High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

Adrian Egli; Nina Goldman; Nicola F. Müller; Myrta Brunner; Daniel Wüthrich; Sarah Tschudin-Sutter; Emma Hodcroft; Richard Neher; Claudia Saalfrank; James Hadfield; Trevor Bedford; Mohammedyaseen Syedbasha; Thomas Vogel; Noémie Augustin; Jan Bauer; Nadine Sailer; Nadezhda Amar-Sliwa; Daniela Lang; Helena M.B. Seth-Smith; Annette Blaich; Yvonne Hollenstein; Olivier Dubuis; Michael Nägele; Andreas Buser; Christian H. Nickel; Nicole Ritz; Andreas Zeller; Tanja Stadler; Manuel Battegay; Rita Schneider-Sliwa

Local cluster identification. To identify sets of sequences from Basel that were likely to have been 759 transmitted locally, we reconstructed the geographic origins of lineages that were introduced into 760 Basel. Therefore, we used the phylogenetic tree distributions for each initial cluster to reconstruct 761 the ancestral states using parsimony. We made some modifications to the standard algorithm for 762 parsimony ancestral state reconstruction to reflect our prior assumption, that Basel is unlikely to 763 act as a relevant source of influenza on a global scale. If any descendent was not in Basel, the 764 node was classified as "not Basel". Since the influenza season covers only a few months, we 765 additionally assumed that lineages are unlikely to persist in Basel for more than 5 weeks (0.1 766 years) without being sampled. To reflect this assumption, we classified internal nodes that are 767 more than 0.1 years from a sample from Basel to be either outside of Basel, or to be in an unknown