Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea.

Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a 'true' transmission history remains unclear. In this study, we compared the transmission trees obtained through contact tracing investigations and various inference methods to identify the contribution and value of each approach. We studied eighty-six sequenced cases reported in Guinea between March and November 2015. Contact tracing investigations classified these cases into eight independent transmission chains. We inferred the transmission history from the genetic sequences of the cases (phylogenetic approach), their onset date (epidemiological approach), and a combination of both (combined approach). The inferred transmission trees were then compared to those from the contact tracing investigations. Inference methods using individual data sources (i.e. the phylogenetic analysis and the epidemiological approach) were insufficiently informative to accurately reconstruct the transmission trees and the direction of transmission. The combined approach was able to identify a reduced pool of infectors for each case and highlight likely connections among chains classified as independent by the contact tracing investigations. Overall, the transmissions identified by the contact tracing investigations agreed with the evolutionary history of the viral genomes, even though some cases appeared to be misclassified. Therefore, collecting genetic sequences during outbreak is key to supplement the information contained in contact tracing investigations. Although none of the methods we used could identify one unique infector per case, the combined approach highlighted the added value of mixing epidemiological and genetic information to reconstruct who infected whom.

Determinants of Transmission Risk During the Late Stage of the West African Ebola Epidemic.

Understanding risk factors for Ebola transmission is key for effective prediction and design of interventions. We used data on 860 cases in 129 chains of transmission from the latter half of the 2013-2016 Ebola epidemic in Guinea. Using negative binomial regression, we determined characteristics associated with the number of secondary cases resulting from each infected individual. We found that attending an Ebola treatment unit was associated with a 38% decrease in secondary cases (incidence rate ratio (IRR) = 0.62, 95% confidence interval (CI): 0.38, 0.99) among individuals that did not survive. Unsafe burial was associated with a higher number of secondary cases (IRR = 1.82, 95% CI: 1.10, 3.02). The average number of secondary cases was higher for the first generation of a transmission chain (mean = 1.77) compared with subsequent generations (mean = 0.70). Children were least likely to transmit (IRR = 0.35, 95% CI: 0.21, 0.57) compared with adults, whereas older adults were associated with higher numbers of secondary cases. Men were less likely to transmit than women (IRR = 0.71, 95% CI: 0.55, 0.93). This detailed surveillance data set provided an invaluable insight into transmission routes and risks. Our analysis highlights the key role that age, receiving treatment, and safe burial played in the spread of EVD.

The Response to and Impact of the Ebola Epidemic: Towards an Agenda for Interdisciplinary Research.

BACKGROUND: The 2013-2016 Ebola virus disease (EVD) epidemic in West Africa was the largest in history and resulted in a huge public health burden and significant social and economic impact in those countries most affected. Its size, duration and geographical spread presents important opportunities for research than might help national and global health and social care systems to better prepare for and respond to future outbreaks. This paper examines research needs and research priorities from the perspective of those who directly experienced the EVD epidemic in Guinea. METHODS: The paper reports the findings from a research scoping exercise conducted in Guinea in 2017. This exercise explored the need for health and social care research, and identified research gaps, from the perspectives of different groups. Interviews were carried out with key stakeholders such as representatives of the Ministry of Health, non-governmental organizations (NGOs), academic and health service researchers and members of research ethics committees (N=15); health practitioners (N=12) and community representatives (N=11). Discussion groups were conducted with male and female EVD survivors (N=24) from two distinct communities. RESULTS: This research scoping exercise identified seven key questions for further research. An important research priority that emerged during this study was the need to carry out a comprehensive analysis of the wider social, economic and political impact of the epidemic on the country, communities and survivors. The social and cultural dynamics of the epidemic and the local, national and international response to it need to be better understood. Many survivors and their relatives continue to experience stigma and social isolation and have a number of complex unmet needs. It is important to understand what sort of support they need, and how that might best be provided. A better understanding of the virus and the long-term health and social implications for survivors and non-infected survivors is also needed. CONCLUSION: This study identified a need and priority for interdisciplinary research focusing on the long-term sociocultural, economic and health impact of the EVD epidemic. Experiences of survivors and other non-infected members of the community still need to be explored but in this broader context.