Surveillance nurses screened all outpatients and inpatients at all health facilities in the BHDSS, 24 hours a day, 7 days per week, using standardized criteria for referral to clinicians (Supplementary Table S1). The study presented here used data and stored specimens collected between February 10 and December 31, 2015. We added the collection of nasopharyngeal (NP) and oropharyngeal (OP) swabs from all surveillance patients from February 2015 onwards with the aim to measure pneumococcal carriage.

Surveillance commenced in 2008 and included all BHDSS residents. Surveillance methodology 10 and results 3, 11 have been previously published. This study was nested within a population-based surveillance study for suspected pneumonia, septicemia and meningitis, designed to measure the impact of PCV introduction. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2009 and replaced by PCV13 in 2011. Transmission of Plasmodium falciparum is associated with a rainy season from June until October. HIV prevalence in antenatal attendees was 1.6% in 2014 9. The Basse Health Centre is a primary and secondary care facility in Upper River Region of The Gambia, providing referral services to five peripheral health facilities in the BHDSS. The Basse Health and Demographic Surveillance Systems (BHDSS) in the rural east of the country had an estimated population of 179 932 in 2015 with 12,318 aged 2–23 months. The Gambia is a small West African country with a population of approximately 2.1 million. We also evaluate specimen collection and storage methodologies and analyse antigenic sites that may impact on vaccination strategies. Here we present the incidence of ALRI associated with RSV, PIV or IV in young children in The Gambia, including the clinical features and temporal circulation. Thus, additional African data are urgently needed as several RSV vaccine candidates are in development with consideration of maternal, neonatal and infant vaccination strategies 8. Incidence varied by location, with only three (two unpublished) African studies reporting disease incidence 7, with none in West Africa. A recent systematic review estimated the global number of cases of RSV-associated ALRI in 2015 at 33.1 million, 3.2 million hospital admissions and 59 600 deaths with 45% of cases occurring before 6 months of age 6. However, these studies could not calculate disease incidence. Recent case-control studies from low-income countries have established an etiologic association between ALRI and respiratory syncytial (RSV), parainfluenza (PIV), influenza (IV) and human metapneumo viruses 4, 5. In order to address the ongoing burden of virus-associated ALRI and to develop evidence-based vaccination strategies, additional data are needed from low-income settings. However, the incidence of all-cause acute lower respiratory infection (ALRI) remains high 3 with an estimated 921,000 deaths due to ALRI in children <5 years of age in 2015, 490 000 of which occurred in sub-Saharan Africa 1. The introduction of pneumococcal conjugate vaccine in The Gambia was associated with a 61% reduction in severe hypoxic pneumonia 3. The introduction of conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae in many countries has contributed to reductions in pneumonia deaths over the last two decades 1, 2. An effective RSV vaccination strategy could have a major impact on the burden of ALRI in this setting. Gambian RSV viruses were closely related to viruses detected in other continents. RSV circulated throughout most of the year and was associated with eight times the number of ALRI cases compared to PIV or IV. Multiple strains of RSV and influenza circulated during the year. The expected incidence of ALRI associated with RSV, PIV or influenza was 140 cases (95% CI, 131–149) per 1000 person-years RSV incidence was 112 cases (95% CI, 102–122) per 1000 person-years. RSV-A was detected in 237 and RSV-B in seven. One or more viruses were detected in 303/519 children (58.4%). 2385 children with ALRI were enrolled, 519 were randomly selected for viral testing. RSV G and F proteins and influenza hemagglutinin genes were sequenced. The expected number of viral-associated ALRI cases in the population was estimated using statistical simulation that accounted for the sampling design. Each month from February through December 2015, specimens from 50 children aged 2–23 months were randomly selected to test for respiratory syncytial (RSV), parainfluenza (PIV) and influenza viruses. Naso- and oropharyngeal swabs were collected.

We conducted population-based surveillance in rural Gambia using standardized criteria to identify and investigate children with acute lower respiratory infection (ALRI). Respiratory viral infections contribute significantly to morbidity and mortality worldwide, but representative data from sub-Saharan Africa are needed to inform vaccination strategies.

Infection detected in on1 resize