A Covid Origin Conspiracy?

 From almost the moment the Covid-19 pandemic broke out in the city of Wuhan, the medical-research establishment in Washington and London insisted that the virus had emerged naturally. Only conspiracy theorists, they said, would give credence to the idea that the virus had escaped from the Wuhan Institute of Virology.

Now a string of unearthed emails—the most recent being a batch viewed by the House Oversight and Reform Committee and referred to in its January 11, 2022 letter—is making it seem increasingly likely that there was, in fact, a conspiracy, its aim being to suppress the notion that the virus had emerged from research funded by the National Institute of Allergy and Infectious Diseases (NIAID), headed by Anthony Fauci. The latest emails don’t prove such a conspiracy, but they make it more plausible, for two reasons: because the expert virologists therein present such a strong case for thinking that the virus had lab-made features and because of the wholly political reaction to this bombshell on the part of Francis Collins, then-director of the National Institutes of Health.

The story begins with a January 31, 2020, email to Fauci from a group of four virologists led by Kristian G. Andersen of the Scripps Research Institute. The genome sequence of SARS-CoV-2 had been published three weeks before, giving virologists their first look at the virus’s structure and possible origin.

Andersen reported to Fauci that “after discussions earlier today, Eddie, Bob, Mike and myself all find the genome inconsistent with expectations from evolutionary theory.” Eddie is Edward C. Holmes of the University of Sydney; Bob is Robert F. Garry of Tulane University; Mike is Michael Farzan at Scripps Research. In their unanimous view, the virus didn’t come from nature and may instead have escaped from a lab.

We knew this much already from emails obtained in June 2021 by a Freedom of Information Act request, as well as from the fact that a teleconference took place the following day (February 1, 2020) to discuss the virologists’ conclusion. But something remarkable happened at the conference, because within three days Andersen was singing a different tune. In a February 4, 2020 email, he derided ideas about a lab leak as “crackpot theories” that “relate to this virus being somehow engineered with intent and that is demonstrably not the case.”

Andersen and his colleagues then prepared an article, published on March 17, 2020, in the journal Nature Medicine, that declared flatly, “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.” The article was highly influential, persuading the mainstream press not to investigate lab-leak theories. That paper, along with an earlier letter in the British medical journal The Lancet, froze into silence any dissenting voices from the scientific community. The Lancet letter was signed by Jeremy Farrar, a powerful research administrator in London who convened the February 1 teleconference.

What happened at the February 1 teleconference to make the virologists change their minds so radically? It was impossible to tell from the emails released in June 2021 because almost every word in them was redacted. The House Oversight and Reform Committee was allowed to view the emails only in camera, meaning members weren’t given copies, but staffers are allowed to transcribe them by hand while viewing them.

A striking feature of the excerpts released in the committee’s January 11, 2022 letter is that the virologists had little doubt that the virus bore the fingerprints of manipulation. The focus of their attention was a genetic element called a furin cleavage site. This short snippet of genetic material is what makes the virus so infectious for human cells. Scientists sometimes add this element to laboratory viruses to make them more virulent, but in nature, viruses usually acquire runs of genetic material like this by swapping them with other members of their family. The furin cleavage site in the Covid virus sticks out like a sore thumb because no other known member of its family—a group called Sarbecoviruses—possesses a furin cleavage site. So how did the virus acquire it?

A member of the Andersen group, Garry of Tulane University, remarks in the latest emails on the fact that the inserted furin cleavage site, a string of 12 units of RNA, the virus’s genetic material, was exactly the required length, a precision unusual in nature: “I just can’t figure out how this gets accomplished in nature . . . it’s stunning. Of course, in the lab it would be easy to generate the perfect 12 base insert that you wanted.”

Another member of the Andersen group, Farzan of Scripps Research, apparently felt much the same way. “He is bothered by the furin cleavage site and has a hard time explain[ing] that as an event outside the lab (though, there are possible ways in nature, but highly unlikely),” the House committee’s letter says of his remarks. Farzan noted that viruses can acquire elements like furin cleavage sites when grown in cultures of human cells, so “instead of directed engineering . . . acquisition of the furin site would be highly compatible with the continued passage of virus in tissue culture.” Both routes— direct insertion of the cleavage site or tissue culture—would mean that the virus came from a lab.

The conferees were clearly aware of the possibility that the virus had originated in the Wuhan lab. “So I think it becomes a question of how do you put all this together,” Farzan wrote, “whether you believe in this series of coincidences, what you know of the lab in Wuhan, how much could be in nature—accidental release or natural event? I am 70:30 or 60:40,” meaning he thought lab origin considerably more likely than not.

You might think that the senior administrators present at the conference would have rushed to investigate the startling inference that their expert advisers had drawn. But just one day after the teleconference at which his experts explained why they thought the virus seemed manipulated, Collins complained about the damage such an idea might cause. “The voices of conspiracy will quickly dominate, doing great potential harm to science and international harmony,” he wrote on February 2, 2020, according to the new emails.

Even after the March 2020 Nature Medicine article, which made the natural-origin theory the mainstream view, Collins still fretted that the lab-leak idea had not been sufficiently suppressed. “Wondering if there is something NIH can do to help put down this very destructive conspiracy,” he emailed Fauci on April 16.

Fauci was less concerned. “I would not do anything about this right now,” he replied the next day. “It is a shiny object that will go away in times.” For many months, it did just that. Natural emergence remained the only possibility on the table in the scientific establishment and mainstream media.

But the lab-leak theory gained in plausibility as more facts emerged about the research NIAID was funding at the Wuhan Institute of Virology. The program followed a debate among virologists as to how far one should go in enhancing a virus’s abilities in the lab in order to study its properties. Collins and Fauci were proponents of “gain-of-function” research, as it is blandly known. “Important information and insights can come from generating a potentially dangerous virus in the laboratory,” they wrote in the Washington Post in 2011.

Some virologists questioned whether the possible gains were worth the substantial risks. But Collins and Fauci prevailed over the doubters, and in 2014 they began supporting a program of manipulating SARS-related viruses in Wuhan. Peter Daszak, president of the EcoHealth Alliance of New York, managed the program, using NIH money to fund Shi Zhengli, the chief expert on coronaviruses at the Wuhan Institute of Virology.

As we know from EcoHealth’s grant applications to the NIAID, Shi collected many types of coronaviruses from wild bats and took them back to her lab. There she manipulated the viruses, principally by taking the gene for the spike protein of one virus and inserting it into the genome of another. The stated goal of this research was to find out how close the wild viruses might be to jumping to humans. To this end, she tested the novel viruses in humanized mice—animals genetically engineered to carry in their airways the proteins that the virus targets. The process adapts the virus to be capable of attacking live humans, even though this is not the intent.

Besides adding novel spike proteins, Shi’s manipulations may well have included insertion of a furin cleavage site. EcoHealth applied for a grant in 2018 for research that proposed to “introduce appropriate human-specific cleavage sites” into SARS-like coronaviruses. Though this grant application, submitted to an agency of the Defense Department, was turned down, Shi’s research team was clearly aware of the technique and may well have conducted such experiments with other funds. It’s common practice for researchers to test out experimental techniques before applying for the grant in which they will be used.

The Andersen group’s detection of the furin cleavage site on January 31, 2020, was a plausible basis for suspecting that SARS-CoV2 was not a natural virus. It’s an enduring puzzle as to why they then ruled out this possibility a mere four days later. There is thus far no counterargument in the public record. Farzan, the one member among Andersen and his three colleagues who did not sign the Nature Medicine article, declined an email request to discuss the episode.

However, Garry said in an email response that his remarks about the furin cleavage site in the emails discussed in the House committee’s January 11 letter were just arguing a position and were taken out of context. “I favored the natural origin and had so for weeks, but the furin cleavage site was hard to rationalize.”

The Andersen group’s change of mind, Garry said, was not precipitate and had developed over several weeks for scientific reasons, not political pressure. A principal factor was “extremely important and compelling” data posted on January 23 about a coronavirus found in pangolins. The pangolin virus’s receptor-binding domain, a critical feature that recognizes a target protein on the cell surface, was almost identical to that of SARS-CoV-2. This was a “big deal,” Garry said, because “if this feature was natural then very likely the whole virus was natural including the furin cleavage site.”

The argument is a little difficult to follow. Just because one part of the virus is natural, why does that show that someone had not inserted a genetically engineered furin cleavage site in another part? Garry replied that engineering such a site would be a “very expensive, labor intensive, multiple month” process, and that in any case the Chinese researchers wouldn’t have used a virus so different from SARS1, the cause of a 2003 epidemic and their primary known focus of interest. But this is a hypothetical, not a clinching argument. If the Andersen group heard compelling new information about the virus’s origin between January 31 and February 4, Garry seems unable to say what it was.

So what induced these virologists to such a radical change of view? “The February 1, 2020, telecon sent a clear message to participants that Fauci and Collins regarded discussion of the lab leak possibility, even though plausible on scientific data, to be politically unacceptable and something that had to be blocked,” says Richard Ebright of Rutgers University, a molecular biologist and a leading critic of gain-of-function research.

Fauci oversees a large portion of funds available for virology research in the U.S. It is not unreasonable to suppose that virologists keen on continuing their careers would be very attentive to his wishes. Both Garry’s and Andersen’s labs receive large sums of money from the NIAID. “Telecon participants with current and pending grants controlled by Fauci and Collins could not have missed or misunderstood the clear message,” Ebright says.

The repudiation by Andersen, Garry, and Holmes of their original conclusion, expressed in the January 31, 2020, email was of enormous benefit to Collins and Fauci. Though primary responsibility for any lab leak would rest with Shi at the Wuhan Institute of Virology and with Chinese regulatory authorities, Collins and Fauci could share a portion of the blame for having funded gain-of-function research despite its obvious risks and then failing to ensure that grant recipients were taking all necessary precautions.

If there really was a conspiracy surrounding the origin of SARS-CoV-2, Congress should search for it—first, in the still-closed records of the National Institutes of Health and the EcoHealth Alliance. Congress then needs to ask scientists free of outside pressures or conflicts to reassess the probable origin of a virus that has now killed some 5 million people worldwide.

Nicholas Wade is a science writer and author who has worked at Nature, Science, and the New York Times.

https://www.city-journal.org/covid-origin-conspiracy

NYC Schools Reported Over 9,600 Students to Child Protective Services Since Aug. 2020

 Paullette Healy can tick off the ways her family’s life has been plunged into uncertainty and fear over the last three months: Her younger child’s repeated nightmares and increased anxiety, the hours she’s poured into collecting forms from her kids’ doctor and psychiatrist to prove she’s a fit parent and an arduous and probably costly legal process that still looms to clear her name.

From early November through Jan. 1, the Bay Ridge, Brooklyn family was under investigation by the Administration for Children’s Services, or ACS, the New York City agency tasked with looking into suspected cases of child abuse and neglect. Healy had been reported for educational neglect for not sending her children to school amid COVID fears, even though she says her kids kept up with their work remotely. 

The report that spurred their investigation was one of more than 2,400 that New York City school personnel made to the New York Statewide Central Register for Child Abuse and Maltreatment during the first three months of the 2021-22 school year, according to data obtained by The 74 through a public record request — about 45 percent more than were reported over the same time span a year prior when most of the city’s nearly 1 million students were learning remotely. From August 2020 to November 2021, records show NYC school staff made a total of 9,674 reports. 

The highest monthly tally, 1,046, came in November 2021, the same month that ACS and the Department of Education issued joint guidance ​​instructing schools to have patience with families keeping their children home due to COVID-19 concerns, and to avoid jumping to allegations of educational neglect when students don’t show up.

About a third of the reports from NYC school personnel from September through November — 839 out of 2,412 — included an allegation of educational neglect. Of that total, just over half named educational neglect as the sole allegation, according to an ACS spokesperson, who pointed out that the rate was actually higher pre-COVID in the fall of 2019, when about 40 percent of reports from city school personnel alleged educational neglect.

Many of the families caught up in COVID-related investigations this school year, including the Healys, say that given the DOE’s statements and guidance, their ACS reports should never have been made.

Child welfare investigations, which disproportionately involve low-income families of color, can have devastating impacts. Charges can stay on parents’ records for years — even in cases like Healy’s where the agency ultimately found no evidence of neglect. Job prospects in fields like child care and education can be erased. And most dire, children can be separated from their parents — a trauma that studies show is later associated with elevated risks of mental health challenges, incarceration and even early death.

ACS has clarified that, on its own, missing class should not be a reason for educators to suspect neglect. “We are … working together (with the DOE) to make sure that families are not reported to the state’s child abuse hotline solely because of [a] child’s absences from school,” a spokesperson wrote in a Jan. 13 email to The 74, adding that the agency is providing training to professionals working with children on ways to support families without calling the hotline.

But now, after New York City student attendance rates plunged in early January amid surging Omicron cases, and with ongoing debate over how the Adams administration will approach remote learning, questions swirl over whether even more families may get entangled in the child welfare web.

“I’m … worried about who’s going to be asked to answer for the decisions that they made in the wake of Omicron,” said Gabriel Freiman, head of education practices at the legal nonprofit Brooklyn Defenders.

Healy echoed the concern, adding that families who kept children home amid the surge may be “vulnerable to possible investigation.”

How did we get here?

Rewind to the fall: New York City announced that schools would open in-person with no option for remote learning, and Healy was terrified. She had suffered massive personal losses through the pandemic — more than a dozen of her relatives had died of the virus, she said, ranging in age from 36 to 87 — and the Brooklyn mother remained unconvinced that sending her children into crowded buildings was a good idea. She quickly submitted applications for home instruction for both of her kids. 

Meanwhile, just before classrooms reopened, the nation’s largest school district made a vow to parents: “The only time ACS will intervene is if there is a clear intent to keep a child from being educated, period,” then-schools Chancellor Meisha Porter said during a September press conference. “We want to work with our families because we recognize what families have been through.”

Even while remote, Healy’s kids were still learning, she said. Both were accessing and submitting coursework via Google Classroom. She had even met with school staff to update both children’s Individualized Education Programs, the plans that spell out their special needs and mandated school services.

“I was in constant contact (with the schools),” Healy said. “​​All of the things that needed to happen were still happening.”

Paullette Healy and her family are still dealing with the fallout of being investigated by ACS for educational neglect. (Asher Lehrer-Small)

So it caught Healy off guard when, in early November, an ACS caseworker knocked on her door. The agency had received a report of suspected educational neglect from a staff member at her younger child’s school.

Healy had understood that a visit from ACS was a possibility. As a member of the advocacy group PRESS, Parents for Responsive Equitable Safe Schools, she knew of numerous other parents keeping their children home from school due to coronavirus concerns who had been investigated. She had even put resources together informing parents of their rights when ACS shows up. But her own investigation still took her by surprise. If anything, she was over-involved in her children’s education, she thought, not neglectful. 

“I’ve always inserted myself into the schools whether they wanted me there or not,” Healy joked.

Familiar with her rights as a parent, Healy did not let the caseworker inside their house. But despite being armed with strategies to navigate the situation, the visit was jarring to the whole family. After the caseworker left, her 14 year-old son, who has autism, paced back and forth for an hour, worried that the unfamiliar woman would return with law enforcement, Healy said. Her 13 year-old child, who identifies as non-binary, had continued nightmares, fearing they would be taken away from the only home they knew. Even Healy herself couldn’t avoid creeping thoughts of the worst-case scenario.

“You automatically think someone’s here to take my kids away,” she told The 74.

‘ACS is like the police’

Just like doctors and nurses, school personnel are mandated by New York state law to report suspected cases of child abuse and neglect to a central hotline. But even before COVID-19, experts and parents alike have critiqued the practice as potentially harmful to families and prone to racial bias.

In New York City, some 90 percent of children named in ACS investigations are Black or Hispanic, while, together, those racial groups make up 60 percent of the city’s youth. In 2019, according to city data, the lower-income, mostly Black and Latino neighborhood of East Harlem saw over six times as many investigations as the nearby Upper East Side, which is mostly white and affluent.

Even among neighborhoods with similar poverty rates, those with greater shares of Black and Hispanic residents face higher rates of child welfare investigations, research shows.

“ACS has long been used to criminalize our families,” said Tanesha Grant, a New York City parent leader who formed the group Parents Supporting Parents for mutual aid throughout the pandemic. Many Black parents, she told The 74, see child protective services as a form of racialized surveillance and punishment. 

“ACS is a curse word in our community. ACS is like the police,” she said.

Tanesha Grant speaks at a New York City protest marking the one-year anniversary of Breonna Taylor’s death at the hands of police. (Stephanie Keith / Getty Images)

“It is deeply concerning to us,” said a spokesperson for the agency, “that, year after year, there are dramatic racial and ethnic disparities in the reports ACS receives from the state and is required [by law] to investigate.” 

As per a 2021 state law, mandated reporters are now required to undergo implicit bias training intended to keep reporters’ assumptions from coloring their assessments of parental fitness.

But just how much of an impact it will make in the K-12 setting remains to be seen. Nationwide, school staff report more allegations to child protective services than any other category of reporters, yet school reports are least likely to be substantiated or lead to family interventions, research shows. In New York City, approximately 1 in 3 calls from school personnel ultimately lead to evidence of abuse or neglect, said ACS. In cases where no evidence is found, families often report that the investigation process can be invasive and disturbing.

There’s often a mismatch, said Freiman, of Brooklyn Defenders, between the typical impacts of child protective services investigations and the purpose they are meant to fulfill.

“Neglect is supposed to cover a category below which we don’t expect any parent to go,” the legal expert explained. 

But the parents keeping their children out of classrooms this school year, from what he has seen, tend to be highly involved and caring, like Healy. Some are even former PTA heads at their children’s schools. 

“These aren’t people who are trying to hurt their children. They’re trying to protect their children,” he told The 74. “ACS is just the wrong tool to employ.”

Even the softer guidance that ACS and DOE offered in November was not enough to sufficiently blunt that tool, advocates said. Healy said she worked with 50 families accused of educational neglect through PRESS and was only able to use the updated guidance to dismiss cases against two of them. 

(JMacForFamilies)

Miranda rights for child welfare

As a way to mitigate some of the worst effects of ACS investigations, state Sen. Jabari Brisport, a former educator from Brooklyn, is sponsoring a bill that would require a Miranda-style reading of parents’ rights at the outset of every child welfare investigation. 

“Parents of color are more likely to be unaware of the rights they have when dealing with [child protective services],” Brisport told The 74. “The bill seeks to address the disparities in the CPS system.”

When, without warning, ACS showed up at the door of Melissa Keaton’s Flatbush, Brooklyn apartment in late October, the mother was taken by surprise. Having lost her father, who was a caregiving adult to her 9-year-old daughter, in April 2020 during the city’s deadly first coronavirus wave, Keaton chose not to return her traumatized child to her sought-after dual language school in Manhattan’s Lower East Side when classrooms reopened. The family was not ready for a two-train commute to and from school each day, Keaton decided. Unlike Healy, she was in the dark about how to navigate the interaction with her caseworker.

“There’s no paperwork. There’s no way of, you know, finding out what is this process? How does it work? What is expected of me?” Keaton told The 74.

Families rally in Brooklyn June 2020, demanding that ACS be defunded. (Erik McGregor/Getty Images)

Parents are not legally obligated to allow caseworkers to enter their homes unless ACS has a warrant. But many parents assent without realizing they have a choice. If caseworkers find evidence of drug use or other outlawed practices, it can lead to compounding charges and increase the likelihood of child separation. 

“Sometimes our families actually find themselves in a deeper hole — not because they’ve done anything wrong — but because ACS comes into the home looking for a problem,” said Taj Sutton, a PRESS organizer. “They’re going through your refrigerator, your cabinets … asking these really invasive and inappropriate questions of your children.”

“This bill doesn’t create new rights,” explained Brisport. “It literally tells parents what their rights are.”

Administration for Children’s Services

‘ACS should not have been called’

Despite the lasting psychological impacts of the neglect investigation upon her children, Healy also acknowledged that her caseworker was kind and actually quite helpful. The staffer fast-tracked her children’s applications for home instruction, helping her younger child recently gain approval for the program. Healy hopes her son will also soon be approved.

But her example, she believes, is an outlier. Not everyone is so fortunate. 

On Dec. 23, Keaton was preparing to lay flowers on the gravestone of her late father. The day marked what would have been his 63rd birthday — and because her dad’s December birthday used to be a part of the family’s holiday rituals, Keaton was feeling his absence even more acutely.

But before she left, she was contacted by her caseworker, who relayed what the mother thought was good news: She was ready to close the case. Keaton told her to come by.

When the caseworker arrived, she told Keaton that the investigation had been completed, but the agency had indeed found evidence of neglect. The news hit her like a thunderclap, Keaton said, stirring fears for how she might appeal, what the findings might mean for her future employment having previously worked at a children’s summer camps, and, most of all, whether it opened the possibility of her daughter being taken away.

The message, Keaton said, was “imprinted in my mind throughout the holidays, along with the thought of, ‘What happens next?’” 

Melissa Keaton’s daughter peers through a shoebox at a 2017 solar eclipse with her grandfather. (Melissa Keaton)

The caseworker instructed her to appeal, Keaton said. When pressed on the evidence behind the finding of neglect, Keaton said, the caseworker explained that her daughter’s school had taken weeks to respond to requests, and when they did, they cited her elementary schooler’s inconsistent 2019 summer school attendance as a strike against the family — data that Keaton said is “completely false.”

Staff at the elementary school did not respond to requests for comment and ACS said that it cannot disclose the details of individual cases. Keaton is awaiting paperwork in the mail that will provide insight into the exact reasons the educational neglect allegation was substantiated by ACS. 

Keaton believes her case was unproductive at best, and inappropriate at worst. She was trying to keep her daughter safe and had been putting together educational assignments for her despite, she said, not being provided materials by her school. She was also applying for medically necessary home instruction — a process through which the November ACS and DOE joint guidance instructs schools to support parents wary of COVID rather than reporting them to child services. 

“Based on the guidelines,” said Keaton, “ACS should not have been called.”

https://www.the74million.org/article/nyc-schools-reported-over-9600-students-to-child-protective-services-since-aug-2020-is-it-the-wrong-tool-for-families-traumatized-by-covid/

The High Cost Of ‘Free’ Covid Testing

 My 4-year-old daughter’s preschool requires weekly Covid testing. We were told not to worry about the cost—the tests are free. On a recent Sunday my family got tested at a pop-up tent outside a gasoline station. The sign on the tent advertised “free Covid testing.”

I didn’t pay for these tests, but they aren’t free. The cost is billed to my health insurance. A few days ago, I received a routine letter from my insurance company summarizing what it paid: $1,140 a month for my daughter’s weekly PCR test. That comes to about $285 per test, 20 times the cost of an at-home rapid test.

Policy makers at both the state and federal levels have opted to finance Covid testing through private health insurance. A California law enacted in November requires insurers to pay for Covid testing without copayments from patients. Insurers must reimburse testing providers, even out-of-network ones, and the state places no restriction on the amount reimbursed.

This gives providers unchecked power to set prices, inflating the societal cost of testing as a tool for controlling the pandemic. Insurance companies will inevitably pass the costs on to policyholders through either higher premiums or reduced benefits.

Let’s revisit the $1,140 per month for testing at my daughter’s preschool. On an annual basis, that would add up to $13,860—a sum that comes close to the $14,974 average yearly expenditure per student in California public schools.

The heart of the problem is that Covid testing isn’t simply a medical service. Regular testing is primarily for the community’s benefit. Policy makers encouraged testing by making it free for individuals, but leaving insurers to pick up the tab established an inefficient system with hidden costs that are likely to haunt us for years to come.

A far better approach would have been for the government to foot the bill for testing. Larger organizations have been able to negotiate lower prices. Last fall the Los Angeles Unified School District provided an estimated nine million Covid tests for students and staff. The price tag was high: $350 million. But that’s $39 a test, or about one-seventh of what my insurer is paying for my daughter.

Like other aspects of healthcare, the current system is also inequitable. Since private insurers are paying more for testing, those pop-up tents on the corner are likely to locate in more-affluent neighborhoods, while testing remains less accessible in lower-income areas.

Another option would be setting a maximum allowable price for Covid testing. Medicare pays up to $100, substantially lower than what some providers charge private insurers. Applying this limit more broadly might be the simplest path, given the way our system has developed. Economists typically don’t advocate price controls, but they can be a viable alternative when markets are already distorted.

Our preschool, the government, and perhaps even those administering the tests are trying to do the right thing. But forcing insurance companies to pay up to 20 times the retail rate for tests creates a sizable moral hazard problem and misallocation of resources that should not be ignored.

Cameron Kaplan, an economist, is an assistant professor of medicine at the University of Southern California’s Keck School of Medicine.

https://vigourtimes.com/the-high-cost-of-free-covid-testing/

Detecting novel SARS-CoV-2 variants in NYC wastewater

 First delta, then omicron. The latest Covid variants have spread like wildfire across the globe in recent months, leading many scientists to wonder when the next variant will appear. Now, scientists may be one step closer to making that determination.

A multi-institutional team of researchers, including virologist Marc Johnson, a professor of molecular microbiology and immunology at the University of Missouri, has detected at least four “cryptic” variants of SARS-CoV-2, the virus that causes COVID-19, in samples of wastewater from New York City’s public sewer system. Their findings were recently published in Nature Communications, a journal of Nature.

According to the Centers for Disease Control and Prevention (CDC), viruses such as SARS-CoV-2 can continually evolve by acquiring mutations. Variants, such as delta or omicron, may contain one or more mutations within their viral sequence that help to distinguish themselves from other variants of SARS-CoV-2.

Johnson, a co-corresponding author on the study, believes the results suggest the “cryptic” mutations they identified in New York City could be linked to possible animal origins. While these origins have not been verified yet, he believes one possible source could be the rats that frequent New York City’s sewer system.

“For instance, we still don’t know where the omicron variant came from, but it had to come from somewhere,” Johnson said. “These variants are bubbling up everywhere, including omicron, which eventually spilled into the general population and wreaked havoc. We think these weird lineages could be where the next variant of concern for COVID-19 comes from.”

Hunting for virus mutations

The idea for this project started in March 2020 after John Dennehy, a virologist and professor of biology at Queens College, City University of New York, began looking for different ways to analyze the impact of the COVID-19 pandemic. Monica Trujillo, an associate professor at Queensborough Community College, City University of New York, shared with Dennehy a study from Australia that described using wastewater to track the spread of a coronavirus, and it inspired Trujillo to ask officials from the New York City Department of Environmental Protection to send her wastewater samples in order to conduct similar work.

In the summer of 2020, Dennehy and Trujillo teamed up with Davida Smyth, the lead author on the study. Smyth, now an associate professor at Texas A&M University-San Antonio, was at The New School, New York at the time. They put together a team of researchers to begin tracking the spread of coronavirus via New York City’s wastewater. Since then, Dennehy, a co-corresponding author on the study, found some interesting results. When he shared some of the more unusual results during a March 2021 episode of Vincent Racaniello’s podcast “This Week in Virology,” a popular podcast with virologists nationwide, Johnson happened to be listening.

Samples of wastewater are ready for testing in the lab of Marc Johnson at the Christopher S. Bond Life Sciences Center.

“The mutations that we were observing in our sample weren’t typical among any of the known sequences circulating at that time,” Dennehy said.

Ironically, Johnson was simultaneously reaching out to various researchers across the United States who were doing similar work with wastewater after he observed some unusual results from his analysis of wastewater in some of his samples from the greater St. Louis area. On the podcast, he heard Dennehy describe their targeted approach, which happened to be the same method MU was using to test samples of wastewater for SARS-CoV-2 in Missouri, but with one key difference — MU was analyzing a larger region of the virus genome for possible mutations. Within a week, Johnson had samples of NYC wastewater delivered to MU for further analysis.

“When we first started with the samples from New York City, I was looking to see if they had the same virus sequences that I saw in some of my samples from St. Louis,” Johnson said. “They were different, but all of them had similar mutations in common at one particular location on the virus — Q498. What’s amazing is that in most of the samples from New York City, the Q in Q498 had turned into a Y, or glutamine into tyrosine. If you look at the database, there was not, and continues to not be, a human patient who has had that mutation.”

In May 2020, MU began working with Missouri officials to assist with statewide tracking of COVID-19 using human waste.

Dennehy believes a possible explanation could be a biological process called convergent evolution.

“An animal in Missouri is not going to mix with the same type of animal in New York City,” Dennehy said. “Therefore, the evolution of the virus in each geographic area is independent of each other, but because it’s the same animal, the virus looks the same in both places. For instance, we think conditions in South Africa that gave rise to the omicron variant are the same conditions in New York City that gave rise to our cryptic variants. As a biologist, I thought the spread of delta was menacing, but the speed in which omicron took over New York City is on another level.”

Marc Johnson's lab (above) is one of two labs used by MU to test wastewater for COVID-19.

Understanding the broader impact

Smyth joined the research team in part due to her passion for taking science from inside a laboratory to showing how it can be applied through a broader, real-world impact. A proud Irish immigrant, she transitioned from studying the basics of biology early in her career to now pursuing her passion by engaging her students in real-world health issues, such as antibiotic resistance, and tracking coronavirus in wastewater.

“I’m interested in how we can take what we know and apply it to the real world where it is needed the most,” said Smyth, who is also the deputy director for the National Center for Science and Civic Engagement. “Wastewater surveillance is really important in the context of community-based, public health measures where we have the ability to communicate health information at a level where decisions, practices and interventions can be implemented. Wastewater surveillance is fast, inexpensive and unbiased, and for that reason it has the ability to be implemented depending on resource availability in a variety of contexts, especially in areas with limited resources such as low testing and vaccine availability.”

“Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater,” was published in Nature Communications. Funding was provided in part by the New York City Department of Environmental Protection, a donation from the Linda Markeloff Charitable Fund, and a grant from the National Institutes of Health (U01DA053893-01).

Co-authors include Devon Gregory, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Terry Lyddon, Clayton Rushford, Reinier Suarez, Emma Teixeiro and Mark Daniels at MU; Davida Smyth and Geena Sompanya at Texas A&M University-San Antonio; Monica Trujillo at Queensborough Community College, City University of New York; Kristen Cheung, Anna Gao, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Michelle Markman, and Kaung Myat San at the City University of New York; and Fabrizio Spagnolo at Long Island University.

The Sewershed Surveillance Project

In May 2020, MU began working with the Missouri Department of Health and Senior Services (DHSS) and the Missouri Department of Natural Resources to assist Missouri officials with statewide tracking of COVID-19 using human waste.

Using the combined resources of Johnson’s lab in the Christopher S. Bond Life Sciences Center and the lab of collaborator Chung-Ho Lin in the College of Agriculture, Food and Natural Resources, Johnson and Lin have tested thousands of wastewater samples from more than 150 participating community water systems across Missouri. Their research method was able to detect the initial wave of community spread of the delta variant in Missouri, and subsequently the initial wave of community spread of the omicron variant in Missouri as well.

In addition, their work has been used outside of Missouri in places like New York City, where they assisted the New York City Department of Environmental Protection with detecting the first omicron case in New York City that is noted in this Centers for Disease Control and Prevention (CDC) Morbidity and Mortality Weekly Report.

https://showme.missouri.edu/2022/mu-scientist-helps-detect-novel-sars-cov-2-variants-in-nyc-wastewater/

Cheap blood test detects lung cancer at an early and treatable stage

 A blood test that can detect lung cancer before people get symptoms may save lives by allowing early treatment.

Lung cancer has a 63 per cent survival rate if it is caught early and hasn’t spread to other parts of the body. Once it spreads, the survival rate drops to 7 per cent.

Catching lung cancer early is difficult because we don’t have any cheap, simple ways to screen for it. Chest CT scans can be used to look for tumours in the lungs, but they are expensive, expose people to radiation and can sometimes make false detections.

Jun Wang at Peking University in Beijing, China, and his colleagues discovered a new way to detect lung cancer by checking people’s blood for unusual levels of nine different lipids – fatty molecules that are present in unusual amounts in tumours.

They trialled the blood test in 1036 people over the age of 40 who didn’t have symptoms of cancer and were going for an annual physical examination. The test was over 90 per cent accurate at detecting those with lung cancer, as determined by a CT scan of each participant’s chest.

The 13 individuals who were found to have lung cancer – mostly early stage – were treated by surgically removing their tumours.

A benefit of the test is that it takes less than 90 minutes to complete, from taking a person’s blood to running it through a mass spectrometry machine to measure lipid levels and crunching the data, says Wang.

The test is also relatively cheap and doesn’t expose people to any radiation, he says.

Kwun Fong at the Prince Charles Hospital in Brisbane, Australia, says the blood test looks promising and could potentially be used to screen people who are at high risk of developing lung cancer – for example, those who have a family history or are heavy smokers.

This in turn could save lives by identifying cancers at a stage where they can still be curatively treated with surgical removal or radiation, says Fong.

“[The test] needs to be validated in other populations first, but if it performs as well, it could be used in addition to CT screening or possibly as a replacement,” he says.

Journal reference: Science Translational Medicine, DOI: 10.1126/scitranslmed.abk2756

https://www.newscientist.com/article/2306773-cheap-blood-test-detects-lung-cancer-at-an-early-and-treatable-stage/#ixzz7K2ktS9jD

Magnetic seeds can be steered into cancer tissue to kill it with heat

 One promising possibility for next-gen cancer treatments involves infiltrating tumors with specially-designed particles and heating them up to destroy the cancerous tissue, and new research from the University of College London (UCL) takes this technology into new terrain. The team's solutions leverages MRI scanning to steer magnetic seeds to the site with a high level of precision, offering new hopes of advanced treatments for hard-to-reach cancers.

The technique at the heart of this research is known as magnetic hyperthermia, and it is a technology that has shown some exciting potential in recent years. The idea is to use carefully placed magnetic particles to heat up targeted cancer cells without harming surrounding healthy tissue, and is currently only used in humans to treat very aggressive forms of brain cancer.

We've seen scientists make promising inroads when it comes to making this technology more effective, such as combining it with chemotherapy to enhance the efficacy of both approaches, heating the particles up with lasers to selectively take out the cancer cells, or delivering clusters of particles intravenously to have them passively accumulate in the tumor.

The UCL team sought to improve on a couple of drawbacks of current techniques, such as the limited ability to manipulate the particles once they are in the body, and a reliance on multiple particles to get the job done. The researchers call their solution “minimally invasive image-guided ablation” (MINIMA), and it instead uses a single ferromagnetic thermoseed that can be steered to the tumor site with an MRI scanner and promptly heated up to deal the damage.

“MINIMA is a new MRI-guided therapy that has the potential to avoid traditional side effects by precisely treating the tumor without harming healthy tissues," said senior author Professor Mark Lythgoe. "Because the heating seed is magnetic, the magnetic fields in the MRI scanner can be used to remotely steer the seed through tissue to the tumor. Once at the tumor, the seed can then be heated, destroying the cancer cells, while causing limited damage to surrounding healthy tissues.”

Artist's impression of a newly developed magnetic seed at the tumor site

Chris Payne, Simon Walker-Samuel, Rebecca Baker and Mark Lythgoe at UCL

The 2-mm seeds are made from a metal alloy, are spherical in shape, and are implanted into tissue before being drawn towards the tumor site. This was demonstrated in mouse models where, while being tracked to within 0.3-mm accuracy, the seeds could be navigated to the cancer and then heated up to take out the tumor.

“We are now able to image and navigate a thermoseed in real-time through the brain using an MRI scanner," said Lythgoe. "As MRI is already used to detect the boundaries of cancers, the seed can be moved precisely to ensure it does not stray into surrounding healthy tissue. As the seed is guided through the tissue it can be heated to destroy the cancer. This combines therapy and diagnosis into a single device, creating a completely new class of imaging therapy.”

The scientists imagine the MINIMA technology finding use in tackling difficult-to-reach and aggressive brain cancers, along with other cancers that call for minimally invasive therapies, such as prostate. The even imagine fashioning the seeds into tiny tools that can be deployed for even more powerful cancer-fighting effects.

“In the longer term, we will change the shape of the seed to act as a tiny cutting scalpel that could be guided through tissue, which would allow surgeons to perform remotely controlled operations, revolutionizing non-invasive surgery," said Lythgoe.

The research was published in the journal Advanced Science. 

https://newatlas.com/medical/magnetic-seeds-cancer-tissue-tumors-heat-mri/

Innovative capsule allows mRNA vaccines to be delivered orally

 A new study from scientists at MIT has demonstrated a way to deliver mRNA directly to the digestive tract using a capsule. The researchers indicate this oral delivery system could be a unique way to administer mRNA therapies directly to the stomach.

Because our digestive system is filled with harsh acids designed to break down complex foods, oral drugs often need protective coatings to get past the stomach. Some drugs, such as insulin, need to be injected as researchers have struggled to develop effective ways to administer them orally.

A few years ago, MIT researchers revealed a unique method of oral drug administration. The innovation was a small capsule coated with microneedles. Upon reaching the intestines the capsule injects its contents directly into the wall of the gut and then harmlessly passes through a person’s digestive system.

In 2019, the MIT team demonstrated the capsule effectively delivered insulin in animal tests. In pig experiments the researchers found the capsule could get the same volume of insulin into the animal's bloodstream as a standard subcutaneous injection.

Now, in light of the remarkable pace of mRNA research due to the COVID-19 pandemic, the researchers have shown this novel drug delivery system can effectively work with mRNA molecules.

“Nucleic acids, in particular RNA, can be extremely sensitive to degradation particularly in the digestive tract,” said co-senior author on the new study, Giovanni Traverso. “Overcoming this challenge opens up multiple approaches to therapy, including potential vaccination through the oral route.”

First, the researchers developed a new kind of nanoparticle to hold the mRNA. This novel nanoparticle is designed to more effectively get into cells and deliver the mRNA payload, meaning fewer nanoparticles are needed to produce therapeutic effects.

After freeze-drying the nanoparticle payloads and packaging them into the microneedle capsules the researchers tested them out in several animal models. The mRNA being delivered in the experiments coded for the production of innocuous reporter proteins, which can signal the tissue is taking up the mRNA blueprint and manufacturing the desired molecules.

The pig experiments successfully demonstrated that stomach cells took up the mRNA molecules and produced reporter proteins. Alex Abramson, co-lead author on the new study, says more work is needed to explore whether mRNA vaccines administered this way can lead to systemic immune responses but it is plausible to think it could work due to the volume of immune cells in the gastrointestinal tract.

“There are many immune cells in the gastrointestinal tract, and stimulating the immune system of the gastrointestinal tract is a known way of creating an immune response,” said Abramson.

Beyond delivering mRNA vaccines in a new way, this new research points to exciting new targeted treatments for gastrointestinal diseases. mRNA can be used to ask cells to produce any number of molecules that could be therapeutically useful and delivering those blueprints directly to intestinal cells promises new ways to treat everything from ulcers to inflammatory bowel disease.

“When you have systemic delivery through intravenous injection or subcutaneous injection, it’s not very easy to target the stomach,” said Abramson. “We see this as a potential way to treat different diseases that are present in the gastrointestinal tract.”

The new study was published in the journal Matter.

https://newatlas.com/medical/capsule-oral-mrna-vaccine-mit/