Pan American Health Organization · 1st edition, 2026 · 51 pages
Operational framework for health authorities to integrate SARS-CoV-2, RSV, and other respiratory viruses into established influenza sentinel surveillance systems.
- Issuer
- Pan American Health Organization
- Edition
- 1st edition, 2026
- Audience
- National and subnational health authorities, epidemiologists, surveillance officers, laboratory focal points, policymakers
- Evidence
- Consensus guidance building on WHO mosaic framework and Global Influenza Surveillance and Response System standards
- Reviewed
- 16 Oct 2026 · GMJ
What this guideline says
GMJ summary
This 2026 PAHO technical guidance provides a comprehensive framework for strengthening routine surveillance of respiratory viruses with epidemic and pandemic potential across the Americas. Building on the WHO mosaic framework Domain II, it guides countries in integrating SARS-CoV-2, respiratory syncytial virus (RSV), and other respiratory viruses into existing influenza sentinel surveillance platforms.
The publication outlines operational components including case definitions (ILI, ARI, SARI, extended SARI), sentinel site selection criteria, sampling strategies, and laboratory protocols. It recommends testing at least 50 specimens per week at the national level for influenza and SARS-CoV-2, and at least 20 specimens per week for RSV in children aged <2 years. The guidance emphasizes weekly data collection, analysis using methods such as the Moving Epidemic Method (MEM) for threshold calculation, and timely reporting to regional systems (FluNet, FluID, PAHOMart).
Beyond sentinel surveillance, the document describes complementary approaches including nonsentinel syndromic surveillance using ICD-10/ICD-11 codes, laboratory-based notifications, healthcare capacity monitoring (bed occupancy, ventilation requirements), all-cause mortality surveillance (PAHoMoMo system), enhanced clinical surveillance, targeted population monitoring (nursing homes, immunocompromised persons, healthcare workers), and wastewater surveillance. The framework supports countries in building flexible, sustainable systems adapted to local contexts while meeting international reporting standards under the International Health Regulations (2005).
Key points
For clinicians — doses and thresholds as stated in the guideline
- Test at least 50 specimens per week at the national level, per case definition (ILI/ARI or SARI) for influenza and SARS-CoV-2; if not feasible, test at least 50 specimens per week from a mix of ILI/ARI and SARI cases
- Test at least 20 specimens per week for RSV from inpatients aged <2 years meeting SARI or extended SARI case definitions
- ILI case definition: acute respiratory infection with measured fever ≥38°C AND cough, with symptom onset within the past 10 days (any age)
- SARI case definition: acute respiratory infection with history or measured fever >38°C AND cough AND onset within the past 10 days (any age)
- Extended SARI for children <2 years: symptom onset within 10 days AND cough or shortness of breath AND hospitalization; for infants <6 months also include apnea or sepsis (fever/hypothermia with shock)
- Collect specimens within 3 days of symptom onset, no later than 7 days; use nasopharyngeal swab or combined nasopharyngeal and oropharyngeal swabs in viral transport medium
- Store specimens at 2–8°C for up to 72 hours if cannot transport immediately; otherwise freeze at −20°C or below; preserve at −70°C for extended periods
- Sentinel sites must report data weekly (by 3:00 p.m. every Friday) to PAHO/WHO using FluNet and FluID templates, stratified by age group and subnational area
Case definitions for respiratory virus surveillance
Table extracted from the guideline
| Syndrome | Case definition | Recommended ages |
|---|---|---|
| WHO ILI | Acute respiratory infection with measured fever ≥38°C AND cough; with symptom onset within the past 10 days | Any age |
| WHO SARI | Acute respiratory infection with history of fever or measured fever >38°C AND cough AND onset within the past 10 days | Any age |
| ARI | Sudden onset of symptoms AND at least one respiratory symptom (cough, sore throat, shortness of breath, coryza) AND clinician's judgement that illness is due to infection | Any age |
| WHO extended SARI (children <2 years) | Symptom onset within 10 days AND cough or shortness of breath AND hospitalization | Children <2 years |
| WHO extended SARI (infants <6 months, additional) | Also include: apnea (temporary cessation of breathing) OR sepsis (fever ≥37.5°C/hypothermia <35.5°C and shock and seriously ill with no apparent cause) | Infants <6 months |
Source: Pan American Health Organization, Technical guidance for an integrated approach to routine surveillance of respiratory viruses in the Americas. Reproduced in summary form.
From the guideline
Verbatim
“WHO recommends testing 50 specimens for each case definition per week at the national level to detect the onset of respiratory virus activity without significant delays.”
Editor’s perspective
Why this matters for Georgia and the region
Prof. Giorgi Pkhakadze, MD, MPH, PhD
Editor-in-Chief, Georgian Medical Journal · Chair, Public Health Institute of Georgia · WHO consultant, health and migration
As Chair of Georgia's Public Health Institute and having worked with WHO on health systems strengthening, I recognize this PAHO framework as directly applicable to our regional context. Georgia's National Influenza Centers and sentinel hospital network, established with WHO EUR support, already report influenza data weekly; the critical recommendation here is expanding laboratory capacity to test 50 specimens weekly for influenza and SARS-CoV-2 combined, and adding 20 weekly RSV tests in pediatric wards—targets that align with Georgia's population of 3.7 million and existing sentinel infrastructure in Tbilisi, Batumi, and regional centers. The guidance's emphasis on the extended SARI case definition for children under 2 years (symptom onset within 10 days, cough or dyspnea, and hospitalization, including apnea or sepsis in infants under 6 months) is particularly relevant given that lower respiratory infections remain a leading cause of child hospitalization across the South Caucasus. However, one realistic implementation challenge for Georgia and neighboring Armenia and Azerbaijan is sustaining year-round cold chain transport from peripheral sentinel sites to reference laboratories and maintaining weekly reporting discipline during low-transmission periods when staff attention shifts to other priorities—issues that require embedding surveillance tasks into routine hospital workflows and ensuring dedicated laboratory technician time, not just seasonal mobilization.
ORCID 0000-0001-7609-4515 · Perspective written for the GMJ Guidelines Library, 16 Oct 2026
Applicability
Georgia and the South Caucasus
For Georgia and the South Caucasus, this guidance offers a roadmap to modernize respiratory virus surveillance systems established during Soviet times and enhanced during the COVID-19 pandemic. The framework is particularly relevant as Georgia operates National Influenza Centers and reports to WHO European Region; adapting the Americas’ weekly specimen targets (50 for influenza/SARS-CoV-2, 20 for RSV in children <2 years) to Georgian catchment populations would require mapping current sentinel hospital capacity and primary care networks. The emphasis on integrating RSV surveillance aligns with regional needs given the burden of lower respiratory infections in young children across the South Caucasus. National programmes would need to assess laboratory capacity for year-round rRT-PCR testing, establish cold chain logistics from sentinel sites to reference laboratories in Tbilisi, and determine whether current reporting systems can accommodate weekly FluNet/FluID-equivalent data flows. The complementary approaches—particularly wastewater surveillance and mortality monitoring via civil registration—could leverage Georgia's existing urban sanitation infrastructure and vital statistics systems, though implementation would require coordination between the National Center for Disease Control and Public Health, municipal authorities, and the National Statistics Office.
Questions this guideline answers
Quick answers
How many specimens should a sentinel site test each week?
At the national level, test at least 50 specimens per week per case definition (ILI/ARI or SARI) for influenza and SARS-CoV-2. If not feasible, test at least 50 specimens per week from a mix of ILI/ARI and SARI cases. For RSV, test at least 20 specimens per week from children aged <2 years meeting SARI or extended SARI definitions. The number per site depends on how many sites are included and their patient volumes; distribute the national target across sites to ensure representativeness.
When should respiratory specimens be collected?
Ideally within 3 days of symptom onset, and no later than 7 days after onset. Use nasopharyngeal swabs or combined nasopharyngeal and oropharyngeal swabs in viral transport medium. Avoid inactivating collection buffers to enable virus isolation. Store at 2–8°C for up to 72 hours if immediate transport is not possible; otherwise freeze at −20°C or below. For long-term storage, maintain at −70°C.
Which case definition should be used for children under 2 years with severe respiratory illness?
Use the WHO extended SARI case definition: children <2 years with symptom onset within 10 days AND cough or shortness of breath AND hospitalization. For infants <6 months, also include apnea (temporary cessation of breathing) or sepsis (fever ≥37.5°C or hypothermia <35.5°C, with shock and seriously ill appearance with no apparent cause). This captures RSV and other respiratory viruses that may not always present with high fever in young children.
How should sentinel surveillance data be reported to PAHO/WHO?
Report aggregated data weekly to PAHO/WHO using FluNet (virological data: number tested, number positive by virus type/subtype) and FluID (epidemiological data: number of ILI/ARI/SARI cases, ICU admissions, deaths) templates. Submit data for the previous complete epidemiological week by 3:00 p.m. every Friday. Data must be stratified by age group and subnational administrative area, indicating whether the source is sentinel or nonsentinel surveillance and the case definition applied.
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- Issuer
- Pan American Health Organization
- Type
- Guidelines and Technical Manuals
- Edition
- 1st edition, 2026
- Status
- Current
- Published
- 2026-07-23
- Languages
- English
- Scope
- Regional (Americas)
- Audience
- National and subnational health authorities, epidemiologists, surveillance officers, laboratory focal points, policymakers
- Pages
- 51
- Licence
- CC BY-NC-SA 3.0 IGO
- ISBN
- 978-92-75-13181-7 (PDF)
- Evidence
- Consensus guidance building on WHO mosaic framework and Global Influenza Surveillance and Response System standards
- Record history
- Created 16 Oct 2026 · updated 16 Oct 2026 · next check Apr 2027
Pan American Health Organization. Technical guidance for an integrated approach to routine surveillance of respiratory viruses in the Americas. Washington, D.C.: PAHO; 2026. Available from: https://doi.org/10.37774/9789275131817GMJ Guidelines Library records are original summaries written by the GMJ editorial team from the issuer’s published document and reviewed by a physician. They do not replace the full guideline. The document is the copyright of its issuer and is linked, not hosted. Spotted an error or a newer edition? Tell the Guidelines Desk.
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