Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic

Patrono, Livia Victoria; Vrancken, Bram; Budt, Matthias; Düx, Ariane; Lequime, Sebastian; Boral, Sengül; Gilbert, M. Thomas P.; Gogarten, Jan F.; Hoffmann, Luisa; Horst, David; Merkel, Kevin; Morens, David; Prepoint, Baptiste; Schlotterbeck, Jasmin; Schuenemann, Verena; Suchard, Marc A.; Taubenberger, Jeffery K.; Tenkhoff, Luisa; Urban, Christian; Widulin, Navena; Winter, Eduard; Worobey, Michael; Leendertz, Fabian H.; Schnalke, Thomas; Wolff, Thorsten; Lemey, Philippe; Calvignac-Spencer, Sébastien

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze the first 1918 IAV genomes from Europe and from the first, milder wave of the pandemic. 1918 IAV genomic diversity is consistent with local transmission and frequent long-distance dispersal events and in vitro polymerase characterization suggests potential phenotypic variability. Comparison of first and second wave genomes shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, phylogenetic estimates based on extended molecular clock modelling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of an intrasubtype reassortment origin. One Sentence Summary Much can be learned about past pandemics by uncovering their footprints in medical archives, which we here demonstrate for the 1918 flu pandemic.