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Guidance for Assessment of Suspected COVID-19 Variant Cases and Breakthrough Disease in Vaccinated Persons
March 3, 2021
COVID-19 variants pose a significant threat to worldwide efforts to end the pandemic; to date, 46 states have reported at least one case of a variant of concern, including cases caused by B1.1.7, B.1.351, and P.1 lineages. The B1.1.7 variant, first identified in the United Kingdom and associated with increased transmission and disease severity, has been identified in Southern California, including Orange County, for several weeks. Based on limited surveillance, this variant has been identified relatively rarely amongst strains genotyped in OC, but CDC modeling indicates that this strain may become predominant here and in the United States in the coming months. OCHCA is working to enhance local surveillance to clarify the presence and prevalence of COVID-19 variants in the county. A summary of variant strains and their epidemiology in California can be found in the attached document. 

OCHCA will also be conducting surveillance to characterize breakthrough disease in vaccinated persons. It will be important to identify how frequently breakthrough disease occurs, particularly severe disease, which populations are affected, and whether COVID-19 variants are disproportionately causing these events. 
Reporting and Assessment of Vaccine Breakthrough Cases and Suspect Variant Cases:
Health care providers are requested to promptly report and submit nasopharyngeal specimens to OCHCA for possible whole genome sequencing from any individuals with SARS-CoV-2 virus infection who meet any of the following criteria:

  • Develop infection between 15 and 90 days after completing a vaccination series (i.e., two doses for the Pfizer or Moderna vaccines, one dose for the Johnson & Johnson vaccine). OCHCA particularly requests reporting of any patients who are hospitalized with post-vaccination infection;
  • Have possible reinfection, with recurrence of symptoms and positive molecular testing at least 90 days after initial infection;
  • Have recent international travel or exposure to persons with recent international travel.
Reporting of Laboratory-Confirmed Variant Cases and Laboratory Results Consistent with a Variant Lineage:
Clinical laboratories and medical providers are asked to report to OCHCA:

  • Laboratory-confirmed cases of variants of concern.
  • Any PCR results which have marked differences in real-time RT-PCR viral target(s) cycle threshold (Ct) values (e.g., ORF1ab target detected, N target detected, and S target NOT DETECTED).
Management of Variant Cases:
  • SARS-CoV-2 cases caused by variants of concern do not need an extended isolation period but should be monitored for isolation adherence.
  • Contacts of cases due to variants of concern should ideally be quarantined for 14 days and be tested during the quarantine period at day 5-7. However, these measures are easier to introduce when variant infections are identified early in the course of illness. It is not necessary to re-quarantine close contacts who do not belong to high-risk groups and have already completed a 10-day quarantine period.
Contact Information:
Please contact the OCHCA Communicable Disease Control Division at 714-834-8180 to report any suspect or confirmed variant cases or with any questions.
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