Welcome to winter virus season! Wastewater shows HIGH levels of COVID across the United States, with Flu and RSV at more MODERATE levels in wastewater, but all are increasing rapidly now as people are together indoors. Flu shots and COVID vaccinations are still available at local pharmacies.
Norovirus (stomach flu) levels are really high across America now as well. Norovirus typically causes projectile vomiting and diarrhea for 24 to 48 hours. It is mostly spread through contaminated food and surfaces. Hand sanitizer does not kill norovirus, so washing your hands for at least 20 seconds with soap and water is key for preventing norovirus. The virus can also occasionally be spread by aerosolization in bathrooms, so in addition to meticulous hand washing, wearing a mask in a bathroom where a person with norovirus has been can also help prevent spread. Some people can become lactose intolerant for weeks to months after a norovirus infection, so it may be important to reintroduce dairy slowly.
COVID
Wastewater levels of SARS-CoV-2 are VERY HIGH in the Midwest as of 12/28/24, although the rest of the country was still at more MODERATE levels. COVID wastewater levels are increasing throughout the United States.
The “Yankee Candle Index” is rising too. When Yankee Candle reviews on Amazon start mentioning candles without much scent, it usually means that there is an increase in COVID infections causing people to lose their sense of smell.
Sara Anne Willette removed her data tracking website and her Twitter and BlueSky accounts this week. I hope that she will be posting again soon as I find her work very helpful.
Variants
The XEC variant is now dominant. But, a new variant called LP.8.1 will probably take over soon as it has been doubling from 2% to 4% to 8% over the last few weeks. According to Yunlong Cao’s lab, LP.8.1 has a growth advantage over other variants including XEC because of its increased ability to bind to the ACE2 receptor on human cells.
A new study in JAMA shows that COVID infection is associated with a more rapid decline in kidney function than pneumonia, especially in people who were hospitalized for COVID. Appropriate follow up after hospitalization is important.
Researchers looked at the blood transcriptome after vaccination for H5N1 to identify factors that influence antibody response and duration. Surprisingly, they found that a platelet signature on day 7 could predict how long antibodies to the vaccine would last. Megakaryocytes are precursor cells in the bone marrow that become platelets. Activation of megakaryocytes led to increased survival of antibody making plasma cells. Using AI, the group found that a platelet signature in the blood from the activated megakaryocytes could predict vaccine durability for six different types of vaccines including some against SARS-CoV-2.
Fig. 7: Summary of proposed mechanism for involvement of megakaryocytes in promotion of durability of antibody responses to vaccination.
An article in Science magazine talked about a recent Cold Spring Harbor Asia conference on preventing pandemics. WHO epidemiologist Maria Van Kerkhove discussed frustration with people acting as if COVID were no longer important. “I feel this massive gravitational pull to go back to what we were doing before,” Van Kerkhove said, “There’s no way we should be going back.”
Scientists at the conference discussed the extraordinarily rapid continued viral evolution of SARS-CoV-2 which makes vaccines and monoclonal antibody (mAb) treatments quickly outdated. Yunlong Cao from Peking University spoke about his lab’s studies looking at antibodies from people who had SARS infection 20 years ago and who were then vaccinated against SARS-CoV-2 (COVID). An antibody from one of these people is a broad spectrum monoclonal antibody called SA55 that is predicted to be effective for at least 2 more years of SARS-2 viral evolution. In an unpublished study, a SA55 mAb nasal spray was 80% effective in preventing COVID infections in 300,000 people exposed. Dr. Cao has licensed the SA55 antibody to Sinovac.
Amyloid proteins in the brain are associated with neurodegenerative diseases like Alzheimer’s disease and Parkinson’s disease. A group from Sweden incubated UV-inactivated herpes simplex 1 virus (HSV-1) and inactivated SARS-CoV-2 virus in human cerebrospinal fluid (CSF) separately and found that the dead viruses still caused proteins in the CSF to make amyloid. The formation of amyloid was not dependent on viral replication, but rather, was dependent on surface properties related to a process called heterogeneous nucleation (HEN).
White arrows indicate viral particles, and black arrows indicate amyloid fibrillar structures.
A small toxicology study from Brazil shows that ingesting water contaminated with SARS-CoV-2 lysate protein is toxic to mice. Giving female mice SARS-2 lysate protein (at 20 µg/L) in their water caused them to show anxiety-like behavior, memory deficits, and reduced activity “which were associated with oxidative stress and dopaminergic and cholinesterase imbalance in the animal brain.” Toxic inflammatory responses were seen in the brain, liver, duodenum, and ovaries. This is concerning for several reasons. Ecological risks of COVID virus contamination in the environment are unknown. From the Erturk study and other studies, we know that the SARS-CoV-2 virus or viral fragments like the spike protein remain in the body and brain of many people who had COVID in the past. If ingesting water tainted with a small amount of SARS-CoV-2 lysate protein can cause this kind of damage, what is the virus or viral fragments like the spike protein doing to our bodies long term?
H5N1
An article from the NEJM this week reported on the Canadian teen who was critically ill with H5N1 bird flu in November. The healthy 13 year old girl with a history of mild asthma and obesity was initially seen in the ER for conjunctivitis and fever. She returned to the emergency department a day later after cough, vomiting and diarrhea developed. She was very ill and was admitted to the hospital in respiratory distress. The teen was put on a ventilator for 3 weeks, was on extracorporeal membrane oxygenation (ECMO) heart and lung bypass machine for 2 weeks, required dialysis for kidney failure and had plasma exchange 3 times. It is very unusual for a teen to need these kinds of critical life saving treatments, but her heart, lungs and kidneys shut down because of the H5N1 bird flu infection.
At this time, the teen is no longer on oxygen, but the article does not state if she is still in the hospital or is at home. “The virus was typed as clade 2.3.4.4b, genotype D1.1, most closely related to viruses detected in wild birds in British Columbia around the same time.” What is concerning is that analysis of the H5 hemagglutinin (HA) gene showed mutations that could allow the H5N1 virus to bind better to human airway receptors. Similar mutations were seen in the critically ill person with H5N1 in Louisiana.
Felines are very sensitive to the H5N1 virus. Twenty big cats including African Servals, bobcats, cougars, Canada Lynxes, a tiger and other species of big cats all died after being infected with H5N1 bird flu at a Washington state big cat sanctuary. It is uncertain how the big cats were infected with H5N1, but it may have been from droppings of migratory wild birds.
The US Department of Health and Human Services (HHS) announced $306 million in new funding to enhance the nation’s preparedness for H5N1 avian flu. The funding includes $183 million for regional and local preparedness, $111 million for CDC monitoring and diagnostic test kit distribution, and $11 million for NIH research on countermeasures. HHS Secretary Xavier Becerra emphasized the importance of these investments in strengthening disease surveillance and response efforts. This is a smart investment because as more and more animals become infected with H5N1 avian flu, this increases the risk of spillover to other animals and to humans.
President Jimmy Carter died at age 100 this week. He was Governor of Georgia and President of the United States. In 1979, he installed solar panels on the roof of the White House for clean energy. Jimmy Carter and his wife Rosalynn volunteered one week a year for Habitat for Humanity into their mid 90s. Mr. Carter was awarded the Nobel Peace Prize in 2002 “for his decades of untiring effort to find peaceful solutions to international conflicts, to advance democracy and human rights, and to promote economic and social development.”
This week, there was an excellent review on how the gut microbiome talks to the brain across the Gut-Brain axis. Gut bacteria are actually able to modulate brain activity and behavior and the brain can influence the gut microbiota as well. Fascinating!
One Heartland, a Minnesota camp founded in 1993 to support children affected by HIV/AIDS, is up for sale due to a dramatic decline in perinatal HIV transmission rates because of effective antiretroviral medicines. The camp will shift its focus to serve other communities in need.
Photo from One Heartland
After a home renovation, a dentist noticed a fossil of a mandible of an ancient human (hominin) in the new travertine floor. Redditors worked together to find the right people to excavate the tile without damaging the fossil. It turns out that the mandible belonged to an ancient hominin and is “potentially of great scientific value to our understanding of the first migration of fossil hominin species outside of Africa after 2 million years ago.”
Green crabs are an invasive species introduced to the San Francisco Bay by trade ships in the 1980s. Sea otters reintroduced to a reserve in Elkhorn Slough, California, have significantly reduced the population of invasive green crabs by consuming up to 120,000 of them annually, according to a recent study. This decline has benefited the ecosystem by allowing native species like snails and sea grass to thrive, which supports young fish and migratory birds. Native predators like sea otters are important, as their return to natural habitats can restore food webs and help control invasive species. Plus, they are cute!
Photo: Michael Yang
Thanks to social media, I just learned about long haired guinea pigs and yes, I am a bit obsessed.
As of January 3, 2025, the amount of acute respiratory illness causing people to seek healthcare is at a high level and continues to increase nationally.
COVID-19 activity is increasing in most areas of the country.
Seasonal influenza activity continues to increase and is elevated across most of the country.
RSV activity is very high in many areas of the country, particularly in young children.
Key takeaway points. Norovirus is very contagious and is spread from hand to mouth and from eating contaminated food. Hand sanitizers do not kill norovirus. You must wash your hands with soap and water for at least 20 seconds to kill the virus. Foods must be cooked at more than 145 degrees F in order to kill the virus.
12/28/24 BioRxiV (Yunlong Cao): Virological and antigenic characteristics of SARS-CoV-2 variants LF.7.2.1, NP.1, and LP.8.1https://buff.ly/4a55PoE
Newcomer LP.8.1 has a growth advantage over other variants including XEC because it can evade antibodies and it has increased ability to bind to the ACE2 receptor to enter human cells.
12/28/24 Nature: Heart rate variability parameters indicate altered autonomic tone in subjects with COVID-19 https://buff.ly/4gyajqh
People hospitalized with COVID had significant autonomic dysfunction showing decreased vagal tone indicating a decrease in parasympathetic activity and increased sympathetic nervous system tone. “Variations in HRV were observed based on demographic factors, with younger patients, females, and non-white individuals showing more pronounced autonomic dysfunction.”
2022 Proceedings of the International AAAI Conference on Web and Social Media: “This Candle Has No Smell”: Detecting the Effect of COVID Anosmia on Amazon Reviews Using Bayesian Vector Autoregression https://buff.ly/3RTMThM
When Yankee Candle reviews start talking about loss of scent, it means that there are more COVID infections where people are losing their sense of smell.
1/2/25 Science: COVID 5 years later: Learning from a pandemic many are forgetting https://buff.ly/4fH4Z2v
recent Cold Spring Harbor Asia conference on preventing future pandemics.
SARS-CoV-2 extraordinarily rapid viral evolution
Yunlong Cao from Peking University studied antibodies from people who had SARS infection 20 years ago and who were then vaccinated against SARS-CoV-2 (COVID). They discovered a broad spectrum monoclonal antibody called SA55 is predicted to be effective for 2 more years of viral evolution. In an unpublished study, 300,000 people exposed to COVID who used the nasal spray monoclonal antibody (mAb) twice daily, the SA55 mAb spray prevented 80% of COVID infections. Dr. Cao has licensed the SA55 antibody to Sinovac.
1/2/25 Nature Immunology: System vaccinology analysis of predictors and mechanisms of antibody response durability to multiple vaccines in humans https://buff.ly/3BWvBP7
Fig. 7: Summary of proposed mechanism for involvement of megakaryocytes in promotion of durability of antibody responses to vaccination.
Explainer:
1/2/25 Nature Immunology: Platelet partnerships and lasting memories https://buff.ly/41Yn20R
"So how do platelets, traditionally known for their role in blood clotting, contribute to long-lasting vaccine immunity?"
Fig 1 from explainer article “Platelet partnerships and lasting memories”: Megakaryocytes support durable vaccine responses by promoting long-lived plasmablasts in the bone marrow via physical interactions and secreted proliferation-inducing ligand (APRIL).
2/19/24 Shinogi to license Ensitrelvir to South Korea
Regarding Filing for Ensitrelvir Fumaric Acid, a Therapeutic Drug for COVID-19 in South Korea https://buff.ly/3BFsZFj
“Ensitrelvir demonstrated a favorable effect in preventing symptomatic COVID-19 in the SCORPIO-PEP trial (post-exposure prophylaxis trial)2.”
Long COVID
12/28/24 Nature: Omics-based analysis of mitochondrial dysfunction and BBB integrity in post-COVID-19 sequelae (PASC, Long COVID) https://buff.ly/3PgbUoE
Mitochondrial dysfunction and blood–brain barrier breakdown
“impaired Mitochondria leads to an accumulation of reactive oxygen species (ROS), triggering endothelial dysfunction, and leading to the passage of harmful molecules across the BBB.”
Fig. 6. The dysfunction of mitochondrial-associated genes harms normal brain homeostasis by targeting the Oxidative phosphorylation mechanism that results in uncontrollable ROS generation.
“In patients who underwent CCI surgery, we recovered Brevundimonas genomes from the C1 ligament,” says Dr. DuPont, who is studying the role of persistent pathogens in #complexchronicillness. “These patients have undergone microbiome translocation from the intestine to ligament.”
?VIDEO Christopher DuPont, JCVI- no link found
12/12/24 Frontiers in Cellular and Infection Microbiology: Connecting dots of Long COVID-19 pathogenesis: vagus nerve- hypothalamic-pituitary- adrenal-mitochondrial axis dysfunction https://buff.ly/3ZPzk9c
This article proposes that reduced vagal tone, cortisol imbalance, and mitochondrial damage may create a feedback loop that perpetuates LC symptoms.
12/19/24 Brain, Behavior and Immunity: COVID-19 may Enduringly Impact cognitive performance and brain haemodynamics in undergraduate studentshttps://buff.ly/3DteWTP
12/7/24 Analytical and Bioanalytical Chemistry: Long-term dysregulation of plasma peptidome in mild and multiple COVID-19 recovered patients revealed by a novel efficient peptidomics workflow https://buff.ly/3PkybBF
Persistent abnormalities in lipid metabolism, coagulation, and immune function peptides, which last longer after secondary infections.
11/7/24 ACS Chemical Neuroscience (Sweden): SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion https://buff.ly/408YBMQ
h/t Jon Douglas
“Importantly, UV-inactivation of SARS-CoV-2 does not affect its ability to induce amyloid aggregation, as amyloid formation is dependent on viral surface catalysis via HEN and not its ability to replicate.”
Graphical Abstract:
Adding HSV-1 or SARS-CoV-2 to CSF causes amyloid fibril formation.
White arrows indicate viral particles, and black arrows indicate amyloid fibrillar structures.
CSF from one individual (CSF 1) was incubated with UV-inactivated HSV-1 and proteins precipitate out into amyloid
11/29/24 Cell Host & Metabolism (Erturk lab): Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19 https://buff.ly/3Va9sTJ
In people who had a COVID infection in the past, 60% were found to have an accumulation of SARS-CoV-2 spike protein in their skull bone marrow or meninges surrounding the brain on post-mortem exam up to 4 years after COVID infection.
Living Long COVID patients were found to have elevated neurodegeneration biomarkers in their cerebrospinal fluid (CSF) including significantly elevated Tau, neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP). The chronic brain inflammation from persistent SARS-2 spike protein may be causing cognitive dysfunction in people with Long COVID, increased risk of strokes and other brain injury. In mice, injection of the SARS-2 spike protein alone induced neuroinflammation and caused anxiety-like behavior. “Findings suggest persistent spike protein at the brain borders may contribute to lasting neurological sequelae of COVID-19.”
1/2/25 Environmental Science and Pollution Research: Beyond the virus: ecotoxicological and reproductive impacts of SARS-CoV-2 lysate protein in C57Bl/6j female mice https://buff.ly/3BW4ML1
Water contaminated with SARS-CoV-2 lysate protein is toxic to female mice.
Anxiety-like behavior, memory deficits, and reduced activity “which were associated with oxidative stress and dopaminergic and cholinesterase imbalance in the animal brain.”
Toxic inflammatory responses were seen in the brain, liver, duodenum, and ovaries.
H5N1
1/3/25 CIDRAP: HHS directs $306 million to avian flu response as virus strikes more US flocks https://buff.ly/4j5znq0
12/31/24 NEJM: Critical Illness in an Adolescent with Influenza A(H5N1) Virus Infection https://buff.ly/425LBc6
Media: Teen with H5N1 off oxygen, no longer infectious. Treatment included temporary tracheal intubation.
Reality: Intubated for 3 weeks, ECMO for 2 weeks, hemodialysis, plasma exchange 3 times.
This kid almost died. Why can't we be transparent about it?
And how many people will be able to afford this treatment in the U.S healthcare system?
12/26/24 CNN: 20 big cats killed by the H5N1 bird flu at Washington sanctuary https://buff.ly/41SvG0S
"The 20 animals that died [from H5N1 bird flu] include: 5 African Servals, 4 bobcats, 4 cougars, 2 Canada Lynxes, 1 Amur-Bengal tiger mix and other species of big cats."
12/25/24 AP: Oregon house cat died after eating pet food that tested positive for bird flu https://buff.ly/41JJpai
"this cat contracted H5N1 by eating the Northwest Naturals raw and frozen pet food" that was contaminated with H5N1 bird flu.
A dentist went to his parents home and saw some new travertine tile that had been put in. He noticed a fossil of a jaw bone and he posted it on Reddit. People there told him who to contact and it turns out that the mandible belonged to an ancient hominin from about 2 million years ago.
12/26/24 Washington Post: Green crabs have invaded habitats. Sea otters might be the solution. https://buff.ly/3Du8snN
Sea otters are eating thousands of invasive green crabs at Elkhorn Slough, a reserve in Monterey County, California, according to a recent study. (Michael Yang)
What H5N1 did to that Canadian teen is terrifying. We should all be paying attention to this. Thank you for including it.
As a long hauler going on five years, I am trying to not let my concerns about a future neurodegenerative disease rule my life, but the concern is always there. I am doing better and better as the years pass, but I still sometimes have cognitive blips that are not normal for a person in their 40’s. I wish more people understood just how much they’re in for by just letting it rip.
What H5N1 did to that Canadian teen is terrifying. We should all be paying attention to this. Thank you for including it.
As a long hauler going on five years, I am trying to not let my concerns about a future neurodegenerative disease rule my life, but the concern is always there. I am doing better and better as the years pass, but I still sometimes have cognitive blips that are not normal for a person in their 40’s. I wish more people understood just how much they’re in for by just letting it rip.
I did not know that someone had produced a mathematical study of Amazon Yankee Candle and Covid rates. Fantastic.
Thanks for the interesting roundup, complete with long-haired guinea pigs.