The current case numbers from the Omicron variant are impressive and scary. We now have almost 1 Million new cases of SARS-CoV-2 each day in the United States. This, of course, does not include all of the home tests that are positive. In places like New York and the UK, after a very steep upward curve, the number of new Omicron cases has taken a U-turn and is starting to descend as fast as the curve went up, similar to South Africa.
Wearing a cloth mask does not provide adequate protection against the more contagious Omicron variant. The best mask protection is to wear a tight-fitting KN95, KF94, or N95 that completely covers your nose and mouth with no gaps. Surgical masks are second best but you may want to double mask.
Starting tomorrow, private insurers will cover 8 home antigen tests per month per person. It is still hard to find them but so far iHealthlabs and On/Go still have tests available online. Remember to order enough tests to be able to test starting day 5 until you get a negative test which may not be until day 10. A new study from UCSF and UC Berkeley show that BinaxNOW rapid antigen test detects Omicron with a sensitivity similar to that observed for prior variants.
In non-COVID news, a new report in Science magazine yesterday shows that Epstein-Barr virus (EBV) is the leading cause of Multiple Sclerosis. If scientists can make a vaccine against EBV, we may be able to prevent new cases of MS.
1/13/22 Science: Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with Multiple Sclerosis (MS)https://buff.ly/3GsCDIB
Risk of MS increased 32-fold after infection with EBV but was not increased after infection with other viruses, including the similarly transmitted cytomegalovirus.
Serum levels of neurofilament light chain, a biomarker of neuroaxonal degeneration, increased only after EBV seroconversion.
These findings cannot be explained by any known risk factor for MS and suggest EBV as the leading cause of Multiple Sclerosis.
SARS-CoV-2 levels in wastewater samples in Santa Clara county have plateaued and are just now starting to fall. It will take a few weeks, but we can assume that SARS-CoV-2 cases will start to fall here soon. But, as Dr. Bob Wachter reminds us, this is not the time to let down our guard- we need to continue to protect ourselves from infection by getting vaccines and boosters, avoiding indoor restaurants, wearing masks and social distancing. Boosters are now recommended 5 months after second doses of Pfizer or Moderna vaccination. To find wastewater SARS-CoV-2 viral levels nationwide, go to https://biobot.io/data/.
The U.S. is reporting 906,713 new coronavirus cases, just below Wednesday's record-high, pushing the seven-day average to 812,208. This means that, every second, more than 9 people are testing positive for COVID-19.
Daily cases continue to rise on the national level, but the Omicron wave appears to have reached a peak in some areas. This includes New York state, where 60,374 new cases were reported on Thursday, down 28% from the week before.
The number of Americans hospitalized with COVID-19 continues to rise and reached 154,131, a new record-high, while the number of people in ICU reached 25,621, the highest since September.
2,136 new deaths were reported, pushing the seven-day average to 1,865, the highest since October3.
Ireland, Iceland, and the UK have U-turn curves now with Omicron. These countries all have some of the highest booster rates in the world.
1/13/22 Harvard DASH: Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant https://buff.ly/3fkOiNy
NBA study, mostly vaccinated cohort
Omicron infections showed a shorter clearance time (5.4 days for Omicron vs 6.2 days for Delta infections) and lower peak viral RNA values than Delta infections.
Increased infectiousness of Omicron is not due to a higher viral load.
Longitudinal mapping of the evolution of an ancestral SARS-CoV-2 infection persisting for over 6 months in a person with advanced HIV.
The SARS-CoV-2 virus mutated over time and gained mutations including those found in Omicron leading to immune escape of vaccines and enhanced escape of Delta immunity, which can affect vaccine breakthroughs and reinfections.
1/13/22 MedRxiV COVID infection severity in children under 5 years old before and after Omicron emergence in the US https://buff.ly/3fjWOfQ
For children under age 5, Omicron infection was associated with significantly less severe outcomes than Delta variant infections.
1/13/22 Nature (Australia): Immunological dysfunction with certain elevated cytokines persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection in Long COVIDhttps://buff.ly/3fnQrbk
Patients with Long COVID (LC) had:
highly activated innate immune cells,
lacked naive T and B cells and
showed elevated expression of type I IFN (IFN-β) and type III IFN (IFN-λ1) that remained persistently high at 8 months after infection.
Combinations of the inflammatory mediators IFN-β, PTX3, IFN-γ, IFN-λ2/3 and IL-6 associated with Long COVID with 80% accuracy.
1/13/22 Nature: SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland https://buff.ly/3trr9kU
79,148 resulting in delivery from March 2020 through October 2021 (pre-Omicron)
32% of pregnant women were vaccinated versus 77% of all women age 18 to 44 yrs.
The death rate for women who gave birth within 28 d of a COVID-19 diagnosis was 22.6 per 1,000 births compared to a pandemic background rate 5.6 per 1,000 births.
Unvaccinated pregnant women accounted for:
77% of infections,
91% of hospitalizations,
98% of ICU admissions,
100% of stillbirths and neonatal deaths.
COVID vaccination protects against infection and is not associated with poor pregnancy outcomes.
The Supreme Court blocked the Biden administration from enforcing its sweeping vaccine-or-test requirements for large private companies.
But the conservative-majority court allowed a vaccine mandate to stand for medical facilities that take Medicare or Medicaid payments.
The OSHA mandate required that workers at businesses with 100 or more employees get vaccinated or submit a negative Covid test weekly to enter the workplace.
CNBC: United Airlines has had zero Covid-related deaths among vaccinated employees for 8 weeks, CEO says https://buff.ly/33CKGUn
United mandated vaccines for staff this summer.
Covid infections have surged among employees, forcing the carrier to cut flights.
Prior to the vaccine mandate, more than one United employee died per week on average.
1/13/22 AP: Kids' low COVID-19 vaccination rates called a 'gut punch' https://buff.ly/3FrlHRo
Distrust, misinformation and delays because of the holidays and bad weather have combined to produce what authorities say are alarmingly low COVID-19 vaccination rates in U.S. children ages 5 to 11.
Only 17% of kids ages 5 to 11 are fully vaccinated in the U.S., more than two months after shots became available to the age group.
While Vermont is at 48%, California is just shy of 19% and Mississippi is at only 5%.
Primary series in children and adolescents ages 5–11 and 12–15 years, and booster doses in adolescents ages 16–24 years https://buff.ly/3qq2XgH
Myocarditis is extremely rare:
For children age 5-11, total of 12 cases of myocarditis for 8.7 million doses
Rate of 4 cases/million in boys is <1/10th the rate in teens
1/13/22 Nature: Inactivated-virus COVID vaccines — which account for nearly half of all shots in arms globally — offer little to no protection against infection from Omicron https://buff.ly/33d5xy2
They include those made by China’s Sinovac and Sinopharm, which together account for nearly 5 billion of the more than 11 billion COVID-19 vaccine doses delivered globally.
1/13/22 BBC: Covid self-isolation in England being cut to five full days with negative antigen test https://buff.ly/3HZTfaU
People will be able to leave isolation after negative lateral flow tests on day 5 and day 6.
1/13/22 BBC: Canada: Unvaccinated father in Quebec loses right to see his child https://buff.ly/3qoJQn7
1/12/22
1/12/22 MedRxiV (France): Screening for SARS-CoV-2 persistence in Long COVID patients using sniffer dogs and scents from axillary sweats samples https://buff.ly/3GE39il
45 Long COVID patients with symptoms for a mean of 15.2 months were tested.
Dogs identified scent in 23/45 (51%) Long COVID patients versus 100% of control individuals (0/188 did not have the scent).
There may be persistence of a viral infection in some Long COVID patients and screening with sniffer dogs may offer a simple, highly sensitive, non-invasive test to detect viral presence, during acute and extended phases of COVID-19.
1/12/22 MedRxiV (Yale): Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain https://buff.ly/3HYp0kC
Long COVID cognitive syndrome shares many features with the syndrome of cancer therapy-related cognitive impairment (CRCI) also known as "chemo brain" as seen by new studies in mice and in humans.
Neuroinflammation, especially white matter microglial reactivity
Elevated CSF cytokines/chemokines, especially CCL11, for weeks post infection
Loss of oligodendrocytes
1/12/22 Stanford Daily: Stanford University introduces 7-day isolation period https://buff.ly/3FpFctr
Students in isolation for COVID-19 can leave after seven days if they test negative on a rapid antigen test and their symptoms are either mild or nonexistent.
Rapid antigen tests are dropped off on day 7 with their meals.
1/13/22 SARS-CoV-2 Sewage Waste water Monitoring Data, County of Santa Clara https://buff.ly/33uBWQi
Palo Alto Water Quality Control Plant processes sewage from Los Altos, Los Altos Hills, Mountain View, Palo Alto, Stanford University and the East Palo Alto.
1/12/22 Palo Alto Online: Santa Clara and San Mateo counties are now seeing more COVID-19 cases than at any other time during the pandemic https://buff.ly/3IgL1vl
Santa Clara County
60% of eligible residents have received a booster shot
82.5% of residents have been vaccinated
>4000 new cases per day, plus positive home tests which are not tracked
State models indicate peak infections could be sometime in early February or later. Hospitalizations peaks will follow.
Wastewater surveillance of SARS-CoV-2 virus has increased sharply in all four sewersheds in the past two weeks.
The current concentration has surpassed last winter's surge.
Unvaccinated residents are hospitalized 20x more often than vaccinated.
Unboosted residents have 2x the case rate of breakthrough infections versus those who have received their boosters.
San Mateo County's increased from an average of 79 new cases per day last week to 905 this week.
1/12/22 MedRxiV (Kaiser So Cal): Clinical outcomes (fewer hospital admissions and less hospitalized days) with Omicron variant than Delta infection in southern California https://buff.ly/3rjXveO
52K Omicron cases vs 17K Delta cases at Kaiser Southern California
Hospital admissions in 0.5% of Omicron cases and 1.3% of Delta cases.
Duration of hospital stay was 3.4 days (70%) shorter for hospitalized cases with Omicron variant than Delta.
1/11/22 NBC news: Hundreds of Parents Step Up to Help Palo Alto Schools During COVID-19 Surge https://buff.ly/3Ka9LqS
PAUSD asked for parent volunteers to help with light custodial work, food services, directing COVID testing lines and even assisting substitute teachers.
The district is missing more than 100 support staff and up to 80 teachers a day. Over 700 parents have volunteered to help.
1/11/22 The Economist: The Omicron wave in New York looks worse than in Englandhttps://buff.ly/3qiIeLL
The United States has fewer people vaccinated and fewer people who have been boosted.
1/11/22 Reuters: Long COVID could become Finland's largest chronic disease, warns minister https://buff.ly/33hOo5E
Finnish expert panel’s summary of more than 4,000 international studies which showed one in two adults and around 2% of children may experience prolonged symptoms connected to COVID-19.
About 20% see long-term cognitive impairment according to Risto Roine, professor of neurology and chairman of the expert panel.
1/11/22 Lancet: Comparison of Moderna Versus Pfizer-Biontech COVID-19 Vaccine Outcomes: A Target Trial Emulation Study In the U.S. Veterans Affairs Healthcare System https://buff.ly/3r7DU12
Moderna vs Pfizer with >900,000 people in each group.
Moderna had a significantly lower hospitalization rate (and infection rate) through the Delta wave than Pfizer.
These differences were greater with longer follow-up time since vaccination.
1/11/22 MedRxiV: Direct Comparison of SARS Co-V-2 Nasal RT- PCR and Rapid Antigen Test (BinaxNOW) at a Community Testing Site During an Omicron Surge https://buff.ly/3Go9y0J
n = 731 at UCSF, UCB
BinaxNOW rapid antigen test detects Omicron with a sensitivity similar to that observed for prior variants.
The assay rapidly identifies persons with highest levels of virus, and thus those likely to pose the greatest risk for transmission at the time of the test.
1/11/22AP: Home COVID tests to be covered by insurers starting Saturday https://buff.ly/31M0x2B
Insurers will be required to cover up to 8 home COVID-19 tests per person per month for people on their plans.
1/11/22 AP: China locks down 3rd city, raising affected to 20 million https://buff.ly/3r74dEB
Anyang's locked down after 2 cases of Omicron reported. Residents are not allowed to go out and stores are closed except those selling necessities.
Xi'an has been in lockdown for 3 weeks and Yuzhou for a week.
1/11/22 Journal of Translational Medicine:Paradoxical sex-specific patterns of autoantibody (AAB) response to SARS-CoV-2 infection https://buff.ly/3nkB0VO
SARS-CoV-2 infection, even in the absence of severe clinical disease, can lead to a broad AAB response that exhibits sex-specific patterns of prevalence and antigen selectivity.
Whereas the overall AAB response was more prominent in women following asymptomatic infection, the breadth and extent of AAB reactivity was more prominent in men following at least mildly symptomatic infection.
Notably, the observed reactivity included distinct antigens with molecular homology with SARS-CoV-2.
Responding to disease outbreaks is about stuff, space and staff.
In March 2020, we didn't have enough of the stuff—PPE, ventilators.
We didn't have enough space. So we built more.
"But now it's healthcare staff that are short."
Omicron’s stunning ability to evade immunity means vaccinated healthcare providers are getting infected at high rates.
Debate re: being hospitalized “WITH Covid” versus “FOR Covid” isn’t a relevant distinction if the hospital doesn’t have the beds or staff needed to care for its patients.
Every Covid positive patient requires a bed with staff to treat them, isolation and use of PPE. And they all represent another infection risk to providers.
The Omicron surge is real. And even if Omicron is 'milder', it's not mild.
It causes severe disease half as often as Delta, but infects 2-4x as many people, potentially washing out any potential 'benefit'.
Unknown Long Covid risks
NY Times Opinion by Craig Spencer: As an E.R. Doctor, I Fear Health Care Collapse More Than Omicronhttps://buff.ly/3GhYnXk
1/10/22 Reuters: Two doses of Pfizer-BioNTech COVID-19 vaccine 91% effective in preventing MIS-C in 12- to 18-year-olds, CDC says https://buff.ly/3r5XbQv
1/10/22 NY Times: A Surge in Hospitalized Young Children Infected With the Coronavirus https://buff.ly/3HRYr0t
The number of hospitalized young children less than age 4 infected with the coronavirus rose precipitously last week to the highest levels since the beginning of the pandemic.
Omicron appears to affect the upper airway more and young children are often more susceptible to bronchiolitis.
1/10/22 CNN: FDA warns against using throat swabs for home Covid-19 tests https://buff.ly/333UdEd
"The FDA has safety concerns regarding self-collection of throat swabs, as they are more complicated than nasal swabs. Throat swabs should be collected by a trained healthcare provider."
1/10/22 Cal Matters: California weighs order canceling elective surgeries as COVID surges https://buff.ly/3r7PTvs
Throughout California, as COVID-19 infections deplete their staff of nurses, anesthesiologists and other essential workers, hospitals are canceling or postponing so-called “elective” surgeries to repair injured knees and aching back, remove kidney stones, repair cataracts or hernias, and even lung transplants.
“Elective” means a surgery is not an emergency and can be scheduled in advance; it does not mean it’s optional. Waiting in some cases can be life-threatening.
Stanford Medical Center in Palo Alto has about 5% of its total workforce out sick. “We have seen a doubling of nurses calling off per shift, reporting that they are ill,” Julie Greicius said.
71% of eligible Californians are vaccinated and 38% of them are boosted.
“This is not about beds, this is about the staff to care for the patients in those beds.”
Hospital staffing shortages are highest in Vermont, New Mexico, Rhode Island, West Virginia and California.
"It feels like I’m starting a job at a new building, except the building is on fire and everyone is rushing outside as they try to save their own lives."
Health Care Providers (HCP) who test positive for SARS-CoV-2 and are asymptomatic, may return to work immediately without isolation and without testing, and HCPs who have been exposed and are asymptomatic may return to work immediately without quarantine and without testing. These HCPs must wear an N95."
UK: 12/30/21 Update on hospitalization and vaccine effectiveness for Omicron https://buff.ly/3FNzqmy
2 doses of Pfizer + Moderna booster had higher VE against symptomatic Omicron than 2 doses of Pfizer + Pfizer booster.
1/9/22 NY Mag: America’s Omicron Wave Already Looks More Severe Than Europe’shttps://buff.ly/3356VTc
“A pandemic is not simply a matter of the biological properties of the virus; it is also determined by the social and immunological context in which that virus spreads.”
A small fraction of a huge number is still a large number.
Omicron spreads proficiently among the vaccinated.
“Incidental” cases found on hospital admission for other things but some patients have other medical issues but have been “tipped over” into hospitalization by the presence of COVID.
Main differences in the US vs Europe:
Lower vaccination rates in US than Europe
Lower booster rates
US is still seeing lingering effects of Delta wave in hospitalizations and deaths
1/9/22 Washington Post: Omicron could have a silver lining by boosting immunity, some experts say. But don’t bet on it. https://buff.ly/3tbUwY5
1/9/22 MedRxiV (Kaiser So Cal): Effectiveness of Moderna mRNA-1273 against SARS-CoV-2 Omicron and Delta variants https://buff.ly/3JT3Fe2
6657 test positive cases (44% delta, 56% omicron) .
3 doses Moderna against Delta infection: 95% VE
Against Omicron infection:
2 doses Moderna against Omicron infection: 30% VE
3 doses Moderna against Omicron infection: 62.5% VE
3 doses Moderna against Omicron infection for immunocompromised: 11% VE
Against Omicron hospitalization:
3 doses Moderna was 100% effective against hospitalization with Omicron, Delta
1/8/22 CDC MMWR: Risk for New Diabetes Diagnosis After SARS-CoV-2 Infection in Children < 18 Years Old https://buff.ly/3qaCK5T
Persons aged <18 years with COVID-19 were more likely to receive a new diabetes diagnosis >30 days after infection than were those without COVID-19 and those with prepandemic acute respiratory infections.
Non–SARS-CoV-2 respiratory infection was not associated with an increased risk for diabetes.
1/8/22 Washington Post: Should you add a throat swab to your at-home covid test? https://buff.ly/3nbIRor
“Virus may start further down,” Mina continued. “Throat swab + nasal may improve chances a swab picks up virus.”
1/9/22 The Stanford Daily: Stanford reports nearly 700 COVID cases, delays start of some in-person undergraduate classes https://buff.ly/3F9ACiQ
400 students have tested positive for COVID-19 since last Friday as have 300 faculty, staff and postdocs.
Designated isolation spaces on campus have reached capacity.
The University is still sending students to off-campus isolation locations, but if those also reach capacity, some undergraduate students who test positive for COVID-19 may be asked to isolate in place, even if they do not have a private living space or bathroom.
In this case, the University would provide roommates who have tested negative with additional living options. These options include an empty room or common space that has been repurposed as a temporary sleeping space, a friend’s room or an off campus hotel. Stanford would also designate shared bathrooms for COVID-positive and COVID-negative students to avoid overlap and exposure.
Stanford surgeon Tiffany Chao:
1/7/22 Newsweek: 125 Plane Passengers Flying from Italy to India Test Positive for COVID https://buff.ly/3t7rRDx
125 out of 160 passengers on the flight were positive
This long, stressful pandemic has been hard on everyone. Let’s try to be kind to others as much as we can. It’s hard to know what things they are carrying around with them.
