The authors thank the study staff and patients involved in this surveillance study and the Department of Climate Change and Meteorological Services in Blantyre for providing meteorological data.
GBD 2015 LRI Collaborators, 2017. Estimates of global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015. Lancet Infect Dis 17: 1133–1161.
Gessner BD, Shindo N, Briand S, 2011. Seasonal influenza epidemiology in sub-Saharan Africa: a systematic review. Lancet Infect Dis 11: 223–235.
WHO, 2012. Vaccines against influenza WHO position paper–November 2012. Weekly epidemiological record/Releve epidemiologique hebdomadaire. Wkly Epidemiol Rec 87: 461–476.
Duque J, McMorrow ML, Cohen AL, 2014. Influenza vaccines and influenza antiviral drugs in Africa: are they available and do guidelines for their use exist? BMC Public Health 14: 41.
Cohen C, Simonsen L, Sample J, Kang JW, Miller M, Madhi SA, Campsmith M, Viboud C, 2012. Influenza-related mortality among adults aged 25–54 years with AIDS in South Africa and the United States of America. Clin Infect Dis 55: 996–1003.
Feikin DR 2012. Etiology and Incidence of viral and bacterial acute respiratory illness among older children and adults in rural western Kenya, 2007–2010. PLoS One 7: e43656.
Cohen C 2015. Epidemiology of severe acute respiratory illness (SARI) among adults and children aged ≥ 5 years in a high HIV-prevalence setting, 2009–2012. PLoS One 10: e0117716.
United Nations Development Programme, 2016. Human Development Report 2016. 1 UN Plaza, New York.
Ministry of Health, Malawi, 2016. Malawi Population-based HIV Impact Assessment (MPHIA) 2015–16: First Report. Lilongwe, Malawi: Ministry of Health. November 2017.
SanJoaquin MA 2013. Surveillance programme of IN-patients and epidemiology (SPINE): implementation of an electronic data collection tool within a large hospital in Malawi. PLoS Med 10: e1001400.
Segula D, Frosch AP, SanJoaquin M, Taulo D, Skarbinski J, Mathanga DP, Allain TJ, Molyneux M, Laufer MK, Heyderman RS, 2014. Prevalence and spectrum of illness among hospitalized adults with malaria in Blantyre, Malawi. Malar J 13: 391.
Mihigo R, Torrealba CV, Coninx K, Nshimirimana D, Kieny MP, Carrasco P, Hedman L, Widdowson MA, 2012. 2009 Pandemic influenza A virus subtype H1N1 vaccination in Africa—successes and challenges. J Infect Dis 206 (Suppl 1): S22–S28.
Peterson I 2016. 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. J Infect Dis 214: 1700–1711.
World Health Organization, 2004. Rapid HIV Tests: Guidelines for Use in HIV Testing and Counselling Services in Resource-constrained Settings. Geneva, Switzerland: WHO.
National Statistics Office (NSO), 2008. Malawi 2008 Population and Housing Census Results. Zomba, Malawi: NSO.
Subbe CP, Kruger M, Rutherford P, Gemmel L, 2001. Validation of a modified early warning score in medical admissions. QJM 94: 521–526.
Subbe CP, Slater A, Menon D, Gemmell L, 2006. Validation of physiological scoring systems in the accident and emergency department. Emerg Med J 23: 841–845.
Burch VC, Tarr G, Morroni C, 2008. Modified early warning score predicts the need for hospital admission and inhospital mortality. Emerg Med J 25: 674–678.
Kruisselbrink R 2016. Modified early warning score (MEWS) identifies critical illness among ward patients in a resource restricted setting in Kampala, Uganda: a prospective observational study. PLoS One 11: e0151408.
Emukule GO, Khagayi S, McMorrow ML, Ochola R, Otieno N, Widdowson MA, Ochieng M, Feikin DR, Katz MA, Mott JA, 2014. The burden of influenza and RSV among inpatients and outpatients in rural western Kenya, 2009–2012. PLoS One 9: e105543.
Cohen C 2013. Severe influenza-associated respiratory infection in high HIV prevalence setting, South Africa, 2009–2011. Emerg Infect Dis 19: 1766–1774.
Desmond NA, Nyirenda D, Dube Q, Mallewa M, Molyneux E, Lalloo DG, Heyderman RS, 2013. Recognising and treatment seeking for acute bacterial meningitis in adults and children in resource-poor settings: a qualitative study. PLoS One 8: e68163.
Scott JA 2000. Aetiology, outcome, and risk factors for mortality among adults with acute pneumonia in Kenya. Lancet 355: 1225–1230.
Hartung TK, Chimbayo D, van Oosterhout JJ, Chikaonda T, van Doornum GJ, Claas EC, Melchers WJ, Molyneux ME, Zijlstra EE, 2011. Etiology of suspected pneumonia in adults admitted to a high-dependency unit in Blantyre, Malawi. Am J Trop Med Hyg 85: 105–112.
Albrich WC 2012. Use of a rapid test of pneumococcal colonization density to diagnose pneumococcal pneumonia. Nephrol Dial Transplant 54: 601–609.
Zar HJ, Madhi SA, Aston SJ, Gordon SB, 2013. Pneumonia in low and middle income countries: progress and challenges. Thorax 68: 1052–1056.
Madhi SA, Schoub B, Simmank K, Blackburn N, Klugman KP, 2000. Increased burden of respiratory viral associated severe lower respiratory tract infections in children infected with human immunodeficiency virus type-1. J Pediatr 137: 78–84.
Ho A 2017. Impact of human immunodeficiency virus on the burden and severity of influenza illness in Malawian adults: a prospective cohort and parallel case-control study. Clin Infect Dis 66: 865–876.
Ope MO, Katz MA, Aura B, Gikunju S, Njenga MK, Ng’ang’a Z, Vulule J, Breiman RF, Feikin DR, 2011. Risk factors for hospitalized seasonal influenza in rural western Kenya. PLoS One 6: e20111.
Remschmidt C, Wichmann O, Harder T, 2014. Influenza vaccination in HIV-infected individuals: systematic review and assessment of quality of evidence related to vaccine efficacy, effectiveness and safety. Vaccine 32: 5585–5592.
Palache A, Oriol-Mathieu V, Abelin A, Music T, 2014. Seasonal influenza vaccine dose distribution in 157 countries (2004–2011). Vaccine 32: 6369–6376.
Pretorius MA 2016. The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV sero-prevalence, South Africa 2012–2015. J Clin Virol 75: 21–26.
Self WH 2015. Respiratory viral detection in children and adults: comparing asymptomatic controls and patients with community-acquired pneumonia. J Infect Dis 213: 584–591.