Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya

Background: Respiratory viruses are primary agents of respiratory tract diseases. Knowledge on the types and frequency of respiratory viruses affecting school-children is important in determining the role of schools in transmission in the community and identifying targets for interventions. Methods: We conducted a one-year (term-time) surveillance of respiratory viruses in a rural primary school in Kilifi County, coastal Kenya between May 2017 and April 2018. A sample of 60 students with symptoms of ARI were targeted for nasopharyngeal swab (NPS) collection weekly. Swabs were screened for 15 respiratory virus targets using real time PCR diagnostics. Data from respiratory virus surveillance at the local primary healthcare facility was used for comparison. Results: Overall, 469 students aged 2-19 years were followed up for 220 days. A total of 1726 samples were collected from 325 symptomatic students; median age of 7 years (IQR 5-11). At least one virus target was detected in 384 (22%) of the samples with a frequency of 288 (16.7%) for rhinovirus, 47 (2.7%) parainfluenza virus, 35 (2.0%) coronavirus, 15 (0.9%) adenovirus, 11 (0.6%) respiratory syncytial virus (RSV) and 5 (0.3%) influenza virus. The proportion of virus positive samples was higher among lower grades compared to upper grades (25.9% vs 17.5% respectively; χ2 = 17.2, P -value <0.001). Individual virus target frequencies did not differ by age, sex, grade, school term or class size. Rhinovirus was predominant in both the school and outpatient setting. Conclusion: Multiple respiratory viruses circulated in this rural school population. Rhinovirus was dominant in both the school and outpatient setting and RSV was of notably low frequency in the school. The role of school children in transmitting viruses to the household setting is still unclear and further studies linking molecular data to contact patterns between the school children and their households are required

Rhinovirus dynamics across different social structures

Rhinoviruses (RV), common human respiratory viruses, exhibit significant antigenic diversity, yet their dynamics across distinct social structures remain poorly understood. Our study delves into RV dynamics within Kenya by analysing VP4/2 sequences across four different social structures: households, a public primary school, outpatient clinics in the Kilifi Health and Demographics Surveillance System (HDSS), and countrywide hospital admissions and outpatients. The study revealed the greatest diversity of RV infections at the countrywide level (114 types), followed by the Kilifi HDSS (78 types), the school (47 types), and households (40 types), cumulatively representing &gt;90% of all known RV types. Notably, RV diversity correlated directly with the size of the population under observation, and several RV type variants occasionally fuelled RV infection waves. Our findings highlight the critical role of social structures in shaping RV dynamics, information that can be leveraged to enhance public health strategies. Future research should incorporate whole-genome analysis to understand fine-scale evolution across various social structures

Replication Data for: Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations

This data was created from a database generated through a surveillance to characterize the transmission pathways of viral respiratory infections in Kilifi County. Data was collected from patients presenting in nine outpatient health facilities within the KHDSS area with symptoms of respiratory infection. The study was conducted from December 2015 to June 2017. However, this dataset includes surveillance conducted in 2016 only. </p

Replication Data for: Absence of Association between Cord Specific Antibody Levels and Severe Respiratory Syncytial Virus (RSV) Disease in Early Infants: A Case Control Study from Coastal Kenya

This dataset was generated from a study nested within a previous Kilifi Birth Cohort (KBC) study, conducted between 1999 and 2007 at KEMRI-Wellcome Trust Research Programme, KEMRI CGMR-C, Kilifi, Kenya. The KBC resulted in an archive of cord and three-monthly follow-up sera from infants. The nested study involved selection from this dataset cases defined as severe RSV antigen confirmed infants admitted to Kilifi County Hospital (KCH), and controls defined as infants without documented severe RSV hospitalization matched to the case by date of birth and geographical location. Stored cord and follow samples from these cases and controls were screened for RSV specific neutralizing antibodies by the plaque reduction neutralisation test (PRNT). A comparison was made between levels of specific antibody at birth (and also rates of specific antibody decay in first 6 months of life) for cases and controls. The study arose out of interest shown by the Program for Appropriate Technology in Health (PATH) in maternal boosting as a vaccination strategy and in quantifying protective levels of neutralizing antibodies

Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations

Background Endemic and seasonally recurring respiratory viruses are a major cause of disease and death globally. The burden is particularly severe in developing countries. Improved understanding of the source of infection, pathways of spread and persistence in communities would be of benefit in devising intervention strategies. Methods We report epidemiological data obtained through surveillance of respiratory viruses at nine outpatient health facilities within the Kilifi Health and Demographic Surveillance System, Kilifi County, coastal Kenya, between January and December 2016. Nasopharyngeal swabs were collected from individuals of all ages presenting with acute respiratory infection (ARI) symptoms (up to 15 swabs per week per facility) and screened for 15 respiratory viruses using real-time PCR. Paediatric inpatient surveillance at Kilifi County Hospital for respiratory viruses provided comparative data. Results Over the year, 5,647 participants were sampled, of which 3,029 (53.7%) were aged <5 years. At least one target respiratory virus was detected in 2,380 (42.2%) of the samples; the most common being rhinovirus 18.6% (1,050), influenza virus 6.9% (390), coronavirus 6.8% (387), parainfluenza virus 6.6% (371), respiratory syncytial virus (RSV) 3.9% (219) and adenovirus 2.7% (155). Virus detections were higher among <5-year-olds compared to older children and adults (50.3% vs 32.7%, respectively; χ2(1) =177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ2(8) =13.38, P=0.072). However, prevalence was significantly higher among inpatients than outpatients in <5-year-olds for RSV (22.1% vs 6.0%; χ2(1) = 159.4, P=0.0001), and adenovirus (12.4% vs 4.4%, χ2(1) =56.6, P=0.0001). Conclusions Respiratory virus infections are common amongst ARI outpatients in this coastal Kenya setting, particularly in young children. Rhinovirus predominance warrants further studies on the health and socio-economic implications. RSV and adenovirus were more commonly associated with severe disease. Further analysis will explore epidemiological transmission patterns with the addition of virus sequence data

Data for Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya

This dataset is acquired from the SPREDstudy which is part of a larger project titled SPReD (Studies of the Pathways of transmission of Respiratory virus Disease) which aims to advance understanding of the nature of spread of respiratory viruses. The study was conducted as a one-year surveillance of respiratory viruses in a rural primary school in Kilifi county, coastal Kenya with the main aim of characterising respiratory virus infection in the school setting and define the role of school-going children in the transmission of these viruses in the general community. The main dataset contains 36 variables and 3384 observations. These data include records of anthropometric measures, acute respiratory infection (ARI) symptoms and laboratory test results from nasal samples obtained from symptomatic school children every week over one school year. Anthropometric measures including the age, grade, weight, height, mid-upper arm circumference, temperature and respiratory rate of each student were recorded every week from a random sample of symptomatic students in each grade. Acute respiratory infection symptoms were also recorded at this time. Nasal samples were screened for 15 virus targets using real-time PCR. Samples were considered positive for a specific target if the ct value was >0 and <=35. The dataset is used to describe the types of respiratory viruses circulating among school-going children

Relationship between Odds of RSV disease and the levels of Cord blood antibody titres.

<p>A scatter plot showing the odds of RSV associated hospitalization against maternally transferred RSV specific antibodies (log₂PRNT titres) from cord blood samples of infants (both cases and controls) born in Kilifi, Kenya; 2002–2007. Black symbols denote individual cord titres for all 90 infants.</p

The estimated rate of decay of RSV specific antibodies from birth to 6 months of life among cases and controls.

<p>The estimated rate of decay of maternally transferred RSV specific antibodies (log₂ transformed PRNT titres) over the first 6 months of life for infants (30 RSV cases and 60 controls) from a birth cohort, Kilifi, Kenya, with best fit linear decay models for samples from cases and controls. Grey symbols denote individual cord titres of cases while black symbols denote individual cord titres of controls.</p

Characteristics of study participants.

<p>Characteristics of study participants.</p

Dynamics of cord titres by time and transmission intensity.

<p>The Red diamond symbols denote individual cord titres by date of birth for RSV A2 strain, Blue diamond symbols denote individual cord titres by date of birth for RSV A Kilifi local strain, Maroon circle markers denote the mean cord titre by quarter (95% CI denoted by Brown whiskers) for RSV A2 strain, Navy blue circle markers denote the mean cord titre by quarter (95% CI denoted by Green whiskers) for RSV A Kilifi local strain. The Grey vertical bars (RSVA) and Orange vertical bars (RSV B) show the number of RSV IFAT positive paediatric severe or very severe pneumonia admissions to Kilifi County Hospital 2002–2005.</p