COVID, H5N1 & more, 12/14/24
Wastewater levels of SARS-CoV-2 are LOW nationally, but are MODERATE in the Midwest as of December 7th according to the CDC. We are just starting to see a rise in virus levels. Through December 7, the CDC reported that New Mexico, Arizona, Massachusetts, and Minnesota were VERY HIGH. Missouri and South Dakota are also VERY HIGH, but there are very few sites reporting in those two states which makes it harder to analyze.
Wastewater SARS-CoV-2 per the CDC (NWSS):
Zoomed in
From: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html
Looking at the CDC wastewater numbers, Mike Hoerger estimates that 1 in every 73 people in the Midwest were actively infectious with COVID on December 7th. If cases continued to rise in a similar way, he calculated that by December 13th, 1 in every 41 people would be actively infectious with COVID in the Midwest. JP Weiland predicts that we will have a much smaller winter COVID wave this year. He predicts a peak under 400,000 new COVID infections per day in early January, but Mike Hoerger believes that the numbers will be higher and expects about 750,000 new infections per day by January 1st. Whichever it is, this winter wave does look like it will be significantly lower than what we have seen in prior years.
From: https://bsky.app/profile/jpweiland.bsky.social/post/3lcw6izzxzs2y
Variants
The US variant tracker only updates every 2 weeks now. Last week, XEC surpassed KP.3.1.1 reaching 44% of COVID cases, while KP.3.1.1 was 39%. Variant hunters on Twitter are watching LP.8 more closely as it is increasing in a Brazilian state. Today, Ben Murrell posted on the growth advantage of LP.8.1 which appears to have about a 30% growth advantage over XEC. Federico Gueli posted, “As expected, very little changed: LP.8.1 is the fastest likely with a slightly more clear advantage over everything.” Even if LP.8.1 takes over, it does not look like it would cause a huge COVID wave.
From: https://github.com/MurrellGroup/lineages?tab=readme-ov-file
Acute COVID infections, General COVID info
Scientists from UCLA created a nanoengineered immunosensor that can quickly see if someone has a blood clot by measuring four markers (CRP, calprotectin, sP-selectin, and D-dimer) in the blood. The sensor was tested on 53 people with acute COVID infection and was rapidly able to predict clotting events with 92% accuracy.
A group from Florida and Italy made an artificial intelligence (AI) model called SARITA which can predict how the SARS-CoV-2 spike protein S1 will mutate. When trained on Alpha, Beta, and Gamma variants, SARITA was able to correctly predict how future S1 mutations would evolve and was able to accurately predict mutations in later variants including Delta and Omicron. Because SARITA is able to predict how the SARS-2 virus will evolve, this technology could be beneficial in designing new COVID vaccines and treatments.
This week, the World Health Organization’s Director-General Dr. Tedros Adhanom Ghebreyesus said at a media briefing on December 10th, "We cannot talk about COVID in the past tense. It’s still with us, it still causes acute disease and Long COVID, and it still kills. The world might want to forget about COVID-19, but we cannot afford to." He is right.
Pediatrics
In a study of about 385,000 children and adolescents, the Pfizer BNT162b2 mRNA COVID vaccine was found to reduce the risk of Long COVID during Delta and Omicron periods. During the Delta wave, the Pfizer mRNA COVID vaccine was 95% effective against Long COVID in teens. During Omicron, it was 60% effective against Long COVID in children and 75% effective in teenagers.
Long COVID
In 2021, the NIH launched the RECOVER initiative with $1 billion allocated for research on Long COVID. Three years later, people were critical because most of the $1 billion funding was spent on observational studies without a focus on treatments or cures.
The NIH has now allocated $147 million to $515 million announced earlier this year for RECOVER, bringing the new total to $662 million in new funding to support ongoing observational studies, pathobiology research, and the RECOVER-Treating Long COVID (RECOVER-TLC) clinical trials program which focuses on developing and testing treatments. $18 million will be directed toward studies exploring biological mechanisms of Long COVID which may help identify potential therapies as well.
An analysis of symptoms from 172,303 people with Long COVID identified ten key symptoms of Long COVID, and categorized them into four subtypes: 30% ENT (smell, taste, and hearing loss), 10% cardiopulmonary (shortness of breath, postural tachycardia, chest tightness or pressure), 23.5% neurological (brain fog and speech difficulty), and 38% with mild general fatigue. Risk factors for Long COVID included severe COVID-19 infection and multiple reinfections. Vaccination reduced the risk.
Long COVID affects women more than men and there are sex differences in immune responses in Long COVID. In a new article, Physical Medicine and Rehabilitation doctors discuss special issues around Long COVID rehabilitation in women stating, "Rehabilitation efforts for long COVID in women must address health equity concerns and consider the historic context of stigmatized infection-associated chronic conditions."
A study from the University of Georgia highlights the financial hardships caused by Long COVID, particularly for lower-income individuals and those without college degrees. Among nearly 10,000 participants with Long COVID, many reported food insecurity, difficulty paying bills, and risk of losing utilities. These challenges disproportionately affected those in lower socioeconomic groups.
A group in British Columbia analyzed health-related quality of life (HRQoL) in 3,463 Long COVID patients using the EQ-5D-5L questionnaire. Results revealed significant reductions in HRQoL, with 95% of participants scoring below 90 and 50% below 60, highlighting Long COVID impacts on mobility, pain, mental health, and daily activities. The study found that social determinants of health (age, sex, employment, and ethnicity) significantly influence HRQoL, emphasizing the need for tailored, equity-focused interventions to support diverse populations affected by Long COVID.
H5N1
On December 10, Marin county reported a child with suspected H5N1 bird flu. “The child presented to a local emergency department with fever and vomiting after drinking raw milk. The child tested positive for Influenza A.” The H5N1 virus is a type of Influenza A. The CDC could not verify if this was due to H5N1 Avian flu or seasonal flu because of low levels of viral RNA in the samples sent. The Marin county health department strongly warned people not to drink raw milk. As Infectious Disease doctor Dr. Titanji posted on BlueSky, “drinking raw milk can expose a person to Listeria, Brucella, Bovine Tuberculosis, Campylobacter, Shigella, E coli, and now H5N1.”
A wildlife rehab in Kansas City reported many calls about "Geese falling out of the sky". H5N1 bird flu has infected migrating wild geese which are now sick and are literally falling out of the sky. “We are not admitting geese to our facility at this time as this is a highly contagious disease that is spread by respiration, fecal matter and contact,” organization leaders said on Friday. “And we must protect the birds already in our care at risk." Who had "Geese falling out of the sky" on their 2024 bingo card?
From: https://www.kctv5.com/2024/12/06/geese-falling-out-sky-avian-flu-begins-infect-birds-kc-metro/
Other news:
This week, the New York Times posted a letter from 77 Nobel laureates asking the Senate to oppose Robert Kennedy Jr’s nomination for Secretary of Health and Human Services stating that he “would put the public’s health in jeopardy.” “In addition to his lack of credentials or relevant experience in medicine, science, public health or administration”, Mr. Kennedy is staunchly against public health measures including life-saving vaccinations, the fluoridation of water and he promotes conspiracy theories about AIDS and other diseases.
Senate Republican Leader Mitch McConnell warned Robert F. Kennedy Jr after one of Kennedy's top advisers had filed petitions to revoke approval for the polio vaccine and other immunizations. McConnell himself had polio as a child and saw what it could do to children.
According to STAT News, “Pediatrics is becoming medicine’s largest skeleton crew”. Thirty-percent of Pediatric residencies did not match this year. Low pay and political pressure on pediatricians by the anti-vaccine movement are causing medical students to choose other medical specialties.
A sophisticated cyberattack called “Salt Typhoon” infiltrated major U.S. telecommunications networks, exposing vulnerabilities in aging infrastructure and compromising sensitive surveillance data. Chinese government hackers breached 8 US telecom and internet services including AT&T and Verizon, as well as many other telecom companies in other countries. The breach is part of a spy operation conducted by China. Last week, the FBI warned Americans to use encrypted messaging like WhatsApp instead of texting. U.S. officials convened industry leaders emphasizing the urgent need for cybersecurity upgrades in our telecom systems despite the risk of significant disruptions.
A new study in JAMA shows that psilocybin, the psychedelic compound found in magic mushrooms, can be used successfully to reduce depression in frontline clinicians who worked during the COVID pandemic. The authors state, “The findings establish psilocybin therapy as a new paradigm of treatment for this postpandemic condition.” I would add that making certain that proper PPE and N95 masks are well stockpiled in case of another pandemic, like H5N1, could also be helpful psychologically to clinicians.
Researchers taught rats to drive small cars and it turns out that the rats love driving. If given a choice to walk directly to a treat or to have to go out of their way to get to their car to drive to the treat, they prefer to drive.
CNN
Have a great rest of your weekend,
Ruth Ann Crystal MD
COVID news notes:
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
CDC Respiratory viruses (COVID, Flu, RSV) Hospitalizations (for those states reporting): https://www.cdc.gov/resp-net/dashboard/index.html
Zoomed in
Walgreens positivity rate: https://www.walgreens.com/businesssolutions/covid-19-index.jsp
Through 12/8/24
Wyoming- Dec 8th, 4 tests of which 50% were positive
New Mexico- Dec 8th: 71 tests of which 39% were positive
Vermont- Nov 21 last reported
US Wastewater Monitoring:
CDC wastewater reporting: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html
Through 12/7/24
Nationally, CDC reports that as of a week ago on 12/7/24, The Midwest is MODERATE and other regions are either LOW or MINIMAL.
Zoomed in
CDC wastewater map: https://www.cdc.gov/nwss/rv/COVID19-currentlevels.html
Through Dec 7, 2024. Arizona and New Mexico were VERY HIGH. Minnesota and Massachusetts were just below that.
South Dakota and Missouri are very high, but there are few sites reporting.
National SARS-CoV-2 data from Sara Anne Willette: https://iowacovid19tracker.org/
Composite SARS-CoV-2 wastewater map [CDC NWSS + WastewaterSCAN data] as of 12/6/24:
Wastewater SCAN: https://data.wastewaterscan.org/
WastewaterSCAN SARS-CoV-2 in wastewater:
In the summer wave, the West Coast started out very high. Now, the Midwest is HIGH and the Northeast has HIGH areas as well, as do parts of the south.
Note, WastewaterSCAN does not include New Mexico or Arizona which are high on the CDC’s NWSS site.
California statewide view https://buff.ly/3YObiul
Palo Alto is the state’s highest SARS-CoV-2 in wastewater at 244 PMMoV which is fairly low.
Sewer Coronavirus Alert Network (SCAN) project by Stanford University:
“This website is no longer being updated as of 11/22/24. To see the latest updates to the national WastewaterSCAN program, please visit data.wastewaterscan.org.”
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
Through 12/9/24
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
https://bsky.app/profile/jpweiland.bsky.social/post/3lcw6izzxzs2y
12/9/24 JP Weiland @jpweiland.bsky.social
Updated December-Early January Forecast:
Given recent data, the expected peak has decreased even further, and the range has shrunk.
This is now guaranteed to be a record low for Holiday infection rates, hospitalization, and deaths.
“A comparison of Holiday surge estimates from 2020 to 2024 shows just how unusual this prediction is.”
Michael Hoerger modeling: http://pmc19.com/data/, https://twitter.com/michael_hoerger
12/13/24 https://x.com/michael_hoerger/status/1867628671978418374
MH: “CDC numbers just dropped:
Covid transmission is picking up rapidly
1 in 73 people in the Midwest were actively infectious on Dec 7 and rising
If following historical trends (no false peak), 1 in 41 people in the Midwest are actively infectious today.”
12/9/24 Mike Hoerger https://x.com/michael_hoerger/status/1866379720255852662
“PMC COVID-19 Forecasting Model, Dec 9, 2024
My over/under for how many daily Covid infections the U.S. will see by the end of the year is 750,000.
Our model has us hitting about 1 million daily by New Year's Eve. The model accounts for historical variation and current trends, but not the atypical state of subvariant evolution. If winter transmission picks up more like usual, such as if LP.8.1. takes off, 1 million is likely spot on.
However, if LP.8.1. does not take off, 700K is probably a better estimate. If the CDC numbers are flat next Friday, take 200k of the model's Dec peak, putting it closer to 800k. If flat in their next two reports, expect closer to 600k.”
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
International from @nichtGenes61287
Look at the date of each map as some are quite old. Also, make sure to note if chart is for wastewater SARS-2 levels or for cases.
Europe variants per Mike Honey
https://bsky.app/profile/mikehoney.bsky.social/post/3lcqtup7qns23
“Here's the latest variant picture for Europe (excluding the UK).
DeFLuQE variants continue to decline, and are no longer dominant.
XEC.* grew to around 45%, and is now dominant.”
Australia https://bsky.app/profile/mikehoney.bsky.social
Variants
US Variant tracker: https://covid.cdc.gov/covid-data-tracker/#variant-proportions
Through 12/7/24. Will update next week.
12/9/24 LP.8 variant https://x.com/SolidEvidence/status/1866298683550999036
12/9/24 LP.8 in Brazil https://x.com/siamosolocani/status/1866098573240070375
Thx for an informal rumour by @es701950 , @Mike_Honey_ and me were able to confirm that LP.8.1 is likely linked to the ongoing wave in Fortaleza in the state of Ceara' Brazil . confirmed by google trends , anectodal tweets and local media sources : https://opovo.com.br/noticias/fortaleza/2024/12/05/covid-19-redes-particulares-registram-aumento-da-demanda-por-atendimento.html…
12/14/24 https://bsky.app/profile/did:plc:pt23sp6i4oj376fljeqqzzlt/post/3ldch4xdayc2t
Federico Gueli:
New update on Sars Cov 2 variant landscape:
@benjmurrell.bsky.social did a great work in updating again his chart this afternoon so now. we have a new different one from this morning.
Acute COVID infections, General COVID info
12/11/24 Science Advances: Rapid prediction of acute thrombosis via nanoengineered immunosensors with unsupervised clustering for multiple circulating biomarkers https://buff.ly/3ORGODn
12/10/24 BioRxiV: SARITA: A Large Language Model for Generating the S1 Subunit of the SARS-CoV-2 Spike Protein https://buff.ly/4gsNxiR
12/10/24 Lucky Tran https://bsky.app/profile/luckytran.com/post/3ld2iq3adtc2a
@who.int Director-General's remarks at a media briefing on 10 December 2024:
"We cannot talk about COVID in the past tense. It’s still with us, it still causes acute disease and Long COVID, and it still kills.
The world might want to forget about COVID-19, but we cannot afford to."
Pediatrics
1/2025 eClinical Medicine: Real-world effectiveness and causal mediation study of BNT162b2 on long COVID risks in children and adolescents https://buff.ly/4g6R3zV
Long COVID
1/2025 Lancet eBioMedicine (Multinational): Refinement of post-COVID condition core symptoms, subtypes, determinants, and health impacts: a cohort study integrating real-world data and patient-reported outcomes https://buff.ly/3ZzzdOK
12/12/24 The NIH adds funds to long COVID-19 research, advances work on new clinical trials https://buff.ly/4fhZF5B
5/31/24 The Sick Times: ‘They bungled it:’ NIH documents reveal how $1.6 billion Long Covid initiative has failed so far to meet its goals https://buff.ly/3VENZTm
12/9/24 Physical Medicine and Rehabilitation Clinics of North America: Considerations for Long COVID Rehabilitation in Women https://buff.ly/4gryFBG
12/6/24 Nature Scientific Reports: Exploring social determinants of health and their impacts on self-reported quality of life in Long COVID-19 patients https://buff.ly/3B6YeJf
12/6/24 CIDRAP: New data highlight the financial burden of long COVID https://buff.ly/4grmbcT
Long COVID symptoms by NY Health https://x.com/nycHealthy/status/1866515772110942283
H5N1
12/10/24 Marin County reports a child with suspected H5N1 bird flu. “The child presented to a local emergency department with fever and vomiting after drinking raw milk. The child tested positive for Influenza A.” https://www.marinhhs.org/h5n1-bird-flu
12/10/24 Marin County Health Department: Health Officials Warn Against Consuming Raw Milk https://buff.ly/4gwZ0hI
https://bsky.app/profile/boghuma.bsky.social/post/3ld27bhoiws2a
12/6/24 KCTV: ‘Geese falling out of the sky’: Avian flu begins to infect birds in the KC metro https://buff.ly/3D6HzWB
H5N1 bird flu has infected migrating geese which are now sick and are literally falling from out of the sky. H5N1 Bird flu is spread by birds breathing, bird poop, or from touching sick birds.
Other news:
12/9/24 NY Times: More than 75 Nobel laureates ask Senate to turn down Kennedy’s nomination for HHS buff.ly/4ivFkwu
“These political attacks on science are very damaging,” laureate Dr. Richard Roberts said. “You have to stand up and protect it.”
12/13/24 CBS: Mitch McConnell warns RFK Jr. against effort to undermine polio vaccines https://buff.ly/41TcTCP
Mia Farrow also responded.
Mia Farrow https://bsky.app/profile/miafarrow.bsky.social/post/3ldabsjdf4s2n
12/12/24 NBC: Phone companies haven't notified most victims of Chinese data hacking campaign, sources say https://buff.ly/41u9wlr
"The hacking campaign, nicknamed Salt Typhoon, is one of the largest intelligence compromises in U.S. history. It has breached eight domestic telecom and internet service providers and dozens of others around the world, and it is still ongoing, a White House official said last week. The U.S., Australia, Canada and New Zealand claim it is part of an intelligence operation conducted by China."
11/22/24 NY Times: Emerging Details of Chinese Hack Leave U.S. Officials Increasingly Concerned https://buff.ly/4fzTrPg
12/9/24 BioRxiV (Scripps): Functional and epitope specific monoclonal antibody discovery directly from immune sera using cryoEM https://buff.ly/4fkIkZw
11/27/24 STAT News: Pediatrics is becoming medicine’s largest skeleton crew https://buff.ly/4gdbWcO
12/11/24 CIDRAP: Trial stops enrollment after Tpoxx (tecovirimat) fails to speed clade 2 Mpox healing or pain relief https://buff.ly/3Dl2sNL
12/6/24 CIDRAP: Psilocybin can lift depression in clinicians who worked on COVID-19 frontlines, trial finds https://buff.ly/4g0cvqb
12/5/24 JAMA: Psilocybin Therapy for Clinicians With Symptoms of Depression After the Pandemic https://buff.ly/3ZEfFtT
12/13/24 CNN: Rats learn to drive miniature cars and seem to enjoy it https://buff.ly/4fji0z7
Deeply, deeply appreciate your continued reporting.
Rats prefer to drive made my day.