Respiratory virus-associated severe acute respiratory illness (SARI) and viral clustering in Malawian children in a setting with a high prevalence of HIV, malaria and malnutrition

Background We used four years of paediatric severe acute respiratory illness (SARI) sentinel surveillance in Blantyre, Malawi to identify factors associated with clinical severity and co-viral clustering. Methods From January 2011 to December 2014, 2363 children aged 3 months to 14 years presenting to hospital with SARI were enrolled. Nasopharyngeal aspirates were tested for influenza and other respiratory viruses. We assessed risk factors for clinical severity and conducted clustering analysis to identify viral clusters in children with co-viral detection. Results Hospital-attended influenza-positive SARI incidence was 2.0 cases per 10,000 children annually; it was highest children aged under 1 year (6.3 cases per 10,000), and HIV-infected children aged 5 to 9 years (6.0 cases per 10,000). 605 (26.8%) SARI cases had warning signs, which were positively associated with HIV infection (adjusted risk ratio [aRR]: 2.4, 95% CI: 1.4, 3.9), RSV infection (aRR: 1.9, 95% CI: 1.3, 3.0) and rainy season (aRR: 2.4, 95% CI: 1.6, 3.8). We identified six co-viral clusters; one cluster was associated with SARI with warning signs. Conclusions Influenza vaccination may benefit young children and HIV infected children in this setting. Viral clustering may be associated with SARI severity; its assessment should be included in routine SARI surveillance