Respiratory Season 2026–27: Planning Your Multiplex RT-PCR Workflow

The 2026–27 respiratory season is beginning, and laboratories are moving into the months when influenza, RSV, SARS-CoV-2 and other respiratory pathogens can place greater demands on molecular testing workflows.

In its September 23, 2026 Respiratory Disease Season Outlook, the CDC said it expects the combined peak hospitalization rate from COVID-19, influenza and RSV this season to be similar to the 2025–26 season. CDC defines “similar” as within 20% of last season’s combined peak, although the agency notes low-to-moderate confidence in that assessment.

The outlook covers the October-through-May respiratory disease season. It is intended as a baseline assessment rather than a forecast, since the timing and intensity of individual respiratory viruses can change considerably from one season to another.

For molecular laboratories, that uncertainty makes flexibility important. As respiratory season gets underway, labs should be looking at the entire workflow—from nucleic acid extraction and multiplex RT-PCR panel selection to instrument capacity, controls, reagents and supply availability.

Last Season Showed Why Timing Matters

Respiratory pathogens do not necessarily peak at the same time.

During the 2025–26 season, the combined hospitalization rate for COVID-19, influenza and RSV peaked during the week ending January 3, 2026. Influenza peaked in late December, while RSV-associated hospitalizations did not peak until the week ending February 21.

That RSV peak was later than the typical national pattern of late December or early January. CDC notes that the reason for the later peak is uncertain and that it could signal another later RSV peak during the 2026–27 season.

For laboratories, the takeaway is straightforward: respiratory season cannot be planned around a single expected peak. Molecular testing needs can shift throughout the fall and winter and extend well into the new year.

Why Multiplex RT-PCR Is Useful for Respiratory Pathogen Research

Many respiratory pathogens circulate during the same period. SARS-CoV-2, influenza A and B, RSV, human metapneumovirus, parainfluenza viruses, adenoviruses and other organisms may all be relevant to respiratory research.

Testing individual targets separately can require multiple reactions, additional reagents and more hands-on processing.

Multiplex real-time PCR takes a different approach. Multiple nucleic acid targets can be amplified and detected within the same assay, allowing laboratories to investigate several respiratory pathogens simultaneously.

For molecular laboratories, a multiplex respiratory PCR panel can offer several workflow advantages:

• Multiple targets in a single assay. Laboratories can investigate several respiratory pathogens without setting up an individual reaction for every target.
• More efficient specimen use. Multiple targets can be evaluated from the same extracted sample, which can be valuable when specimen volume is limited.
• Reduced hands-on processing. Consolidating targets may reduce the number of individual reactions that need to be prepared.
• Greater throughput potential. Multiplex workflows can help laboratories evaluate more targets without increasing the number of reactions proportionally.
• Flexible target selection. Depending on the panel, laboratories can focus on major respiratory viruses or investigate a broader combination of viral and bacterial respiratory targets.

The right approach depends on the laboratory’s research objectives, sample volume, instrumentation and desired target coverage.

Start With the Respiratory Targets You Need

Not every laboratory needs the same respiratory panel.

For research focused on major seasonal respiratory viruses, a targeted panel covering SARS-CoV-2, influenza A, influenza B and RSV may provide the appropriate level of coverage.

Jant Pharmacal offers the Accutest Standard COVID/Flu/RSV RT-PCR Panel, which includes SARS-CoV-2, influenza A, influenza B and RSV A/B targets. It is available in pre-spotted 384-well plates for higher-throughput workflows as well as tubes for 100 reactions.

Explore the Accutest Standard COVID/Flu/RSV RT-PCR Panel →

Other respiratory research may require broader target coverage.

The Accutest Standard Respiratory RT-PCR Panels I & II provide options for investigating a wider range of respiratory organisms, including influenza viruses, RSV, SARS-CoV-2, human metapneumovirus, parainfluenza viruses, seasonal coronaviruses and additional respiratory targets.

Explore Accutest Standard Respiratory RT-PCR Panels →

The PCR Panel Is Only Part of the Workflow

Choosing the panel is important, but it is only one part of a molecular testing workflow.

As respiratory season begins, laboratories should consider how the panel fits with extraction, instrumentation, throughput requirements and controls.

1. Review Nucleic Acid Extraction

Consistent nucleic acid extraction is critical to downstream PCR performance.

Laboratories should consider specimen type, anticipated volume and whether the current extraction workflow can support the number of samples expected during respiratory season.

Explore Nucleic Acid Extraction Solutions →

2. Confirm Instrument Compatibility

Multiplex assays can differ in fluorophore requirements, cycling conditions and reaction formats.

Before implementing a panel, laboratories should confirm compatibility with their real-time PCR platform, including the instrument’s available detection channels.

3. Match the Panel to the Research Question

More targets are not necessarily better.

A focused COVID/Flu/RSV panel may be appropriate for one project, while another may require a broader respiratory panel covering additional viral or bacterial targets.

Selecting the appropriate panel starts with defining what the laboratory actually needs to investigate.

4. Consider Throughput

Panel format becomes increasingly important as sample volume increases.

A laboratory processing a small number of samples has different requirements from one running hundreds of reactions. Plate configuration, extraction capacity, available instruments and staff time should be considered together when evaluating the workflow.

5. Review Controls and Validation Requirements

Controls are an important component of molecular workflows and help laboratories monitor amplification performance, inhibition and run validity.

Laboratories should follow the applicable assay instructions and establish appropriate verification or validation procedures for their intended research applications.

Is Your Molecular Workflow Ready for Respiratory Season?

With October approaching, now is a good time to confirm that the entire workflow is ready—not just the PCR assay.

Review:

• RT-PCR reagent inventory and expiration dates
• Extraction reagents and consumables
• Anticipated sample and reaction volume
• Instrument availability and maintenance
• Panel and fluorophore compatibility
• Control materials
• Staff training
• Supplier lead times

It is also worth reviewing whether the panel currently in use still matches the laboratory’s research objectives. A workflow built around a limited number of targets may not be the most efficient option when a project requires broader respiratory pathogen coverage.

Molecular Testing Solutions from Jant Pharmacal

Jant Pharmacal has supplied laboratory and diagnostic products since 1986 and offers a growing portfolio for molecular laboratories.

Our molecular testing portfolio includes:

• Standard Multiplex RT-PCR Panels
• Lyophilized Multiplex RT-PCR Panels
• Custom Pre-Plated RT-PCR Panels
• Respiratory RT-PCR Panels
• COVID/Flu/RSV RT-PCR Panels
• Nucleic Acid Extraction Systems and Reagents
• Real-Time PCR Products
• Molecular Testing Solutions

Respiratory panel options range from focused SARS-CoV-2, influenza and RSV configurations to broader panels for investigating multiple viral and bacterial respiratory targets.

Explore Jant Pharmacal Molecular Testing Solutions →

Accutest molecular testing products referenced in this article are for Research Use Only (RUO) and are not validated for diagnostic procedures. Refer to individual product information for intended use.

Frequently Asked Questions

What is a multiplex respiratory PCR panel?

A multiplex respiratory PCR panel uses real-time PCR to amplify and detect multiple respiratory pathogen targets within the same assay. The number and type of targets vary depending on the panel.

What pathogens can be included in a respiratory RT-PCR panel?

Depending on the panel, targets may include SARS-CoV-2, influenza A and B, RSV A/B, human metapneumovirus, parainfluenza viruses, adenoviruses, seasonal coronaviruses and bacterial respiratory organisms.

What is the difference between a COVID/Flu/RSV panel and a broader respiratory panel?

A COVID/Flu/RSV panel focuses on several major respiratory viruses. Broader respiratory panels can include additional viral and bacterial targets. The appropriate configuration depends on the laboratory’s research objectives and workflow.

Can multiplex RT-PCR reduce the number of PCR reactions?

Potentially. Because multiplex assays can detect several targets within the same reaction, they may reduce the number of separate reactions required compared with testing every target individually. Actual workflow efficiency depends on the assay configuration and laboratory process.

How do I choose a respiratory PCR panel for my laboratory?

Start with the targets required for your research, then consider sample volume, desired throughput, extraction method, real-time PCR instrumentation, available fluorescence channels and assay format. Panel selection should be based on the laboratory’s specific research objectives rather than simply choosing the panel with the largest number of targets.

Are Jant Pharmacal respiratory RT-PCR panels for clinical diagnosis?

The Accutest Standard Respiratory RT-PCR Panels and Accutest Standard COVID/Flu/RSV RT-PCR Panel referenced in this article are for Research Use Only (RUO) and are not validated for diagnostic procedures. Review the intended use and regulatory status of each individual product before use.

References

1. Centers for Disease Control and Prevention, Center for Forecasting and Outbreak Analytics.
   
   2026–2027 Respiratory Disease Season Outlook.
   
   September 23, 2026.
2. Centers for Disease Control and Prevention, Center for Forecasting and Outbreak Analytics.
   
   2025–2026 Respiratory Disease Season Outlook Evaluation.
   
   May 4, 2026.