COVID news 5/20/22
COVID news 5/20/22
Hi all,
I know that we all have terrible pandemic fatigue, but unfortunately this is not over. With BA.2.12.1 now dominant in many places, cases are rising significantly again as are hospitalizations. Wastewater shows that the virus levels are rising in many cities in the United States. When Omicron BA.1 hit, we still had people in the hospitals with the Delta variant, but at least now we are starting this wave with fewer people in the hospital.
Yesterday, the CDC recommended that people start wearing masks indoors especially in high risk areas like the Northeast and Finger Lakes areas. More than one third of the U.S. is in the high community spread range which refers to the fact that hospital beds are filling up. BA.2.12.1 is dominant in at least 3 regions of the United States and we know that this variant is even more contagious than all previous variants. BA.2.12.1 in the U.S. and BA.4/BA.5 in South Africa all carry the L452 mutation in the receptor binding domain (RBD) allowing the virus to escape our immunity. There is little cross-immunity between BA.1 and BA.2.12.1, BA.4 or BA.5, so reinfections will be more common. Some people infected with the first Omicron variant BA.1 are already reporting second infections with the newer versions of the variant just a few months later. So, it is time to get out your masks and wear them indoors, turn on your air filtration systems or open windows, and get your booster vaccines if you are eligible.
Paxlovid went through clinical trials during the Delta wave and only 1-2% had a rebound of their infection. But, many more people are reporting infection relapse after taking Paxlovid for Omicron infections. This may be due to a higher viral load with Omicron. Fortunately, it does not appear that the virus is becoming resistant to Paxlovid at this time. People who have a relapse of COVID after taking Paxlovid do have a high enough viral load to infect others, so precautions need to be taken if one rebounds. In the future, a longer course of Paxlovid may be prescribed. For now, we do not know the optimal length of treatment and people should definitely take a COVID antigen test if they feel like they are getting symptoms again 3 to 7 days after stopping Paxlovid.
Some people on Twitter report that their doctors are telling them not to worry about a positive rapid antigen test after a certain number of days of infection. PCR tests can remain falsely positive, but if you test positive on a rapid antigen test, no matter what day of illness, you are still contagious and need to continue isolating so as to not infect others. In some good news, the FDA has extended expiration dates of several home rapid antigen tests listed in the chart here. For example, Binax NOW tests expire at 15 months, Cue Health tests expire at 4 months, and iHealth Labs tests expire at 9 months. In addition, the government is giving out 8 more free home antigen COVID tests again which you can order at https://special.usps.com/testkits.
Nasal spray boosters after an initial mRNA vaccine are showing promise in initial trials. The original mRNA intramuscular vaccine primes the immune system and the nasal spray containing the spike protein boosts immunity in the nose and other mucosal surfaces. Nasal vaccines can prevent people from getting infected to begin with and may allow scientists to develop a single vaccine for a broader range of coronaviruses with protection against future variants too.
Two other infectious diseases of interest have come up in the news, Monkeypox and Pediatric Hepatitis of Unknown Origin. I am including articles on both.
Have a great weekend,
Ruth Ann Crystal MD
Twitter: https://twitter.com/CatchTheBaby
5/19/22 Monkeypox 101, unanswered questions, and the bigger picture by Katelyn Jetelina and Dr. Anne Rimoin https://buff.ly/3PAK45e
Great summary of what you need to know about Monkeypox
Long incubation: no symptoms for 5 to 21 days. Rare to transmit before symptoms.
Then, sick for 2 to 4 weeks in 2 phases:
0 to 5 days: Flu-like symptoms (fever and body aches) and swollen lymph nodes.
Then, vesicular rash or pox. Can be associated with fever.
Transmission:
Respiratory droplets and aerosols from prolonged face-to-face contact;
Contact with bodily fluids or monkeypox lesions;
Indirect contact with items that have been contaminated with fluids or sores, like clothing or bedding.
Demographics and Severity:
So far, there are at least 110 suspected cases, in 11 countries.
The majority are male, younger, and presenting with classic skin lesions.
Appears to be transmitting sexually among gay and bisexual men.
Some patients have had genital lesions and the rash may be hard to distinguish from syphilis, herpes simplex virus (HSV) infection, chancroid, varicella zoster, and other more common infections.
36% of cases have been hospitalized so far in this outbreak.
During a 2003 outbreak in the U.S., 26% of cases were hospitalized and 15% had severe disease, but none died.
Treatments and Prevention:
This is not a new or novel virus like SARS-CoV-2 so we have some available.
We have vaccines to prevent monkeypox (85% VE) either before or after an exposure if given within 3 days.
Antiviral ST-246 (tercovirimat) for smallpox can treat monkeypox.
Masks and improved ventilation and filtration, will help with reducing spread.
In 2021, a monkeypox case landed in Dallas from Nigeria. It’s largely hypothesized that the mask mandate helped contain the virus.
Reasons for increase in infections with global outbreaks:
Climate change: People and animals are moving into areas that have never been inhabited before.
Technological change: Humans and goods are traveling more than ever due to globalization and increased travel. Viruses can hitch a ride.
Demographic change: Population growth, change in land use, urbanization, and aging populations, immunosuppression.
Typical clinical presentation of human monkeypox in a 7-y-old female child, Sankuru District, Democratic Republic of Congo. Source here.
5/19/22 The Atlantic: So, Have You Heard About Monkeypox? https://buff.ly/3wFJnyR
Not from monkeys but from rodents like squirrels and prairie dogs.
Reported in 7 countries.
R0 is <1 (each infected person will only infect 1 or 0 other people)
Transmitted via contaminated surfaces or prolonged proximity with other people
Some of the new cases may be sexually transmitted.
Fatality rate 1% in poor, rural populations, but none in high-resource settings so far.
One smallpox vaccine is 85% effective at preventing monkeypox.
5/20/22 UKHSA: Investigation into acute hepatitis of unknown aetiology in children in England https://buff.ly/3wIcF00
I haven’t had time to read this yet but am including it for reference.
MedRxiV: Pediatric Hepatitis of Unknown Origin: Elevated liver enzymes and bilirubin following SARS-CoV-2 infection in children under 10 https://buff.ly/3FPRg94
Nationwide retrospective cohort study using US EHR records.
Children ages of 1-10 years, 245,675 with COVID-19 and 550,694 with non-COVID other respiratory infection.
Children infected with COVID-19 infection were at significantly increased risk for elevated liver enzymes AST or ALT and total bilirubin which may be related to the current increase in pediatric hepatitis cases of unknown origin.
COVID News:
World
United States
US cases: https://www.nytimes.com/interactive/2021/us/covid-cases.html
CDC: Community Transmission Risk
5/20/22 Masking is needed again per CDC. Map in Dr. Walensky’s tweet below shows communities where hospital beds are filling up.
5/17/22 COVID Data Tracker on Variant Proportions https://buff.ly/3zMdWE5
BA2121 is in Orange.
Santa Clara County: https://covid19.sccgov.org/dashboard-wastewater
San Mateo County: https://soe-wbe-pilot.wl.r.appspot.com/charts
5/20/22 Yes, it’s a surge: Wastewater tests reveal high level of COVID-19 in East Bay https://buff.ly/3LxABsq
Alameda County
5 to 11 year olds may be eligible for a booster vaccine. ACIP has recommended it.
5/19/22 NY Times: Biden Health Officials Warn of Substantial Increase in Virus Cases https://buff.ly/3sMSuN7
Over the past week, there has been a jump in cases and in hospitalizations.
The CDC director Dr. Walensky recommends wearing masks indoors, especially in higher risk areas like the Northeast.
President Biden is no longer wearing masks.
The president “is managing a war overseas, the economy, inflation, infant formula and as these things go, the pandemic is now seen by the public as one more thing,” he said. “Of all the things going on, most people don’t perceive this to be the problem that it probably is.” said Andy Slavitt
Boosters: 62% of those aged 50 to 64 have not received a booster in the past six months, nor have 57% of those 65 or older. They will be less protected if there is a Fall surge.
5/19/22 ABC: Nearly every state expected to see increase in COVID-19 hospitalizations, CDC forecast shows https://buff.ly/39DA8Y8
5/19/22 Many rapid antigen COVID tests have longer expiration dates than what’s on the box. Check here for your test's NEW expiration date from the FDA here: https://buff.ly/3v3PcW7
Extended Expiration Dates:
Binax NOW test: expires at 15 months
Cue Health: 4 months
iHealth Labs: 9 months
5/19/22 Proceedings of the National Academy of Sciences (PNAS): How local partisan context conditions prosocial behaviors: Mask wearing during COVID-19 https://buff.ly/3MrbatH
Differences between Democrats and Republicans in rates of wearing a mask to stop the spread of COVID-19 are associated with the partisan balance of a neighborhood.
Wearing a mask can be seen by one’s peers, but other COVID-19 mitigation strategies, like vaccination are not.
Neighborhood partisan composition was only weakly related to uptake of the COVID-19 vaccine and unrelated to uptake of flu vaccines.
5/19/22 Eric Topol MD tweet re: BA.2 hospitalizations are rising like Delta did
5/19/22 MedRxiV: Neutralization Escape by the SARS-CoV-2 Omicron Variants BA.2.12.1 and BA.4/BA.5 https://buff.ly/3LvHL0a
BA.2.12.1 and BA.4/BA.5 substantially escape NAbs induced by both vaccination and infection.
Moreover, BA.4/BA.5 NAb titers, and to lesser extent BA.2.12.1 NAb titers, were lower than BA.1 and BA.2 NAb titers, suggesting that the SARS-CoV-2 Omicron variant has continued to evolve with increasing neutralization escape.
This significant immune escape helps to explain the current US BA.2.12.1 surge despite vaccinations and considerable prior Omicron BA.1 infections.
5/19/22 Nature (A. Iwasaki’s lab): Unexplained Post-Acute Infection Syndromes (PAIS) https://buff.ly/38zncTh
Excellent review article summarizes what is known about unexplained PAISs, including ME/CFS, provides context for post-acute sequelae of SARS-CoV-2 infection (PASC), a.k.a. Long COVID, and delineate the need for basic biomedical research into the underlying mechanisms.
Hypotheses on what causes PAIS:
Viral (or bacterial) remnants
Autoimmunity
Dysbiosis of gut with Reactivation
Tissue damage from acute disease
Paxlovid rebound/relapse seems more common than when it was tested during the Delta wave
5/17/22 Research Gate: Rapid Relapse of Symptomatic Omicron SARS-CoV-2 Infection Following Early Suppression with Paxlovid (Nirmatrelvir/Ritonavir) https://buff.ly/3ljDfax
8 patients took Paxlovid for 5 days, had negative tests, but relapsed and were then positive again days 9 - 12.
Viral loads during relapse were high and one person transmitted the virus to 2 family members.
Rebound was not due to a treatment-emergent mutation or infection with a different viral strain.
5/18/22 SF Chronicle: Why is the COVID case rate in San Francisco so much higher than the U.S. right now? https://buff.ly/3wtfyTD
San Franciscans are more vaccinated than the U.S. as a whole, but vaccines have become less effective at preventing infections as coronavirus strains have mutated.
SF residents are taking more risks as local pandemic-era restrictions and messaging wane.
Hospitalizations have increased in San Francisco since April, but are still far below that of previous waves.
5/18/22 Yahoo news: Future COVID variants will likely reinfect us multiple times a year, experts say — unless we invest in new vaccines https://buff.ly/3wI03Gi
Four different sub lineages (including BA.2.12.1, BA.4 and BA.5 that all carry the L452 mutation in the RBD) happened in 4 different locations (Belgium, France, South Africa and NY) almost simultaneously. This strongly suggests that the mutations weren’t random, but rather a Darwinian adaptation allowing the virus to escape our immunity and available monoclonal antibodies.
There’s little cross-immunity between BA.1 and BA.2.12.1, BA.4 or BA.5, so reinfections will be more common.
Some infected with the first Omicron variant are already “reporting second infections with the newer versions of the variant” just a few months later.
Previously, vaccines protected 95% against hospitalization and death. Now, vaccines and boosters protect 80% against hospitalization and death and even less against breakthrough infections.
The US should be focusing money and time on making new vaccines, including nasal vaccine boosters that can help the body make antibodies that capture the virus before it even has a chance to attach to our cells, but the government has not approved new funding.
5/18/22 The United States Congress has not approved more money to fight COVID-19. We should be preparing for the Fall surge now like Germany.
5/18/22 Bloomberg: FDA Authorizes First DTC Covid-19, Flu, RSV Combination Test https://buff.ly/3MxZMwi
5/18/22 Nature: The pandemic’s true health cost: how much of our lives has COVID stolen? https://buff.ly/3yPAG7U
We measure cases, hospitalizations and deaths, but the disability toll as seen by disability-adjusted life years (DALYs) is significant and may represent 30% of the health burden of COVID-19.
DALYs ( disability-adjusted life years) = totalling the years of life lost due to illness, disability or premature death gives an estimate of the burden. They vary in countries because of different age structures and political responses to the pandemic.
In 2020 and 2021, 4.6 million people in the United States had symptoms (fatigue, cognitive problems and ongoing respiratory issues) that persisted for at least three months.
>85% of these Long COVID were from milder cases that did not require hospital treatment.
5/18/22 PNAS (France): The risk of COVID-19 death is much greater and age dependent with type I Interferon autoantibodies https://buff.ly/38sF5Df
Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in:
20% of deceased patients across age groups, and in
1% of individuals aged <70 y
>4% of those >70 y old in the general population.
Autoantibodies against type I IFNs are strong predictors of life-threatening COVID-19 and have a much greater predictive value for death, and, by inference, hospitalization and critical COVID-19, than sex, comorbidities, and common genetic variants.
5/17/22 BMJ (Finland Airport): Scent dogs in detection of COVID-19: triple-blinded randomised trial and operational real-life screening in airport setting https://buff.ly/3G2Yh6Q
Four trained scent dogs screened airport passenger samples with high accuracy of 92%, sensitivity of 92% and specificity of 91% compared with RT-PCR.
It is important to retrain the dogs to new variants as they emerge.
From 3/2022 Research Gate : Screening for SARS-CoV-2 Persistence in Long COVID Patients using Sniffer Dogs and Scents from Axillary Sweats Samples https://buff.ly/3llJLgJ
Dogs discriminated in a positively 51.1% of long COVID patients versus 0/188 (0%) control healthy individuals (p<.0001).
Conclusion: Our data provide arguments for the persistence of viral antigens at least in some long COVID patients.
5/18/22 Gauteng, South Africa @rid1tweets
For week ending 14 May = 24.1% test positivity (down from 31%)
New hospital admissions during this BA.4 / BA.5 wave rising to 34% or 1/3rd of peak hospitalisation during recent Omicron BA.1 wave
As expected: High number of infections (underestimated), but significantly fewer hospitalisations and deaths due to high level of population immunity.
5/16/22 NY Times Opinion by Dr. Iwasaki | The Answer to Stopping the Coronavirus May Be Up Your Nose https://buff.ly/37NbN1w
Animal studies show that giving a nasal spray vaccine booster of viral spike protein after an initial mRNA vaccination in the arm, is effective for blocking virus entry.
Nasal vaccines can prevent people from getting infected to begin with and may allow scientists to develop a single vaccine for a broader range of coronaviruses with protection against future variants, too.
5/16/22 Eric Topol MD: The Covid Capitulation https://buff.ly/3PkG4pD
We can't surrender to the virus. We need to:
Increase vaccines and boosters especially in the elderly.
Fund nasal vaccines (3 are in late stage trials), to decrease transmission by increasing mucosal immunity.
Have rapid access to Paxlovid, while understanding the virus may become resistant to it like it has to Redesivir in select cases.
De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient https://buff.ly/355PhzM
5/16/22 NY Times: How Often Can You Be Infected With the Coronavirus? https://buff.ly/3Pmy1Zb
With Omicron, you can be reinfected repeatedly, sometimes within months.
Omicron infection produces a weaker immune response, which seems to wane quickly, compared with infections with previous variants.
Each infection may bring with it the possibility of long Covid.
Vaccines and boosters help protect against severe infection.
5/16/22 VOX: 4 questions about long Covid experts wish they could answer https://buff.ly/3FTRso8
Survivor Corps, a long Covid research group affiliated with Dr Iwasaki of Yale.
Theories on causes of Long COVID:
Viral reservoir triggers chronic inflammation
Reactivation of viruses other than SARS-CoV-2
Dysbiosis — an imbalance in the microbiome of the lungs or the gut
Autoantibodies
Microclots prevent the body’s oxygen supply from meeting organs’ demands.
Lack of tests for Long COVID
Treatment and prevention of Long COVID
Anti-microclot therapy
Paxlovid
Hyperbaric oxygen
Vaccination
Experimental drugs (like Oxford’s trial of AXA1125 https://buff.ly/3CsOfsU)
Doctors who see long Covid patients are in such demand that patients might wait six months for an appointment.
Remember, if the rapid antigen test is positive, you are infectious!
5/18/22 FT: How can Covid-19 affect the human brain? https://buff.ly/39AP899
A study from Oxford university researchers published in March 2022 found tissue damage and shrinkage in parts of the brain related to smell in people who had only mild bouts of Covid-19.
Loss of the sense of smell may have been caused by damage to the olfactory nerve which extends into the brain, according to a study published in JAMA Neurology April 2022.
5/16/22 Nature: Pfizer BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality https://buff.ly/3wsJ4Jb
Vaccine-induced memory T cells exhibited substantial responses to the Omicron spike protein.
Infection plus vaccination boosted memory T cell response.
5/15/22 NY Times: How Australia Saved Thousands of Lives While Covid Killed a Million Americans https://buff.ly/3wyk5D3
The United States and Australia share similar demographics, but their pandemic death rates point to very different cultures of trust.
Australians tend to do what is right for the community not just the individual and this saved lives during the pandemic.
Americans often lack trust in science, institutions and one another. Putting personal "freedoms" over the community can lead to deaths in a public health crisis.