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BA.2.12.1 is on the rise in New York…

A recently named sub-strain represents the latest twist in the ongoing evolution of SARS-CoV-2. It’s currently active in the United States and looks…

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A recently named sub-strain represents the latest twist in the ongoing evolution of SARS-CoV-2. It’s currently active in the United States and looks to be very capable of spreading, outpacing the base model BA.2. As usual, it’s early days so we don’t know a lot about BA.2.12.1 and disease severity or how much protection is offered by previous vaccination. It seems BA.2.12.1 is likely to visit a host near you in 2022.

Analysis of some genomes shows the rise of BA.2.12.1

The US CDC genomic sequencing data page shows this variant’s rise to the week ending 23rd of April. They also model its likely ongoing rapid spread.[2,5]

Graph from the US Centers for Disease Control and Prevention (CDC) COVID data tracker, variant proportions website.[2]

BA.2.12.1 has also been highlighted on NEXTSTRAIN – a gold standard resource for following the emergence and changes of a range of important viruses.[2]

Dr Emma Hodcroft notes NEXTSTRAIN has made a place for some new clades in the forest of SARS-CoV-2, and this includes BA.2.12.1 (22C).[3] See the NEXTSTRAIN blog on this image.[4]

Remember that sequencing is a lagging indicator – what we see now, happened in the past. The lag can be bigger or smaller depending on the source.

Genomic sequencing usually shows only the tip of the iceberg. It shouldn’t be used to define the number of cases in an area unless every case is a) captured (some sites are better than others) and b) can be sequenced (depends on sampling, sample handling, whereabouts in the course of the disease the person is, CT, sequencing method, data analysis, etcetera).

Drawing conclusions about changes in virus proportions based on viral genome sequencing is subject to from whom, where and when samples were collected; do they represent what we assume when we look at the data? What proportion cam from hospitalised patients, cases of special interest, asymptomatic cases, are they from a fixed percentage of cases, are they from all over the land, is there a proportional representation of locals and travellers…and so on.

Hospitalised cases are on the rise in New York

Given this apparent rise in BA.2.12.1 viruses in New York COVID-19 cases, it’s also very interesting to look at hospitalisations. Here we find that there’s been a rise in hospitalised cases as well.[1]

Graph from New York State Health Department’s novel coronavirus hospitalisation summary.[1]

BA.2.12.1 is already travelling

With an estimated transmission advantage of 23% – 27% over the original BA.2,[14] it’s no surprise BA.2.12.1 is on the move. Other States in the US have already reported cases,[13] and it’s been detected in a case in Delhi, India [17], among two local cases in Singapore [16] and in the wastewater of the Australian State of Victoria.[15,6]

We know what we can do

There are a few things we know can help us avoid getting sick from circulating respiratory viruses like SARS-CoV-2.

Getting boosted is top of the list

Our immunity to anything drops off over time.

We’ve learned in the pandemic that the first to go is the relatively short-lived immunity that protects from infection (virus getting a foothold in our airways).

The next to go is immunity against more severe disease but that isn’t necessarily because the vaccine-generate immunity has disappeared, but more because SARS-CoV2 keeps evolving. That other slippery virus we know so well, the influenza virus, does a similar thing. So we have to change the flu vaccine annually to keep up with the rapidly evolving flu viruses.

When viruses like SARS-CoV-2 and influenza virus spread through so many humans, each infection giving rise to a swarm of mutants, there are more chances (because more hosts) that a “fitter” virus will emerge. In this context, fitness relates to a virus changed enough to be able to doge some of our immune response. We’ll learn more about what BA.2.12.1 can do as time goes by.

Air purity

While not accessible to everyone,[18-19] even in richer nations, we expect our food to be fresh and clean and we expect our water to be toxin and pathogen-free. These two things, when present and working, save lives and prevent a lot of diseases.

The next big revolution in public health is to purify pathogens out of the air we share.[9-12]

If we did this, we would dramatically reduce acute and chronic diseases, reduce sick days and lost education days and hospital and aged care disease outbreaks.

Masks

They don’t hurt and, if you use good ones (e.g. P2/N95) and they fit well and you wear them whenever there is a risk, you’ll reduce the likelihood of inhaling enough virus to get sick.

References

  1. Novel coronavirus, Daily Hospitalisation Summary
    https://coronavirus.health.ny.gov/daily-hospitalization-summary
  2. COVID Data Tracker – Variant Proportions
    https://covid.cdc.gov/covid-data-tracker/#variant-proportions
  3. Genomic epidemiology of SARS-CoV-2 with subsampling focused globally over the past 6 months
    https://nextstrain.org/ncov/gisaid/global/6m
  4. SARS-CoV-2 clade naming strategy for 2022 9last visited, 02MAY2022 AEST)
    https://nextstrain.org/blog/2022-04-29-SARS-CoV-2-clade-naming-2022
  5. New Omicron Variant BA.2.12.1 Now Dominant In New York, Driving Infections; Strain Up 47% Nationwide In Past Week
    https://deadline.com/2022/04/new-omicron-variant-ba-12-1-dominant-new-york-1235010160/
  6. COVID-19 Omicron subvariant BA.2.12.1 detected in Australia in Victorian wastewater
    https://www.abc.net.au/news/2022-04-30/covid-19-omicron-subvariant-ba-2-12-1-detected-in-victoria/101027818
  7. Survival Of The Fittest: The Rise Of BA.2.12.1
    https://www.forbes.com/sites/williamhaseltine/2022/04/22/survival-of-the-fittest-the-rise-of-ba2121/?sh=29687b5b413d
  8. Portable air cleaners and residential exposure to SARS-CoV-2 aerosols: A real-world study
    https://pubmed.ncbi.nlm.nih.gov/35481935/
  9. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals
    https://www.nature.com/articles/s41586-020-2271-3
  10. Use of portable air purifiers as local exhaust ventilation during COVID-19
    https://pubmed.ncbi.nlm.nih.gov/35290164/
  11. Airborne SARS-CoV-2 in hospitals – effects of aerosol-generating procedures, HEPA-filtration units, patient viral load and physical distance
    https://pubmed.ncbi.nlm.nih.gov/35226740/
  12. Use of portable air cleaners to reduce aerosol transmission on a hospital coronavirus disease 2019 (COVID-19) ward
    https://www.cambridge.org/core/journals/infection-control-and-hospital-epidemiology/article/abs/use-of-portable-air-cleaners-to-reduce-aerosol-transmission-on-a-hospital-coronavirus-disease-2019-covid19-ward/17C5199D3903ABD465017C34AA741826
  13. A new omicron subvariant is spreading in North Texas: What we know about BA.2.12.1
    https://www.star-telegram.com/news/coronavirus/article260860897.html
  14. New York State Department of Health Announces Emergence of Recently Identified, Highly Contagious Omicron Subvariants in New York and Urges Continued Vigilance Against COVID-19
    https://www.health.ny.gov/press/releases/2022/2022-04-13_covid-19.htm
  15. Coronavirus update for Victoria – 29 April 2022
    https://www.health.vic.gov.au/media-releases/coronavirus-update-for-victoria-29-april-2022
  16. 2 S’pore Covid-19 cases infected with new Omicron sub-variant BA.2.12.1
    https://www.straitstimes.com/singapore/health/two-singapore-covid-19-cases-infected-with-new-sub-variant-of-omicron-ba2
  17. Omicron’s BA.2.12.1 mutant found in a Delhi patient, all you need to know about the sub-variant
    https://www.dnaindia.com/india/report-omicron-ba-2-12-1-mutant-found-in-a-delhi-patient-all-you-need-to-know-about-the-sub-variant-2947595
  18. Calls for clean water continue
    https://nit.com.au/calls-for-clean-water-continue/
  19. Uranium Detectable in Two-Thirds of U.S. Community Water System Monitoring Records
    https://www.publichealth.columbia.edu/public-health-now/news/uranium-detectable-two-thirds-us-community-water-system-monitoring-records

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RFK Jr. Reveals Vice President Contenders

RFK Jr. Reveals Vice President Contenders

Authored by Jeff Louderback via The Epoch Times,

New York Jets quarterback Aaron Rodgers and former…

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RFK Jr. Reveals Vice President Contenders

Authored by Jeff Louderback via The Epoch Times,

New York Jets quarterback Aaron Rodgers and former Minnesota governor and professional wrestler Jesse Ventura are among the potential running mates for independent presidential candidate Robert F. Kennedy Jr., the New York Times reported on March 12.

Citing “two people familiar with the discussions,” the New York Times wrote that Mr. Kennedy “recently approached” Mr. Rodgers and Mr. Ventura about the vice president’s role, “and both have welcomed the overtures.”

Mr. Kennedy has talked to Mr. Rodgers “pretty continuously” over the last month, according to the story. The candidate has kept in touch with Mr. Ventura since the former governor introduced him at a February voter rally in Tucson, Arizona.

Stefanie Spear, who is the campaign press secretary, told The Epoch Times on March 12 that “Mr. Kennedy did share with the New York Times that he’s considering Aaron Rodgers and Jesse Ventura as running mates along with others on a short list.”

Ms. Spear added that Mr. Kennedy will name his running mate in the upcoming weeks.

Former Democrat presidential candidates Andrew Yang and Tulsi Gabbard declined the opportunity to join Mr. Kennedy’s ticket, according to the New York Times.

Mr. Kennedy has also reportedly talked to Sen. Rand Paul (R-Ky.) about becoming his running mate.

Last week, Mr. Kennedy endorsed Mr. Paul to replace Sen. Mitch McConnell (R-Ky.) as the Senate Minority Leader after Mr. McConnell announced he would step down from the post at the end of the year.

CNN reported early on March 13 that Mr. Kennedy’s shortlist also includes motivational speaker Tony Robbins, Discovery Channel Host Mike Rowe, and civil rights attorney Tricia Lindsay. The Washington Post included the aforementioned names plus former Republican Massachusetts senator and U.S. Ambassador to New Zealand and Samoa, Scott Brown.

In April 2023, Mr. Kennedy entered the Democrat presidential primary to challenge President Joe Biden for the party’s 2024 nomination. Claiming that the Democrat National Committee was “rigging the primary” to stop candidates from opposing President Biden, Mr. Kennedy said last October that he would run as an independent.

This year, Mr. Kennedy’s campaign has shifted its focus to ballot access. He currently has qualified for the ballot as an independent in New Hampshire, Utah, and Nevada.

Mr. Kennedy also qualified for the ballot in Hawaii under the “We the People” party.

In January, Mr. Kennedy’s campaign said it had filed paperwork in six states to create a political party. The move was made to get his name on the ballots with fewer voter signatures than those states require for candidates not affiliated with a party.

The “We the People” party was established in five states: California, Delaware, Hawaii, Mississippi, and North Carolina. The “Texas Independent Party” was also formed.

A statement by Mr. Kennedy’s campaign reported that filing for political party status in the six states reduced the number of signatures required for him to gain ballot access by about 330,000.

Ballot access guidelines have created a sense of urgency to name a running mate. More than 20 states require independent and third-party candidates to have a vice presidential pick before collecting and submitting signatures.

Like Mr. Kennedy, Mr. Ventura is an outspoken critic of COVID-19 vaccine mandates and safety.

Mr. Ventura, 72, gained acclaim in the 1970s and 1980s as a professional wrestler known as Jesse “the Body” Ventura. He appeared in movies and television shows before entering the Minnesota gubernatorial race as a Reform Party headliner. He was a longshot candidate but prevailed and served one term.

Former pro wrestler Jesse Ventura in Washington on Oct. 4, 2013. (Brendan Smialowski/AFP via Getty Images)

In an interview on a YouTube podcast last December, Mr. Ventura was asked if he would accept an offer to run on Mr. Kennedy’s ticket.

“I would give it serious consideration. I won’t tell you yes or no. It will depend on my personal life. Would I want to commit myself at 72 for one year of hell (campaigning) and then four years (in office)?” Mr. Ventura said with a grin.

Mr. Rodgers, who spent his entire career as a quarterback for the Green Bay Packers before joining the New York Jets last season, remains under contract with the Jets. He has not publicly commented about joining Mr. Kennedy’s ticket, but the four-time NFL MVP endorsed him earlier this year and has stumped for him on podcasts.

The 40-year-old Rodgers is still under contract with the Jets after tearing his Achilles tendon in the 2023 season opener and being sidelined the rest of the year. The Jets are owned by Woody Johnson, a prominent donor to former President Donald Trump who served as U.S. Ambassador to Britain under President Trump.

Since the COVID-19 vaccine was introduced, Mr. Rodgers has been outspoken about health issues that can result from taking the shot. He told podcaster Joe Rogan that he has lost friends and sponsorship deals because of his decision not to get vaccinated.

Quarterback Aaron Rodgers of the New York Jets talks to reporters after training camp at Atlantic Health Jets Training Center in Florham Park, N.J., on July 26, 2023. (Rich Schultz/Getty Images)

Earlier this year, Mr. Rodgers challenged Kansas City Chiefs tight end Travis Kelce and Dr. Anthony Fauci to a debate.

Mr. Rodgers referred to Mr. Kelce, who signed an endorsement deal with vaccine manufacturer Pfizer, as “Mr. Pfizer.”

Dr. Fauci served as director of the National Institute of Allergy and Infectious Diseases from 1984 to 2022 and was chief medical adviser to the president from 2021 to 2022.

When Mr. Kennedy announces his running mate, it will mark another challenge met to help gain ballot access.

“In some states, the signature gathering window is not open. New York is one of those and is one of the most difficult with ballot access requirements,” Ms. Spear told The Epoch Times.

“We need our VP pick and our electors, and we have to gather 45,000 valid signatures. That means we will collect 72,000 since we have a 60 percent buffer in every state,” she added.

The window for gathering signatures in New York opens on April 16 and closes on May 28, Ms. Spear noted.

“Mississippi, North Carolina, and Oklahoma are the next three states we will most likely check off our list,” Ms. Spear added. “We are confident that Mr. Kennedy will be on the ballot in all 50 states and the District of Columbia. We have a strategist, petitioners, attorneys, and the overall momentum of the campaign.”

Tyler Durden Wed, 03/13/2024 - 15:45

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The SNF Institute for Global Infectious Disease Research announces new advisory board

From identifying the influenza virus that caused the pandemic of 1918 to developing vaccines against pneumococcal pneumonia and bacterial meningitis in…

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From identifying the influenza virus that caused the pandemic of 1918 to developing vaccines against pneumococcal pneumonia and bacterial meningitis in the 1970s, combating infectious disease has a rich history at Rockefeller. That tradition continues as the Stavros Niarchos Foundation Institute for Global Infectious Disease Research at Rockefeller University (SNFiRU) caps a successful first year with the establishment of a new advisory board.

Credit: Lori Chertoff/The Rockefeller University

From identifying the influenza virus that caused the pandemic of 1918 to developing vaccines against pneumococcal pneumonia and bacterial meningitis in the 1970s, combating infectious disease has a rich history at Rockefeller. That tradition continues as the Stavros Niarchos Foundation Institute for Global Infectious Disease Research at Rockefeller University (SNFiRU) caps a successful first year with the establishment of a new advisory board.

This international advisory board was created in part to give guidance on how to best use SNFiRU’s resources, as well as bring forward innovative ideas concerning new avenues of research, public education, community engagement, and partnership projects.

SNFiRU was established to strengthen readiness for and response to future health crises, building on the scientific advances and international collaborations forged in the context of the COVID-19 pandemic. Launched with a $75 million grant from the Stavros Niarchos Foundation (SNF) as part of its Global Health Initiative (GHI), the institute provides a framework for international scientific collaboration to foster research innovations and turn them into practical health benefits.

SNFiRU’s mission is to better understand the agents that cause infectious disease and to lower barriers to treatment and prevention globally. To speed this work, the institute launched numerous initiatives in its inaugural year. For instance, SNFiRU awarded 31 research projects in 29 different Rockefeller laboratories for over $5 million to help get collaborative new research efforts off the ground. SNFiRU also supports the Rockefeller University Hospital, where clinical studies are conducted, and brought on board its first physician-scientist through Rockefeller’s Clinical Scholars program. “One of the surprises was the scope of interest from Rockefeller scientists in using their talents to tackle important infectious disease problems,” says Charles M. Rice, Maurice R. and Corinne P. Greenberg Professor in Virology at Rockefeller and director of SNFiRU. “The research topics range from the biology of infectious agents to the dynamics of the immune response to pathogens, and also include a number of infectious disease-adjacent studies.”

In the past 12 months, SNFiRU often brought together scientists studying different aspects of infectious disease as a way to spur new collaborations. In addition to hosting its first annual day-long symposium, SNFiRU initiated a Young Scientist Forum for students and post-doctoral fellows to meet regularly, facilitating cross-laboratory thinking. A bimonthly seminar series has also been established on campus.

Another aim of SNFiRU is to develop relationships with community-based organizations, as well as design and participate in community-engaged research, with a focus on low-income and minority communities. To that end, SNFiRU is helping develop a research project on Chagas disease, a tropical parasitic infection prevalent in Latin America that can cause congestive heart failure and gastrointestinal complications if left untreated. The project will bring together clinicians practicing at health centers in New York, Florida, Texas, and California and basic scientists from multiple institutions to help the communities that are most impacted.

“The SNFiRU international advisory board convenes globally recognized leaders with distinguished biomedical expertise, unrivalled experience in pandemic preparedness and response, and a shared commitment to translating scientific advancements into equitably distributed benefits in real-world settings,” says SNF Co-President Andreas Dracopoulos. “The advisory board will advance the institute’s indispensable mission, which SNF is proud to support as a key part of our Global Health Initiative, and we look forward to seeing breakthroughs in the lab drive better outcomes in lives around the globe.”

The new advisory board will hold its first meeting on April 11th, 2024, following the second annual SNF Institute for Global Infectious Disease Research Symposium at Rockefeller.

Its members are: Rafi Ahmed of Emory University School of Medicine, Cori Bargmann of The Rockefeller University, Yasmin Belkaid of the Pasteur Institute, Anthony S. Fauci, the former director of the National Institute of Allergy and Infectious Diseases, Peter Hotez of Baylor College of Medicine and Texas Children’s Hospital Center for Vaccine Development, Esper Kallas of of the Butantan Institute, Sharon Lewin of the University of Melbourne Doherty Institue, Carl Nathan of Weill Cornell Medicine, Rino Rappuoli of Fondazione Biotecnopolo di Siena and University of Siena, and Herbert “Skip” Virgin of Washington University School of Medicine and UT Southwestern Medical Center.


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Congress’ failure so far to deliver on promise of tens of billions in new research spending threatens America’s long-term economic competitiveness

A deal that avoided a shutdown also slashed spending for the National Science Foundation, putting it billions below a congressional target intended to…

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Science is again on the chopping block on Capitol Hill. AP Photo/Sait Serkan Gurbuz

Federal spending on fundamental scientific research is pivotal to America’s long-term economic competitiveness and growth. But less than two years after agreeing the U.S. needed to invest tens of billions of dollars more in basic research than it had been, Congress is already seriously scaling back its plans.

A package of funding bills recently passed by Congress and signed by President Joe Biden on March 9, 2024, cuts the current fiscal year budget for the National Science Foundation, America’s premier basic science research agency, by over 8% relative to last year. That puts the NSF’s current allocation US$6.6 billion below targets Congress set in 2022.

And the president’s budget blueprint for the next fiscal year, released on March 11, doesn’t look much better. Even assuming his request for the NSF is fully funded, it would still, based on my calculations, leave the agency a total of $15 billion behind the plan Congress laid out to help the U.S. keep up with countries such as China that are rapidly increasing their science budgets.

I am a sociologist who studies how research universities contribute to the public good. I’m also the executive director of the Institute for Research on Innovation and Science, a national university consortium whose members share data that helps us understand, explain and work to amplify those benefits.

Our data shows how underfunding basic research, especially in high-priority areas, poses a real threat to the United States’ role as a leader in critical technology areas, forestalls innovation and makes it harder to recruit the skilled workers that high-tech companies need to succeed.

A promised investment

Less than two years ago, in August 2022, university researchers like me had reason to celebrate.

Congress had just passed the bipartisan CHIPS and Science Act. The science part of the law promised one of the biggest federal investments in the National Science Foundation in its 74-year history.

The CHIPS act authorized US$81 billion for the agency, promised to double its budget by 2027 and directed it to “address societal, national, and geostrategic challenges for the benefit of all Americans” by investing in research.

But there was one very big snag. The money still has to be appropriated by Congress every year. Lawmakers haven’t been good at doing that recently. As lawmakers struggle to keep the lights on, fundamental research is quickly becoming a casualty of political dysfunction.

Research’s critical impact

That’s bad because fundamental research matters in more ways than you might expect.

For instance, the basic discoveries that made the COVID-19 vaccine possible stretch back to the early 1960s. Such research investments contribute to the health, wealth and well-being of society, support jobs and regional economies and are vital to the U.S. economy and national security.

Lagging research investment will hurt U.S. leadership in critical technologies such as artificial intelligence, advanced communications, clean energy and biotechnology. Less support means less new research work gets done, fewer new researchers are trained and important new discoveries are made elsewhere.

But disrupting federal research funding also directly affects people’s jobs, lives and the economy.

Businesses nationwide thrive by selling the goods and services – everything from pipettes and biological specimens to notebooks and plane tickets – that are necessary for research. Those vendors include high-tech startups, manufacturers, contractors and even Main Street businesses like your local hardware store. They employ your neighbors and friends and contribute to the economic health of your hometown and the nation.

Nearly a third of the $10 billion in federal research funds that 26 of the universities in our consortium used in 2022 directly supported U.S. employers, including:

  • A Detroit welding shop that sells gases many labs use in experiments funded by the National Institutes of Health, National Science Foundation, Department of Defense and Department of Energy.

  • A Dallas-based construction company that is building an advanced vaccine and drug development facility paid for by the Department of Health and Human Services.

  • More than a dozen Utah businesses, including surveyors, engineers and construction and trucking companies, working on a Department of Energy project to develop breakthroughs in geothermal energy.

When Congress shortchanges basic research, it also damages businesses like these and people you might not usually associate with academic science and engineering. Construction and manufacturing companies earn more than $2 billion each year from federally funded research done by our consortium’s members.

A lag or cut in federal research funding would harm U.S. competitiveness in critical advanced technologies such as artificial intelligence and robotics. Hispanolistic/E+ via Getty Images

Jobs and innovation

Disrupting or decreasing research funding also slows the flow of STEM – science, technology, engineering and math – talent from universities to American businesses. Highly trained people are essential to corporate innovation and to U.S. leadership in key fields, such as AI, where companies depend on hiring to secure research expertise.

In 2022, federal research grants paid wages for about 122,500 people at universities that shared data with my institute. More than half of them were students or trainees. Our data shows that they go on to many types of jobs but are particularly important for leading tech companies such as Google, Amazon, Apple, Facebook and Intel.

That same data lets me estimate that over 300,000 people who worked at U.S. universities in 2022 were paid by federal research funds. Threats to federal research investments put academic jobs at risk. They also hurt private sector innovation because even the most successful companies need to hire people with expert research skills. Most people learn those skills by working on university research projects, and most of those projects are federally funded.

High stakes

If Congress doesn’t move to fund fundamental science research to meet CHIPS and Science Act targets – and make up for the $11.6 billion it’s already behind schedule – the long-term consequences for American competitiveness could be serious.

Over time, companies would see fewer skilled job candidates, and academic and corporate researchers would produce fewer discoveries. Fewer high-tech startups would mean slower economic growth. America would become less competitive in the age of AI. This would turn one of the fears that led lawmakers to pass the CHIPS and Science Act into a reality.

Ultimately, it’s up to lawmakers to decide whether to fulfill their promise to invest more in the research that supports jobs across the economy and in American innovation, competitiveness and economic growth. So far, that promise is looking pretty fragile.

This is an updated version of an article originally published on Jan. 16, 2024.

Jason Owen-Smith receives research support from the National Science Foundation, the National Institutes of Health, the Alfred P. Sloan Foundation and Wellcome Leap.

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