COVID, H5N1 news & more, 12/22/24

As of 12/14/24, wastewater levels of SARS-CoV-2 virus are MODERATE across America with the Midwest now with HIGH levels of COVID in wastewater according to the CDC NWSS. According to Sara Anne Willette’s composite data using both the CDC and WastewaterSCAN data, the highest levels of wastewater SARS-CoV-2 are in New Mexico, followed by South Dakota and Arizona.

US Wastewater SARS-CoV-2

As of 12/14/24

From: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html

Composite SARS-CoV-2 map with CDC NWSS and WastewaterSCAN data through 12/16/24

From: https://iowacovid19tracker.org/

According to JP Weiland, there are approximately 370,000 new COVID cases per day and about 1 in every 90 people in the US are currently infected. This is much lower than what was seen during the same week in 2023 and 2022. The peak of COVID cases is expected to be between 400,000 to 800,000 cases per day according to JP Weiland, while Mike Hoerger predicts 800,000 to 1,100,000 cases per day. Predicted case numbers are less than what was seen in the last 2 winters. Emergency department visits for COVID are still fairly low across the US so far.

From: https://x.com/JPWeiland/status/1870201070041084339

According to Mike Hoerger, if no one tests or isolates prior to a Christmas event, there would be about a 1 in 8 chance of someone having COVID at a gathering of 10 people. This number would be expected to be higher at a New Year’s party because more people would be infected by then.

The CDC has a new “Respiratory Illness Data Channel” where you can look up levels of COVID, Flu and RSV for your state. The site is updated on Fridays. Here is this week’s data for California vs. Massachusetts:

______________________________________________________________

From: https://www.cdc.gov/respiratory-viruses/data/index.html

SARS-CoV-2 Variants

The XEC variant is now at 45% of cases and KP.3.1.1 is down to 24% of COVID cases. The newest COVID vaccines should protect against these variants. Newcomer variant LP.8.1 has been doubling every 2 weeks (1% to 2% to 4% to 8%) and now is at 8% of COVID cases.

Acute COVID infections, General COVID info

In a new study, close household contacts of people with symptomatic acute COVID infection were followed longitudinally. Exposed individuals who did not contract COVID from household members were found to have an early increase in interferons, a part of the innate immune system. “Ultra-early interferon-associated innate immune responses correlate with, and may contribute to, protection against SARS-CoV-2 infection.” The authors validated their findings in two additional cohorts.

A new review from Italy looks at what SARS-CoV-2 does at the cellular level and finds that the virus can hijack and remodel the endoplasmic reticulum (ER) of cells to form specialized compartments called double-membrane vesicles (DMVs). The DMVs shield viral RNA from being detected by immune cells and help facilitate viral replication. The SARS-2 virus also alters autophagy processes and rewires lipid metabolism in cells to fuel viral replication and spread. Understanding these cellular processes may help scientists to develop new antiviral medications.

From: https://www.nature.com/articles/s44298-024-00076-8

A 2020 paper from Didier Raoult and colleagues was retracted this week on ethical and scientific grounds. The study claimed that hydroxychloroquine, especially when combined with the antibiotic azithromycin, reduced COVID-19 virus levels, but critics showed that the study was flawed by a small sample size, misreported data, lack of informed consent, and potential conflicts of interest involving the journal’s editor. The now-discredited study led to widespread, unnecessary use of hydroxychloroquine, which led to almost 17,000 deaths in 5 countries studied. Hydroxychloroquine can be toxic to the heart.

Social, Advocacy, Inequality

COVID infections spread rapidly in California prisons, affecting nearly 67,000 residents between 2020 and 2022, with higher per capita infection rates than in the general population. Overcrowded, poorly ventilated environments and ineffective control measures contributed to widespread transmission, with Black and Indigenous individuals disproportionately impacted. Approximately 15% of prison residents developed Long COVID.

Lil Wayne and other wealthy musicians received pandemic relief funds intended for struggling arts organizations through the Shuttered Venue Operators Grant program. Instead of aiding entertainment crews, much of the money was spent on shopping sprees and luxury hotels prompting criticism about the misuse of federal resources and highlighting broader issues with the oversight of pandemic-relief funds.

Long COVID

1 in 5 adults with Long COVID report significant limitations in daily activities according to a new report by the CDC. In 2023, 6.4% of adults had activity limiting Long COVID overall, with higher levels in the District of Columbia (12.8%) and Puerto Rico (29.4%). These findings highlight the importance of tools like vaccination and improved air quality to reduce Long COVID risk. They can also guide policymakers to make programs to help people with Long COVID.

Natural Killer (NK) cells are part of the immune system that destroy infected and diseased cells, including cancer cells, early so that they do not spread. Researchers from UCSF looked at PBMCs (peripheral blood mononuclear cells) in 21 people with Long COVID and 14 people who fully recovered after acute COVID infection in 2020. People with Long COVID had significantly fewer mature, cytotoxic NK cells compared to fully recovered individuals. Lower NK cell levels also were linked to more Long COVID symptoms including fatigue and neurocognitive issues and to more severe Long COVID symptoms. These findings suggest that reduced NK cell cytotoxicity may hinder the clearance of infected cells, potentially contributing to viral persistence and Long COVID development. Further research is needed to explore the relationship between immune responses, viral persistence, and Long COVID.

Golden hamsters infected with SARS-CoV-2 demonstrate persistent neurological and behavioral changes resembling Long COVID. The SARS-CoV-2 virus was found to be neuroinvasive and persisted in the brainstem of the hamsters for up to 80 days, leading to neuroinflammation, disrupted neurotransmission (affecting dopaminergic and glutamatergic systems), and altered energy metabolism. Hamsters with Long COVID had a distinct neurodegenerative transcriptome signature in the brainstem and demonstrated anxiety, depression, and memory impairments.

The RECOVER project updated their research index for 2024 incorporating additional data from nearly 4,000 new participants. Five Long COVID subtypes (loss smell/taste, chronic cough, brain fog, palpitations and multisystem symptoms) that tracked quality-of-life measures were noted in cluster analysis. The 2024 RECOVER updated index introduced a new "possible Long COVID" category, which 39% of participants with prior known SARS-CoV-2 infection had, and adjusted classification thresholds, helping researchers better study Long COVID's heterogeneity and guide future investigations.

On 12/7/24, Dr. Funmi Okunola of “Long COVID The Answers” interviewed Dr. Nancy Klimas regarding her upcoming study using monoclonal antibodies to treat Long COVID. The study will be a placebo controlled trial of a long acting monoclonal antibody against SARS-CoV-2 from AstraZeneca and will include 100 patients with Long COVID. Dr. Klimas plans on obtaining samples for a biorepository and will check for SARS-CoV-2 viral persistence. The study is based on work by Dr. Scheppke who reported a case study of 3 Long COVID patients treated with Regeneron’s monoclonal antibodies who had resolution of their disease. According to Dr. Klimas, Dr. Scheppke treated 21 Long COVID patients total with Regeneron monoclonal antibodies, 19 of whom responded to the treatment.

A new study from the Mayo Clinic and ASU shows that people who went on to get Long COVID had a specific gut microbiome signature during acute COVID infection. Researchers followed 380 people who were positive for SARS-CoV-2 and 419 people who were negative. Microbiome data alone was more accurate in predicting Long COVID than the addition of clinical information. Specific gut bacterial changes during acute COVID could also predict specific Long COVID symptom clusters. I am especially interested in this study as I made a synbiotic preparation (low FODMAP prebiotic plus probiotic bacteria shown in the Hong Kong randomized control trial to help reduce Long COVID symptoms) that has helped my family member with Long COVID.

Rob Wust’s lab wrote a comprehensive review of what we know about skeletal muscle abnormalities in people with Long COVID including discussions about mitochondrial dysfunction, endothelial abnormalities, and shifts towards glycolytic muscle fibers which contribute to reduced exercise capacity. Although the exact mechanisms of post-exertional malaise (PEM) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) remain unclear, PEM is hypothesized to involve immune dysregulation, hypoxia, and neurological factors. In addition, the group looked at five possible mechanisms causing Long COVID skeletal muscle symptoms including local hypoxia, deconditioning, electrophysiological alterations, autoimmunity, and central fatigue. Current treatments are limited, with ongoing research exploring therapies like immunoadsorption, dietary supplements, and anti-inflammatory drugs.

Figure 1 Long COVID symptoms (blue boxes) and possible pathophysiologic mechanisms (red boxes)

Figure 3 Possible causes of Long COVID skeletal muscle symptoms

From: https://www.cell.com/trends/endocrinology-metabolism/fulltext/S1043-2760(24)00298-4

Between October 2022 and October 2023, 20 Long COVID ME/CFS patients with elevated autoantibodies to receptors in the autonomic nervous system called β2 adrenergic autoantibodies (β2 AR-AB) were treated with five immunoadsorption (apheresis) sessions over 10 days. The patients answered questionnaires and underwent handgrip strength and EndoPAT testing to evaluate muscle fatigue and vascular dysfunction. This was a small study, but 70% of patients responded with improvement of fatigue, post-exertional malaise, pain, cognitive dysfunction and autonomic dysfunction. The authors concluded, "Immunoadsorption may improve symptoms in post-COVID ME/CFS patients. The beneficial effects of IgG depletion suggest a significant role for autoantibodies and disturbed B-cell function in the condition's pathophysiology."

Dr. Akgun from UCLA reviewed Therapeutic Plasma Exchange (TPE) as a treatment for Chronic Fatigue Syndrome (CFS) and Long COVID, conditions characterized by persistent fatigue, cognitive impairment, and autonomic dysfunction. TPE works by filtering out autoantibodies and pro-inflammatory cytokines. While preliminary studies show promising results, further research is needed to identify ideal candidates, standardize treatment protocols, and determine long-term effectiveness.

From: https://onlinelibrary.wiley.com/doi/10.1111/trf.18099

H5N1

Governor Newsom declared a State of Emergency for H5N1 Bird Flu for California this week as 300 more dairy herds in California tested positive for H5N1 in the last 30 days. Uncontrolled spread of the virus increases the risk of spillover into humans.

A person from Louisiana has been hospitalized with severe H5N1 bird flu after exposure to infected backyard poultry. The genotype of the hospitalized case is D1.1 which was also seen in the hospitalized Canadian teen last month and has been spreading in birds. The genotype infecting cattle is B3.13. Although most cases in America have been mild to date, these critical cases remind us that certain types of the H5N1 virus can cause severe illness and even death in humans.

This week, the Los Angeles County Department of Public Health confirmed that 2 indoor cats died from H5N1 after drinking raw milk. Three other cats from another household may have H5N1 bird flu as well. Two of those cats died and were not able to be tested. The third living cat has tested positive for Influenza A which is rare in felines. The source of the infection for that household is unknown but may have come from raw meat.

H5N1 Bird flu also killed at least two wild cougars in Washington state. One of the dead cougars was tracked with a collar and the other was found nearby. It is not known how many cougars may be infected in the area as most are not tracked.

Labcorp announced a new commercially available H5 Bird Flu (nucleic acid amplification) test that can be ordered by a physician (test code 140046).

A new preclinical study in ferrets shows that an mRNA vaccine against H5N1 successfully protected the animals from the virus. The vaccine would need to be tested in humans before being approved by the FDA.

Other news

Cases of whooping cough (Pertussis) surged six-fold in the United States in 2024. Most people do not realize that pertussis and whooping cough are the same disease or that the Tdap vaccine prevents whooping cough. Public health experts emphasize the need for clear messaging, urging the use of familiar terms like "whooping cough" and highlighting the effectiveness of vaccines as the best defense against the disease. Whooping cough can cause severe coughing fits so violent that sometimes people break ribs from coughing.

At a November 14th meeting, public health workers from Louisiana were told they should no longer advertise or promote COVID, flu or Mpox vaccines to the public. "Employees could not send out press releases, give interviews, hold vaccine events, give presentations or create social media posts encouraging the public to get the vaccines. They also could not put up signs at the department's clinics that COVID, flu or mpox vaccines were available on site."

The FDA approved Zepbound (tirzepatide) for the treatment of moderate to severe obstructive sleep apnea (OSA) in adults with obesity. Tirzepatide is a GLP-1 receptor agonist and a gastric inhibitory polypeptide analog.

On 12/16/24, the FDA added a "Boxed Warning", their most prominent warning, because of a rare but serious liver injury associated with use of menopause medicine Veozah (fezolinetant). Veozah is used to reduce hot flashes without hormones. The FDA states that health care providers should order liver tests before prescribing Veozah, then every month for 3 months, then at 6 months and 9 months of treatment and should warn patients of symptoms of fatigue, nausea, vomiting, jaundice, or right upper quadrant pain.

This week, Gukesh Dommaraju, 18 years old, became the youngest winner of the Chess World Championship. The previous record was held by chess master Garry Kasparov who won his first title when he was 22 years old in 1985.

Gukesh Dommaraju

Photo by Frans Peeters - https://www.flickr.com/photos/suspeeters/53467032837/

Have a great rest of your weekend and Happy Holidays! I’ll be taking next week off.

Ruth Ann Crystal MD

---

NEW CDC’s Respiratory Illnesses Data Channel

Updated on Fridays. https://www.cdc.gov/respiratory-viruses/data/index.html

As of 12/20/24 in the United States:

_________________________________________________________________

CDC Respiratory viruses (COVID, Flu, RSV) Hospitalizations (for those states reporting): https://www.cdc.gov/resp-net/dashboard/index.html

Hospitalizations through 12/14/24

COVID news notes:

US Variant tracker: https://covid.cdc.gov/covid-data-tracker/#variant-proportions

XEC is now at 45% of cases and KP.3.1.1 is down to 24% of COVID cases.

LP.8.1 is doubling every 2 weeks. (1% to 2% to 4% to 8%)

CDC COVID data tracker: https://covid.cdc.gov/covid-data-tracker/index.html#datatracker-home

Through 12/14/24

COVID Emergency Dept visits: https://covid.cdc.gov/covid-data-tracker/#ed-visits_all_ages_combined

Through 12/15/24

Walgreens positivity rate: https://www.walgreens.com/businesssolutions/covid-19-index.jsp

Many states do not do that many tests.

US Wastewater Monitoring:

CDC wastewater reporting: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html

As of 12/14/24

CDC wastewater map: https://www.cdc.gov/nwss/rv/COVID19-currentlevels.html

National SARS-CoV-2 data from Sara Anne Willette: https://iowacovid19tracker.org/

Through 12/16/24

12/16/24

Wastewater SCAN: https://data.wastewaterscan.org/

SARS-CoV-2

Bay Area SARS-CoV-2

Oceanside is at 262 PMMoV of SARS-CoV-2.

Wastewater virus levels for each US region

Santa Clara County wastewater: https://publichealth.santaclaracounty.gov/health-information/health-data/disease-data/covid-19/covid-19-wastewater

Marin county: https://coronavirus.marinhhs.org/surveillance

COVID deaths per week: https://covid.cdc.gov/covid-data-tracker/#trends_weeklydeaths_weeklypctdeaths_00

JP Weiland: https://twitter.com/JPWeiland

12/20/24 https://x.com/JPWeiland/status/1870201070041084339

“Dec 20th update:

• Remarkably, we are now in mid December, and numbers in August were 150% higher than now. Increases mainly from holiday gatherings, currently trending toward my Nov 19th model.

  • 371,000 new infections/day

  • 1 in every 90 people currently infected”

12/20/24 JWeiland:

“I updated the model on Dec 9th with what I now believe to be an under-sampled data point on Dec 9 from NWSS. This did throw the trajectory off a bit, should have trusted my gut and stuck with the original. I like the fit so far of the Nov 19th shown here”

“To note, here are some other current trends that do show a slower rise than NWSS. (WWscan, Emergency Dept Data, Positivity Rates, Walgreens Positivity Rates)

It's a bit unclear what the *exact* trajectory is, probably somewhere in between NWSS/the rest.”

____________________________________________________________________________

12/20/24 https://x.com/JPWeiland/status/1870516067715715464

______________________________________________________________________

Michael Hoerger modeling: http://pmc19.com/data/

12/16/24 https://x.com/michael_hoerger/status/1868550160105841149

Michael Hoerger:

“PMC COVID-19 Dashboard, Dec 16, 2024

• 1 in 64 (1.6%) actively infectious in the U.S.

• 750,000 new daily infections and rising

• Highest % increase in transmission in nearly 3 years

• 10th wave is the "silent surge," coming on late out of nowhere

12/15/24 https://x.com/michael_hoerger/status/1868407551878152519

MH: “Covid transmission is projected to be very high around New Year's Eve.

At a party of 25 without testing or isolation, it's a coin toss of getting a Covid exposure.

(Airplane) Flight? All but guaranteed.”

Canada

Canada wastewater https://health-infobase.canada.ca/wastewater/

Canada RSV

UK

UKHSA Dashboard:

https://ukhsa-dashboard.data.gov.uk/

UK COVID PCR Test Positivity Map: https://jamestindall.info/skeuomorphology/ladb_covid/index.html

International @nichtGenes61287

Some graphs are wastewater SARS-CoV-2, some are COVID cases

Australia

https://bsky.app/profile/mikehoney.bsky.social

Acute COVID infections, General COVID info

1/2025 eBioMedicine: An ultra-early, transient interferon-associated innate immune response associates with protection from SARS-CoV-2 infection despite exposure https://buff.ly/49OK7VR

12/17/24 npj Viruses (Italy): A portrait of the infected cell: how SARS-CoV-2 infection reshapes cellular processes and pathways https://buff.ly/4gg29T6

• SARS-CoV-2 hijacks the Endoplasmic Reticulum

From: https://www.nature.com/articles/s44298-024-00076-8

12/17/24 Science: Infamous paper that popularized unproven COVID-19 treatment finally retracted https://buff.ly/4gjfA4R

Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds

1/4/24 The Hill: Nearly 17,000 people may have died from hydroxychloroquine: study https://buff.ly/48k9vB2

Social, Advocacy, Inequality

12/16/24 MedRxiV: COVID-19 Reproduction Numbers and Long COVID Prevalences in California State Prisons https://buff.ly/401gzRu

12/18/24 Business Insider: How rich musicians billed American taxpayers for luxury hotels, shopping sprees, and million-dollar bonuses https://buff.ly/4a0W8HT

Long COVID

12/19/24 CDC MMWR: Long COVID and Significant Associated Activity Limitation Among Adults, By Jurisdiction https://buff.ly/3P6zm7K

12/17/24 JCI (UCSF): Long COVID is associated with lower percentages of mature, cytotoxic NK cell phenotypes https://buff.ly/41DNhcX

12/17/24 PolyBio Research Foundation: Study first to document dysfunctional natural killer cells in long COVID - https://buff.ly/3ZSKJoS

12/16/24 BioRxiV (Institut Pasteur): Hamsters with long Covid exhibits a neurodegenerative signature in the brainstem https://buff.ly/3OYz173

12/18/24 JAMA (Geng et al.): 2024 Update of the RECOVER-Adult Long COVID Research Index https://buff.ly/400G3hR

12/7/24 Long COVID The Answers Podcast

On 12/7/24, Dr. Funmi Okunola of Long COVID The Answers interviewed Dr. Nancy Klimas regarding her upcoming study using monoclonal antibodies to treat Long COVID.

1/2024 American Journal of Emergency Medicine: Remission of severe forms of long COVID following monoclonal antibody (MCA) infusions: A report of signal index cases and call for targeted research https://buff.ly/4gH7naZ

12/11/24 BioRxiV (Mayo Clinic): Gut Microbiome Signatures During Acute Infection Predict Long COVID https://buff.ly/4gA9n4k

12/17/24 Trends in Endocrinology & Metabolism (Wust lab): Skeletal muscle adaptations and post-exertional malaise in long COVID https://buff.ly/3BPSNhR

Figure 1 Common long coronavirus disease 2019 (COVID) symptoms (blue boxes) and pathophysiological hypotheses on the mechanisms underlying tissue alterations (red boxes)

Figure 2. Contribution of skeletal muscle cell types in long coronavirus disease 2019 (COVID).

(A) Capillary basal lamina thickening observed in patients with long COVID (from Aschman et al., 2023 [28]).

(B) Lower succinate dehydrogenase activity in patients with long COVID compared with healthy controls (from Colosio et al., 2023 [18]).

(C) CD68+ macrophage infiltration between muscle fibers (from Aschman et al., 2023 [28]).

(D) High skeletal muscle sodium content, as viewed using 3T magnetic resonance imaging (from Petter et al., 2022 [70]).

(E) Connective tissue content was similar in long COVID as in healthy controls (from Colosio et al. 2023 [18]).

(F) Patients with long COVID have abnormal mitochondria imaged using electron microscopy (from Bizjak et al., 2023 [19]).

(G) Amyloid-containing deposits can be found in skeletal muscle and blood of patients with long COVID (unpublished data).

(H) Patients with long COVID have more glycolytic, type II muscle fibers. Dark blue represents type I fibers, yellow represents type IIa fibers, turquoise represents type IIa/IIx fibers (Appelman et al., 2024 [21]).

Figure 3 Schematic illustration of the five predominant mechanisms underlying long COVID skeletal muscle symptoms: local hypoxia, deconditioning, electrophysiological alterations, autoimmunity, and central fatigue.

2/2025 Lancet Regional Health Europe (Charite Berlin): Efficacy of repeated immunoadsorption (apheresis) in patients with post-COVID myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and elevated β2-adrenergic receptor autoantibodies: a prospective cohort study https://buff.ly/49KOoJC

12/14/24 Transfusion: The potential of plasma exchange in treating Chronic Fatigue Syndrome and long COVID: Targeting autoimmune and inflammatory mechanisms https://buff.ly/4gp0efi

H5N1

12/17/24 Labcorp Launches H5 Bird Flu Test in the U.S., Now Available for Order through Physicians https://buff.ly/3BPIXMZ

• Influenza A and Influenza B With Reflex to H5 Subtyping, NAA, Labcorp TEST: 140046

12/18/24 NPR: Bird flu update: California declares emergency and U.S. sees 1st severe human case https://buff.ly/402rb2A

12/18/24 CDC Confirms First Severe Human Case of H5N1 Bird Flu in the United States https://www.cdc.gov/media/releases/2024/m1218-h5n1-flu.html

• D1.1 genotype

12/18/24 LACPD: Confirmed H5 Bird Flu Detected in Los Angeles County Cats That Consumed Recalled Raw Milk - Public Health Investigating Additional Possible Cases in Cats https://buff.ly/4goE1h4

12/19/24 Bird flu kills Olympic Peninsula cougars in Washington state https://buff.ly/4gGgfwX.

12/18/24 https://bsky.app/profile/kakape.bsky.social/post/3ldlqy7hkok2d

Kai Kupferschmidt: CDC just confirmed the first severe case of #H5N1 in the US in a patient in Louisiana. This virus seems to be the same genotype D1.1 that is spreading in birds at the moment (so not the cattle genotype B3.13) that severely sickened the teenager in Canada.

12/5/24 Science: Why hasn’t the bird flu pandemic started? https://buff.ly/3BlqPuj

12/15/24 CIDRAP: Positive avian flu bulk-tank tests prompt another raw-milk recall in California https://buff.ly/4gm0xHp

12/20/24 STAT News: Rapid spread of H5N1 bird flu through California dairy herds suggests unknown paths of transmission https://buff.ly/3BJNXTt

12/19/24 Infectious disease doctor BK. Titanji

12/18/24 Science: An influenza mRNA vaccine protects ferrets from lethal infection with highly pathogenic avian influenza A(H5N1) virus https://buff.ly/4iNKpQy

Other news:

12/20/24 FDA Approves First Medication for Obstructive Sleep Apnea https://buff.ly/3VSDhIS

• Zepbound (tirzepatide)

12/20/24 NPR: Louisiana forbids public health workers from promoting COVID, flu and mpox shots https://buff.ly/4gIlw73

12/17/24 CIDRAP: US whooping cough cases soar, but public knowledge of the contagious disease remains low https://buff.ly/3VMLKxm

12/16/24 FDA warns menopause drug Veozah can cause rare but serious liver injury. https://buff.ly/41J9ZjE

12/17/24 Youngest ever chess world champion Gukesh Dommaraju returns home to rock star welcome in India | CNN https://buff.ly/4a6V59n