COVID-19 Vaccine Breakthrough Case Investigation and Reporting

For local health departments, healthcare providers, and clinical laboratories

• CDC encourages local health departments, healthcare providers, and clinical laboratories that identify a COVID-19 vaccine breakthrough case to:
  • Request the respiratory specimen be held for further testing.
  • Report the case to the state health department where the individual resides for further investigation and reporting to the national system.
• COVID-19 vaccine breakthrough cases that result in hospitalization or death should be reported to the Vaccine Adverse Event Reporting System (VAERS)external icon.

For state health departments

• If a possible vaccine breakthrough case is identified:
  • Request that the clinical or public health laboratory hold any residual respiratory specimens from the positive SARS-CoV-2 test.
  • Report the available case data to NNDSS, per normal procedures.
  • Review CDC’s screening questions to assess whether the case meets the COVID-19 vaccine breakthrough investigation criteria.
• If the reported case meets those criteria, CDC encourages state health departments to:
  • Follow the steps for initiating a COVID-19 vaccine breakthrough case investigation.
  • Record the case in the COVID-19 vaccine breakthrough REDCap database.
• Because CDC would like to characterize the SARS-CoV-2 lineages responsible for COVID-19 vaccine breakthrough cases, including variants, CDC requests state health departments to:
  • Report sequence results from a state public health laboratory, commercial reference laboratory, or academic laboratory by entering the PANGO lineage and GenBank or GISAID accession number into the COVID-19 vaccine breakthrough REDCap database.
  • If SARS-CoV-2 sequencing will not be performed locally and an acceptable clinical respiratory specimen is available, provide instructions for the testing laboratory to send the residual respiratory specimen to CDC.
  • For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value ≤28 to CDC for sequencing. (Sequencing is not feasible with higher Ct values.)
  • If the Ct value is not known (e.g., positive by antigen test only or by a molecular test that does not provide a Ct value), submit the positive specimen may still be submitted to CDC for RT-PCR and possible sequencing.

How to send CDC sequence data or respiratory specimens from suspected vaccine breakthrough cases

• CDC would like to receive sequence data and respiratory specimens from COVID-19 vaccine breakthrough cases to assess the SARS-CoV-2 lineage, including variants. When a vaccine breakthrough case is identified, the health department will contact the laboratory to request that any residual respiratory specimen from the positive test be held for sequencing at CDC.
• The health department also will request the specimen ID numbers and the Ct value for positive RT-PCR results.
• If SARS-CoV-2 sequencing will not be performed locally and a specimen is available, the state public health laboratory should request the residual clinical respiratory specimen for subsequent shipping to CDC.
  • For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value ≤28 to CDC for sequencing.
  • If the Ct value is not known (e.g., positive by antigen test only or by a molecular test that does not provide a Ct value), the positive specimen may still be submitted to CDC for RT-PCR and potential sequencing.
• If your laboratory identifies a COVID-19 vaccine breakthrough case, please report it to your state health department so it can initiate the investigation with CDC.
• These instructions can also be found here: NS3 Submission Guidance Documentsexternal icon.