COVID-19 Update for Virginia


Clarification from December 7, 2021: This clarification provides additional information about the mutation present in Omicron that leads to a failure of one of the targets on certain PCR diagnostic assays (e.g., Thermo Fisher Scientific TaqPath™ COVID-19 Combo Kit diagnostic assay).  This failure is called the S-gene target failure (SGTF).  The overall sensitivity of the test should not be affected by the Omicron variant because the test detects multiple genetic targets.  The presence of the SGTF provides a clue that the Omicron variant might be present, but sequencing is needed to confirm the Omicron variant.

COVID-19 Update for Virginia

December 3, 2021

Dear Colleague:

Thank you for your continued partnership in responding to the COVID-19 pandemic.  Please visit the Virginia Department of Health (VDH) website for current clinical and public health guidance, epidemiologic data, and other information.  Updates on the following topics are included in this correspondence:

  • Update on the Omicron Variant
  • CDC’s Health Alert Network (HAN) Health Advisory About Increasing Seasonal Influenza A (H3N2)
  • Upcoming Webinars on Monoclonal Antibodies and COVID-19 Vaccines

Update on the Omicron Variant

On November 26, 2021, the World Health Organization (WHO) classified the variant Omicron (B.1.1.529) as a Variant of Concern.  The U.S. government’s SARS-CoV-2 Interagency Group classified it as a Variant of Concern in the United States on November 30.  The variant is concerning because it has a large number and an unusual profile of mutations.  Some of these mutations have been seen before with other variants and may be associated with immune escape potential and increased transmissibility; other mutations are not well understood.  On December 1, the Centers for Disease Control and Prevention (CDC) announced the first confirmed case of COVID-19 caused by the Omicron variant detected in the United States and issued a Health Alert Network health advisory.  The case occurred in a fully vaccinated person in California who recently traveled to South Africa.  On December 2, additional cases were identified in California, Colorado, Hawaii, Minnesota, and New York, and it is very likely that more cases will continue to emerge in the U.S.  The Division of Consolidated Laboratory Services and VDH continue to work with laboratory partners to conduct genomic surveillance on a subset of PCR positive samples to detect variants circulating in Virginia.

We are very early in our understanding of this new variant, and much is still unknown.  We will learn more in the coming days and weeks.  At this time, it is unknown if Omicron is more transmissible, if it causes more severe disease than other variants or if it evades immunity by either vaccine or natural infection.  For diagnostic testing, it is thought that widely used PCR tests detect infection with Omicron, and studies are underway to determine the impact on other tests, like antigen tests.  One mutation present in Omicron leads to a failure of one of the targets on certain PCR diagnostic assays (e.g., Thermo Fisher Scientific TaqPath™ COVID-19 Combo Kit diagnostic assay).  The effectiveness of monoclonal antibodies and other therapeutics for infected patients is being evaluated.  Providers are advised to closely follow the National Institutes of Health’s COVID-19 Treatment Guidelines.

The recent emergence of the Omicron variant is a good reminder of the importance of layered prevention strategies such as getting vaccinated and getting a booster dose if eligible, physical distancing, masking, avoiding crowds and poorly ventilated spaces, washing hands, and testing and isolating if needed.  Vaccination remains the most important tool to help prevent the spread of variants.  Please continue to encourage your patients aged 5 years and older to receive their primary vaccine series and all individuals aged 18 years and older to receive a booster dose.

To slow the spread of Omicron, the President issued a proclamation that took effect on November 29 to restrict noncitizens from entering the United States if they have been in certain southern African countries in the past 14 days.  Yesterday,  CDC amended an Order effective December 6 to require all inbound international air passengers aged 2 years and older to have a negative test conducted within one day of departure or to present documentation of recent recovery.  These air passengers must also complete an Attestation.  As VDH and CDC try to identify potential cases of Omicron, VDH recommends that healthcare providers take a travel history for any patient with suspected or confirmed COVID-19.

CDC recently strengthened booster recommendations in response to the Omicron variant.  All individuals 18 years and older should receive a booster dose at least six months after completing their mRNA (i.e., Pfizer or Moderna) series or at least two months after receiving the Johnson & Johnson vaccine.  Previously, CDC stated that people aged 18 to 49 years may receive a booster dose at least six months after completing their mRNA series.  CDC updated the Interim Clinical Considerations for the Use of COVID-19 Vaccines Currently Approved or Authorized in the United States to reflect this change.

CDC’s Health Alert Network (HAN) Health Advisory: Increasing Seasonal Influenza A (H3N2) Activity, Especially Among Young Adults and in College and University Settings, During SARS-CoV-2 Co-Circulation

 In this November 24 health advisory, CDC informed providers about a recent increase in influenza activity, which may signal the start of the 2021–2022 influenza season in the United States.  Activity is still low overall, but there have been recent increases in influenza A(H3N2) infections, especially in young adults, and outbreaks in colleges and universities across multiple states.  As of November 20, 2021, 67 confirmed influenza laboratory reports have been reported, with 86.6% of the influenza viruses detected in Virginia identified as Flu A and 10.4% identified as Flu B.  So far, one outbreak due to influenza has been reported in Virginia this influenza season.  No pediatric deaths associated with influenza have yet been reported in Virginia.  The timing and intensity of the 2021–2022 influenza season is difficult to predict.  Because influenza activity was low throughout the 2020–2021 season, there will likely be a lower level of community protection this year than is typical.  For the most current information about activity in Virginia, refer to VDH’s weekly surveillance reports.

To ensure the best protection, please recommend and offer influenza vaccines now to your patients aged six months and older who have not yet received the vaccine this season.  Evidence suggests that even when the vaccine does not prevent infection, it can help to prevent severe illness, hospitalization, and death.  So far, U.S. influenza vaccination coverage is lower this year compared to this time period in 2020 among certain higher risk groups like pregnant people and children.  As a reminder, flu vaccines can be given at the same time as the primary series or booster doses of COVID-19 vaccines.

For patients with influenza-like illness, healthcare providers should test for influenza and SARS-CoV-2 when both are co-circulating.  CDC recommends treatment with influenza antiviral medications as soon as possible to patients who are hospitalized, outpatients at increased risk for complications, or outpatients with progressive disease.

In the context of SARS-CoV-2 co-circulation, during an influenza outbreak in a congregate setting (e.g., long-term care facility, shelter, university dormitory, prison), healthcare providers can consider antiviral postexposure prophylaxis (PEP) to prevent influenza infection among exposed individuals and to reduce strain on healthcare services in these institutions during influenza outbreaks.  In general, CDC recommends initiating influenza antiviral PEP within 48 hours of contact with someone who has influenza.

Non-pharmaceutical interventions to prevent COVID-19 will also be effective against influenza, including staying home when sick, masking, physical distancing, covering coughs and sneezes, and washing hands.

Upcoming Webinars on Monoclonal Antibodies and COVID-19 Vaccines

Join VDH for upcoming webinars for healthcare providers.  A Monoclonal Antibody Update will be held on December 6 and December 7 from 12–1pm and a COVID-19 Vaccine Update will be held on December 15 from 6–7pm.  Details will be available on the Healthcare Professionals page under Events.

Thank you again for your continued partnership as we respond to the COVID-19 pandemic.  I hope you have a safe and happy holiday season.


M. Norman Oliver, MD, MA
State Health Commissioner