Tag Archives: Pavitra Roychoudhury

COVID cases fueled by Omicron skyrocket globally, nationally, and in Washington

December 20, 2021 David Obelcz

Texas officials report the first Omicron related fatality in the United States

Editor’s Note: As a policy, Malcontent News does not quote or publish data from pre-print studies. The transmission rate of the Omicron SARS-CoV2 variant is so high it is spreading at a rate faster than the scientific review process. For this reason, we are using pre-print studies in our reporting and analysis for the Omicron variant. We will continue to backlink to all quoted sources to support transparency in reporting.

Updated: Story edited to report first Omicron death in the United States

[KIRKLAND, Wash.] – (MTN) Washington state moved back to high transmission risk for COVID as new cases fueled by the Omicron variant grew 32 percent over the weekend. The highly contagious variant was discovered in South Africa, spreading to over 90 countries in six weeks.

The United States was reminded how serious Covid-19 is this evening, with Texas reporting the first Omicron-related death in the nation. Judge Lina Hidalgo of Harris County, Texas, tweeted that a man in his 50s had died of Omicron. He was unvaccinated and had health issues. It is reported he was treated with monoclonal antibodies, which have been rendered ineffective against the Omicron variant.

The U.S. Centers for Disease Control (CDC) reported 73% of new COVID cases across the United States are the Omicron variant, swamping Delta cases. The World Health Organization estimated cases are doubling every 1.5 to three days.

The CDC estimates that Omicron is 90% of new COVID cases in the New York City area, the Southeast, the Ohio River Valley and Great Lakes states, and the Pacific Northwest. Omicron cases have been detected in 48 of 50 states, with Montana, Indiana, and Vermont confirming cases this afternoon.

On December 20, North Dakota, Montana, Indiana, and Vermont reported their first confirmed Omicron cases and Texas reported an Omicron-related death – Oklahoma and South Dakota lag the rest of the country in genomic sequencing of test samples

In Miami, lines of cars waited for hours to get COVID tests. Governor Ron DeSantis had boasted Florida had conquered coronavirus on Oct. 27, using data from the New York Times. On Monday evening, Florida reported more than 7,000 new cases a day, an increase of almost 300% in two weeks – second only to Hawaii.

The Washington State Department of Health (WSDoH) reported a sharp increase in COVID cases. The counties with the highest rates were distributed across Washington from the Olympic Pennisula to the Palouse. Only Wahikakum County reported low community spread on Monday.

Percent of Total Population Fully Vaccinated	Percentage of Vaccinated People with Booster Dose	Total Population in Group	Average 7-Day New Case Rate
70.00% or above	39.15%	2,343,250	170.1
60.00% to 69.99%	35.36%	1,669,300	136.0
50.00% to 59.99%	32.23%	3,339,300	111.6
40.00% to 49.99%	29.41%	268,975	77.6
32.70% to 39.99%	35.38%	151,850	85.5

7 Day New Covid-19 Cases per 100K average by Vaccination Rate for Total Population, Adjusted for Population by County, Booster percentage is based on totally fully vaccinated, not eligible, Average 7-day New Case Rate <25 normal, =>25 to 99.9 moderate, => 100, high transmission

Federal officials believe the actual case count is much higher due to asymptomatic carriers and home testing, which isn’t reported to county and state health departments.

According to the University of Washington Virology Lab, the genomic sequencing of SGTF COVID test samples was 70% positive for Omicron on Dec. 16. Data provided by Pavitra Roychoudhury, MSc, Ph.D., of the University of Washington Virology Division, showed Omicron cases had been lab-confirmed in Benton, Franklin, King, Pierce, Snohomish, Thurston, Walla Walla, Whatcom, and Yakima Counties.

Researchers had looked at test samples as far back as Nov. 7 from Idaho, Oregon, and Washington.

Frustration was building on social media as Western Washington residents tried to find rapid COVID antigen tests, booster shots, and appointments for children 5 to 11 to get vaccinated. People waited for hours in long lines to get lab tested for Covid-19 and worried about travel plans as the time to get test results back grew past 72 hours.

Seattle Mayor Jenny Durkan announced that the Rainier Beach and West Seattle vaccination clinics will remain open for boosters and vaccinations into January 2022. Tests sites across the city run in cooperation with the University of Washington are expanding hours to try and meet growing demand. There are fixed test sites at Aurora, SODO, Rainier Beach, and West Seattle, as well as seven Curative kiosks placed throughout the City. In partnership with the City of Seattle, UW Medicine has also opened a site at City Hall, which is available to the public. Appointments are encouraged at all locations, and sites will be closed on Christmas Day.

Area hospitals are at capacity even though COVID hospitalizations are low

The number of hospitalized COVID patients in Washington has slowly dropped through December. The WSDoH reported there were 640 hospitalized Covid-19 patients on Sunday, and 81 were on ventilators. The numbers are significantly higher than the end of the Fifth Wave in late May, and area hospitals are already filled with non-COVID patients.

Data from the U.S. Health and Human Services (HHS) found regional hospitals have scant resources to manage another surge. Almost half of the regional hospital beds available are at Swedish on Broadway in Seattle and St. Joseph’s Medical Center in Tacoma. The report indicated there were 730 beds available, but that includes resources for pediatric patients and neonatal incubators. Available ICU beds include NICU incubators, PICU beds, and critical care resources for post-surgical, transplant, trauma, and burn patients.

Hospital	City	Acute Care Total	Acute Care Available	ICU Total	ICU Available
Overlake	Bellevue	264	17	34	4
Swedish – Cherry Hill	Seattle	170	2	42	16
Seattle Children’s	Seattle	308	29	96	12
U.W. Medical Center	Seattle	641	58	139	98
Swedish – Broadway	Seattle	568	90	79	55
Harborview	Seattle	400	9	97	10
Virginia Mason	Seattle	238	20	33	13
EvergreenHealth	Kirkland	251	8	37	2
Swedish – Issaquah	Issaquah	100	8	30	26
Valley Medical	Renton	292	36	50	27
St. Anne’s	Burien	161	44	31	23
Swedish – Edmonds	Edmonds	173	14	9	5
Harrison Memorial	Bremerton	281	36	49	6
MultiCare	Auburn	138	31	16	1
St. Francis	Federal Way	155	45	15	1
St. Anthony’s	Gig Harbor	108	0	16	3
Providence	Everett	611	47	77	8
Tacoma General	Tacoma	310	-9	46	2
Mary Bridge Children’s	Tacoma	83	34	11	4
St. Joseph’s	Tacoma	573	234	76	14

Data is through December 9, 2021, as reported to the U.S. Health and Human Services for all hospitals with more than 50 beds and ICU resources within 30 miles of downtown Bellevue – acute care beds include adult, pediatric, and neonatal, ICU beds include NICU, PICU, and specialized critical care units for post-surgical, trauma, and burns

In a worrying sign from New York, officials reported on Monday night that while many people are experiencing breakthrough cases and having mild symptoms, unvaccinated individuals were 11 times more likely to be hospitalized.

More data released on vaccine and monoclonal antibody effectiveness against Omicron

In an announcement early Monday, Moderna said preliminary data from lab testing found that a booster of the currently available vaccine increased antibody levels to an effective level. The drugmaker said its currently FDA-approved 50 microgram booster increased neutralizing antibody levels 37-fold against Omicron and 83-fold with a 100 microgram “full dose” booster.

An independent study released last week that evaluated the effectiveness of the Pfizer, Moderna, and Johnson & Johnson vaccines had similar results. Vaccine effectiveness appears to be significantly impacted by how long ago someone received their final dose or booster. Multiple studies have found the Johnson & Johnson vaccine is significantly less effective.

Results from a study that reviewed the effectiveness of the Moderna, Pfizer, and Johnson & Johnson vaccines after three months, more than six months, with the previous infection, and with a booster. The Johnson & Johnson vaccine was evaluated using a Modern 50 microgram dose as a booster

A study from the U.K. found that relying on immunity from a previous COVID infection was only 19 percent effective against preventing symptomatic reinfection and 20 percent when relying on vaccination without a booster. The same study found that a booster dose increased protection by 50 to 85 percent. Overall the risk for reinfection was 5.4 times greater than Delta. The study done by the Imperial College of London used PCR test data from Nov. 29 to Dec. 11.

In New York, hospitalists at Mount Sinai Hospital were advised to stop administering monoclonal antibodies because they were ineffective against Omicron. The memo reported that most people seeking treatment had breakthrough infections with mild symptoms that didn’t warrant hospitalization.

Washington state is waiting for the first 552 doses of the monoclonal antibody sotrovimab. Granted Emergency Use Authorization (EUA) by the U.S. Food and Drug Administration (FDA) in May, it is the only remaining effective early treatment for Omicron in the United States.

Concern grows as the hopes of Omicron being “only a cold” fade away

South Africa officials reported 105 COVID-related deaths across the nation on Monday. The number of ICU patients has increased 144 percent since Nov. 25. Omicron appears to have peaked in Gauteng Province but continues to spread rapidly across the nation of almost 60 million.

United Kingdom officials reported another five Omicron COVID-related deaths, bringing the total to 12. Hospitalizations of children under 5 increased 39% week over week, and thousands of healthcare workers have been stricken with Covid-19 infections, causing staffing issues.

A study by the University of Texas Austin for the CDC was made public on Dec. 16. It looked at 18 different scenarios for the spread of Omicron. In ten of those scenarios, the healthcare system in the United States is overrun by patients.

President Joe Biden will address the nation on Tuesday to outline the administration’s new steps to aid states and communities while trying to curb the spread of COVID.

Yesterday, former President Donald Trump addressing a crowd of admirers in Dallas told the audience he had received his booster. A smattering of jeers and boos rippled across American Airlines Center.

“Don’t, don’t, don’t, don’t …” he said.

“There’s a very tiny group over there,” the former President added.

Breaking News, Health and Lifestyle, Local, National

Where London goes with Omicron Seattle will follow, with the rest of the US close behind

December 19, 2021 David Obelcz

[KIRKLAND, Wash.] – (MTN) A record 93,000 new COVID cases were reported in the United Kingdom by the National Health Service just hours after Trevor Bedford, Ph.D., an Associate Professor, Biostatistics, Bioinformatics and Epidemiology Program Vaccine and Infectious Disease Division, at Fred Hutchinson Cancer Research indicated that where London goes, Seattle will follow five days later.

France closed its borders to the UK on Friday evening and on Saturday, London Mayor Sadiq Khan declared a “major incident” as Covid-19 hospital admissions rose 30% in a week. The National Health Service reported seven people have died from the Omicron variant and believe that “hundreds of thousands” of cases are going unreported. Cases are expected to grow at a dizzying rate well into January.

On Friday, Bedford told reporters that 50 percent of new Covid-19 cases in King County, were likely Omicron and doubling every 2.4 days. The next day, Pavitra Roychoudhury, MSc, Ph.D., of the University of Washington Virology Division tweeted that Omicron was 50 percent of all cases in Washington.

In an interview published on Saturday in the New York Intelligencer, Bedford shared his prediction on what is to come. “I can expect caseloads that are huge. I can easily expect a 50 percent attack rate from Omicron. I can easily expect that.”

“Attack rate,” is how much of the population will be infected – and Bedford predicts that half of the United States population will catch the Omicron variant. Because the United States does not take a national approach to genomic sequencing, and not all hospitals test patients for COVID at admission, the number of people already hospitalized is murky. From the earliest reports, the hospitalization rate was between 2% to 5%.

There was little good news to be found over the weekend on the impact the new wave is going to have on the United States. In the Northeast, Mid-Atlantic, and Great Lakes Region hospitals are already at or over capacity and receiving additional aid from FEMA. Many states are struggling with dwindling testing funds and a lack of data because tracking systems were dismantled over the summer.

A cascade of drug makers indicated late in the week that the current version of monoclonal antibodies in distribution aren’t effective against the Omicron variant. Unlike vaccines, which target all antibodies, monoclonal antibodies only target one. The antibody that was “cloned” in the process was effective against previous variants but doesn’t produce a significant immune response with Omicron.

In a series of studies, only Sotrovimab, produced by GlaxoSmithKline, showed promise against the fast-spreading variant. The monoclonal antibody received Emergency Use Authorization ( EUA) from the U.S. Food and Drug Administration (FDA) on May 26. Health and Human Services (HHS) reported they would be distributing 55,000 doses across the United States this week, with Washington receiving 552.

Back in the UK, the National Health Service reported that on any given day, about one percent of the national health force would be absent from work due to illness. In London, the number of workers calling out sick surged 40 percent. In the United States, healthcare workers have been fleeing the profession for years, while nurses have complained about short staffing for over a decade. Area hospitals will be impacted dramatically if Omicron starts to infect their workforces.

HHS reported over 68,000 people were hospitalized with COVID across the United States. Statewide on Friday, only eight percent of acute care and 12 percent of ICU beds were available. In King County many hospitals are already at or above capacity, but not due to COVID patients. A shortage of staffed skilled nursing and rehabilitation beds has left patients ready for discharge nowhere to go.

Over the summer when patient loads were lower, the Delta wave brought Oregon and Washington hospitals to the brink of crisis standards of care while collapsing the healthcare systems in Idaho and Alaska. Hospitalization rates for COVID and non-COVID patients are already much higher as the region prepares to face the biggest challenge yet.

According to HHS, EvergreenHealth Kirkland had 19 acute care beds available while Overlake had 17. Both hospitals were reporting ICUs near capacity with 3 beds at Evergreen and 4 at Overlake.

During the Delta surge, states learned that activating the National Guard for nurses and doctors was a poor option. Trained hospital staff who are “weekend warriors” were frequently already supporting surging hospital admissions. The activation in some cases made staffing situations worse.

King County residents vented their frustration on social media about the inability to get a booster shot, find home COVID antigen tests, and PCR test results being delayed. In other circles, Seahawks fans raged against the scheduling change against the Rams due to coronavirus.

Officials in the UK pleaded with government officials to implement further public health restrictions to stem the tide of new cases, as models indicate that by January, the island nation could see 3,000 to 4,000 new hospitalizations a day. Londoners were already starting to deal with closed shops and restaurants, and delays in services because so many people have been sickened.

It is unlikely any additional restrictions will be implemented across the United States, where COVID has been turned into a political weapon. The U.S. Department of Homeland Security (DHS) indicated in a Nov. 10 memo, “If a new COVID-19 variant emerges and new public health restrictions are imposed as a result, anti-government violent extremists could potentially use the new restrictions as a rationale to target government or public health officials or facilities.“

Numerous studies and growing real-world data from Africa and Europe indicate that immunity from prior COVID infections or vaccination without a booster provides enough protection to prevent severe COVID symptoms that result in hospitalization and death. Booster shots ideally received within the previous 12 weeks, boost immunity for more.

For people relying on viral vector vaccines such as Johnson & Johnson, AstraZeneca, or Russia’s GNCEM, there appears to be even less protection without a booster. On Thursday, The Centers for Disease Control (CDC) endorsed the recommendation from the Advisory Committee on Immunization Practices (ACIP) to recommend the mRNA Pfizer and Moderna vaccines over Johnson and Johnson. The decision was made due to the waning effectiveness of the J&J vax and nine confirmed fatalities, seven women including one from Seattle, and two men, from vaccine-induced immune thrombotic thrombocytopenia (VITT).

A study published on Dec. 14 found that Moderna with a booster provided the best protection from Omicron, followed by Pfizer with a booster, and then Johnson & Johnson with a Moderna booster. The study also evaluated individuals who had a previous COVID infection and then got vaccinated. They found that immunity was better than vaccination without a booster, but not as robust.

Real-world data from Europe and Africa indicate that relying on immunity from a previous COVID infection is offering little protection from becoming symptomatic. Epidemiologists have stated it is possible to be infected with the Delta and Omicron variants at the same time. It also appears that natural immunity from Omicron won’t protect a person from a later Delta infection.

There is mounting evidence that Omicron is no more severe than Delta, but little evidence it is less so. On Friday the Imperial College of London released a report that found no evidence that Omicron is “mild.”

“The study finds no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms or by the proportion of cases seeking hospital care after infection. However, hospitalisation data remains very limited at this time.”

The challenge for the public and health experts is comparing the current global wave to previous spikes in COVID cases. During the original wave in the spring of 2020, no one had any type of immunity. When the Alpha and Beta waves came in the winter of 2020, vaccines were just rolling out. When Delta arrived the variant was more transmissible and more severe than prior strains. It also was capable of nibbling around the edges of vaccine protection due to its mutations.

Omicron has arrived in a population that has received a variety of mRNA and viral-vector vaccines with different doses as well as disease acquired immunity from different strains. The timing of receiving a vaccine, prior infection, or a combination also impacts how much immunity a person has.

Many people are more mobile and have returned to work and school while simultaneously taking fewer precautions. An additional challenge is the rate of vaccination is not homogenous, with highly vaccinated communities adjacent to vaccine-resistant populations.

All of these factors are obscuring the true nature of Omicron and because the United States does a poor job of genomic sequencing in some states, little is known about the current hospitalized population and which variant patients have.

Although data out of South Africa has been more encouraging, experts had warned that the recent end of the Delta wave, a higher than understood vaccination rate, and the youthful nature of the South Africa population would favor better outcomes. Although only 26% of South Africa’s total population is vaccinated, over 34% of the county was ineligible due to age. On Oct. 20, the nation expanded vaccination to 12 to 17-year-olds and introduced booster shots to adults on Dec. 9. In reality, 44% of South African adults are fully vaccinated, including 61 percent of people over 50. Additionally, only 5.7% of South African residents are 60 or older.

Researchers are watching King County closely for several reasons. The region is a leader in genomic sequencing and research. As Omicron moves through the region it will provide critical data to build a better understanding of transmissibility, the impact on public health measures, prevention and treatment, and how severe Omicron is. King County is highly vaccinated, but has pockets of low vaccine acceptance, providing a more realistic cross-section. Finally, New York City is almost unique compared to other US cities due to its size, reliance on public transit, and the number of people who live in buildings with communal areas.

Dr. Cameron Webb, the senior policy advisor for equity for the White House COVID Response Team shared early symptoms to look for if you start feeling ill.

Sore throat, espeically if it is more than mild
Headache
Fatigue – severe fatigue appears more common in children
Runny nose
Sneezing
Dry cough

County health officials continue to appeal for people to get vaccinated and get a booster shot if they are eligible. They recommend frequent hand washing and wearing an N-95, KN-94, or KN95 mask whenever you’re out of your home, and to stop using cloth masks. When it comes to Christmas and New Year’s celebrations and travel plans, it is recommended to test the day off and celebrate outside or in well-ventilated indoor areas.

Because of the systems put in place by King County Public Health and supported by County Executive Dow Constantine, the region is better prepared to provide vital data to the rest of the nation. It is very likely that by Christmas, Seattle will feel a lot more like March 2020 than December 2021.

Health and Lifestyle, Local, National

Omicron variant 20% of Washington COVID cases

December 15, 2021 David Obelcz

[SEATTLE, Wash.] – (MTN) Pavitra Roychoudhury, MSc, Ph.D., of the University of Washington Virology Division, reported 20% of tests samples submitted for genomic sequencing are positive for the Omicron variant. From Dec. 6 to Dec. 10, Omicron jumped from 1% to 20% of samples tested using an S Gene Target Failure (SGTF) test.

The Washington State Department of Health reported on Dec. 13, 75.3% of residents 12 and older are fully vaccinated. Multiple studies have shown that three months after vaccination, Pfizer, Moderna, and Johnson and Johnson had low neutralizing antibodies against the Omicron variant but enough of a secondary response to prevent severe infections. On Dec. 15, the WSDoH reported 1.48 million people of 3.3 million eligible had received a booster shot. Boosters doses have been shown to increase neutralizing antibodies and add additional protection.

Percent of Total Population Fully Vaccinated	Percentage of Vaccinated People with Booster Dose	Total Population in Group	Average 7-Day New Case Rate
70.00% or above	33.67%	2,343,250	72.1
60.00% to 69.99%	30.67%	1,669,300	93.6
50.00% to 59.99%	28.79%	3,339,300	87.4
40.00% to 49.99%	25.62%	268,975	76.5
32.70% to 39.99%	31.51%	151,850	102.6

Statewide, the 7 day moving average for new COVID cases was 84.1, indicating moderate coronavirus transmission across the state. Ferry and Columbia Counties are hot spots, while a surge in new cases in Garfield County was winding down.

On Wednesday, the WSDoH reported four super spreader events on Dec. 4, involving high school wrestling tournaments in Yelm, Puyallup, Sumner, and Lacey. Participants and spectators came from Clark, Cowlitz, Grays Harbor, King, Kitsap, Lewis, Mason, Skagit, Snohomish, Pierce, Thurston, Whatcom, and Yakima Counties, and one school from Oregon.

Officials reported that 80 to 90 people had confirmed COVID cases so far, and they expect to find more infections. Infections were among vaccinated and unvaccinated individuals, and three genomic sequenced tests were positive for the Omicron variant.

On Tuesday, the U.S. Centers for Disease Control (CDC) presented two potential national scenarios in a closed-door media briefing. The first predicted a continued Delta surge followed by a smaller wave of Omicron cases spiking in the early spring. The second had Delta, Omicron, and Influenza surging simultaneously in January, potentially overwhelming hospitals.

Omicron has world leaders and health officials increasingly worried as cases surge around the globe. Seventy-seven countries and 36 states have confirmed cases.

In South Africa, over 7,300 people are hospitalized, an increase of 81% from a week ago, with cases exploding outside of Gauteng Province. The South Africa Department of Health reported 26,976 positive cases today, and the 7 day moving average jumped to over 23,000 – a new record.

The United Kingdom reported a single-day record for new COVID cases – 78,610. National Health Services leaders said 60% of all cases in London are the Omicron variant and 35% of cases nationwide. British prime minister Boris Johnson told reporters that cases of Omicron are doubling in less than two days.

“I’m afraid we’re also seeing the inevitable increase in hospitalizations up by 10 percent nationally week on week and up by almost a third in London.”

In a political blow, the conservative members of his party voted down stricter measures meant to curb the growing number of hospitalizations.

The European Centre for Disease Prevention and Control Rapid Risk Assessment from Dec. 15 issued a stark warning to the European Union members.

“Although current data on the severity of the infection associated with the Omicron [Variant of Concern] (VOC) remain limited, evidence to date raises concern that the Omicron VOC may be associated with a significant reduction in vaccine effectiveness against SARS-CoV-2 infection,” the report stated.

“Even in the case of lower infection/disease severity with the Omicron VOC, a steep, exponential increase in cases caused by the Omicron VOC will result in a growing number of cases with severe disease. As EU/EEA countries are still facing the severe impact of the Delta VOC wave, a further rise in hospitalisations could quickly overwhelm healthcare systems.”

Many pundits have rushed to declare Omicron as mild relying on abstracts, articles, and soundbites. Many doctors believe the early data is encouraging but caution against rushing to conclusions.

Several publications are quoting an article from the LKS Faculty of Medicine from the University of Hong Kong by Dr. Michael Chan Chi-wai, Associate Professor of School of Public Health and Principal Investigator, and Professor John Nicholls, Professor of Department of Pathology.

The research paper and study data have not been published and currently is under peer review. The article suggested that the Omicron variant can replicate 70 times faster in the lungs’ airways when compared to the Delta variant, creating a higher viral load. Dr. Chan also suggested that Omicron may infect multiciliated cells found in the deep lungs at a slower rate when compared to the Delta variant.

Dr. Chan stressed that COVID infections are complicated, and only looking at the ability to infect lung cells was too narrow to reach a broader conclusion on severity. “It is important to note that the severity of disease in humans is not determined only by virus replication but also by the host immune response to the infection, which may lead to dysregulation of the innate immune system.”

He went on to add, “By infecting many more people, a very infectious virus may cause more severe disease and death even though the virus itself may be less pathogenic. Therefore, taken together with our recent studies showing that the Omicron variant can partially escape immunity from vaccines and past infection, the overall threat from Omicron variant is likely to be very significant.”

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Omicron variant identified in 13% of recent Washington COVID tests

December 14, 2021 David Obelcz

Editor’s Note: As a policy, Malcontent News does not quote or publish data from pre-print studies. The transmission rate of the Omicron SARS-CoV2 variant is so high it is spreading at a rate faster than the scientific review process. It is for this reason, we are using pre-print studies in our reporting and analysis for the Omicron variant. We will continue to backlink to all quoted sources to support transparency in reporting.

[SEATTLE, Wash.] – (MTN) Pavitra Roychoudhury, MSc, Ph.D., of the University of Washington Virology Division, reported 13% of tests samples submitted for genomic sequencing on Dec. 8 were positive for the Omicron variant. Tentative confirmation was made using an S Gene Target Failure (SGTF) test, with Dr. Roychoudhury indicating in a tweet that it will take a few days for genomic sequencing confirmation.

Using the data provided by the University of Washington, Omicron variant cases in Washington doubled every 24 hours from Dec. 6 to Dec. 8. The total number of new COVID cases being detected indicates that the Omicron variant is rapidly replacing Delta, not adding to confirmed cases at this time.

At @UWVirology, we continue to screen positive specimens using SGTF. Confirmation by sequencing usually lags by a few days, but we expect the majority of these SGTFs to be Omicron. If so, definitely seeing a rapid rise similar to reports from South Africa, UK, Denmark, etc. https://t.co/Qb1LrEdT6t pic.twitter.com/1d7Rheqoe6
— Pavitra Roychoudhury (@pavitrarc) December 13, 2021

Nathan Grubaugh, Ph.D., Associate Professor of Epidemiology at the Yale School of Public Health, tweeted researchers were seeing a similar trend among samples collected in Connecticut.

If the rate of new case growth for Omicron continues at the current rate in Washington, it would be the fastest case growth rate observed to date. In South Africa and across the United States, Omicron cases have been doubling every three days. In the United Kingdom, cases have been doubling every two-and-a-half days and in Denmark, every two days.

Sikhulile Moyo, director at the Botswana Harvard AIDS Institute Partnership (BHP) lab in Gaborone and a research associate in immunology and infectious diseases at Harvard T.H. Chan School of Public Health was the first person to sequence the Omicron variant on Nov. 8. He shared his findings on GISAID on Nov 11, which caught the attention of virologists around the world.

Lancet Labs in South Africa started seeing an alarming number of PCR tests from the Gauteng Province missing the target S gene in mid-November. Lancet shared the findings with the Network for Genomics Surveillance in South Africa (NGS-SA), which called an urgent meeting on 23 November. “We were shocked by the number of mutations,” says Tulio de Oliveira in a report in Science, a virologist at the University of KwaZulu-Natal and NGS-SA’s principal investigator.

On Nov. 24, Dr. Alex Sigal of the Africa Health Institute received three test swabs with the Omicron variant and started growing the virus to test it against sera from vaccinated and recovered individuals.

On the same day, Lancet sequenced another 100 samples with the missing S gene, and all were positive for the newly discovered variant. The South Africa Department of Health sent their findings to the World Health Organization (WHO) on Nov. 24, and Omicron was labeled a Variant of Concern (VOC) on Nov. 26.

Despite the first three cases appearing in Botswana, Omicron was likely circulating undetected on several continents by late October. The Centers for Disease Control (CDC) reported last week that the first symptomatic Omicron case in the United States was on Nov. 15. The implementation of international travel restrictions likely had no impact on slowing the spread of the highly infectious variant.

*Nevada became the most recent state to report an Omicron variant COVID case on December 14*

Preliminary data has emerged over the last week on transmissibility, treatment efficacy, and vaccine effectiveness for Omicron.

A study out of South Africa published on Dec. 2, found that Omicron was 2.5 to 3.5 times more transmissible than Delta. The study, which has not been peer-reviewed, indicated the Rt, a measure of how quickly a communicable disease can spread, is between R12 and R17, which is comparative to measles. On Dec. 8, Hiroshi Nishiura, professor at Kyoto University released a study that found Omicron is 4.2 times more transmissible than Delta with an Rt of R20. If additional research were to find this true, the Omicron COVID variant would be the most transmissible disease observed in the modern medicine era.

Omicron is forecasted to become the dominant strain in the United Kingdom and Denmark this week and was already 44% of detected COVID cases in the UK on Tuesday. The CDC reported tonight Omicron represents 3% of all detected COVID cases in the United States.

Eleven studies and reports, none of which have been peer-reviewed, have been published on vaccine effectiveness in the last 10 days. Studies have evaluated the Pfizer, Moderna, Johnson and Johnson, and AstraZeneca vaccines.

Studies that reviewed the effectiveness of the Pfizer vaccine found that the effectiveness of preventing symptomatic illness dropped from 80% to zero to 35%, depending on the study. Very limited real-world data out of South Africa from Discovery Health released today showed that the Pfizer vaccine was only 33% effective at preventing infection.

The same study found that the Pfizer vaccine was 70% effective at preventing “severe complications of Covid-19,” down from 93% with the Delta variant.

Dr. Peter English, Retired Consultant in Communicable Disease Control, Former Editor of Vaccines in Practice, past Chair of the BMA Public Health Medicine Committee had this to say about the findings.

“Two doses of vaccine are 70% effective at preventing hospitalization. They are not ineffective, but they are much less effective than the 90-95% protection that two doses provided against hospitalization. With a highly infectious variant, this still risks a catastrophic number of hospitalizations.”

A non-peer-reviewed study published on Tuesday evening provided the first data on the effectiveness of the Moderna vaccine, and more data for the Johnson & Johnson/Jassen vaccine.

Researchers evaluated the sera from 239 vaccinated healthcare workers in the Boston area. The study found that for the Moderna and Pfizer vaccine, more than 50% of individuals had no neutralizing antibodies three months after vaccination. The Moderna vaccine showed a 43-fold decrease in antibodies while the Pfizer vaccine had a 122-fold decrease. The Johnson and Johnson vaccine performed better against the Omicron variant versus Delta but had significantly reduced effectiveness versus the original COVID strain.

For individuals who had a prior Covid-19 infection and then got vaccinated more than six months ago, the Moderna vaccine had a 9-fold decrease in neutralizing antibodies, the Pfizer vaccine had a 12-fold decrease, and the Johnson & Johnson vaccine had a 17-fold decrease.

The study also found an mRNA booster within the last three months provided a significant increase in neutralizing antibodies but did not provide the same level of protection versus the Delta variant. The samples from the Johnson and Johnson test subjects were all boosted with a half-dose of the Moderna vaccine.

Two studies on disease acquired immunity found that protection declined significantly compared to previous variants. A study published on Dec. 2 out of South Africa, which has not been peer-reviewed, found that protection against Omicron dropped 240% for individuals who were previously infected by the original strain, Beta, or Delta, and had never been vaccinated. Another study released on Dec. 9 reached a similar conclusion, and in an alarming find, reported up to 40% of individuals who had a previous Delta infection were experiencing reinfection with Omicron. The Delta wave ended on Sep. 19 in South Africa, suggesting it took less than three months for protection to wane.

Scientists, public health officials, and policymakers have been attempting to determine if Omicron is less severe than the Delta variant. The study released from Discovery Health today reported that Omicron was 29% less severe than the original COVID strain.

“Without seeing a preprint or the report on which this press release is based it is difficult to get a clear understanding of the validity of these conclusions,” said Prof. Paul Hunter, Professor in Medicine at the University of East Anglia and a member of the National Institute of Health Research in the U.K. “If these are valid conclusions then there are both reassuring and worrying findings. The report that reinfections are more common with Omicron has already been published and the evidence is strong that Omicron can increase the risk of infection in people who have already had a COVID infection.”

Other experts warned against reading too much into the Discovery Health report.

Dr. Simon Clarke, Associate Professor in Cellular Microbiology, University of Reading, said, “This press release outlines preliminary observations of Covid-19 in South Africa during the first three weeks of the wave of infections caused by the Omicron. It shouldn’t be forgotten that in the UK, during the initial epidemic there was a 5-week gap between the first diagnosis and the first death. A situation report taken in those first few weeks would not have given us an accurate picture of what was about to happen, so we shouldn’t expect these preliminary indications to be a portent of how the Omicron epidemic will play out here.”

The Centers for Disease Control (CDC) provided detailed information on Dec. 10 about the first 43 Omicron variant cases detected in the United States. The report found that one person required hospitalization and was released after two days. Almost 60% were 39 years old or younger and 33% had recently traveled internationally. Forty of the 43 cases were vaccinated or had a previous COVID infection. Among the 34 who were vaccinated, 14 had received a booster.

Officials believe the high infection rate for vaccinated individuals has created a data fallacy. International travelers are more likely to be vaccinated, younger, and healthier and many were not eligible for a booster.

The Washington State Department of Health (WSDoH) reported 75.3% of all Washingtonians 12 and older are fully vaccinated and almost one in four children five to eleven have received their first dose of the Pfizer COVID vaccine. An estimated 3.5 million residents are eligible for boosters, but only 1.35 million have received one to date.

WSDoH reported the 7 day moving average for new cases is 1,333, and the statewide 7 day moving average new case rate is 83.5 per 100K residents – moderate transmission. The state has been averaging 650 to 700 hospitalized COVID patients a day, with roughly 100 requiring ventilators.

Statewide new admissions for COVID-related illness started increasing on Nov. 27, and through Dec 7. was averaging 92 new admissions a day. On Tuesday there were approximately 642 available staffed acute care and 144 staffed ICU beds throughout Washington.

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