Sunday, June 6, 2021

SARS-CoV-2: Convergent Evolution by Deletions


Have you noticed that the same or very similar mutations are emerging across the globe?

For example, the  E484K mutation emerged in the US (with California and Arizona variants), South African, and Brazil, among other locales.

SARS-CoV-2 mutation is being driven by deletions according to several research studies. Here is one:

Ribes, M., Chaccour, C. & Moncunill, G. Adapt or perish: SARS-CoV-2 antibody escape variants defined by deletions in the Spike N-terminal Domain. Sig Transduct Target Ther 6, 164 (2021).

Rapid evolution by deletion toward more hazardous mutations is unusual.

One analyst notes that mutations in the E protein are not subject to evolutionary pressures and therefore suggest pre-progammed change:

RaTG13 – The undeniable evidence that the Wuhan coronavirus is man-made. Nerd Power,

The E protein of β coronaviruses is a structural protein that is tolerant of mutations as evidenced both in SARS and in bat coronaviruses. 
However, on the amino acid level, E protein of the Wuhan coronavirus identified at the beginning of the outbreak is 100% identical to those of the suspected templates, ZC45 and ZXC21 (Figure 4). 
What is striking is that, after a short two-months spread of the virus in humans, the E protein is already mutating. Sequence data obtained within the month of April indicate that mutations have occurred to four different locations (Figure 4). 
Note that the E protein makes very limited interactions with host proteins and thus is not under evolutionary pressure to adapt to a new host. Not only the E protein can tolerate mutations but also its mutational rate is held constant across different coronavirus species. 
The fact that the E protein of the Wuhan coronaviruses is already mutating in the short period of human-to-human transmission is consistent with its evolutionary feature. In stark contrast, while ZC45/ZXC21 and the Wuhan coronavirus are more distant evolutionarily, the E proteins within them are 100% identical. In no way this could be a result of natural evolution.

Interesting speculation.

In the spring of 2020 I read an interesting discussion about the potential for SARS-CoV-2 to be a bioweapon. One commentator suggested it was a total dud as weapon. Another commentator responded (I paraphrase):

Imagine a bioweaponized virus with an initially low-kill rate. It disrupts society but low mortality eventually reassures health authorities that the hazard is ultimately low and manageable.

Then the virus shapeshifts by shedding protein encumbrances, deleting excess RNA code to reveal the real weapon at the heart of the Trojan Horse.

I certainly hope this imaginary is purely dark fantasy because the on-the-ground convergent evolution by deletions followed by reassortment of mutations in new and more hazardous variants certainly raise questions.

The future will tell.




  1. I tolerate diverse points of view at my blog because I believe in political pluralism. Allowing people to post comments that I disagree with is dialogue. However, comments that are personal slurs will not be allowed.

  2. Officers said they wanted to come in and talk to his kids, and Jones said he let them. Within seconds they had their flashlights on and were, Jones said, “running rampant” without a search warrant.

    The police report stated that Jones consented to a search. But he disputes this.

    They scoured the house and found empty zip-close bags in his son’s room that later tested positive for traces of marijuana. Bobby was arrested and spent three weeks in juvenile detention before his trial, where the judge dismissed the charges due to the lack of measurable marijuana. He had been at his new school for just over a week.

    Image: Robert Jones looks over documents relating to his son's arrests.
    Robert Jones looks over documents relating to his son's arrests.Bob Croslin / for NBC News
    What Jones didn’t realize at the time was that his son had been identified as a target by the Pasco Sheriff’s Office's “intelligence-led” policing program. Police had gathered records of Bobby’s previous interactions with law enforcement and were using his history to predict that he would be a troublemaker in Pasco County.

    After Bobby was released, a monthslong ordeal followed, which Jones described as a “horror story” of police showing up at the family home, sometimes multiple times a day or in the middle of the night, to inquire about Bobby or ask to enter the home. Any time there was a crime in the neighborhood, such as a burglary,

  3. Bobby was a suspect. On some occasions, described in a lawsuit filed in March by Jones and others targeted bythe Pasco Sheriff’s Office, as many as 18 officers would show up at the home, “banging on windows and yelling at his young daughters while they were hiding under the bed.”

    Jones, who had studied to be a paralegal, said he tried to stand his ground and refused to allow officers to conduct any more warrantless searches of his property. But police interpreted this behavior, the lawsuit states, as uncooperative and he was repeatedly cited — and eventually arrested — for property code violations such as having overly long grass, missing numbers on his mailbox and a Jet Ski trailer on the property.

    From October 2015 through April 2016, Jones, who had no previous criminal history, was arrested five times. None of the arrests resulted in a conviction. His home was ransacked, laptops and phones seized, and he ultimately fled their home in the middle of the night to avoid further harassment by police, the lawsuit alleges.

    “My family will never be made whole from this atrocity,” he said. “Where does anyone in my family get their presumption of innocence back?”

    Image: Robert Jones' former home in Pasco County.
    Robert Jones' former home in Pasco County.Bob Croslin / for NBC News
    The sheriff’s office disputed the idea that its intelligence-led policing was “predictive policing” in the sense characterized by the science fiction movie "Minority Report," where people are arrested by a police department’s "pre-crime" division before they have the chance to carry out illegal deeds. It said the Pasco Sheriff’s Office used historical data to “work with those who have shown a consistent pattern of offending to attempt to break the cycle of recidivism” but said Bobby was not added to its “prolific offender program,” which results in random visits from deputies, until 2017 — long after the period of harassment alleged by Jones.

  4. A spokesman said Bobby had interacted with the sheriff’s office three times before they showed up at the family home in September 2015. The spokesman said officers went to the house to discuss “involvement in criminal activity in the area” and searched his room to look for a stolen GPS device, which is how they found the empty baggies.

    In a lengthy statement released by the agency in response to reporting on the program, a spokesman said the individuals accusing the sheriff’s office of harassment all had “lengthy criminal histories, often with a multitude of arrests and victims.”

    Predictive analytics
    Jones' family and civil liberties experts believe his case is emblematic of a broader effort by law enforcement agencies across the United States to predict criminality based on a wide range of data points that are crunched together and used to assign a risk score to individuals or places. While some law enforcement agencies say it can be a useful approach to efficient resource allocation and early intervention, critics say these programs can enter into the alarming realm of "pre-crime," where the presumption of innocence is lost, and that they encode existing racial and social biases.

    Pasco County’s approach to “intelligence-led” policing, developed over a decade, has drawn particular concern from civil liberties experts because of a data-sharing arrangement with the local school district, which was first reported by Tampa Bay Times. That partnership gave police access to data relating to students’ grades, attendance and behavior as well as any history of abuse or other “adverse childhood experiences.” School records were used to allocate students one of four labels: on track, at risk, off track or critical. Getting a D grade or having a parent or sibling go to prison could be enough to put a child in the “at risk” category, according to Pasco’s own 83-page “Intelligence-Led Policing Manual,” first obtained by the Tampa Bay Times.

  5. The manual, last updated in January 2018, states that the data-sharing was designed to identify “at-risk youth who are destined to a life of crime” and intervene to “set them on the right path.”

    The sheriff’s office took the list of 20,000 students determined to be at risk, according to school data, and cross-referenced it with its own records of law enforcement interactions to come up with a smaller list of a few hundred students to be monitored closely and offered “positive mentorship and support” by school resource officers — sheriff’s office deputies contracted to work at the school. The agency does not notify parents of children added to the list but said parents can file a public records request to find out.

    Bobby and his dad say they were never offered any kind of diversion program or support at school or home, only harassment and punishment. The sheriff’s office said the program to identify at-risk students was entirely separate from the "prolific offender" program but that Bobby and other adolescent offenders were given a “resource card” featuring details about “opportunities in our community” relating to mental health and substance abuse.

    Criminal justice advocates say programs like these targeting adolescents, and the broader trend to increase surveillance in schools under the guise of school safety, fuel the so-called school-to-prison pipeline. This is where instead of letting children and teenagers make and learn from their mistakes, they are marked as criminals at an early age — even if they are only interacting with school resource officers. Once they are in the criminal justice system, it’s almost impossible to escape.

    “This idea that you can predict criminality is very worrisome and extremely troubling. You cannot,” said Jason Nance, professor of law at the University of Florida Levin College of Law. “These are real kids with real lives. If you have extra scrutiny on a child and that child does something minor or untoward, you may set that student on a pathway in which that student will become more involved in the criminal justice system later on.”

    After the Tampa Bay Times disclosed the existence of the program in late 2020, the program received widespread criticism from civil liberties and legal experts.

    “It is really, as someone who has studied this, it is jaw-droppingly bad in all aspects,” said Andrew Ferguson, a law professor at American University. “They basically built this system as a justification to chase the bad kids out of town, to monitor them in over-aggressive ways with no intention to help them but to make their lives so miserable that they would leave.”

    The intelligence-led policing program, which is the subject of the lawsuit in which Jones and three other parents are named as plaintiffs, alleges that the sheriff’s office repeatedly violated property rights with its unwarranted, suspicionless visits to targets’ homes.

    “Having a policy of harassment and intimidation and constitutional violations of a county’s own residents is not a legitimate way to do police work,” said Ari Bargil, an attorney at the Institute for Justice, the legal nonprofit bringing the case.

    Federal notice
    Pasco’s program has also attracted the attention of the U.S. Departments


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