Health Advisory: COVID-19 Updates – Omicron Variant, Multisystem Inflammatory Syndrome, and Vaccination

Requested actions

  • Be aware of quickly evolving information about the new SARS-CoV-2 variant, Omicron.
  • Consider Omicron as part of your differential diagnosis for patients who present with generalized fatigue or malaise. Many cases of Omicron are linked with mild, generalized symptoms. Preliminary evidence suggests no unusual symptoms are associated with Omicron.
  • Take a travel history for all suspected or confirmed COVID-19 cases before community transmission of Omicron becomes more prevalent.
    • Notify the Health District of a confirmed case with history of international travel within 14 days before symptom onset or positive test, if asymptomatic.
    • Notify the Health District of all close contacts of a confirmed case of Omicron infection.
  • Certain PCR tests can screen for Omicron because of its S gene deletion. Ask your labs if they can monitor for Omicron. Labs should send possible Omicron specimens to CDC for sequencing.
  • Remind patients how to prevent COVID-19 infection and stop its spread: wear a mask, maintain physical distance, get vaccinated, ensure good ventilation and get tested if you have symptoms.
  • Be aware, Food and Drug Administration (FDA) may soon grant emergency use authorization (EUA) to Molnupiravir, the first oral antiviral developed to prevent severe COVID-19 illness in adults 18 years or older with mild to moderate illness at high risk of progressing to severe illness.
    • Be prepared, Health and Human Services (HHS) will allocate supply to each state and DOH will distribute doses to enrolled providers. HHS created Healthcare Partner Ordering Portal (HPoP) to manage COVID-19 therapeutics.
    • Register for training on HPoP. Email to become an enrolled provider. Training is given 9–10 a.m. on Tuesdays in December.
  • Be aware that reports of Multisystem Inflammatory Syndrome in children (MIS-C) have increased in Washington State (MIS-C WA Monthly Report) and Multisystem Inflammatory Syndrome in adults (MIS-A) has subsequently been documented (Morris, October 2020).
    • Report any cases to Kitsap Public Health by calling 360-728-2235.
  • Reach out to your pediatric patients and their caregivers and strongly recommend COVID vaccination for all children five and older. Additionally, promote all Vaccines for Children (VFC) doses. Utilize provider resources from the CDC and Washington State Department of Health.
  • Promote COVID-19 vaccine booster doses for everyone 18 years or older who are at least 6 months after completion of primary vaccination series with Pfizer or Moderna or at least 2 months after completion of a primary Johnson & Johnson (J&J) vaccine.
    • Offer the same or different vaccine for the booster dose than the patient received for their primary vaccination.
    • Report all COVID-19 vaccine doses administered into the Washington Immunization Information System (IIS).
    • FDA expanded booster eligibility press release
  • Continue to promote COVID-19 vaccine and booster among people who are pregnant, lactating or who are trying to become pregnant now or might become pregnant. Educate these patients on the safety and effectiveness of COVID-19 vaccine during pregnancy, emphasize that the benefits of vaccination outweigh known or potential risks.
  • Enroll as a vaccine provider and administer COVID vaccines to all your eligible patients. Assess and document vaccination status as a standard of care and quality measure at every healthcare encounter.
  • Be aware of and participate in the Washington State Department of Health Power of Providers program.
  • Assist patients to find a COVID vaccine location:
  • Report COVID-19 and other notifiable conditions to Kitsap Public Health 24/7 by calling 360-728-2235 or use the Reportable Disease Fax Form and fax to 360-813-1168 with any corresponding lab results.


CDC HAN ADVISORY: SARS-CoV-2 Variant of Concern Identified: Omicron (B.1.1.529) Variant

Distributed via the CDC Health Alert Network
December 1, 2021, 11:00 PM ET


Omicron, a new SARS-CoV-2 variant, has been identified in many countries and categorized as a Variant of Concern by the U.S. government and the World Health Organization (WHO). Because little is known about Omicron currently, it is important for the public health and medical communities as well as the general public to remain vigilant to reduce potential exposure. This Health Alert Network (HAN) Health Advisory summarizes current knowledge about Omicron and provides recommendations on how to detect the Omicron variant within the United States as soon as possible to mitigate its spread.


A new SARS-CoV-2 variant, lineage B.1.1.529, was first detected in Botswana on November 11, 2021, and South Africa on November 14, 2021. This new variant has a large number of mutations in portions of the genome that can potentially increase infectivity and transmissibility, confer resistance to certain therapeutics, and reduce neutralization by convalescent and vaccinee sera1. For these reasons, on November 26, 2021, WHO classified B.1.1.529 as a variant of concern and named it Omicron2. By December 1, the Omicron variant had been detected in at least 20 countries in addition to those in Southern Africa, including the United States, Israel, Hong Kong, Nigeria, Saudi Arabia, South Korea, Australia, Canada, the United Kingdom, and several European countries. In some countries, such as Germany and Portugal, there is evidence of community transmission of Omicron. On November 30, 2021, the U.S. SARS-CoV-2 Interagency Group (SIG), which includes the Centers for Disease Control and Prevention (CDC), the National Institutes of Health, the Food and Drug Administration, the Biomedical Advanced Research and Development Authority, and the Departments of Defense, Agriculture, and Health and Human Services, classified the Omicron variant as a Variant of Concern.

Currently, it is unknown how efficiently the Omicron variant can spread from person to person. It is unknown whether Omicron is more transmissible than other variants, but preliminary data from South Africa suggest that the mutations to the receptor binding protein of the variant virus will confer increased infectivity. Currently, there is limited information about the clinical manifestations of infection due to the Omicron variant and given the small number of identified cases attributed to the Omicron variant to date, current assessment of disease severity and response to vaccines and therapeutics is difficult. Preliminary information from South Africa indicates that there are no unusual symptoms associated with Omicron variant infection, and as with other variants, some patients are asymptomatic3. Symptoms may be milder in persons who have been vaccinated or previously infected with SARS CoV-2.

Some SARS-CoV-2 variants, including the Omicron variant, have Δ69-70 deletion in the spike (S) gene. This particular mutation leads to failure of one of the polymerase chain reaction (PCR) targets (sometimes called S-gene target failure (SGTF)) when the virus is tested with assays that include an S gene target, including the Thermo Fisher Scientific TaqPath™ COVID-19 Combo Kit diagnostic assay4. This particular assay tests for three different SARS-CoV-2 genes so will still detect the virus but will fail to detect the S gene target specifically. Such assays can be used as a screen to presumptively identify SARS-CoV-2 variants that have the Δ69-70 deletion, including the Omicron variant. Delta, currently the predominant variant in the United States, does not have this Δ69-70 deletion; therefore, infections due to Delta variant would not produce a SGTF profile.


Case identification and reporting
Public health departments should follow existing state guidelines for case investigations. Case investigation and contact tracing can help ensure compliance with mitigation measures, such as isolation for people who test positive, and identify close contacts for public health follow-up including testing, masking, and quarantine based on vaccination status and history of prior infection. Jurisdictions that are interested in partnering with CDC to conduct enhanced case investigation to identify and characterize initial Omicron cases in the United States should contact their CDC health department liaison officer (HD LNOs). Case investigation will enable better understanding of the characteristics of the initial cases identified in the United States and will provide data on early symptoms, vaccination status, and travel history of these infected persons. In the initial weeks, collecting data on travel history, including any international locations where the infected person was present during the 14 days before illness onset (or date of positive test if asymptomatic), will help monitor importation versus domestic community transmission. All cases should be reported to CDC through existing systems, such as Epi-Info surveys and case surveillance, and using established communication channels, such as HD LNOs.

CDC is collaborating with Xprescheck and Gingko Bioworks on a SARS-CoV-2 surveillance program that involves voluntary testing of arriving international travelers at select U.S. airports. Arriving air travelers are offered both pooled sample collection in the airport and take-home kits for saliva sampling done 3-5 days after arrival; all samples are returned to the laboratory for PCR testing. All positive samples are sequenced, enabling detection of novel COVID-19 variant strains among travelers entering the United States. On November 28, 2021, the program began expanding to test air travelers entering the United States from Southern Africa, including passengers making connections through Europe.


Laboratory testing is a critical component of public health response to and surveillance of emerging variants, including the Omicron variant. The presence of the SGTF profile can signal the need for sequencing to characterize the variant in that specimen. Consideration of epidemiological factors, including recent travel history, for patients who test positive for SARS-CoV-2 can also indicate that a specimen should be prioritized and sent to CDC for sequencing.

In partnership with U.S. public health laboratories and the Association of Public Health Laboratories, CDC has implemented enhanced surveillance for specimens with SGTFs and specimens with sequencing data available that indicate a mutation profile resembling Omicron. CDC requests that public health laboratories send SGTF specimens or specimens that are possible Omicron variant by sequencing to CDC through National SARS-CoV-2 Strain Surveillance (NS3) external iconES21-01 (SGTF) and ES21-03 (specimens with sequence data available) as quickly as possible for rapid confirmation of presumptive Omicron cases and subsequent virological characterization.

Delta variant specimens do not yield an SGTF result using the TaqPath COVID-19 Combo Kit. Given that nearly 100% of viruses circulating in the United States are the Delta variant, specimens with an SGTF using this diagnostic test may be presumptive Omicron variants and should be prioritized for sequencing confirmation. There are other lineages that may contain the Δ69-70 deletion and give the SGTF profile, such as the Alpha variant which is uncommon currently but was predominant in the United States earlier this year.


Clinical diagnosis and treatment  
Early reports are that the clinical signs and symptoms of COVID-19 from infection with the Omicron variant are similar to those of other variants and may also be absent (asymptomatic). As CDC and public health officials work to identify cases of COVID-19 with the Omicron variant, it is important to take a travel history for all suspected or confirmed COVID-19 cases. If the case is confirmed and there is a history of international travel within 14 days before symptom onset or positive test (if asymptomatic), the local health department should be notified about the travel history. Health departments should also be notified about household contacts or close contacts of individuals who are confirmed to have the Omicron variant.

The utility of travel history to identify Omicron cases will likely decline as domestic community transmission becomes more prevalent. With low levels of domestic community transmission, travel history may be a good screening tool to identify cases of possible Omicron.

There are no data yet available about the effectiveness of monoclonal antibodies and antiviral therapies (e.g., molnupiravir) against the Omicron variant. Whether severity of disease due to Omicron will differ from that of disease caused by other variants is currently unknown. At this time, CDC recommends providers continue to closely follow NIH treatment guidelinesexternal icon for COVID-19.



  1. SARS-CoV-2 Interagency Group, Situation Report for B1.1.529 – November 28, 2021.
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  3. Frequently asked questions for the B.1.1.529 mutated SARS-CoV-2 lineage in South Africa – NICDexternal icon
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Data released by the American Association of Pediatrics (AAP) showed that the number of newly diagnosed COVID-19 cases in children peaked at 252,000 the week of September 2, 2021. A corresponding increase in the number of children who tested positive for COVID-19 was seen in Washington. Although case numbers have been declining in Washington and nationwide, rates remain high (DOH WA COVID-19 data).

Since September, reports of Multisystem Inflammatory Syndrome in children (MIS-C), which is a rare but severe complication that can occur weeks after a symptomatic or asymptomatic COVID-19 infection have also increased. The number of MIS-C cases among children who reside in Washington State that were reported September 1 through November 30, 2021 (n=24) was three times the number of cases reported during the same time period in 2020, and 33 percent greater than the most cases reported in any three month period (n=18) since surveillance began. (See MIS-C WA Monthly Report.)

Although MIS-C was  initially characterized in children, Multisystem Inflammatory Syndrome in adults (MIS-A) has subsequently been documented (Morris, October 2020). The CDC has developed a working case definition for MIS-A which includes:

  • Age 21 years or older.
  • Presence of a severe illness requiring hospitalization.
  • Recent positive test result for SARS-CoV-2 infection (PCR, antigen, or antibody).
  • Severe extrapulmonary organ system dysfunction.
  • Markedly elevated acute inflammatory markers; and/or
  • Absence of severe respiratory illness (to exclude patients where tissue hypoxia causes organ system dysfunction).

MIS-A is likely underdiagnosed due to symptoms that overlap those seen with severe COVID-19. If identified, any MIS-A cases should be reported in the same manner as MIS-C case, and the same case report form is used.

To report a case or for more information, contact Kitsap Public Health District by calling 360-728-2235.


Cases continue to decrease, dropping into the “substantial” transmission range over the past few days. Hospitalizations appear to be approaching pre-delta levels (prior to August 2021).

The rate of infection among unvaccinated individuals was 3.6 times higher than among fully vaccinated. In the past 30 days, unvaccinated people age 12-59 were 11.2 times more likely and adults age 60 and older were 6.1 times more likely to be hospitalized for COVID-19 than those fully vaccinated.

As of November 27, 73.7% of Kitsap residents age 5+ had initiated vaccination, 66.7% were fully vaccinated. Vaccination initiation rates are lowest in adults age 19-34 (63%), residents of Bremerton (64%) and Central Kitsap (68%), Black/African American (48%), and males (64%). So far, 20% of Kitsap resident children age 5-11 have initiated vaccination.

The chart below provides trend over time of vaccine doses administered to Kitsap County residents. On the right, light blue indicates number of additional/booster doses administered.


Our phone lines are open Monday – Friday from 8:00 am to 4:30 pm, providers can report notifiable conditions 24/7 using our main number

  • Main (360) 728-2235
  • Fax (360) 813-1379

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