used it to replace the RBM in RaTG13. Talk about Intelligent Design!
Royal Genealogy
In order to better understand CoV2 origins, let’s take a look at spike protein sequences of our Unholy Trinity: CoV2, RaTG13 and MP789 (pangolin-2019). Let’s compare the pairwise differences between them (identical amino acids are marked with dots, red letters denote differences, and dashes indicate deleted/inserted amino acids):
The comparisons illustrate what previously quoted papers have noted: that in the first quarter of the sequence, the pangolin strain is far from CoV2 and RaTG1, and if it weren’t for the RBM region (red rectangle), RaTG13 would have been very close to CoV2. But, as I already said, the RBM in CoV2 is closest to that of the pangolin strain.
What about other pangolin strains? So far we’ve only analyzed the MP789 strain isolated from pangolins confiscated by customs in 2019. But there was another batch of pangolins confiscated in 2017, and they also had a similar coronavirus strain isolated. Let’s compare it to RaTG13 and MP789:
In the first quarter of the S protein, the 2017 pangolin strains are closer to RaTG13 (and CoV2) than their 2019 pangolin counterpart (MP789). At the same time, all three have a clear recent common ancestor in the areas marked by green rectangles, and in these areas RaTG13 and pangolin-2019 (MP789) are closer to each other than to pangolin-2017, since they have several common mutations (marked by red and blue ellipses), which are absent from pangolin-2017. But the RBM for all three is different, and different in approximately the same proportion, and in similar places.
Maybe after ancestors of RaTG13 and MP789 diverged, the MP789 ancestor had the first quarter of its protein replaced (which did not occur in RaTG13 or pangolin-2017), and the rest of the protein remained common for all three strains. Later the paths of the RaTG13 and MP789 gene pools crossed again and produced CoV2. It is also possible that the ancestor of RaTG13 arose as a result of recombination of ancestral pangolin strains.
It is also interesting to see a rather unique identical mutation (QTQTNS) in RaTG13 and pangolin-2019 right in front of the spot where CoV2 has a new furin cleavage site. That furin site, as I mentioned, arose via an insertion of 4 new amino acids (PRRA). If we look at the nucleotide sequence around this insertion, we can see that RaTG13 and CoV2 are closer to each other in that area than to pangolin-2019, since they possess several common mutations (highlighted in blue):
Alright, I'm done c/pasting - click the link to read the rest.
Oh yeah - thanks for the link. You know who you are. :^)
