Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study

Agua-Agum, Junerlyn; Ariyarajah, Archchun; Aylward, Bruce; Bawo, Luke; Bilivogui, Pepe; Blake, Isobel M.; Brennan, Richard J.; Cawthorne, Amy; Cleary, Eilish; Clement, Peter; Conteh, Roland; Cori, Anne; Dafae, Foday; Dahl, Benjamin; Dangou, Jean-Marie; Diallo, Boubacar; Donnelly, Christl A.; Dorigatti, Ilaria; Dye, Christopher; Eckmanns, Tim; Fallah, Mosoka; Ferguson, Neil M.; Fiebig, Lena; Fraser, Christophe; Garske, Tini; Gonzalez, Lice; Hamblion, Esther; Hamid, Nuha; Hersey, Sara; Hinsley, Wes; Jambei, Amara; Jombart, Thibaut; Kargbo, David; Keita, Sakoba; Kinzer, Michael; George, Fred Kuti; Godefroy, Beatrice; Gutierrez, Giovanna; Kannangarage, Niluka; Mills, Harriet L.; Moller, Thomas; Meijers, Sascha; Mohamed, Yasmine; Morgan, Oliver; Nedjati-Gilani, Gemma; Newton, Emily; Nouvellet, Pierre; Nyenswah, Tolbert; Perea, William; Perkins, Devin; Riley, Steven; Rodier, Guenael; Rondy, Marc; Sagrado, Maria; Savulescu, Camelia; Schafer, Ilana J.; Schumacher, Dirk; Seyler, Thomas; Shah, Anita; Van Kerkhove, Maria D.; Wesseh, C. Samford; Yoti, Zabulon

We explored the relationship between district-level (second administrative division) transmission intensity and (1) the proportion of cases reporting funeral attendance amongst those reporting any exposure and (2) the proportion of cases ever hospitalised and the proportion of cases hospitalised 4 days (4 days was the median delay from symptom onset to hospitalisation; see Figure m in S1 Text for sensitivity analysis to that threshold). The transmission intensity was quantified by the reproduction number, R, which estimates the average number of secondary cases per index case [11, 18] (see section 1.6 in S1 Text). We estimated the reproduction number (R d m ) and the proportion (p d m ), for every district (d) in all three countries over monthly intervals (m). (R d m was estimated with the R package "EpiEstim" [19] using districtlevel incidence, presented in Fig 1 at the country level; see section 1.6 in S1 Text.) The relationship between (R d m ) and the proportions was explored using linear regressions. As these quantities were estimated from a sample of data with a level of uncertainty, we used a custom linear regression method that accounts for measurement error [20, 21] . The method to compute the correlation coefficient was also adapted to account for measurement error (see section 1.7 in S1 Text).