Biology subjects

Kucharski, A.

Publications and source records attributed to Kucharski, A..

6 recordsLinked to original sources

bioRxiv2018

Structure and consistency of self-reported social contact networks in British secondary schools

Self-reported social mixing patterns are commonly used in mathematical models of infectious diseases. It is particularly important to quantify patterns for school-age children given their disproportionate role in transmission, but it remains unclear how the structure of such social interactions changes over time. By integrating data collection into a public engagement programme, we examined self-reported contact networks in year 7 groups in four UK secondary schools. We collected data from 460 unique participants across four rounds of data collection conducted between January and June 2015, with 7,315 identifiable contacts reported in total. Although individual-level contacts varied over the study period, we were able to obtain out-of-sample accuracies of more than 90% and F-scores of 0.49-0.84 when predicting the presence or absence of social contacts between specific individuals across rounds of data collection. Network properties such as clustering and number of communities were broadly consistent within schools between survey rounds, but varied significantly between schools. Networks were assortative according to gender, and to a lesser extent school class, with the estimated clustering coefficient larger among males in all surveyed co-educational schools. Our results demonstrate that it is feasible to collect longitudinal self-reported social contact data from school children and that key properties of these data are consistent between rounds of data collection.

epidemiology↗

bioRxiv2018

Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis

Background Zika virus (ZIKV) emerged in Latin America & the Caribbean (LAC) region in 2013, and has had serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and a lack of a comprehensive collation of data from affected countries.\n\nMethods Our analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 91 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vector capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories.\n\nResults There was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (p<0.05) with the reported peak in incidence. The reporting rate varied across countries, with lower reporting rates for those with only confirmed cases compared to those who reported both confirmed and suspected cases.\n\nConclusions The findings suggest that the ZIKV epidemic is by and large over, with incidence projected to be low in most cities in LAC in 2018. Local low levels of transmission are probable but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.

epidemiology↗

bioRxiv2018

Guiding Vaccine Efficacy Trial Design During Public Health Emergencies: An interactive web-based decision support tool

The design and execution of rigorous, fast, and ethical vaccine efficacy trials can be challenging during epidemics of emerging pathogens, such as the 2014-2016 Ebola virus and 2015-2016 Zika virus epidemics. Response to an urgent public health crisis requires accelerated research even as emerging epidemics themselves change rapidly and are inherently less well understood than well-established diseases. As part of the World Health Organization Research and Development Blueprint, we designed a web-based interactive decision support system (InterVax-Tool) to help diverse stakeholders navigate the epidemiological, logistical, and ethical decisions involved in designing a vaccine efficacy trial during a public health emergency. In contrast to existing literature on trial design, InterVax-Tool offers high-level visual and interactive assistance through a set of four decision trees, guiding users through selection of 1) the Primary Endpoint, (2) the Target Population, (3) Randomization, and (4) the Comparator. Guidance is provided on how each of fourteen key considerations-grouped as Epidemiological, Vaccine-related, Infrastructural, or Sociocultural-should be used to inform each decision in the trial design process. The tool is not intended to provide a black box decision framework for identifying an optimal trial design, but rather to facilitate transparent, collaborative and comprehensive discussion of the relevant decisions, while recording the decision process. The tool can also assist capacity building by providing a cross-disciplinary picture of trial design using concepts from epidemiology, study design, vaccinology, biostatistics, mathematical modeling and clinical research ethics. Here, we describe the goals and features of InterVax-Tool as well as its application to the design of a Zika vaccine efficacy trial.\n\nOne Sentence SummaryAn interactive web-based decision support tool was developed to assist in the design of vaccine efficacy trials during emerging outbreaks.

epidemiology↗

bioRxiv2017

Timescales of influenza A/H3N2 antibody dynamics

Human immunity influences the evolution and impact of novel influenza strains. Because individuals are infected with multiple influenza strains during their lifetime and each virus can generate a cross-reactive antibody response, it is challenging to quantify the processes that shape observed immune responses, or to reliably detect recent infection from serological samples. Using a Bayesian model of antibody dynamics at multiple timescales, we explain complex cross-reactive antibody landscapes by inferring participants histories of infection with serological data from cross-sectional and longitudinal studies of influenza A/H3N2 in southern China and Vietnam. We show an individuals influenza antibody profile can be explained by a short-lived, broadly cross-reactive response that decays within a year to leave a smaller long-term response acting against a narrower range of strains. We also demonstrate that accounting for dynamic immune responses can provide a more accurate alternative to traditional definitions seroconversion for the estimation of infection attack rates. Our work provides a general model for explaining mechanisms of influenza immunity acting at multiple timescales based on contemporary serological data, and suggests a two-armed immune response to influenza infection consistent with competitive dynamics between B cell populations. This approach to analysing multiple timescales for antigenic responses could also be applied to other multi-strain pathogens such as dengue and related flaviviruses.

epidemiology↗

bioRxiv2017

Identifying Human Encounters That Shape The Transmission Of Streptococcus Pneumoniae And Other Respiratory Infections

Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, there is little empirical evidence to back this up. Indeed, no previous study has linked individuals risk of respiratory infection with their current pattern of social contacts. We explored whether the frequency of different types of social encounters were associated with current pneumococcal carriage and self-reported acute respiratory symptoms (ARS), though a survey in Uganda in 2014. In total 566 participants were asked about their daily social encounters and about symptoms of ARS in the last two weeks. A nasopharyngeal specimen was also taken from each participant. We found that the frequency of physical (i.e. skin-to-skin), long ([≥]1h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact -, was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 9% (1-18%) respectively. In contrast, the number of casual contacts (<5 minutes long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people with ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Such results strengthen the evidence for public health measures based upon assumptions of what contacts are important for transmission, and are important to improve disease prevention and control efforts, as well as inform research on infectious disease dynamics.\n\nAuthor summaryAlthough social contacts are an important determinant for the transmission of many infectious diseases it is not clear how the nature and frequency of contacts shape individual infection risk. We explored whether frequency, duration and type of social encounters were associated with someones risk of respiratory infection, using nasopharyngeal carriage (NP) of Streptococcus pneumoniae and acute respiratory symptoms as endpoints. To do so, we conducted a survey in South-West Uganda collecting information on peoples social encounters, respiratory symptoms, and pneumococcal carriage status. Our results show that both pneumococcal carriage and respiratory symptoms are independently associated with a higher number of social encounters, irrespective of a persons age. More specifically, our findings strongly suggest that the frequency of close contacts is important for transmission of respiratory infections, particularly pneumococcal carriage. In contrast, our study showed no association with the frequency of short casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models.

epidemiology↗

bioRxiv2017

Characteristics Of Human Encounters And Social Mixing Patterns Relevant To Infectious Diseases Spread By Close Contact: A Survey In Southwest Uganda

Quantification of human interactions relevant to infectious disease transmission through social contact is central to predict disease dynamics, yet data from low-resource settings remain scarce. We undertook a social contact survey in rural Uganda, whereby participants were asked to recall details about the frequency, type, and socio-demographic characteristics of any conversational encounter that lasted for [≥]5 minutes (henceforth defined as contacts) during the previous day. An estimate of the number of casual contacts (i.e. <5 minutes) was also obtained. A total of 568 individuals were included. On average participants reported having routine contact with 7.2 individuals (range 1-25). Children aged 5-14 years had the highest frequency of contacts and the elderly ([≥]65 years) the fewest (P<0.001). A strong age-assortative pattern was seen, particularly outside the household and increasingly so for contacts occurring further away from home. Adults aged 25-64 years tended to travel more and further than others, and males travelled more frequently than females. Our study provides detailed information on contact patterns and their spatial characteristics in an African setting. It therefore fills an important knowledge gap that will help more accurately predict transmission dynamics and the impact of control strategies in such areas.

epidemiology↗