Dataset Information

Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016-2018.

ABSTRACT:

Purpose

The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission.

Participants

We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice-weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.

Findings to date

There were 122 113 potential individual follow-up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR-confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case.

Future plans

Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016-2018 were eligible for inclusion in a study of SARS-CoV-2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS-CoV-2 infection and the role of asymptomatic infection in virus transmission.

SUBMITTER: Cohen C

PROVIDER: S-EPMC8542945 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant's age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9-80.5%) than older children (5-17 years-old) (31.7-50.0%) or adults (11.5-23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7-15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91-1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2-12.8 vs 6.0 days, 95%CI: 5.6-6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507-714 vs 389, 95%CI: 311.1-435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.

Project description:ObjectivesRespiratory syncytial virus (RSV) is one of the most important causes of lower respiratory tract illnesses. In this study, we examined the number and severity of RSV infections among adult patients. The underlying diseases and background information of patients with RSV were examined and compared with the patients with influenza.DesignRetrospective cohort study.SettingPatients receiving tertiary care services in Kuopio University Hospital (KUH) district in Eastern Finland.Participants725 patients (152 with RSV infection and 573 with influenza) treated in KUH between November 2017 and May 2018.Primary and secondary outcome measuresHospitalisation and mortality.ResultsCompared with influenza, RSV caused a more serious disease in terms of hospitalisation (84.2% vs 66.0%, p<0.001), incidence of pneumonia (37.5% vs 23.2%, p<0.001), need for antibiotics (67.1% vs 47.3%, p<0.001) and supplemental oxygen (50.7% vs 31.2%, p<0.001). The all-cause mortality during hospitalisation and 30 days after discharge was higher among the RSV-infected patients (8.6% vs 3.5%, p=0.010). Solid malignancies (23.1% vs 5.0%, p=0.042) and chronic kidney disease (30.8% vs 5.8%, p=0.011) were more common among the RSV-infected non-survivors compared with survivors. RSV was an independent risk factor for hospitalisation (adjusted OR (aOR) 2.035; 95% CI 1.17 to 3.55) and mortality (aOR 2.288; 95% CI 1.09 to 4.81) compared with influenza.ConclusionsAmong all the screened patients, those with RSV infection were older and had more underlying conditions than patients with influenza. They had increased likelihood of hospitalisation and mortality when compared with influenza. Solid malignancies and chronic kidney disease seemed to be independent risk factors for death among RSV-infected patients. During RSV and influenza epidemics, it is important to test patients with respiratory symptoms for RSV and influenza to prevent the spread of the infections among elderly and chronically ill patients.

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