Recommendations for Local Public Health Laboratories: Influenza, RSV, SARS-CoV-2, and Other Respiratory Virus Surveillance Testing and Reporting 2025–2026
November 2025
This California Department of Public Health (CDPH) guidance summarizes surveillance testing and reporting guidelines for influenza, respiratory syncytial virus (RSV), SARS-CoV-2, and other respiratory viruses for the 2025–2026 respiratory season. While SARS-CoV-2 is common during the summer, influenza and RSV activity typically starts increasing in the fall and peaks during winter months. For data visualization and reporting purposes, the respiratory virus surveillance season is June 29, 2025–July 4, 2026 (MMWR Weeks 27–26).
Highlights
Public Health
Labs (PHLs) should continue working with local health jurisdictions and
clinical laboratory partners to prioritize influenza specimens from severe
cases, suspect novel influenza cases, and respiratory outbreaks for further
subtyping and characterization.
- PHLs should continue to follow influenza subtyping goals according to the right size roadmap to ensure an adequate number of samples are subtyped weekly based on population.
- Influenza A unsubtypable results on samples with influenza A Ct <35 must be communicated immediately to VRDL to seek technical advice and to facilitate the submission of those samples to VRDL for confirmatory testing.
- Local PHLs should send specimens of any severe case (hospitalized/intensive care unit (ICU) cases) of influenza, RSV, enterovirus/rhinovirus, adenovirus, or other viral pathogen to VRDL for further characterization.
- CDPH recommends reporting of respiratory virus data via Electronic Laboratory Reporting (ELR) platforms where possible. Aggregate spreadsheet reporting will continue through the 2025-2026 season with anticipated sunsetting in June 2026. Reporting will fully transition to ELR only starting in the 2026-2027 season.
Respiratory Virus Testing Overview
When to submit specimens to VRDL:
- PHLs that are members of the Respiratory Laboratory Network (RLN) are advised to submit specimens as part of national influenza surveillance efforts. Further information can be found in the “Recommendations for Right Size Surveillance” section below.
- For severe cases or respiratory outbreak specimens that test NEGATIVE by rRT-PCR for both SARS-CoV-2 and influenza, the VRDL will accept specimens for further non-influenza respiratory virus testing. Specimens submitted to VRDL must be accompanied with a hard copy of the completed VRDL General Purpose Specimen Submittal Form for each specimen or a form generated in the VRDL Lab Web Portal.
- For fatal cases, submitters may refer available fresh frozen autopsy tissues to VRDL for further testing and histopathologic analysis at CDC. On a case-by-case basis, refer to VRDL specimens for antiviral resistance testing (e.g., a patient on treatment with persistently positive influenza PCR results).
Testing at PHLs:
Specimen collection and storage:
- Upper respiratory specimens suitable for rRT-PCR include: nasopharyngeal (NP) swabs, nasal swabs, throat swabs, nasal aspirates, nasal washes, NP washes, and NP aspirates. For patients hospitalized with pneumonia, specimens from the lower respiratory tract should also be obtained. Lower respiratory tract samples suitable for rRT-PCR include: bronchoalveolar lavage, bronchial wash, tracheal aspirate, and lung tissue.
- Swab specimens should be collected using swabs with a synthetic tip (e.g., polyester or Dacron®) and an aluminum or plastic shaft. Swabs with cotton tips and wooden shafts are NOT recommended. Specimen collected with swabs made of calcium alginate are NOT acceptable. For more information about the collection of samples see VRDL's test catalog.
- Place appropriate swab specimen in a standard container with 2–3 ml of viral transport media (VTM) or universal transport media (UTM).
- Freeze or refrigerate specimens promptly after collection. Delivery to VRDL after 72 hours from date of collection must be at -70°C; please ship to VRDL overnight on dry ice. The CDPH-VRDL can receive specimens Monday through Friday.
Review of influenza testing algorithm for seasonal influenza and the presumptive detection of novel influenza viruses:
- The following algorithm applies to laboratories using the CDC In-Vitro Diagnostic (IVD) kit or the Research Use Only (RUO) kit (provided by CDPH-VRDL) for influenza testing
- Screening for influenza A, influenza B, and RNase P (RP)
- Influenza A positives should be subtyped as follows: repeat influenza A with the full subtyping panel, H3, pdmA and pdmH1. The pdmA target detects swine origin viruses and must be included to identify possible influenza variants strains.
- Typical seasonal influenza testing results are shown below:
Influenza real-time RT-PCR results for seasonal influenza viruses
A/H1 2009 pdm virus [1]
| POS
| NEG
| POS
| POS
|
A/H3 seasonal virus
| POS
| POS
| NEG
| NEG
|
- We request the labs to perform B lineage discrimination on all influenza B positive samples if possible.
- Influenza A unsubtypable results on samples with Flu A Ct <35 must be communicated immediately to the VRDL Respiratory and Gastroenteritis Diseases Section (RGDS) to seek technical advice and to facilitate the submission of those samples for confirmatory testing.
- Influenza B inconclusive (no genotype detected) results on samples with Flu B Ct<35 should also be reported to the RGDS.
- Influenza and SARS-CoV-2 Testing: The CDC developed an emergency use authorization (EUA)-approved rRT-PCR multiplex assay that simultaneously tests for influenza A, influenza B, and SARS-CoV-2 (Flu SC2). The CDC has proposed different scenarios in which state and local PHLs may include the Flu SC2 assay for either influenza diagnostic or surveillance testing systems. The algorithm includes testing specimens: (1) with no test results for influenza or SARS-CoV-2, (2) for confirmation of rapid influenza diagnostic test (RIDT), and (3) with negative results for SARS-CoV-2 by a CLIA approved rRT-PCR assay. If a specimen tests positive for influenza A or B, influenza A subtyping or B-lineage genotyping should be completed in a timely manner regardless of the algorithm followed by the PHL.
- Do not batch specimens for testing:
- Batching specimens for influenza A subtyping is NOT recommended because this may delay the detection of a novel virus and is counter to the aim of having PHLs perform influenza subtyping testing.
- To detect novel and possible reassorted influenza viruses, it is important that PHLs NOT batch test influenza specimens and that a full rRT-PCR subtyping panel (Inf A, H3, pdm Inf A, and pdm H1) is used to determine the subtype.
How to submit specimens to VRDL for additional testing
- Respiratory Laboratory Network (RLN) laboratories must use the VRDL General Purpose Specimen Submittal form or the VRDL Lab Web Portal to create specimen requisitions for testing at VRDL (the Influenza Reference Examination Form (PDF) may be included for influenza positive specimens being submitted for further characterization at CDPH-VRDL as part of national influenza surveillance efforts). These forms and the Lab Web Portal provide instructions on submission of specimens to CDPH-VRDL. If additional guidance is needed, please contact Alice Chen (alice.chen@cdph.ca.gov) for instructions on submission of specimens for further characterization at CDPH-VRDL.
- Required information to be provided when submitting Influenza Reference samples:
- Please provide demographic information, PCR method used, testing results (Ct values), and your laboratory information.
- Please include the patient county of residence and the submitting laboratory's contact information (i.e., how to contact you).
- Please include information about SARS-CoV-2 testing Status: Detected, Not Detected, Unknown. This information is required.
Additional specimen considerations:
- For ideal specimen quality, specimens should have a cycle threshold (Ct) value of <30 by rRT-PCR and at least 1.0mL of clinical material.
- During the season, the VRDL may contact PHLs requesting the submission of additional influenza positive specimens from specific jurisdictions.
- INFLUENZA REFERENCE SAMPLES SHOULD ONLY BE IN VTM or UTM. Specimens in other media, including, but not limited to, saline, PBS, or Molecular Transport Media (MTM) are not acceptable. Additionally, clinical specimens that have been heat inactivated are not acceptable.
Recommendations for Right Size Surveillance
Influenza
During the 2025–2026 respiratory season, PHL laboratories are advised to continue receiving specimens from clinical labs for enhanced influenza surveillance testing for:
- Hospitalized, ICU, and/or fatal cases with Influenza-like illness (ILI)
- Acute respiratory illness outbreaks of public health concern
- Cases with recent close contacts, or exposures within 10 days of symptom onset that suggest concern for avian, variant, or novel influenza infection (e.g., variant influenza A (H3N2)v, (H1N2)v, or (H1N1)v, or avian influenza H5N1 or H7N9)
Influenza Right Size Surveillance
The Right Size Roadmap (PDF, 4.6MB) provides guidance on the minimum level of influenza virologic testing for novel virus detection, and antiviral resistance (AVR) and vaccine strain selection.
Influenza Virologic Testing
Weekly influenza virologic testing goals for each jurisdiction are outlined in the Right Size Roadmap. Aim to reach weekly testing goals as best you can. The sample sizes will be distributed to all RLN labs in a separate document.
Antiviral Resistance Testing and Vaccine Strain Selection
To meet goals for AVR and strain-typing, CDPH requests the submission of at least two specimens each of laboratory-confirmed positive influenza A subtypes (i.e., H1pdm09 and H3) and one specimen each of laboratory-confirmed positive B-lineage genotypes (i.e., Victoria B-lineage).
- Submit laboratory-confirmed influenza positive specimens to CDPH-VRDL as follows:
- At the beginning of the respiratory season: submit specimens to VRDL as they are detected in your laboratory; please do NOT batch specimens for a single shipment;
- During the peak of the respiratory season; and
- At the end of the respiratory season
Surveillance Reporting
Facilities conducting testing for SARS-CoV-2, influenza A, influenza B, or RSV are required by California Code of Regulations ,Title 17, Section 2025 to report all test results - including negative (not detected), non-reactive, inconclusive, and other non-positive outcomes - through complete and timely Electronic Laboratory Reporting (ELR). This includes reporting of subtyping results for Influenza A, Influenza B lineage, and RSV when performed.
Please see CalREDIE's ELR HL7 specifications guide (PDF, 1MB) for complete instructions, including example HL7 messages, to help ensure your facility's ELR submissions meet required content and formatting specifications. Additionally, visit the CalREDIE Laboratory Reporting Resources webpage for further materials, including LOINC code references and other helpful tools.
When reporting influenza results in ELR, please ensure that the specimen collection date is accurately recorded for each sample, as this information is critical for surveillance and epidemiologic analysis.
RLN laboratories should additionally continue to report influenza, RSV, and other respiratory virus data via aggregate spreadsheets throughout the 2025-2026 season. Data modernization efforts are ongoing to ensure all PHLs are effectively reporting via ELR, but aggregate spreadsheet reporting will be maintained for data validation and quality assurance. It is anticipated that spreadsheet reporting will sunset in June 2026 with reporting via ELR only starting in the 2026-2027 respiratory virus season.
Additional reporting considerations for specimens concerning for Novel Influenza:
Specimens with rRT-PCR test results that meet any of the following criteria should be reported and submitted to CDPH-VRDL for further characterization AS SOON AS POSSIBLE (contact VRDL at 510-307-8585 or the VRDL.Submittal@cdph.ca.gov):
- Unsubtypable results: with Ct value for Flu A ≤35, which might suggest a novel influenza virus infection
- Inconclusive results: for influenza A(H1N1)pdm09 PCR target with Flu A Ct ≤35, which might suggest a variant influenza virus infection (see table below)
- Co-Infections: specimens with results suggesting the presence of more than one influenza virus (co-infections)
- Suspect or probable avian influenza results: for influenza A positive specimens collected from a person meeting clinical and epidemiological criteria for avian influenza should be tested using the CDC H5 Dx Assay. Public health laboratories using the VRDL RUO reagents for the initial influenza A testing and subtyping should submit the specimen to CDPH-VRDL for testing using the CDC H5 Dx Assay or the CDC H7 Dx Assay, depending on patient history
- Suspect variant (swine origin) results: specimens with results suggestive of variant influenza
Influenza real-time RT-PCR results suggestive of variant (swine origin) influenza virus
| A/H1 variant virus | POS
| NEG | POS | NEG |
| A/H3 variant virus | POS
| POS | POS | NEG
|
Respiratory Syncytial Virus (RSV) and Other Respiratory Viruses
Other respiratory virus data are used for virologic, genomic, and epidemiologic purposes. VRDL offers a diagnostic respiratory viral PCR panel including adenovirus, coronaviruses, human metapneumovirus, parainfluenza virus, and RSV. For any severe cases (hospitalized/ICU) or outbreaks of public health concern of entero/rhinovirus, adenovirus, or other viral pathogen, PHLs should send specimens to VRDL for further characterization.
COVID-19
PHLs are welcome to send VRDL up to 25 SARS-CoV-2 positive samples for Whole Genome Sequencing (WGS) every two weeks. Please contact VRDL with specific questions about submissions for WGS.
Additional Questions or Assistance
Laboratory Testing Information or Questions
Contact CDPH-VRDL:
- For general specimen submission questions:
- For urgent or specific laboratory testing inquiries:
- Contact Hugo Guevara of the CDPH-VRDL for routine lab questions by email at Hugo.Guevara@cdph.ca.gov or by phone at 510-307-8565 (desk).
Reporting or Surveillance Questions
Contact the COVID Control Branch by email: