Updated 22/05/2026
During epidemiological week 19 (May 4–10, 2026), 13 countries across the WHO African Region reported respiratory virus surveillance data, revealing a 9% influenza positivity rate against a backdrop of minimal SARS-CoV-2 circulation. According to WHO surveillance data, influenza A and B viruses dominated clinical respiratory specimens, while COVID-19 testing showed a sustained decline across the region.
Influenza subtypes detected across 13 African countries, week 19
Distribution of 86 positive specimens by influenza type and subtype, May 4–10, 2026
Source: WHO African Region Respiratory Virus Surveillance, Week 19, 2026 | Georgian Medical Journal News
Influenza A and B drive regional disease burden
Among 86 confirmed influenza cases, WHO data show that 59 specimens were influenza A and 27 were influenza B. Influenza A without full subtyping accounted for the largest group (36 specimens), followed by influenza B Victoria lineage (24 specimens) and influenza A H3 (19 specimens). Pandemic H1N1 (H1N1)pdm09 represented only 4 cases, with 3 influenza B viruses remaining untyped.
This composition reflects the typical seasonal and endemic patterns observed across sub-Saharan Africa, where multiple influenza subtypes circulate simultaneously. The regional surveillance network continues to track genetic variants and lineage evolution to inform vaccine strain recommendations.
SARS-CoV-2 positivity falls to 2% in acute surveillance
In week 19, laboratories across the African Region processed 908 specimens for SARS-CoV-2, yielding only 18 positive cases—a 2% positivity rate, according to WHO African Region surveillance. This represents a marked decline from pandemic-era levels and signals sustained control of acute COVID-19 transmission across participating countries.
Cumulatively from weeks 1 to 19, the influenza laboratory network tested 25,293 specimens for SARS-CoV-2, with 785 positive results—a cumulative positivity of 3.1%. The persistent low-level circulation of SARS-CoV-2 aligns with global trends showing endemic rather than epidemic transmission, though ongoing surveillance remains essential to detect emerging variants.
Laboratory capacity and regional participation strengthen surveillance
The week 19 surveillance snapshot represents data from 13 countries—Algeria, Burkina Faso, Cameroon, Ethiopia, Ghana, Kenya, Mali, Mauritania, Nigeria, Senegal, South Africa, Togo, and the United Republic of Tanzania. A total of 961 specimens were collected and processed, with 951 tested for influenza and 908 tested for SARS-CoV-2, demonstrating sustained laboratory participation across the region.
Consistent regional surveillance underpins early warning systems for pandemic influenza and emerging respiratory threats. The WHO emphasizes that maintaining sentinel surveillance networks—particularly among hospitalized patients and healthcare facility-based samples—remains critical to detect antigenically novel influenza viruses and variants of concern before rapid spread occurs.
Influenza positivity reached 9% in week 19 across 13 African countries, with influenza A and B co-circulating, while SARS-CoV-2 remained at 2% positivity—underscoring a shift toward endemic influenza dominance and sustained COVID-19 control in the African Region.
— WHO African Region Respiratory Virus Surveillance Network (WHO AFRO, May 2026)
Key takeaways
- Influenza positivity of 9% (86 of 951 specimens) demonstrates significant seasonal circulation of both A and B viruses across 13 African countries in week 19.
- Influenza A H3 (19 cases) and influenza B Victoria (24 cases) were the most commonly detected subtypes, while pandemic H1N1 remained rare (4 cases).
- SARS-CoV-2 positivity fell to 2% in acute surveillance (18 of 908 specimens), with a cumulative year-to-date rate of 3.1%, indicating sustained endemic control rather than epidemic transmission.
- Continued participation by 13 countries and 12 laboratories demonstrates strengthened regional surveillance capacity essential for early detection of respiratory threats.
Frequently asked questions
Why is influenza positivity higher than SARS-CoV-2 in African surveillance?
Influenza circulates year-round in tropical and subtropical Africa, with intensity varying by season and region. SARS-CoV-2, by contrast, has transitioned to endemic circulation at much lower levels globally, as population immunity from vaccination and prior infection has increased. The 9% influenza positivity versus 2% for SARS-CoV-2 reflects this epidemiological shift rather than a novel threat.
What does “subtyping not performed” mean for 36 influenza A specimens?
Subtyping identifies whether influenza A is H1N1, H3N2, or another subtype. When resources or time constraints prevent full characterization, specimens are reported as influenza A without subtype designation. This is common in high-volume surveillance weeks and does not indicate a detection failure—further testing can be conducted if needed for epidemiological investigations.
Should African countries maintain respiratory surveillance at current levels?
Yes. The WHO recommends continuous sentinel surveillance for influenza and other respiratory viruses to detect antigenic drift, novel reassortants, and emerging pathogens. Early detection enables rapid public health response and vaccine strain selection. The current 13-country network provides critical epidemiological intelligence for the region and informs global pandemic preparedness.
As respiratory surveillance systems across Africa mature and laboratory capacity strengthens, the week 19 data underscore the importance of sustained, real-time monitoring. With influenza remaining the dominant respiratory threat in the region and SARS-CoV-2 in endemic decline, public health authorities can refine seasonal prevention strategies—including timely influenza vaccination campaigns—while maintaining heightened alertness for unexpected shifts in viral epidemiology.
Source: Respiratory virus surveillance in the WHO African Region Epidemiological Week 19, May 4 to 10 2026
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Medically reviewed by Prof. Giorgi Pkhakadze, MD, MPH, PhD. Spotted an error? Contact the editorial team.
