From https://covid.cdc.gov/covid-data-tracker/#variant-proportions
Walgreen’s COVID testing shows that positivity in their store testing sites is up 4.2% this week for the entire nation. Across the U.S., emergency department visits for COVID are up 16.2% for the most recent week reported, but E.R. test positivity is only at 4.5%.
The wastewater data from this week was a bit confusing because of some inconsistencies in reporting. The CDC reports that US wastewater is at the “LOW” level, but the West and the South are higher than the national average. National SARS-CoV-2 data from Sara Anne Willette shows that Hawaii wastewater levels of SARS-CoV-2 is still “VERY HIGH”. Florida levels are “SUBSTANTIAL”, followed by California, Vermont, Alaska and Idaho which are right behind at a “MODERATE” level.
In his June 14 update, JP Weiland states that there is an “8% increase this week. Hawaii continues to be near their highest levels in over a year. Continental US at low levels [of COVID infections], but the West Coast and Florida are at medium” levels. Approximately 1 in every 155 people is currently infected with COVID on a national level.
From JP Weiland: https://x.com/JPWeiland/status/1801711110636376494
Wastewater levels in different states:
From National SARS-CoV-2 data from Sara Anne Willette: https://iowacovid19tracker.org/
Wastewater SCAN reports that nationally there has been an upward trend over the last 21 days and that there is a medium concentration of SARS-CoV-2 at the national level. As of Friday 6/14/24, the highest SARS-CoV-2 wastewater levels in the nation in PMMoV are:
Brunswick, ME at 2346 PMMoV
Honolulu at 2282 PMMoV
Concord NH at 1717 PMMoV
Oceanside, San Francisco, CA at 1715 PMMoV
San Rafael CA at 1482 PMMoV
Ithaca NY at 1402 PMMoV
South Parker CO at 1137 PMMoV
Boise ID at 1108 PMMoV
Novato CA at 1081 PMMoV
Orange Co FL at 1031 PMMoV
New Orleans at 837 PMMoV
In the Bay Area, Palo Alto, San Jose, and Sunnyvale wastewater sheds are at the “HIGH” level for COVID, and Gilroy is at the “MEDIUM” level according to the Santa Clara county website. However, looking at the California statewide view on Wastewater SCAN, we see that levels of SARS-CoV-2 virus in PMMoV are much lower in Palo Alto (368 PMMoV), San Jose (327 PMMoV), San Mateo county (290 PMMoV) than in other places like Oceanside, San Francisco (1715 PMMoV) or San Rafael (1482 PMMoV). Marin is at the MEDIUM level, but is increasing overall.
Variants
In Spain, Portugal, Scotland, Hawaii and Australia, KP.3 (the “FLuQE” variant) is driving a significant COVID wave. According to Kei Sato, deFLiRT variants LB.1 and KP.2.3 exhibited higher pseudovirus infectivity in the lab and more robust immune resistance than KP.2. But, pseudovirus studies do not always translate into real world findings, so we will have to wait to see if either of them will push out KP.3.
Vaccines
On Thursday, the FDA changed its recommendation to COVID vaccine manufacturers telling them to use KP.2 for the Fall 2024 vaccine formulas instead of JN.1 if possible. This makes a lot of sense since KP.2 [JN.1 + F456L + R346T mutations] is expected to protect better against all of the newer variants that contain F456L mutations. Basing the vaccines on an older variant (JN.1) would not be expected to protect against the newer variants as well. Moderna and Pfizer will be able to change their vaccine formula to use the KP.2 antigen because of the agility of mRNA vaccines.
Novavax will supply JN.1 protein-based vaccines because those take at least 6 months to make. Novavax put out a statement that they hope to have their JN.1 COVID vaccine available in pre-filled syringes for US distribution by mid-July. They also stated that in non-human primates, their JN.1 vaccine provided good protection against KP.2 and KP.3 in animals that had received the XBB.1.5 vaccine previously.
A new study shows that the more symptoms (chills, malaise and headache) that a person got after their second dose of the COVID vaccine, the more long-lasting neutralizing antibodies they produced. Increased heart rate and temperature after the vaccine was also associated with higher levels of neutralizing antibodies made.
The common cold is caused by endemic coronaviruses (eCoVs), including human coronavirus OC43 (HCoV-OC43). Researchers found that prior infection with SARS-CoV-2 protected against the OC43 virus infection, but that SARS-CoV-2 vaccination did not. Prior COVID infection caused CD8+ T cell responses against two eCoV proteins, nsp12 and nsp13. COVID vaccination did not produce these T cell responses. Other studies have shown the reverse- that high levels of HCoV-OC43-nucleocapsid antibodies from infection with the common cold coronavirus OC43 can provide some protection against SARS-CoV-2. These clues can give us insight into pancoronavirus vaccines.
Moderna is planning to offer a combination COVID and Flu vaccine in 2025. The combination vaccine was found to be more effective than existing standalone shots for those viruses in a late-stage clinical trial.
Masks
North Carolina’s House of Representatives passed a mask ban bill this week with a health exemption. According to the Herald Sun, “The bill arose out of Republican concerns over Black Lives Matter and pro-Palestinian protesters wearing masks during marches and demonstrations. Its justification is that restricting masks will make it easier for police to identify protesters who engage in obstructive, destructive or violent behavior.” The bill will now allow people to wear medical masks to prevent the spread of contagious disease, but added language stating that “on public or private properties, like at grocery stores or at a workplace, people can be required to remove masks if requested.”
New York Governor Kathy Hochul said at a news conference that she is also considering a ban on masks in the NYC subway because of worries about crime. Dr. Stella Safo and Lucky Tran responded on Twitter that mask bans will not stop crime, but will put people at risk of airborne pathogens like COVID.
Pediatrics
In a study of 3,568 patients under age 18 from ten countries who were hospitalized with acute SARS-CoV-2 or with MIS-C, severe neurological manifestations like acute encephalopathy, seizures, and delirium were prevalent, leading to new neurocognitive impairments at hospital discharge. Although not as many children are hospitalized with COVID infections as adults, the rates of new onset severe neurological conditions were found to be 18.0% for children hospitalized with acute COVID infection and 24.8% for kids with MIS-C.
Paxlovid is approved for people age 12 and over, but it is not commonly prescribed in teenagers. In a target trial emulation study looking at 49,378 mostly vaccinated adolescents age 12 to 17, Paxlovid decreased all-cause hospitalization risk and no safety concerns were noted. The risk of hospitalization for 12 to 17 year olds was small, but it was statistically lower for the group that took Paxlovid (0.45%) as compared to controls (0.68%).
Long COVID
Last week, The National Academies of Sciences, Engineering, and Medicine (NASEM) released a 250 page document for the Social Security Administration on long term health effects and disability caused by Long COVID. At the request of the White House, NASEM released a new document with a consensus definition of Long COVID. Until now, different government bodies (WHO, CDC, etc) had different definitions of Long COVID that varied in length of duration required and whether a positive COVID test was needed. The NASEM came up with 5 key elements on the definition of Long COVID which was summarized by Lisa McCorkell below.
“Long COVID is an infection-associated chronic condition that occurs after SARS-CoV-2 infection and is present for at least 3 months as a continuous, relapsing and remitting, or progressive disease state that affects one or more organ systems.”
From Lisa McCorkell https://x.com/LisaAMcCorkell/status/1800578860670747045
On page 75 of the 2024 NASEM Long COVID Definition Implementation,Table 2 includes key considerations for clinicians on what should be evaluated in people with Long COVID.
Chief Data Scientist from the University of California healthcare system Atul Butte tweeted that researchers can now access deidentified data on 14,000 adults participating in Long COVID research through NIH RECOVER. The studies include data from 92,000 study visits at 79 locations throughout the United States in 2021 to 2023.
Post-viral syndromes, Long COVID & ME/CFS
This week, there was an excellent NEUROLOGY Podcast where Dr. Avindra Nath discussed Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (PI-ME/CFS), including Long COVID. He relayed that in PI-ME/CFS, there is a defect in B cells where they cannot switch from making IgM to IgG easily. This leads to problems with T cell maturation, so that T cells cannot respond to antigens well. The T cells become exhausted because of this. When cellular immunity (B cells and T cells) have issues, the innate immune system is triggered leading to release of cytokines and activation of macrophages. Dr. Nath spoke of possible treatments to assess in future clinical trials including checkpoint inhibitors to reverse T cell exhaustion and blocking specific cytokines that are elevated in PI-ME/CFS like TNF, IL-1 or IL-6.
Last week, there was an outstanding mega review of ME/CFS. The article reviews the probable predisposition and causes of ME/CFS, the complex pathophysiology of ME/CFS, Gut dysbiosis, Systemic inflammation, Redox imbalance and oxidative stress, Dysfunction of the vasculature, endothelium, and coagulation, Neuroinflammation, Impaired energy metabolism in ME/CFS, Hormonal alterations, Immune dysfunction, Autoimmunity, Management of ME/CFS, and future research recommendations.
H5N1 Avian Flu (HPAI)
This week, the USDA announced that more house mice and more cats have tested positive for H5N1. With the spread of bird flu H5N1 to more and more mammals, there are more chances for the virus to start infecting more humans as well. A new article in the NEJM shows that there is “ the potential for a relatively small but detectable quantity of HPAI A(H5N1) virus to remain infectious in milk after 15 seconds at 72°C if the initial titer is sufficiently high." Two weeks ago, it was reported in Science magazine that there are huge amounts of H5N1 influenza virus in raw milk. It is imperative that regulatory bodies test commercial milk to make sure that the pasteurization process is strong enough to kill off all H5N1 virus in milk. According to Cornell’s College of Agriculture and Life Sciences, “Ultra-pasteurized means that the milk is heated to a minimum of 280°F for a minimum of 2 seconds. This temperature and time combination is much more lethal to bacteria, killing virtually all of concern. Ultra-pasteurized milk is also packaged under near sterile conditions.” Perhaps we should consider drinking ultra-pasteurized milk, although I could not find any studies on ultra-pasteurized milk and the H5N1 virus yet.
Other news
GLP-1 drug Tirzepatide (Mounjaro, Zepbound) was found to reduce Metabolic dysfunction–Associated SteatoHepatitis (MASH), also known as fatty liver, in a Phase 2 trial. A review of GLP-1 medications for obesity and for diabetes reported that GLP-1 drugs decrease major adverse cardiovascular events (MACE), including heart failure, kidney disease, and cardiovascular death and these drugs have been well studied in people with Type II diabetes showing that they are safe and effective.
The Supreme Court preserved access to Mifepristone pills for medical abortions this week. The state of Connecticut mandated that people be offered a chance to donate their endometriosis samples to a biorepository so that the disease can be better studied. An excellent review of mitochondrial function in health and in disease came out recently in Cell magazine.
People diagnosed with schizophrenia or another psychotic disorder were found to be 3-fold more likely to have Bartonella DNA in their blood. Bartonella is spread via fleas and ticks and animals that harbor them. Cat scratch disease is caused by Bartonella henselae. Eighteen types of Bartonella are known to infect humans. In this study of 116 people, they found Bartonella henselae, Bartonella vinsonii subsp. berkhoffii, Bartonella quintana, Bartonella alsatica, and Bartonella rochalimae in some of the patients with psychosis.
A few weeks before her husband Robert died of a brain tumor, Karen Coffman won $1 Million on a scratcher. This was a great relief to Robert who had worried that she would not have enough money to live on after he was gone.
African elephants were discovered to call each other by unique names using low rumbling sounds that can be heard from a distance.
Lakota legend says that 2,000 years ago, a White Buffalo Calf Woman prophet brought the “Seven Sacred Rites” to the Lakota people. She told them that someday, when times are hard, prosperity shall return when a white buffalo calf with a black nose, black eyes, and black hooves appears. She also told them that they needed to take care of the earth. This week, a white buffalo calf, with a black nose, black eyes, and black hooves was born in Yellowstone National Park. An albino calf would have pink eyes, unlike this one. Photographer Erin Braaten was able to capture a photo of the white buffalo calf with its mother.
Photo by Erin Braaten
Have a good rest of your weekend,
Ruth Ann Crystal MD
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