Estimating household contact matrices structure from easily collectable metadata

Contact matrices are a commonly adopted data representation, used to develop compartmental models for epidemic spreading, accounting for the contact heterogeneities across age groups. Their estimation, however, is generally time and effort consuming and model-driven strategies to quantify the contacts are often needed. In this article we focus on household contact matrices, describing the contacts among the members of a family and develop a parametric model to describe them. This model combines demographic and easily quantifiable survey-based data and is tested on high resolution proximity data collected in two sites in South Africa. Given its simplicity and interpretability, we expect our method to be easily applied to other contexts as well and we identify relevant questions that need to be addressed during the data collection procedure.

Incidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018

Data on respiratory syncytial virus (RSV) incidence and household transmission are limited. To describe RSV incidence and transmission, we conducted a prospective cohort study in rural and urban communities in South Africa over two seasons during 2017-2018. Nasopharyngeal swabs were collected twice-weekly for 10 months annually and tested for RSV using PCR. We tested 81,430 samples from 1,116 participants in 225 households (follow-up 90%). 32% (359/1116) of individuals had ≥1 RSV infection; 10% (37/359) had repeat infection during the same season, 33% (132/396) of infections were symptomatic, and 2% (9/396) sought medical care. Incidence was 47.2 infections/100 person-years and highest in children <5 years (78.3). Symptoms were commonest in individuals aged <12 and ≥65 years. Individuals 1-12 years accounted for 55% (134/242) of index cases. Household cumulative infection risk was 11%. On multivariable analysis, index cases with ≥2 symptoms and shedding duration >10 days were more likely to transmit; household contacts aged 1-4 years vs. ≥65 years were more likely to acquire infection. Within two South African communities, RSV attack rate was high, and most infections asymptomatic. Young children were more likely to introduce RSV into the home, and to be infected. Future studies should examine whether vaccines targeting children aged <12 years could reduce community transmission.

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

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.

Asymptomatic transmission and high community burden of seasonal influenza in an urban and a rural community in South Africa, 2017-18 (PHIRST): a population cohort study

Background

Data on influenza community burden and transmission are important to plan interventions especially in resource-limited settings. However, data are limited, particularly from low-income and middle-income countries. We aimed to evaluate the community burden and transmission of influenza in a rural and an urban setting in South Africa.

Methods

In this prospective cohort study approximately 50 households were selected sequentially from both a rural setting (Agincourt, Mpumalanga Province, South Africa; with a health and sociodemographic surveillance system) and an urban setting (Klerksdorp, Northwest Province, South Africa; using global positioning system data), enrolled, and followed up for 10 months in 2017 and 2018. Different households were enrolled in each year. Households of more than two individuals in which 80% or more of the occupants agreed to participate were included in the study. Nasopharyngeal swabs were collected twice per week from participating household members irrespective of symptoms and tested for influenza using real-time RT-PCR. The primary outcome was the incidence of influenza infection, defined as the number of real-time RT-PCR-positive episodes divided by the person-time under observation. Household cumulative infection risk (HCIR) was defined as the number of subsequent infections within a household following influenza introduction.

Findings

81 430 nasopharyngeal samples were collected from 1116 participants in 225 households (follow-up rate 88%). 917 (1%) tested positive for influenza; 178 (79%) of 225 households had one or more influenza-positive individual. The incidence of influenza infection was 43·6 (95% CI 39·8–47·7) per 100 person-seasons. 69 (17%) of 408 individuals who had one influenza infection had a repeat influenza infection during the same season. The incidence (67·4 per 100 person-seasons) and proportion with repeat infections (22 [23%] of 97 children) were highest in children younger than 5 years and decreased with increasing age (p<0·0001). Overall, 268 (56%) of 478 infections were symptomatic and 66 (14%) of 478 infections were medically attended. The overall HCIR was 10% (109 of 1088 exposed household members infected [95% CI 9–13%). Transmission (HCIR) from index cases was highest in participants aged 1–4 years (16%; 40 of 252 exposed household members) and individuals with two or more symptoms (17%; 68 of 396 exposed household members). Individuals with asymptomatic influenza transmitted infection to 29 (6%) of 509 household contacts. HIV infection, affecting 167 (16%) of 1075 individuals, was not associated with increased incidence or HCIR.

Interpretation

Approximately half of influenza infections were symptomatic, with asymptomatic individuals transmitting influenza to 6% of household contacts. This suggests that strategies, such as quarantine and isolation, might be ineffective to control influenza. Vaccination of children, with the aim of reducing influenza transmission might be effective in African settings given the young population and high influenza burden.

Source apportionment of ambient PM10−2.5 and PM2.5 for the Vaal Triangle, South Africa

The Vaal Triangle Airshed Priority Area (VTAPA), like other priority areas in South Africa, has an air pollution problem. Understanding the sources contributing to air pollution in this priority area will assist in the selection and implementation of appropriate control strategies. For this study, aerosol samples in the coarse (PM10-2.5) and fine (PM2.5) fraction were collected at four sites in the VTAPA during summer/autumn, winter, and spring. The contributing sources were identified and characterised based on the elemental and ionic compositions obtained through X-ray fluorescence and ion chromatography analysis. The highest seasonal median concentrations of PM10-2.5 (116 μg/m3) and PM2.5 (88 μg/m3) were observed in Sharpeville during the winter. The lowest median concentrations of PM10-2.5 (25 μg/m3) and PM2.5 (18 μg/m3) were detected in Zamdela during the summer/autumn period. At all sites, there was a high abundance of crustal elements in PM10-2.5 and a dominance of coal and biomass combustion-related elements in PM2.5. The Positive Matrix Factorisation receptor model identified dust-related and secondary aerosols as the major contributing sources of PM10-2.5. PM2.5 contributions were predominantly from coal burning for Sebokeng and Sharpeville and from industry, wood and biomass burning, and secondary aerosols for Kliprivier and Zamdela. The results of this study identify the main sources contributing to particulate air pollution in the VTAPA and provide local authorities with valuable information for decision-making.

Contrasting indoor and ambient particulate matter concentrations and thermal comfort in coal and non-coal burning households at South Africa Highveld

One of the key challenges noted in the sustainable development goals for good health and wellbeing (SDGs 3) is both ambient and household air pollution. Household solid fuel combustion represents one of the biggest threat to human health in South Africa. This study helps to understand the impact of solid fuel burning in an indoor and ambient environment. Continuous monitoring of particulate matter (PM₄) was carried out in two houses, one used coal as a primary source of energy, while the other did not. For solid fuel burning (SFB) house the winter PM₄ average 24-h concentration ranges between 60.9 μg m^-3 and 207.5 μg m^-3 while at non-solid fuel burning (NSFB) house it ranges between 15.3 μg m^-3 and 84.2 μg m^-3. In both houses, the national ambient air quality standard (NAAQS) for PM2.5 (40 μg m^-3) were exceeded during winter. The summer PM₄ levels ranged between 17.4 μg m^-3 and 36.6 μg m^-3 in the solid fuel burning house and between 14.2 μg m^-3 and 39.9 μg m^-3 at the non-solid fuel-burning house. During mornings and evenings, indoor concentrations were higher than the outdoor; these periods coincide with the fuel-burning pattern in this community. In the mid-afternoon, the outdoor PM levels sometimes went higher than the indoor levels, perhaps as a result of the pollution from the power plants in the neighbourhood. Using the linear regression model, there were no significant correlations between indoor/outdoor PM₄ concentrations during the winter, but there were good correlations for both houses during the summer. There was an observed difference in the thermal comfort at the SFB and NSFB. The temperature at SFB went below the World Health Organisation standard in winter and above during the summer while at NSFB, the temperature was managed within the standard in both seasons.