This week, case numbers are decreasing although we still have 330,000 new cases daily in the United States. Unfortunately, unlike other high income countries, the U.S. COVID death rate continues to increase and is presently 3,300 per day. Why is the United States so different from other countries? The vaccination and booster rate is much lower in the U.S. compared to other countries.
For example,
In California, the death rate is 3x higher in Southern California as compared to the Bay Area where there are higher rates of vaccination and boosters. In Santa Clara county, the most populous county in Northern California, 84% of people are vaccinated with 2 doses and 58% are boosted.
There is a controversy among public health scientists, whether or not we should continue mask mandates especially in schools. Dr. Leana Wen believes that since cases overall are decreasing, we should ditch the masks for now and save them for the future if we have another COVID wave. While I respect Dr. Wen, I think that it is premature to remove masks in schools. After all, in the U.S. only 19% of kids ages 5 to 11 are fully vaccinated with 2 doses and only 28% have received 1 dose of vaccine. There is a lot of variation in child COVID vaccination rates across different states in the U.S.
Sweden joins Denmark and Norway in dropping mask mandates and other COVID restrictions, but as seen in the table above and graphs below and on Our World In Data, these countries have much higher vaccination and booster rates than the United States and so their people are better protected from hospitalizations and deaths. I am surprised that Denmark has decided to drop restrictions now since they have the highest number of cases per capita of any country right now. Vaccinations are made to reduce hospitalizations and deaths and they are working for that against Omicron. But, vaccinated people can still get Long COVID albeit at a much lower rate.
This week, there are several articles reviewing the human immune system and how it relates to SARS-CoV-2. Articles include reviews of children vs adult immunity, the innate immune system and a breakdown of B cells, Plasma cells, antibodies and T cells.
Medicare will cover up to 8 free tests per month, starting in early spring for people with Medicare’s “Part B” outpatient benefit.
2/4/22 Reuters: In world first, South Africa's Afrigen makes mRNA COVID vaccine using Moderna data https://buff.ly/3uqBbTL
Afrigen used the publicly available sequence of Moderna's mRNA COVID-19 vaccine to make its own version, which could be tested in humans before the end of this year.
2/4/22 Palo Alto Online: COVID-19 outbreaks hit 12 local long-term care facilitieshttps://buff.ly/3GrTLxi
Vaccines are making the difference between mild illness and hospitalization.
A dozen residential and skilled nursing facilities in Palo Alto, Mountain View and Los Altos have experienced outbreaks of COVID-19, mostly around or just after the Christmas holiday.
Outbreaks were mostly among workers- housekeepers to dining and nursing staff. Many of the staff became infected from their children after they went back to school.
A California state order that went into effect on Jan. 7 and is set to expire Feb. 7 requires visitors to show proof of a negative PCR test within 48 hours of coming to the facility or a negative rapid test in the presence of staff. Difficulties finding COVID tests made it hard for families to visit.
2/4/22 Nature: Does Omicron hit kids harder? Scientists are trying to find out https://buff.ly/3LlgP4u
Although there has been an increase in kids hospitalized with Omicron, especially those < 1 year old, they are less sick and require less oxygen therapy and ventilators.
The individual risk of a child with Omicron being hospitalized is, in fact, lower — by one-third to one-half — than it was when the Delta variant was dominant.
2/4/22 Technology Review: How Pfizer made an effective anti-covid pill Paxlovid in record time https://buff.ly/3B0QTpL
2/3/22 Nature Review: Immunology of SARS-CoV-2 infection in Children https://buff.ly/3GmZAMh
Children tend to have fewer comorbidities than adults.
Protective innate immune factors include reduced expression of ACE2 and a more robust Interferon (IFN) response.
Compared with adults, children also have more T cells owing to greater thymic output, more T cells that recognize non-structural viral proteins, and less T cell exhaustion.
2/3/22 Nature: Innate immunity: the first line of defense against SARS-CoV-2 https://buff.ly/3L3ypK6
Comprehensive review of the innate immune system which acts as the first line of defense, sensing the virus through pattern recognition receptors and activating inflammatory pathways that promote viral clearance.
2/3/22 MedRxiv (Berlin): Durability of Omicron-neutralizing serum activity following PfizermRNA booster immunization in elderly individualshttps://buff.ly/3ulYJJl
37 individuals with a median age of 82 years
Detectable Omicron-neutralizing activity was nearly absent after two vaccinations but was seen in 89% of individuals by the booster immunization.
81% of individuals maintained detectable activity against Omicron at 4.5 months.
2/3/22 Pathology: Acute SARS-CoV-2 Infection in Pregnancy Is Associated with Placental ACE2 Sheddinghttps://buff.ly/34kW3ky
Although human placental tissues may be infected by SARS-CoV-2, the rate of fetal transmission is low, suggesting either viral neutralization or a barrier at the maternal-fetal interface to protect the fetus.
In acute maternal SARS-CoV-2 infections, decreased placental ACE2 protein may be the result of ACE2 shedding.
ACE2 levels decreased in the placenta and soluble ACE2 significantly increased in the maternal serum in 3rd Trimester COVID infections compared with control pregnancies and those 2nd Trimester people with COVID.
2/3/22 NY Times: In New York City Sewage, a Mysterious Coronavirus Signal https://buff.ly/35DfYvq
Article pieces together the data trying to figure out where these mutated viral pieces are coming from.
There is no evidence that the lineages, which have been circulating for at least a year without overtaking Delta or Omicron, pose an elevated health risk to humans.
Original study in Nature: Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater https://buff.ly/3saawb4
To monitor New York City (NYC) for the presence of novel variants, scientists sequence the receptor binding domain (RBD) of the S protein of SARS-CoV-2 in New York City wastewater.
Increasing frequencies of novel cryptic SARS-CoV-2 lineages with mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern were noted.
Potential sources could include an immunosuppressed person or an animal such as a rat.
2/3/22 AP: Strained US hospitals seek foreign nurses amid visa windfall https://buff.ly/3AXFdUI
Twice as many green cards are available this year. That’s because U.S. consulates shut down during the coronavirus pandemic weren’t issuing visas to relatives of American citizens, and, by law, these unused slots now get transferred to eligible foreign professionals, including nurses.
2/3/22 AMA Updates CPT Codes for Pediatric Pfizer COVID-19 Vaccine or children in the age range of six months to five years https://buff.ly/3IY4oti
0081A: First dose Pfizer 3 mcg vaccination
0082A: Second dose Pfizer 3 mcg vaccination
91308: Pfizer 3 mcg/0.2 mL vaccine
Remove mask restrictions now or wait?
2/1/22 Washington Post Opinion by Leana Wen MD: Yes, more variants may emerge in the future. That’s why we should lift restrictions now. https://buff.ly/3J9g7p3
Two approaches to removing mask mandates:
One is gradual and based on case numbers and test positivity.
Another approach, which I am beginning to favor, is to state that every person 5 and older can be vaccinated, and high-quality masks can protect individuals well.
Therefore, masks can be optional, not required, even at high rates of community transmission.
The threshold for re-implementing indoor masking would shift from case numbers to hospital capacity.
(Of course, masking could also return if a deadlier variant arises that evades prior immunity.)
2/2/22 Two Houston doctors nominated for Nobel Peace Prize for low-cost COVID vaccine https://buff.ly/3Ho18a8
Dr. Peter Hotez and Dr. Maria Elena Bottazzi of Baylor college were nominated for their work to develop and distribute the low-cost Corbevax vaccine to people of the world — without patent limitation.
2/2/22 MedRxiV: High Rates of Rapid Antigen Test (RAT) Positivity After 5 Days of Isolation for COVID-19 https://buff.ly/3om6Cea
CDC recommendations allow healthcare workers to return to work after day 5 if symptoms have improved, without a requirement for a negative rapid antigen test.
In this study, 43% of all RAT overall were positive between days 5-10.
58% positive on day 6 vs 26% positive on days 8 and 9.
A substantial proportion of individuals with COVID-19 are likely still contagious after day 5 of illness regardless of symptom status. Early liberation from isolation may increase the risk of COVID-19 spread, resulting in more sick workers.
2/3/22 Cell: T-cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals https://buff.ly/3AVaqbp
T-cell responses to Omicron are preserved in most infected and vaccinated individuals.
However, a subset of people (∼21%) have a >50% reduction in T-cell reactivity to the Omicron spike.
2/3/22 Nature Immunology: The T cell immune response against SARS-CoV-2 https://buff.ly/3robwcj
Comprehensive review of T cell and COVID with a focus on T cell role in protection from severe disease.
2/2/22 Nature: What the Omicron wave is revealing about Human Immunity https://buff.ly/3gl84Jm
B cells make antibodies to tag intruders and stop them from entering (infecting) a cell.
It takes a few days to call in and make more B and T cells, so with Omicron, vaccinated people may get sick, but they aren’t hospitalized because their B and T cells kick in to stop an overwhelming infection.
Some infections and immunizations elicit lifelong protection, but for others, the response requires regular reminders in the form of booster shots or new, reformulated vaccines.
During a first exposure to a pathogen, B cells that get activated divide rapidly and differentiate into plasma cells that churn out antibodies.
Antibodies can flag intruders for destruction. ‘Neutralizing’ antibodies prevent the virus from entering cells altogether.
Long-lived B cells develop Germinal Centers in the lymph nodes and serve as a sort of B-cell training camp.
Long-lived plasma cells that reside mainly in the bone marrow and secrete a small-but-steady stream of high-quality antibodies.
After vaccination, when re-exposed to a virus or booster, Memory T cells “proliferate like crazy” and in a 24-hour period, you can get a 10x increase in the number of memory T cells.
That’s probably not fast enough to have much of an effect on getting sick. But it could be fast enough to prevent hospitalization.
A third booster shot increases antibody levels but also increases the breadth of the response.
Although Sweden is experiencing a record-breaking surge in coronavirus cases, the situation in hospitals remains stable as Swedes are more vaccinated and boosted.
Neighboring countries such as Denmark and Norway have already dropped nearly all of their restrictions against COVID-19.
Our World In Data: Which countries are on track to reach global COVID-19 vaccination targets? https://buff.ly/3igWAb6
Not the U.S.
2/2/22 NY Times: U.S. Has Far Higher Covid Death Rate Than Other Wealthy Countries https://buff.ly/34rwi1Y
Two years into the pandemic, the coronavirus is killing Americans at far higher rates than people in other wealthy nations, a sobering distinction.
Vaccines and boosters work and we simply haven't given enough of them.
2/2/22 LA Times Coronavirus Today: What the Bay Area teaches us about the value of vaccineshttps://buff.ly/3HnHYkF
Percent of residents fully vaccinated and boosted by county:
Los Angeles County, 69.8% fully vaccinated, and 46.4% boosted
Orange County, 69.8% vaccinated and 50.2% boosted.
Riverside county 56.7% fully vaccinated
San Bernardino County 55.6% fully vaccinated.
San Francisco county: 82% fully vaccinated and 63.9% boosted.
Santa Clara County, 84.1% are fully vaccinated and 57.9% boosted.
With higher vaccination and booster rates, the Bay Area experienced fewer coronavirus cases in January, and that lower case rate resulted in a lower COVID-19 death rate.
Deaths were 3x higher in Southern California compared to the Bay Area.
Other factors besides vaccines and boosters contribute, but their impact is likely much less.
2/1/22 KRON: What you need to know about San Francisco’s updated COVID-19 guidelines https://buff.ly/3GpFbpT
San Francisco offices and gyms will no longer require masks indoors as of Feb. 1, as long as people’s vaccination records, including boosters, are “up to date“.
People will also now be allowed to enter indoor “mega-events” of 500 people or more with a negative COVID-19 test as an alternative to being up to date on vaccinations, but masking would still be required.
2/1/22 CDC MMWR: SARS-CoV-2 Infection and Hospitalization by Vaccination Status in Los Angeles Countyhttps://buff.ly/3L2gMdz
Los Angeles County has > 10 million people which is larger than Israel (9.4M), Denmark (5.8M) and Ireland (5 M).
Hospitalizations, compared to unvaccinated people:
Hospitalizations have always been higher for unvaccinated individuals, but the gap took off like a hockey stick about a week after Omicron became the dominant coronavirus strain.
2/1/22 BioRxiV: SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathologyhttps://buff.ly/3HAckjW
small study, n = 5 patients
SARS-CoV-2 can induce or enhance Alzheimers-like neuropathology with manifestations of beta-amyloid aggregation and plaque formation, tauopathy, neuroinflammation and cell death.
2/1/22 FDA Advisory Committee Meeting on Feb 15, 2022 Will Discuss Request for Authorization of Pfizer-BioNTech COVID-19 Vaccine for Children 6 Months Through 4 Years of Age https://buff.ly/3ssS7qj
2/1/22 Eric Topol: The Omicron wave begins a global descent after >90 million confirmed cases in 10 weeks, more than all of 2020
2/1/22 Politico: Medical boards get pushback as they try to punish doctors for Covid misinformation https://buff.ly/3AQV9s3
Medical boards and other regulators across the country are scrambling to penalize doctors who spread misinformation about vaccines or promote unproven cures for Covid-19. But they are unsure whether they’ll prevail over actions by state lawmakers who believe the boards are overreaching.
Giving a high dose flu shot with a Moderna COVID booster at the same time was safe and did not affect immune responses in adults aged 65 years and older.
That boosters work against an outdated strain work so well against omicron is amazing.
The U.S. has a much lower booster (3 dose) rate than other countries.
In this essay, Dr. Topol reviews all of the data on why it is important to increase boosters.
1/31/22 Financial Times: ‘Pandemic of the unboosted’: low US Covid jab uptake piles pressure on hospitals https://buff.ly/32JJJcW
‘If the US had matched the vaccination coverage of leading European countries, it would have halved its COVID-19 hospitalizations’
1/31/22 MedRxiV: Acute upper airway disease in children with the Omicron (B.1.1.529) variant of SARS-CoV-2: a report from the National COVID Cohort Collaborative (N3C) https://buff.ly/3gezNeA
Pediatric acute upper airway infection (UAI) cases have increased during the Omicron variant surge with many developing severe disease.
Omicron is more likely to cause croup (laryngotracheobronchitis) in small children because they have smaller airway calibers.
1/31/22 Nature Immunology (via Eric Topol): Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules https://buff.ly/3ugs487
12 human humoral fluid-phase pattern recognition molecules (PRMs) were studied in patients with severe COVID.
The long pentraxin 3 (PTX3) and mannose-binding lectin (MBL) bound the SARS-CoV-2 viral nucleocapsid and spike proteins, respectively.
Select humoral fluid-phase PRMs can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.
1/31/22 Nature: Equitable access to COVID-19 vaccines makes a life-saving difference to all countries https://buff.ly/3KRY1JI
Sharper disparities in vaccine allocation between high-income countries (HICs) and low- and middle-income countries (LMICs) lead to earlier and larger outbreaks of new waves.
Equitable vaccine allocation strategies, in contrast, substantially curb the spread of new strains.
1/30/22 T cell immunologist Anthony Leonardi weighs in on vaccines and T cell response against Omicron
1/30/22 NY Times: ‘Stealth’ BA.2 Variant No Cause for Alarm, but Could Slow Case Decline https://buff.ly/3Ge6PWS
So far, BA.2 doesn’t appear to cause more severe disease, and vaccines are just as effective against it as they are against other forms of Omicron. But it does show signs of spreading more readily.
In a small study of Long COVID patients with breathlessness but whose other tests were normal, gas (oxygen) transfer was less effective than in healthy controls as seen on Xenon MRI.
People who had been hospitalized for COVID had similar abnormalities.
Xenon MRI scans:
Original study NIHR Oxford: Pulmonary Abnormalities using Hyperpolarized Xenon Magnetic Resonance Imaging (MRI) in Patients with Long COVID https://buff.ly/3rb1Thd
In long COVID patients with breathlessness but whose other tests are normal, Xenon MRI and TLco (transfer capacity of the lung test) demonstrate significantly impaired gas transfer.
1/30/22 Nature: Human genetic and immunological determinants of critical COVID-19 pneumoniahttps://buff.ly/3GhX9KN
Insufficient Type I Interferon (IFN) immunity in the respiratory tract during the first few days of infection may account for critical COVID-19 pneumonia.
Inborn errors of type I IFNs, including autosomal TLR3 and X-linked TLR7 deficiencies, are found in 1-5% of patients with critical pneumonia under 60 years old, and a lower proportion in older patients.
Pre-existing autoantibodies neutralizing IFN-α, –β, and/or –ω, which are more common in men than in women, are found in 15-20% of patients with critical pneumonia over 70 years old, and a lower proportion in younger patients.
At least 15% of cases of critical COVID-19 pneumonia can be explained with a combination of age, sex and Type I IFN immunity issues.
1/30/22 Nature : Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants https://buff.ly/3GahFwU
24 monoclonal antibodies (mAbs) from memory B cells from 3 dose vaccineesneutralized all VOCs, including Omicron and could provide a target for a universal vaccine against all sarbecoviruses.
1/29/22 NY Times: As Covid Shots for Kids Stall, Appeals Are Aimed at Wary Parents https://buff.ly/3rcSuWw
Getting more young school-age children vaccinated is crucial for ending the pandemic, public health officials say, and many are focusing on that group.
School principals and peer “vaccine ambassadors” try to persuade families to vaccinate their kids.
For 5 to 11 year olds, only 18.8 percent are now fully vaccinated and only 28.1 percent have received one dose. The disparity of rates among states is stark.
1/30/22 Two Long Island nurses made more than $1.5 million in a fake vaccine card scheme, prosecutors say. https://buff.ly/3ISGxvc
The nurses sold fake vaccination cards and entered false information into New York’s immunization database.
1/29/22 Lancet pre-print (Hong Kong): Transmission of SARS-CoV-2 (Variant Delta) from Pet Hamsters to Humans and Onward Human Propagation of the Adapted Strain: A Case Study https://t.co/wYArRR298T
Two separate hamster-to-human transmission events are documented, one leading to onward household spread.
What not to do to help doctors with burnout and mental health issues:
1/30/22 The Hill: Australia says Kanye West must be fully vaccinated to perform https://buff.ly/3u940UF
