COVID and Medical News 6/29/25
COVID levels have increased in the southern states which are now considered high by WastewaterSCAN, although older data from the CDC reports levels overall as low. Florida has high levels of SARS-CoV-2 in wastewater in many sites and emergency department visits for children ages 0 to 11 in Florida are higher than those for people over age 75. These are the highest levels of COVID emergency room visits for kids in Florida since last September. It is expected that the summer wave may be more significant in the South and in the West as these regions did not have as large of a COVID winter wave this year.
From: https://covid.cdc.gov/covid-data-tracker/#ed-visits_separated_by_age_group
Nationally, there are only about 148,000 new COVID infections per day in America, with about every 1 in 225 people currently infected according to JP Weiland. The CDC states on their COVID variant website that they do not have enough samples to accurately predict SARS-CoV-2 variants now. Although the CDC reported that variant NB.1.8.1 is highest, JP Weiland posted that actually XFG is higher in the United States now and is growing faster. XFG was also made a Variant Under Monitoring (VUM) by the WHO this week.
According to WastewaterSCAN, which omits 12 states, COVID in wastewater in southern states of Florida and Louisiana and the Houston area in Texas are high. Mike Hoerger reports that he expects US COVID transmission will increase quickly and that it may be a good idea to restock on good masks, COVID tests and air filters now.
In California, WastewaterSCAN reports that SARS-CoV-2 in wastewater is highest in Vallejo at 200 PMMoV, Novato 182 PMMoV, Oceanside San Francisco 191 PMMoV, Palo Alto 151 PMMoV and San Jose 120 PMMoV. Los Angeles remains low at 39 PMMoV. Santa Clara County reports Palo Alto and San Jose wastewater levels as high, but they have not yet risen to SARS-CoV-2 wastewater levels seen last summer (yet).
Acute COVID infections, General COVID info
Researchers from Mexico analyzed sweat from COVID patients using solid-phase microextraction (SPME) to detect metabolic biomarkers. They identified unique chemical signatures in acute COVID infection, including elevated levels of ketones and aldehydes, that may offer a non-invasive way to monitor infection and disease progression. This reminds me of past studies that showed that scent dogs could detect COVID infection in people’s sweat as accurately as PCR tests.
A new preprint shows that the SARS‑CoV‑2 nucleocapsid (N) protein drives microglial cells into a senescent state by shifting their metabolism toward glycolysis which led to cognitive deficits in mice. In both cell culture and animal models, inhibiting glycolysis (with 2‑DG) blocked microglial senescence and preserved learning and memory function.
A new review from Italy and the US reviewed how viruses like Epstein-Barr virus (EBV) and SARS-CoV-2, and bacteria such as H. pylori, contribute to gut inflammation that can lead to cancer. The viruses and bacteria disrupt immune responses, promote genetic instability, and intensify chronic inflammation which are key drivers of tumor development.
A comprehensive review in Virology maps how SARS‑CoV‑2 interacts with human proteins beyond ACE2, highlighting additional entry co‑receptors like C‑type lectins, neuropilin‑1, CD147, and tyrosine‑kinase receptors. It also details viral tactics to subvert immune responses, including disrupting type I interferon signaling and hijacking host machinery for replication and assembly (e.g. polymerases, lipid regulators, ATP processes, vesicle trafficking). The membrane (M) protein and NSPs are shown to manipulate ER, Golgi, and mitochondrial pathways to promote infection and syncytia formation.
Vaccines
A group from the La Jolla Institute for Immunology and UCSD followed 78 people longitudinally over three years to track how repeated mRNA COVID-19 boosters shaped immunity. They found that while antibody levels rose with each booster, spike-specific CD4+ and CD8+ T cell responses increased early and then plateaued, remaining stable without signs of exhaustion. People with asymptomatic infections developed more diverse T cell profiles, suggesting that repeated vaccination plus mild exposure may strengthen and balance long-term immune defenses.
From: https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00678-3
Antiviral treatments
Invivyd, maker of the COVID monoclonal antibody Pemgarda, tested a new monoclonal antibody against COVID called VYD2311 in Phase 1 and 2 studies. VYD2311 was found to have a long half-life and remained active in the blood for 6 months with no severe side effects reported.
Long COVID
In a new preprint, researchers analyzed multimodal MRI scans (structural, diffusion, functional, and cerebral blood flow) of 76 COVID survivors versus 51 healthy controls. The study found focal atrophy in the right basal ganglia and limbic regions, and decreased white matter integrity in tracts like the uncinate fasciculus and cingulum that was more pronounced in hospitalized cases. Brain changes correlate with common post-COVID symptoms such as fatigue, memory loss, attention issues, and insomnia.
From: https://www.medrxiv.org/content/10.1101/2025.06.20.25329994v1.full.pdf
Researchers from Saudi Arabia looked at the gut microbiome in people who had heart attacks after COVID infection and sometimes after vaccination. They found that beneficial bacteria like Faecalibacterium prausnitzii (F. Prau) and Bifidobacterium longum were significantly reduced, while opportunistic pathogens such as Escherichia coli and Enterococcus faecalis increased in these patients. They concluded that shifts in the gut microbiome could alter metabolite production and contribute to systemic inflammation and increased cardiovascular risk.
A report from the 5th symposium on regulatory autoantibodies against G-protein coupled receptors (RAB-GPCRs) shows that “RAB-GPCRs have emerged as key players in the pathogenesis of complex diseases, including systemic sclerosis, myalgic encephalomyelitis/chronic fatigue syndrome, post-COVID syndrome (ME/CFS/PCS), vasculitis, and transplant rejection.” SARS-CoV-2 can trigger autoantibodies targeting GPCRs which can disrupt vascular, neurological, and autonomic functions and contribute to fatigue and brain fog. Overlap with ME/CFS suggests shared autoimmune pathways, pointing to potential benefits from treatments targeting these autoantibodies.
Fig. 2: Anti-AT1R Autoantibodies and Endothelial Damage with SARS-CoV-2
From: https://www.sciencedirect.com/science/article/pii/S1568997225001156
Fibrinaloid (amyloid-containing) microclots are resistant to degradation and are found in a variety of diseases including Long COVID, ME/CFS, and sepsis. A new review looks at the use of laser speckle imaging (LSI) and laser Doppler imaging (LDI) to assess how fibrinaloid microclots can disrupt the microcirculation.
A group from the University of Washington at Tacoma used 3 RNA-seq datasets of 142 samples from Australia, the US and Russia to look at gene expression signatures in acute COVID infection and in Long COVID. They found that TNF-α/NF-κB pathway signatures could identify patients at risk of severe disease progression from acute COVID infection and that OXPHOS and Myc pathway-associated signatures reflecting metabolic changes may be used as a biomarker for Long COVID diagnosis and severity stratification. “Acute severe COVID-19 benefits from anti-inflammatory interventions targeting the dominant TNF-α/NF-κB pathway, consistent with the proven efficacy of corticosteroids and immunomodulators. Conversely, PASC management should prioritize mitochondrial function restoration and cellular repair mechanisms.”
Measles
As of June 24, 2025, a total of 1,227 confirmed measles cases were reported by 36 states, 12% of cases have been hospitalized (148 of 1227) and there have been 3 confirmed measles deaths.
A measles outbreak at a jail in New Mexico has infected five inmates, prompting quarantines, visitor restrictions, and vaccine/testing efforts by New Mexico health authorities.
A new review of Measles outlines the global resurgence of measles as vaccination coverage dips with nearly 396,000 confirmed measles cases globally in 2024 and over 16,000 in the first two months of 2025 alone. It details measles’ clinical features (like Koplik spots, rash, and severe complications), updated diagnostic methods, and current immunization recommendations. “Because measles is a systemic infection, it can affect the skin, eyes, gut, and respiratory system. Complications that occur in approximately 30% of measles cases — and frequently occur up to 1 month after infection.” Measles complications (see Table 1) include pneumonia, diarrhea, inflammation of the cornea and conjunctivitis, corneal ulceration, blindness, ear infection, death, malnutrition, encephalitis, subacute sclerosing panencephalitis and immune system amnesia. The review emphasizes strengthening immunization programs, improving surveillance, and countering hesitancy to address this disease’s resurgence.
Clinical Features and Pathogenesis of Measles.
From: https://www.nejm.org/doi/full/10.1056/NEJMra2504516
Government Medical News
The American Academy of Pediatricians (AAP) posted that the Advisory Committee on Immunization Practices (ACIP) meeting this week was an “orchestrated effort to sow distrust in immunizations and the vaccine approval process.” Therefore, the AAP will continue to publish their own vaccine guidelines.
From: https://x.com/AmerAcadPeds/status/1938239291139735733
US Representative and pediatrician Dr. Kim Schrier schooled HHS Secretary Kennedy about her personal experience of what vaccine preventable diseases (measles, meningitis, whooping cough) does to children in this important video post.
The National Science Foundation (NSF) was blindsided this week when they found out from media reports, and not internal channels, that they would be ousted from their headquarters in Alexandria. The Department of Housing and Urban Development (HUD) will take over the space that the NSF presently occupies, and NSF staff report there is no new site or budget yet identified, raising concerns for the agency’s future operations.
Other Medical News
A team at the University of Edinburgh engineered Escherichia coli bacteria to convert PET plastic from plastic bottles into paracetamol (acetaminophen), the active ingredient in Tylenol. They used a modified biochemical pathway to turn plastic-derived compounds into the drug at room temperature with up to 92% efficiency.
An adjuvant is a substance added to vaccines to boost the body’s immune response to make the vaccine more effective. A U.K.-U.S. study of 436,788 patients found that vaccines containing the AS01 adjuvant (like the Shingrix vaccine for shingles and Arexvy for RSV) are linked to a roughly 29% lower dementia risk over 18 months, suggesting the adjuvant itself may offer brain-protective benefits.
Eric Topol MD wrote an excellent article this week on the Gut-Brain axis. He discussed four ways that the gut talks to and influences the brain including 1) neural pathways via the Vagus nerve and the autonomic nervous system, 2) hormones such as GLP-1, GIP, and Gherlin, 3) neurotransmitters and short-chain fatty acids (SCFAs) and 4) via the immune system where inflamed T cells from the gut can go to the brain and cause inflammation.
Regarding neuroinflammation, a new review in Science is a “comprehensive overview of the contribution of neuroinflammation during the course of a range of neurologic disorders, including multiple sclerosis, stroke, Alzheimer’s disease, and Parkinson’s disease.”
From: https://www.science.org/doi/10.1126/science.adx0043
APOE ε4 carriers with atrial fibrillation on apixaban (Eliquis) were found to have a higher risk of brain bleeding. Genetic testing may help personalize anticoagulation decisions.
Researchers developed an AI model trained on over 10 million ECGs to predict heart conditions with high accuracy. The model generalizes across populations and could help detect arrhythmias, cardiomyopathies, and other silent conditions using ECGs.
The Arc Institute unveiled STATE, a machine learning model trained on 270 million single-cell profiles that predicts how cells change under genetic or drug perturbations. It showed about 50% better discrimination of perturbation effects and twice the accuracy in finding differentially expressed genes compared to older models.
The Turing Test, proposed by Alan Turing, is a test of a machine's ability to exhibit intelligent behavior equivalent to, or indistinguishable from, that of a person. Researchers from the Arc Institute propose the Virtual Cell Challenge- a "Turing test" for computer models of cells, to see how closely simulations can mimic real cellular behavior. The Virtual Cell Challenge is a public competition, “sponsored by Nvidia, 10x Genomics, and Ultima Genomics, with a grand prize worth $100,000 for the machine learning model that best predicts how cells will respond to genetic perturbations.”
Students at a middle school in the UK are raising money to train their teacher's puppy Nellie to be a therapy dog for the student body by holding Nellie-themed bake sales.
Nellie the future therapy dog
BBC: Nellie-themed cake sales have been held to help the cause
Have a great week and Happy July 4th! I will be taking next week off for the holiday.
Take care,
Ruth Ann Crystal MD
Notes and References
CDC COVID data tracker: https://covid.cdc.gov/covid-data-tracker/index.html#datatracker-home
COVID Emergency Dept visits: https://covid.cdc.gov/covid-data-tracker/#ed-visits_all_ages_combined
Florida emergency department visits for COVID are highest for children age 0 to 11
COVID deaths per week: https://covid.cdc.gov/covid-data-tracker/#trends_weeklydeaths_weeklypctdeaths_00
JP Weiland: https://twitter.com/JPWeiland https://bsky.app/profile/jpweiland.bsky.social
Michael Hoerger modeling: http://pmc19.com/data/, https://twitter.com/michael_hoerger
https://x.com/michael_hoerger/status/1938423951291473944
We are entering wave 11 in the U.S. The average is about 4 infections, so a fair number are on their 7th infection, unfortunately.
https://x.com/michael_hoerger/status/1938318163479040352
Mike Hoerger, PhD MSCR MBA @michael_hoerger
U.S. COVlD transmission is expected to increase quickly. Today is a good day to restock on masks, tests, and air filters. Check your blood pressure. If you can afford it, get an indoor air quality monitor. Track nearby transmission via the new links on our dashboard.
Walgreens positivity rate: https://www.walgreens.com/businesssolutions/covid-19-index.jsp
US Wastewater Monitoring:
CDC wastewater reporting: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html
CDC wastewater map: https://www.cdc.gov/nwss/rv/COVID19-currentlevels.html
Wastewater SCAN: https://data.wastewaterscan.org/
WastewaterSCAN, which omits 12 states, says that SARS-CoV-2 levels are high.
St Petersburg FL 802 PMMoV
Anchorage AK 457 PMMoV
E Bank New Orleans LA 444 PMMoV
Coralville IA 431 PMMoV
Woodlands TX 404 PMMoV
California statewide view https://buff.ly/3YObiul
California SARS-CoV-2 in Wastewater from CDPH: https://skylab.cdph.ca.gov/calwws/
California: CDC California | WastewaterSCAN California
Central Valley Area: WastewaterSCAN Central Valley
Los Angeles Area: WastewaterSCAN Greater LA
San Francisco Bay Area:
Vallejo 200 PMMoV
Novato 182 PMMoV
Oceanside San Francisco 191 PMMoV
Palo Alto 151 PMMoV
San Jose 120 PMMoV
Los Angeles composite 39 PMMoV
International Surveillance
Mike Hoerger https://pmc19.com/data/index.php#international
International Surveillance Data
Austria: Federal Government of Austria |
Canada: C19 Resources Canada * | World Health Network (WHN) Canada **
Finland: WHN Finland **
Germany: WHN Germany **
Netherlands: WHN Netherlands **
Canada
Tara Moriarty Canadian COVID data: https://x.com/MoriartyLab
Canada wastewater https://health-infobase.canada.ca/wastewater/
UK
UKHSA Dashboard:
https://ukhsa-dashboard.data.gov.uk/
UK COVID PCR Test Positivity Map: https://jamestindall.info/skeuomorphology/ladb_covid/index.html
Wastewater monitoring in Scotland
Bob Hawkins UK and Europe https://substack.com/@bhawkins3
European CDC https://www.ecdc.europa.eu/en/news-events/epidemiological-update-sars-cov-2-and-nb181-variant-assessment
Australia
https://bsky.app/profile/mikehoney.bsky.social
Variants
US Variant tracker: https://covid.cdc.gov/covid-data-tracker/#variant-proportions
JPWeiland @jpweiland.bsky.social
The only thing that makes sense to me is they accidentally included inbound international travel seq, of which a large portion from Asia is NB.1.8.1. This is not local sampling and should not be included for US prevalence estimates.
6/27/25 CIDRAP: WHO adds XFG to SARS‑CoV‑2 variants under monitoring https://buff.ly/r6nOdaJ
Weekly variant roundup by Mike Honey:
Acute COVID infections, General COVID info
6/25/25 Nature Sci Reports preprint (Mexico): Solid-phase microextraction of sweat components of patients positive for Sars-Cov-2 for identification of possible biomarkers https://buff.ly/42DwZ8Q
7/2023 CIDRAP: Study shows dogs can detect COVID-19 faster, better than most PCR tests https://buff.ly/7iW0aR1
6/26/25 Gut Microbes (Italy): Gastrointestinal inflammation and cancer: viral and bacterial interplay https://buff.ly/cpqp7JG
6/20/25 Preprint for BMC Molec Med: The SARS-CoV-2 nucleocapsid protein induces microglia senescence- mediated cognitive impairment via glycolysis https://buff.ly/vH94ojV
Sept 2025 (out 6/23/25) Virology (S. Africa): SARS-CoV-2 host-pathogen interactome: insights into more players during pathogenesis https://buff.ly/RZnwtr7
Vaccines
7/22/25 (really 6/27/25) Cell Reports: Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters https://buff.ly/pqD6d8x
Antiviral treatments
6/26/25 Invivyd press release: Invivyd Announces Positive Full Phase 1/2 Clinical Data for VYD2311, a Next Generation COVID-19 Monoclonal Antibody for Potential Use as a Non-Vaccine Preventative and for Treatment of Active Infection | Invivyd https://buff.ly/lNboKCO
Long COVID
6/20/25 MedRxiV (India): Multimodal MRI Reveals Consistent Basal Ganglia and Limbic System Alterations in COVID-19 Survivors https://buff.ly/bF8lyq1
6/25/25 World Journal of Microbiology and Biotechnology (Saudi Arabia): Biochemical insight into gut microbial imbalance in Covid-19 and post vaccination heart attacks https://buff.ly/dRihklH
6/25/25 Frontiers of Neuroscience: REGAIN- A Randomized Controlled Clinical Trial of Oxaloacetate for Improving the Symptoms of Long COVID https://buff.ly/EjRDjrA
6/24/25 Autoimmunity Reviews: Advancing research on regulatory autoantibodies targeting GPCRs: Insights from the 5th international symposium https://buff.ly/RrqI7pC
6/26/25 Preprint (Kell, Zhao, Pretorius): Assessment of the Impacts of Fibrinaloid Microclots on the Microcirculation and Endothelial Function, Using Laser Speckle and Laser Doppler Imaging https://buff.ly/NheLwhG
6/20/25 BioRxiV (UW Tacoma): Uncovering the Pathophysiological Pattern of Expression from Integrated Analysis across Uniformly Processed RNA Sequencing COVID-19 Datasets https://buff.ly/7PpOZDP
Measles
Measles CDC Measles updates (on Fridays): https://www.cdc.gov/measles/data-research/index.html
As of June 24, 2025, a total of 1,227 confirmed* measles cases were reported by 36 states.
12% of cases hospitalized (148 of 1227).
3 confirmed deaths.
6/27/25 CIDRAP: Measles outbreak strikes New Mexico jail as US total climbs https://buff.ly/BmWxDZd
NEJM: Measles 2025 https://www.nejm.org/doi/full/10.1056/NEJMra2504516
Clinical Features and Pathogenesis of Measles.
From: https://www.nejm.org/doi/full/10.1056/NEJMra2504516
Incidence of Severe Complications Associated with Measles.
Government Medical News
6/26/25 AAP will continue to publish its own vaccine recommendations after CDC advisers sow distrust https://buff.ly/MUSLD4b
6/26/25 https://x.com/AmerAcadPeds/status/1938239291139735733
American Academy of Pediatrics
Pediatrician Dr. Schrier schools HHS Secretary RFK Jr about specific cases of vaccine preventable diseases (measles, meningitis, whooping cough) that she has treated. He has treated none. Video in Aaron Rupar’s Bluesky post below:
6/23/25 HHS Secretary Kennedy, CMS Administrator Oz Secure Industry Pledge to Fix Broken Prior Authorization System https://buff.ly/z4dQjk6
6/29/25 Scientific American: Trump Administration Ousts National Science Foundation from Headquarters https://www.scientificamerican.com/article/trump-administration-ousts-national-science-foundation-from-headquarters/
6/25/25 STAT News: NIH halts grant terminations ‘effective immediately,’ email says https://buff.ly/hDtyXkj
Other news:
6/26/25 Nature: Everyday painkiller made from plastic — by E. coli https://buff.ly/izwkx2k
6/25/25 npj Vaccines: Lower risk of dementia with AS01‑adjuvanted vaccination against shingles and respiratory syncytial virus infections https://buff.ly/19dyYMi
6/22/25
Excellent new article by @erictopol.bsky.social on the Gut-Brain axis!
Neural paths via Vagus Nerve and ANS
Hormones like GLP-1, GIP, Gherlin and others
Microbiome neurotransmitters, SFCAs
Immune system: inflamed T cells in Gut➡️ Brain inflammation
6/19/25 Science Review: Neuroinflammation across neurological diseases https://buff.ly/8E1ReGb
From: https://www.science.org/doi/10.1126/science.adx0043
6/23/25 JAMA Neurology: APOE ε4 and Risk of Intracranial Hemorrhage in Patients With Atrial Fibrillation Taking Apixaban (Eliquis) https://buff.ly/TU3hpVC
6/26/25 NEJM AI: An Electrocardiogram Foundation Model Built on over 10 Million Recordings https://buff.ly/J6OkzZO
6/26/25 Nature: Everyday painkiller made from plastic — by E. coli https://buff.ly/izwkx2k
6/23/25 Arc Institute: Predicting cellular responses to perturbation across diverse contexts with STATE https://buff.ly/c9JuZ7x
6/26/25 Cell (Arc Institute): Virtual Cell Challenge: Toward a Turing test for the virtual cell https://buff.ly/KHu1bEL
6/26/25 Gen Eng News: Arc Institute Launches Virtual Cell Challenge to Accelerate AI Model Development https://buff.ly/P2lR6c7
6/26/25 BBC: Ovingham students fundraise for their own therapy dog Nellie https://buff.ly/fMPnp8D
Thank you, as always.
This is the most accessible, thorough, and relevant COVID (and other medical) news aggregator out there. Don't be fooled by the small number of responses; I know a number of people who rely on this newsletter every week, and are too busy to respond -- or just don't think to do so. You are very appreciated, Dr. Crystal, and this newsletter is immensely valuable!