There are presently at least 900,000 new COVID infections each day in the United States, with 1 in every 37 people infected. Some areas like California, Texas and Florida appear to be peaking, but with the addition of KP.3.1.1, we may see another bump in numbers. The West and the South have almost double the level of virus in wastewater as compared to last summer’s COVID wave. Per Sara Anne Willette, wastewater levels of SARS-2 virus are “Excessively High” in Utah, followed by “Very High” in Louisiana, Arkansas, Florida, Texas, Oregon, California, North Carolina and Oregon. In the Bay Area, San Jose, San Mateo, Sacramento and parts of San Francisco show higher levels of virus in wastewater than the winter wave last December/January. The San Francisco Department of Health is advising people to wear masks indoors.
Eric Topol came out with a new essay yesterday that I highly recommend reading. He discusses this large wave, why waves continue to happen and what we should be doing about it.
People have asked me how to look up information on their state. I recommend these 3 sources:
Pick your state under Location (see highlighted below)
Variants
The KP.3.1.1 variant is pushing out KP.3 in America and around the world. KP.3.1.1 is the JN.1 variant with DeFLuQE mutations = [S31 deletion + F456L+ Q493E mutations]. It is dominant in most of Europe and is rapidly increasing in Canada and the United States. The DeFluQE mutations make KP.3.1.1 more immune evasive against our antibodies and more infectious.
KP.3 and KP.3.1.1 have evolved to be very different antigenically from the original SARS-CoV-2 virus and even from the original Omicron BA.1 virus. That is why it is important to get updated booster vaccines when they are available. A group in Germany made an antigenic map using a hamster model which shows that all pre-Omicron variants are clustered together. The original Omicron BA.1 and the Omicron subvariants show a lot more antigenic diversity. The current dominant variant (KP.3 and KP.3.1.1) are more antigenically different from the original Omicron (BA.1) than Omicron (BA.1) was to the original wildtype SARS-CoV-2 virus.
A team from Virginia Tech found that SARS-CoV-2 is spreading from humans to wild animals, especially in places with high human activity. They found SARS-2 in six different wildlife species, the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat from 2022 to 2023 across Virginia and Washington, D.C. Areas with more people had a higher rate of animals infected. Human-to-animal transmission was seen in seven cases where the animal had a variant that matched those circulating in humans at the time.
A US veterinary hospital network tested 1000 dogs and cats belonging to employees in 2020 to 2022. Positive SARS-CoV-2 antibodies were seen in 33% of 747 dogs and 27% of 253 cats and positive COVID antibodies correlated with US human case waves. "Antibodies persisted longer than previously documented (828 days in dogs; 650 days in cats)." Cats were more likely to have COVID symptoms.
COVID vaccines are safe and reduce the risk of COVID infection. COVID vaccines were also found to decrease the risk of major cardiovascular thrombotic disease. In a study of 46 million adults in England, both arterial thrombotic events (heart attacks and stroke) were lower after COVID vaccination. Similarly, venous clotting events (pulmonary embolism, leg deep vein thrombosis) were also lower after COVID vaccination.
Scientists discovered two complementary antibodies that they called Cv2.3194 and Cv2.3132 from the memory B cells of a single person who had recovered from a COVID infection with ancestral SARS-CoV-2. "When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail" that work together to neutralize many different beta coronaviruses including SARS-CoV-2 variants.
Recently, I found a great resource from NYC Health called the NYC Health COVID-19 Isolation and Exposure Guidance Tool which gives guidance for isolation after COVID exposure. The tool calculates the specific dates that one should isolate and test. They recommend isolating and masking for 10 days after exposure and to test on day 5. For symptoms, they recommend testing every 48 hours twice or three times before coming out of isolation. Using a molecular COVID test like Lucira allows people to come out of isolation sooner.
Bernie Sanders and other senators proposed a bill this week called The Long COVID Research Moonshot Act of 2024 to provide $1 billion in funding each year for 10 years for Long COVID research, treatments and for the expansion of care for patients. More than 22 million adults and 1 million children have Long COVID in the United States and there are no treatments or cures for this disabling disease. I truly hope that this bill becomes a law, but we will need to advocate at each of the 9 steps that it will go through to be approved.
Dr. Trisha Greenhalgh and colleagues wrote a massive review article on Long COVID this week which looked at risk factors, symptoms, phenotypes, clinical rehab services and prevention for Long COVID. She wrote a tweet thread discussing the article here. In addition, Dr. Greenhalgh wrote a substack post called “Long COVID – a dystopian game of pinball” that explained the review article for lay people. She also gave some great advice for avoiding Long COVID:
Get vaccinated against COVID-19, and make sure your boosters are up to date.
Try not to catch COVID-19. Avoid crowded indoor spaces (wear a well-fitting mask if you can’t avoid them), especially when local rates of COVID-19 are high.
If you catch COVID-19, rest up until you feel better and take anti-virals if you’re eligible.
In June 2024, the National Academies of Sciences, Engineering, and Medicine (NASEM) Committee published a consensus definition for Long COVID in a 166 page document. This week, the Long COVID definition was published in the NEJM. First author Dr. Wes Ely also wrote a tweet thread about the definition here.
NASEM 2024 Long COVID definition:
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.
Using the Adult Developmental Eye Movement Test, people with Long COVID were found to have abnormal oculomotor results. This may relate to cognitive dysfunction in the brain or possibly to issues with muscles of the eye.
People usually know when they have loss of taste or loss of smell after a COVID infection. Healthcare professionals should also be aware that there is a significant risk of hearing loss in young adults after COVID infection too. In 6.7 million young adults aged 20–39 years in South Korea, COVID infection was associated with a 3.5x increased risk of hearing loss and sudden sensorineural hearing loss (SSNHL).
COVID and the Heart
A new study from Hong Kong shows that different SARS-CoV-2 variants affect heart muscle cells differently. "Omicron BA.2 most efficiently infected and injured cardiomyocytes in vitro and in vivo, and induced expression changes consistent with increased cardiac dysfunction, compared to other variants tested."
COVID and the Placenta
A group from Italy studied individuals who had COVID in pregnancy, including a group who had COVID infection at the time of delivery. "SPIKE protein was detected in villi and decidua from women with ongoing infection." Autophagy was seen in COVID infected placentas with an increase in LC3B that decreased once the COVID infection had resolved. CD147 levels were increased in the placental villi of people with active COVID infection and also in those with recent COVID infection that had resolved. Proangiogenic marker VEGF was seen in placentas that were SARS-CoV-2 spike protein positive.
COVID and the Thyroid
In a retrospective cohort study, scientists from China found that severe COVID-19 was a risk factor for Euthyroid Sick Syndrome (ESS) (OR=22.5). ESS and low thyroid function were associated with increased risk of death from COVID, while high levels of FT3 and FT4 were associated with a lower risk of death, especially in women. Hyperthyroidism was uncommon after COVID infection, but 7.7% of people became chronically hypothyroid after COVID infection.
COVID and the Lungs and Kidneys
Patients hospitalized with severe COVID infection in China during the first COVID wave were followed for 1 year (n=73) and 2 years (n=57). Pulmonary Long COVID with fibrous stripes seen on CT scan was found in 8.7% of hospitalized patients at 1 year and 17.8% of patients at 2 years and was related to low serum surfactant-associated protein B. Renal Long COVID was seen in 15.2% of hospitalized patients at 1 year and 23.9% of patients at 2 years. It was associated with lower urinary protein expression. Using machine learning, data collected during the 1st month of the original severe COVID infection could predict Pulmonary Long COVID and Renal Long COVID with an accuracy of 87.5%.
COVID and the Testes
One in ten men with mild COVID infections were found to have SARS-CoV-2 RNA in their semen, "which persisted for up to 90 days in one patient." Sperm count and motility were lower when the viral RNA was present, but normalized with long term follow up.
H5N1 Avian Flu
In a small study, 15% of workers (2 of 14 workers) from two Texas dairy farms were found to have antibodies to H5N1 and one person continued to have a lingering cough. One of the two people who tested positive worked in the cafeteria on the farm and not with animals. This is concerning. The article did not say if the cafeteria worker got H5N1 from another person, or if she had consumed raw milk. "I am very confident there are more people being infected than we know about," senior author Gregory Gray, MD, MPH, a UTMB infectious disease researcher, said "Largely, that's because our surveillance has been so poor."
An article in Lancet Public Health shows that younger people appear to be getting cancer at earlier ages than prior generations. People born in the 1990s had cancer rates ranging from 12% to 169% higher than those born in the generation with the lowest rates. The mortality rates (MRRs) for some cancers like liver, uterine, gallbladder, testicular, and colorectal also increased in younger generations, while for other cancers, the mortality rates either stabilized or decreased.
Mpox infections are spiking in ten African nations, but 96% of cases are reported in the Democratic Republic of the Congo DRC. "As of July 28, 2024, a total of 14,250 cases (2,745 confirmed; 11,505 suspected) and 456 deaths (case fatality rate [CFR]: 3.2%) have been recorded in 10 African nations."
A study of 1525 adults followed longitudinally since the early 1990s found that certain Alzheimer's disease biomarkers (Aβ42:β40 ratio and p-Tau181) in midlife were linked to dementia in later life. Changes in the Aβ42:β40 ratio and p-Tau181 and in NfL and GFAP from midlife were linked to all-cause dementia.
Olympics
There are so many amazing Olympic stories, but here are a few of my favorites. Katie Ledecky won her 13th Olympic medal this week making her the most decorated female US Olympian of all-time. Simone Biles showed us why she is the GOAT (Greatest Of All Time) as she won the Olympic gold medal in individual all-around gymnastics.
I highly recommend that you read Eric Topol's new essay on COVID. He discusses this large wave, why waves continue to happen and what we should be doing about it.
“As of July 30, 2024, we estimate that COVID-19 infections are growing or likely growing in 35 states and territories, declining or likely declining in 2 states and territories, and are stable or uncertain in 7 states and territories.”
California
7/29/24 Los Angeles Times: COVID surging in California, nears two-year summer high. 'Almost everybody has it' https://buff.ly/3Wiwpnu
“If you have cough-and-cold symptoms, at this point, living in Los Angeles, you should really think that they are COVID until proven otherwise,” she said.
Between new very immune variants and people no longer taking precautions, it is not a surprise that we are in a large COVID wave. The summer 2022 wave lasted 16 weeks at HIGH and VERY HIGH and summer 2023 lasted 8 weeks. This year, wastewater levels of SARS-2 in California have been at the “HIGH” or “VERY HIGH” level for seven straight weeks and does not appear to be peaking soon.
At the end of the 12th week of the current COVID-19 wave in Portugal, cases and deaths keep decreasing but are still above last winter's peak. In fact, weekly deaths for this wave were the highest since August 2022, a clear sign that SARS-2 remains a very dangerous virus.
DeFLuQE (KP.3.1.1) is now dominant in much of Europe and rising rapidly in the US and Canada, so they are likely to drive the next wave in Australia.
Here are the leading countries reporting DeFLuQE (KP.3.1.1). Strong growth continued in Spain and Denmark, followed by the Netherlands, France and the UK. The curves for Canada and the US appear to be lagging by a few weeks.
The KP.3.1.1 is the JN.1 variant with DeFLuQE = [S31 deletion + F456L+ Q493E mutations].
Evolution of #SARSCoV2. The current dominant variant (KP.3/KP.3.1.1), derived from JN.1, is further away in antigenic distance from original Omicron BA.1 than BA.1 was to all the prior major variants
COVID and Animals
7/29/24 Nature: Widespread exposure to SARS-CoV-2 in wildlife communities https://buff.ly/3ydwyRr
Virginia Tech scientists found that SARS-CoV-2 was spreading from humans to wild animals, especially in places with high human activity. They found SARS-2 in six different wildlife species, the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat from 2022 to 2023 across Virginia and Washington, D.C. Areas with more people had a higher rate of animals infected. Human-to-animal transmission was seen in seven cases where the animal had a variant that matched those circulating in humans at the time.
7/18/24 Viruses: The Transmission of SARS-CoV-2 from COVID-19-Diagnosed People to Their Pet Dogs and Cats in a Multi-Year Surveillance Project https://buff.ly/46MOijv
A US veterinary hospital network tested 1000 dogs and cats belonging to employees in 2020 to 2022. Positive COVID antibodies were seen in 33% of 747 dogs and 27% of 253 cats and positive COVID antibodies correlated with US human case waves.
"Antibodies persisted longer than previously documented (828 days in dogs; 650 days in cats)." Cats were more likely to have COVID symptoms.
Vaccines
7/31/24 Nature: Cohort study of cardiovascular safety of different COVID-19 vaccination doses among 46 million adults in England https://buff.ly/3A6pztZ
COVID vaccines are not only safe, they reduce the risk of COVID and also decrease the risk of major cardiovascular thrombotic disease. In a study of 46 million adults in England, both arterial thrombotic events (heart attacks and stroke) were lower after COVID vaccination. Similarly, venous clotting events (pulmonary embolism, leg deep vein thrombosis) were also lower after COVID vaccination.
7/17/24 Frontiers Immunology: Tetanus-diphtheria vaccine can prime SARS-CoV-2 cross-reactive T cells https://buff.ly/3WPQLX1
A group from Spain found that tetanus-diphtheria vaccines can prime SARS-CoV-2 cross-reactive T cells and likely contribute T cell against the SARS-CoV-2 virus.
Antiviral treatments and Prevention
6/22/24 Cell iScience: Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2 https://buff.ly/3SuheGH
Scientists discovered two complementary antibodies called Cv2.3194 and Cv2.3132 from the memory B cells of a single person who had recovered from a COVID infection with ancestral SARS-CoV-2.
8/2/24 ACS Sensors (Italy): Functionalized N95 Face Mask with a Chemical-Free Paper-Based Collector for Exhaled Breath Analysis: SARS-CoV-2 Detection with a Printed Immunosensor as a Case Study https://buff.ly/3ypwYnE
A group in Italy made a paper-based sensor that could collect exhaled breath inside a mask. Combining the paper sensor with a printed magnetic immunoprobe, they were able to detect SARS-CoV-2 in exhaled breath. The virus was detected by a miniaturized electrochemical MB-based printed immunosensor and could be used for detecting other viruses as well.
Isolate and mask for 10 days and test on day 5 after exposure.
For someone exposed to a person with COVID:
For 10 days wear a well-fitting mask when unable to separate from others and monitor for symptoms.
Test 5 days after the COVID exposure.
If you develop symptoms, test for COVID.
If you take a molecular test (like Lucira) and it is negative, you can stop isolating from others.
If you take a home antigen test and it is negative, continue to isolate and test after 48 hours. If that test is negative, you can stop isolating. If you are still concerned that you might have COVID-19, consider doing a third test 48 hours after the second test.
Note: Health care personnel, congregate setting staff and individuals who work in or attend childcare or school settings should check with their workplace or school about their policies for returning to work or school.
Long COVID
8/2/24 Bernie Sanders and other senators proposed a bill called The Long COVID Research Moonshot Act of 2024 to provide $1 billion in funding each year for 10 years for Long COVID research, treatments and for the expansion of care for patients. More than 22 million adults and 1 million children have Long COVID in the United States and there are no treatments or cures for this disabling disease.
National Academies of Sciences, Engineering, and Medicine Committee definition of Long COVID
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.
7/27/24 PolyBio Research Foundation: “Multiple hit” model shows that COVID protein potentiates subsequent infection-related neuroinflammation and other physiological problems https://buff.ly/4d4k4uA
A new study from the University of Colorado shows that the SARS-CoV-2 S1 protein can prime the immune system in the brain, making rats more vulnerable to another “hit” (another viral infection, bacterial infection or even a concussion) which then leads to more neuroinflammation, autonomic dysfunction (heart rate and body temperature control) and low cortisol hormone levels in the hippocampus.
Original article: 10/2024 issue Brain, Behavior and Immunity (U Colorado): SARS-CoV-2 S1 subunit produces a protracted priming of the neuroinflammatory, physiological, and behavioral responses to a remote immune challenge: A role for corticosteroids https://www.sciencedirect.com/science/article/abs/pii/S0889159124005105
Young Adults (20 to 39 years old)
7/29/24 eClinical Medicine: Incidence of hearing loss following COVID-19 among young adults in South Korea: a nationwide cohort study https://buff.ly/3AhcMot
In 6.7 million young adults aged 20–39 years in South Korea, COVID infection was associated with a 3.5x increased risk of hearing loss and sudden sensorineural hearing loss (SSNHL). Healthcare professionals should be aware of this risk for this age group.
COVID and the Heart
8/2/24 Cell & Bioscience: SARS-CoV-2 variants divergently infect and damage cardiomyocytes in vitro and in vivo https://buff.ly/4cabuJl
"Omicron BA.2 most efficiently infected and injured cardiomyocytes in vitro and in vivo, and induced expression changes consistent with increased cardiac dysfunction, compared to other variants tested."
COVID and the Placenta
8/1/24 Journal of Molecular Histology: Effects of SARS-COV-2 on molecules involved in vascularization and autophagy in placenta tissues https://buff.ly/4ft8kmS
A group from Italy studied women who had COVID in pregnancy, including a group who had COVID infection at delivery. "SPIKE protein was detected in villi and decidua from women with ongoing infection." Autophagy was seen in COVID infected placentas with an increase in LC3B that decreased once COVID infection had resolved. CD147 levels were increased in the placental villi of people with active COVID infection and also in those with recent COVID infection that had resolved. Proangiogenic marker VEGF was seen in placentas that were SARS-CoV-2 spike protein positive.
COVID and the Thyroid
7/15/24 Frontiers | Thyroid dysfunction in the wake of Omicron: understanding its role in COVID-19 severity and mortality https://buff.ly/3WvaYA1
Patients hospitalized in China during the first COVID wave were followed for 1 year (n=73) and 2 years (n=57). Pulmonary Long COVID (fibrous stripes on CT scan) was found in 8.7% of hospitalized patients at 1 year and 17.8% of patients at 2 years. It was related to low serum surfactant-associated protein B. Renal Long COVID was seen in 15.2% of hospitalized patients at 1 year and 23.9% of patients at 2 years. It was associated with lower urinary protein expression. Using machine learning, data collected during the 1st month of the original severe COVID infection could predict Pulmonary Long COVID and Renal Long COVID with an accuracy of 87.5%.
COVID and the Testes
8/2/24 Andrology (Toulouse, France): Mild coronavirus disease 2019: Results of a multicentric prospective study on severe acute respiratory syndrome coronavirus 2 presence in semen fractions and cells and its effects on semen parameters https://buff.ly/3Wzgxgy
11% of men with mild COVID infections were found to have SARS-CoV-2 RNA in their semen, "which persisted for up to 90 days in one patient." Sperm count and motility were lower when the viral RNA was present, but normalized with long term follow up.
H5N1
7/31/24 NPR: Bird flu cases among farm workers may be going undetected, a study suggests https://t.co/OgYNOE60cX
In a small study, 15% of workers (2 of 14 workers) from two Texas dairy farms were found to have antibodies to H5N1 and one person continued to have a lingering cough. One of the two people who tested positive worked in the cafeteria on the farm and did not work with animals. Did she get H5N1 from another person, or did she perhaps drink raw milk? This is concerning. Tip of the iceberg.
"I am very confident there are more people being infected than we know about," senior author Gregory Gray, MD, MPH
Study: 7/31/24 MedRxiV: A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms https://buff.ly/3A56RmH
8/2024 Lancet Public Health: Differences in cancer rates among adults born between 1920 and 1990 in the USA: an analysis of population-based cancer registry data https://buff.ly/4fuCGFy
23 million people age 25 to 84 studied from 2000 to 2019.
17 of 34 cancers had an increasing incidence in younger birth cohorts, including nine that previously had declining incidence in older birth cohorts.
These findings add to growing evidence of increased cancer risk in younger generations, highlighting the need to identify and tackle underlying risk factors.
Mpox Clade 1b has been seen in the Democratic Republic of the Congo (DRC) where 96% of African cases have been reported. "As of July 28, 2024, a total of 14,250 cases (2,745 confirmed; 11,505 suspected) and 456 deaths (case fatality rate [CFR]: 3.2%) have been recorded in 10 African nations."
7/28/24 JAMA: Alzheimer Disease Blood Biomarkers and Incident Dementia https://buff.ly/4caPYnG
A study of 1525 adults followed longitudinally since the early 1990’s found that certain Alzheimer's disease biomarkers (Aβ42:β40 ratio and p-Tau181) in midlife were linked to dementia in later life. In late life, changes in these biomarkers and others (NfL and GFAP) from midlife were linked to all-cause dementia.
9/2023 The Guardian: Covid hunters: the amateur sleuths tracking the virus and its variants https://buff.ly/3A7mIkp
Olympics
Katie Ledecky won her 13th Olympic medal this week making her the most decorated female US Olympian of all-time.
Simone Biles showed us why she is the GOAT (Greatest Of All Time) as she won the Olympic gold medal in individual all-around gymnastics.
Badminton gold medalist Huang Ya Qiong said yes to teammate Li Yuchen when he proposed marriage after the Olympic medal ceremony.
I'm elderly, disabled and got Long Covid after suffering a benign case in July 2020. Life changing.
Now I can see the resurgence all around me: My own daughter (mid 40's) succumbed to her own case of covid a few weeks ago. The most careful, masked, vaccinated, hand-washing & considerate person, it was bound to happen. She's fine.
I'm scheduled for updated vax in a few weeks but not soon enough for me.
I had a wonderful visit with some sweet, adorable neighbors yesterday. Elementary school kids all over my house. Just back from the first day at school. I wouldn't have even let them into the house few years ago...oops.
I did not run around with Lysol disinfecting the door knobs but you know I thought about it.
These girls joyfully bounded off a crowded school bus to visit this old woman who welcomes them always.
Anyway I've ordered some more free test kits just in case. Thanks for the chance to respond. What's a friendly granny to do....
As always, thank you! I know I speak for many when I say how deeply appreciated your posts are.
I'm elderly, disabled and got Long Covid after suffering a benign case in July 2020. Life changing.
Now I can see the resurgence all around me: My own daughter (mid 40's) succumbed to her own case of covid a few weeks ago. The most careful, masked, vaccinated, hand-washing & considerate person, it was bound to happen. She's fine.
I'm scheduled for updated vax in a few weeks but not soon enough for me.
I had a wonderful visit with some sweet, adorable neighbors yesterday. Elementary school kids all over my house. Just back from the first day at school. I wouldn't have even let them into the house few years ago...oops.
I did not run around with Lysol disinfecting the door knobs but you know I thought about it.
These girls joyfully bounded off a crowded school bus to visit this old woman who welcomes them always.
Anyway I've ordered some more free test kits just in case. Thanks for the chance to respond. What's a friendly granny to do....