COVID, H5N1 & more, 11/24/24

Nov 24, 2024

Wastewater levels of SARS-CoV-2 are still LOW in most places across the U.S. according to the CDC and WastewaterSCAN. As of 11/22/24, JP Weiland predicts that there are approximately 182,000 new COVID infections per day in the US and that about 1 in every 183 people is currently infected. Overall, COVID wastewater levels and COVID cases are almost 4x less than we had during the same week in prior years of the pandemic. So, although we expect a COVID wave during and after the winter holidays when people mingle together indoors, hopefully it will be a smaller wave than in past years.

This week, Mike Hoerger noticed that the CDC did something wacky to their SARS-CoV-2 wastewater graph. It appears that the CDC changed the y-axis on their curve to make wastewater levels appear lower. There is no longer a zero on the y-axis.

From: https://x.com/michael_hoerger/status/1858985224836968583

Here in the Bay Area and in California, SARS-CoV-2 wastewater levels are low overall.

Variants

Regarding SARS-CoV-2 variants, KP.3.1.1 is now at 44% of cases, down from 52% two weeks ago. XEC is at 38% of cases. XEC has a growth advantage, but it is not growing as fast as other variants have in the past. More good news is that the updated COVID vaccines should protect against the XEC variant.

Acute COVID infections, General COVID info

A zoo in Brazil reported that 19% of their animals tested positive for SARS-CoV-2. The Alpha variant was found in a maned wolf and a fallow deer and Omicron was seen in a western lowland gorilla. Genetic analysis suggests human-to-animal viral transmission from the people who take care of the animals.

Pregnancy

Comparing 11 million births from before the pandemic to 7 million births during the COVID pandemic (2020 to 2022), the number of infants born with a congenital heart condition had increased by 16%. Professor Asma Khalil said, "Studying this large US dataset has revealed an unexpected picture for how the pandemic has affected the hearts of unborn babies...These results act as an important reminder for pregnant women to get their Covid-19 vaccinations to help protect themselves and their baby."

A study from China looked at the impact of maternal COVID vaccination before pregnancy on fetal immunity by analyzing umbilical cord blood samples at birth from vaccinated and unvaccinated people who contracted SARS-CoV-2 during pregnancy. Vaccination before pregnancy increased neutralizing antibody levels against COVID and enhanced immune regulation in the fetal circulation as measured by cytokine levels found in umbilical cord blood at birth. A single prior vaccine dose was associated with persistent immune dysregulation and platelet activation in the fetal circulation, but two or three doses provided protective effects for the fetus. These findings support the benefits of pre-pregnancy COVID vaccination to help protect the fetus against COVID infection in utero.

The UK’s Joint Committee for Vaccination and Immunisation (JCVI) announced that they will stop offering free COVID vaccines to pregnant individuals in the UK starting in 2025, raising concerns about maternal and infant health. Vaccination during pregnancy reduces severe COVID risks for mothers, lowers risks of miscarriage and stillbirth, and protects newborns during their vulnerable early months by passing on antibodies. Data show infants, especially those under six months of age, are at higher risk of severe COVID than most age groups, but maternal vaccination can significantly reduce these risks.

Vaccines

A Pew Research Center survey reveals that approximately 60% of Americans do not plan on getting the updated 2024-25 COVID vaccine. This is despite CDC recommendations for everyone aged 6 months and older to get the updated vaccine to protect against severe illness from COVID. As mentioned above, the new COVID vaccines protect well against variants that are circulating now. Vaccine uptake is sharply divided along partisan lines, with Democrats more likely than Republicans to say they will get the vaccine- a trend especially pronounced among older adults. Key reasons for not getting the updated vaccine include concerns about side effects and a belief that the vaccine is not necessary for them.

A new study shows that people with rheumatoid arthritis or spondyloarthritis who stopped their JAK or IL-17 inhibitor medications for 2 weeks at the time of COVID mRNA booster vaccination, did not significantly increase the amount of COVID neutralizing antibodies made. Stopping these medications did, however, cause a significant number of patients to have a flare of their arthritis.

Long COVID

A group from USC has made a mouse model of Long COVID (Post-acute Sequelae of COVID infection, PASC) using C57BL/6 mice and a SARS-CoV-2 virus strain that was adapted to mice. The “C57BL/6J mice developed neurological impairments, including behavior changes related to sensorimotor coordination, depression- and anxiety-like behaviors, and inflammation in multiple organs including lung, liver and brain” that persisted for at least 4 weeks after mild infection.

A press release from Dogwood Therapeutics reported on a small double-blinded, placebo controlled study completed at the Bateman Horne Center on 29 people with Long COVID who received either IMC-2 (valacyclovir 750 mg + celecoxib 200 mg twice daily) or placebo. People in the IMC-2 treatment group showed “clinically meaningful reduction” in Long COVID fatigue and sleep disturbances. Larger studies are planned.

Tryptophan is an essential amino acid that the body uses to produce serotonin, melatonin and niacin. A group from Cork, Ireland found that tryptophan and its microbial indole metabolites in the gut are linked to dysregulated immune responses in both hospitalized COVID patients and those with Long COVID 6 months after acute infection. Reduced expression of bacterial genes involved in tryptophan metabolism may lead to altered levels of indole metabolites which can affect innate and adaptive immune responses.

H5N1

The California Department of Public Health (CDPH) reported on November 19th, that a child in Alameda County with mild upper respiratory symptoms tested positive for several viruses including H5N1 Bird Flu. The child was treated and is doing well at home. They had no known contact with farm animals and all of their human contacts have tested negative for H5N1.

So far, there have been three people infected by H5N1 Bird Flu without an obvious source of infection including the person hospitalized in Missouri several weeks ago, the Canadian teenager who is critically ill in the ICU with ARDS, and now a young child in Alameda County in California who tested positive. If these people did not get H5N1 Avian Flu from farm animals or from human contacts, where did they get it from?

New data shows that the Canadian teen in Vancouver is infected with several variants of the H5N1 bird flu including one with mutations that make it easier to infect human cells and to replicate more easily in human cells. It appears that the teen was originally infected with H5N1 seen in poultry that led to conjunctivitis symptoms. But, the H5N1 virus may have evolved within the teenager’s body to cause a severe lung infection days later. “It’s not the time to panic,” said immunologist Scott Hensley at the University of Pennsylvania. “But this should serve as a warning: this virus has the capacity to switch very quickly into a form that can cause severe disease.” According to CIDRAP, public health officials are monitoring the situation and are testing vaccines to prepare for potential outbreaks.

The USDA has confirmed 62 new dairy cattle herds in California with H5N1 avian flu, bringing the total since late August to 398 herds in California and 612 infected cattle herds in the nation. California is the nation’s largest dairy producer and one-third of its dairy herds have been infected. Regarding poultry, new H5N1 outbreaks have been reported in four states, including major cases in California in Kern County and in a Marin County duck meat producer.

In an essay entitled “The World Is Watching the U.S. Deal With Bird Flu, and It’s Scary”, South African virologist Tulio de Oliveira discusses the subpar response by the United States to contain the spread of H5N1 bird flu. He says, “Failure to control H5N1 among American livestock could have global consequences, and this demands urgent attention. The United States has done little to reassure the world that it has the outbreak contained.” He asks us to imagine how America would respond if there was uncontrolled spread of a highly pathogenic virus in another country like China.

Researchers from Wake Forest University warn that as the highly pathogenic avian influenza (HPAI) H5N1 spreads quickly on American dairy farms, this threatens our food supply and our safety. They show that viral spread between farms is happening more rapidly than what current surveillance methods can keep up with. They recommend biosecurity practices to be put in place instead of passive surveillance measures.

Scientists from around the world are sounding alarm bells for H5N1’s rapid spread in cattle and poultry in the United States. Bird flu also spreads by wild birds as they migrate to new locations. As seen by the case of the previously healthy Canadian teenager, the H5N1 virus is able to evolve within people to cause more severe infections in humans. If H5N1 obtains another mutation to make it more transmissible from animal-to-human or from human-to-human, we potentially could have another global pandemic. We really need to get this under control now.

Norovirus

Levels of Norovirus in wastewater is HIGH in most of the US now, as seen by orange on the map below. Norovirus is very contagious and is spread by eating contaminated food or by touching infected people or contaminated surfaces. It causes nausea and vomiting. People are most contagious when they have these symptoms and for the first few days after they feel better. In some cases, norovirus can still spread for 2 weeks after the nausea and vomiting have resolved.

Artificial Intelligence (AI)

A new AI foundation model called BiomedParse is able to analyze nine different medical imaging modalities (CT, MRI, Xray, Ultrasound, Pathology, Fundus exam, Dermoscopy, Endoscopy and OCT in the eye) for diagnosis. It makes me wonder if we could use BiomedParse to find Long COVID biomarkers or to better understand the pathophysiology of Long COVID.

From: https://www.microsoft.com/en-us/research/blog/biomedparse-a-foundation-model-for-smarter-all-in-one-biomedical-image-analysis/

Open Evidence is an AI medical information platform that can “aggregate, synthesize, and visualize clinically relevant [medical] evidence in understandable, accessible formats that can be used to make more evidenced-based decisions and improve patient outcomes.” It is free for healthcare professionals and provides references for each answer.

Other news

Measles is one of the most contagious diseases known. But, many people don’t know that measles can also cause “immune amnesia”. “When you're infected with measles, your immune system abruptly forgets every pathogen it's ever encountered before – every cold, every bout of flu, every exposure to bacteria or viruses in the environment, every vaccination. The loss is near-total and permanent. Once the measles infection is over, current evidence suggests that your body has to re-learn what's good and what's bad almost from scratch.” It appears that this is due to long term infection of memory T cells by the measles virus.

Most people know to dial 911 for emergencies, but there is also a special phone number to call if someone feels suicidal. 988 is the National Suicide Prevention Hotline and we need to spread the word about this important service.

How can you solve the problem of tons of plastic in the ocean? By making a plastic that can be broken down by salt water. A group from Japan has done just that and is featured in Science magazine.

Finally, I wanted to share our new article, "Reimagining Kangaroo Care for Preterm Infants: A Novel Garment for Safe and Comfortable Bonding," that was published in the journal Children. Kangaroo care, or skin-to-skin care, has been shown to have numerous benefits for premature babies and their parents. But, it can be difficult to do in the neonatal intensive care unit (NICU) because it is hard to secure the baby’s lines and breathing tube. Using human-centered design with feedback from nurses, neonatologists, respiratory therapists and parents, we invented the Kangarobe. This study completed in the NICU at Stanford shows that parents and nurses found that using the Kangarobe was a safer, easier and more comfortable way to do kangaroo care with premature babies.

The Kangarobe™

From: https://www.mdpi.com/2227-9067/11/11/1392#

I will be taking next week off from the newsletter for Thanksgiving.

Wishing you a wonderful holiday,

Ruth Ann Crystal MD

COVID news notes:

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

KP.3.1.1 now at 44% of cases, down from 52% 2 weeks ago
XEC is at 38% of cases. It went from 10% of cases, to 16%, to 26% and now to 38% over 6 weeks. So, it has a growth advantage, but it is not as significant as other variants in the past.
Also, the JN.1 and KP.2 updated COVID vaccines should protect against XEC, so it is not expected to cause as large a wave as other variants in the past.

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

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

Vermont and Hawaii have the most increases in positive COVID tests now.

US Wastewater Monitoring

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

11/19/24 Mike Hoerger https://x.com/michael_hoerger/status/1858985224836968583

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

National SARS-CoV-2 data from Sara Anne Willette:

https://iowacovid19tracker.org/

Combined risk from CDC and WastewaterSCAN from November 17, 2024

11/9/24 (2 weeks ago!) COVID hospitalization data:

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

SARS-CoV-2 is LOW nationally.

SARS-CoV-2 California statewide view https://buff.ly/3YObiul

Sewer Coronavirus Alert Network (SCAN) project by Stanford University:

SARS-CoV-2 in wastewater

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

11/22/24 Update https://x.com/JPWeiland/status/1860118075305263186

Nov 22nd update:

The US is maintaining unseasonably good numbers. Almost 4x lower than the same week average of prior years. Good news going into a week of Thanksgiving travel and gatherings.

182,000 new infections/day
1 in every 183 people currently infected

11/20/24 https://x.com/JPWeiland/status/1859448708082868610

“This holiday season will have the lowest Covid hospitalization and death rates so far.

This should help the hospital capacity going into flu and RSV season.”

11/19/24 https://x.com/JPWeiland/status/1859014108747886866

Holiday Season Forecast:

The wildest forecast I've ever made was for Dec 2021, predicting multiple millions of daily infections. This one is easily second place. A very muted holiday wave relative to all prior years, due to weak evolution and large summer numbers.

Michael Hoerger modeling: http://pmc19.com/data/, https://twitter.com/michael_hoerger

Canada

Canada wastewater https://health-infobase.canada.ca/wastewater/
Tara Moriarty Canadian COVID data: https://x.com/MoriartyLab

UKHSA Dashboard:

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

UK COVID PCR Test Positivity Map: https://jamestindall.info/skeuomorphology/ladb_covid/index.html
- This site hasn’t been working in the last few days.

International @nichtGenes61287

Wastewater SARS-CoV-2 or COVID cases in different countries. Some are last updated in October, while others have been updated on November 20th.

Australia:

https://bsky.app/profile/thecovidinfoguy.bsky.social/post/3lazja4ueus27

Acute COVID infections, General COVID info

11/20/24 CIDRAP: 1 in 5 animals at zoo tested positive for SARS-CoV-2, perhaps from people https://buff.ly/4eExr4n

Pregnancy

11/15/24 Medical Life Sciences News: Pandemic linked to 16% rise in babies born with heart defects https://buff.ly/4g2qqf7

Original article:
9/27/24 Ultrasound in Ob/Gyn (UK): Congenital heart defects during COVID‐19 pandemic https://buff.ly/4g2lruV

11/20/24 Nature, Signal Transduction and Targeted Therapy: A comprehensive proteomic analysis of umbilical cord blood supports COVID-19 vaccination before pregnancy https://buff.ly/3ATBxYE

11/20/24 The Conversation: The UK is no longer offering COVID vaccines to pregnant women– here’s why that might be a bad idea https://buff.ly/4eHVW0J

Vaccines

11/19/24 Pew Research Center: 60% of Americans say they probably won’t get an updated COVID-19 vaccine https://buff.ly/4eG7QZ5

11/17/24 Healio Rheumatology: Withholding JAK, IL-17 inhibitors fails to improve COVID-19 vaccine booster response https://www.healio.com/news/rheumatology/20241116/withholding-jak-il17-inhibitors-fails-to-improve-covid19-vaccine-booster-response

Long COVID

11/11/24 BioRxiV (USC): A Mouse-adapted SARS-CoV-2 Model for Investigating Post-acute Sequelae of COVID infection https://buff.ly/4fwa3Hx

11/17/24 Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2429754#abstract

11/18/24 Press Release Dogwood Therapeutics: Dogwood Therapeutics, Inc. Announces Low Dose IMC-2 Treatment Reduces Long-COVID Related Fatigue and Sleep Disturbance in an Investigator-Initiated Study https://www.globenewswire.com/news-release/2024/11/18/2982814/0/en/Dogwood-Therapeutics-Inc-Announces-Low-Dose-IMC-2-Treatment-Reduces-Long-COVID-Related-Fatigue-and-Sleep-Disturbance-in-an-Investigator-Initiated-Study.html

IMC-2 treatment, dosed as valacyclovir 750 mg + celecoxib 200 mg twice daily

H5N1

Nationally, Turlock is top, then Los Angeles county, but both are decreasing now.

11/19/24 CDPH: California Reports Single, Possible Case of Bird Flu Virus in Child with Mild Symptoms https://buff.ly/4eDJK12

11/20/24 Nature: Why a teenager’s bird-flu infection is ringing alarm bells for scientists https://buff.ly/4hXZBu5

11/21/24 CIDRAP: Avian flu confirmed at 62 more California dairy farms as virus strikes more poultry https://buff.ly/3Zh2UFw

The USDA has confirmed 62 new H5N1 avian flu outbreaks in dairy cattle herds in California, bringing the state’s total since late August to 398 herds and the national total to 612 cattle herds. California is the nation’s largest dairy producer and one-third of its dairy herds have been infected.

11/19/24 NY Times Opinion by Dr. Tulio de Oliveira: The U.S. Response to Bird Flu Is Not Reassuring the World https://buff.ly/4fD5V8V

11/15/24 BioRxiV (Wake Forest Univ.): Time is of the essence: effectiveness of dairy farm control of H5N1 is limited by fast spread https://www.biorxiv.org/content/10.1101/2024.11.15.623774v1

Norovirus

AI:

11/18/24 Microsoft Blog: Introducing BiomedParse, a groundbreaking foundation model for biomedical image analysis https://buff.ly/3OmShKZ

h/t Eric Topol

Original article:
11/18/24 Nature Methods: A foundation model for joint segmentation, detection and recognition of biomedical objects across nine modalities https://buff.ly/4i4qqNh
Explainer article in Nature Methods: A foundation model unlocks unified biomedical image analysis https://buff.ly/3OosSAy

Open Evidence https://www.openevidence.com/

“The leading AI-powered medical information platform” for healthcare providers.

Other news:

Measles

2/2024 BBC: Measles: The race to understand 'immune amnesia'

https://www.bbc.com/future/article/20211112-the-people-with-immune-amnesia

Samoa state of emergency in 2019 from a measles outbreak that quickly spread with “In all, 5,667 people were infected – including 8% of the population under 15 years old. Of those, 81 died, including three children from the same family.”
Immune amnesia. Years later, scientists investigated blood samples taken from patients and confirmed that they contained memory T cells infected with measles.
It's not surprising, then, that measles doesn't just increase the risk of illness, but also death. In fact, childhood mortality from other viruses is strongly linked to the incidence of measles.

11/19/24 The Hill: Public awareness of 988 national suicide prevention hotline low, but growing: Poll https://buff.ly/4gfngVt

11/21/24 Science: Mechanically strong yet metabolizable supramolecular plastics by desalting upon phase separation https://buff.ly/3CIlnlu

How can you solve the problem of tons of plastic in the ocean? A plastic that can be broken down by salt water.

11/16/24 Children: Reimagining Kangaroo Care for Preterm Infants: A Novel Garment for Safe and Comfortable Bonding https://buff.ly/4fzbXr0

https://www.mdpi.com/2227-9067/11/11/1392#

A Stanford NICU study on the Kangarobe shows that nurses and parents find that it is safer, easier to set up and more comfortable for kangaroo care in the NICU.