Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014–15

• DOI: 10.3201/eid2403.171499
• Publication Date: 2018-01-30T14:06:55Z
• Authors: Derek R. MacFadden; Allison McGeer; Taryn Athey; Stephen Perusini; Romy Olsha; Aimin Li; AliReza Eshaghi; Jonathan B. Gubbay; William P. Hanage
• Keywords: Pandemic

Abstract Adequacy of the current clinical definition institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis that occurred during 2014–15 season in Toronto, Canada. sequenced 2 earliest submitted samples positive for A(H3N2) from each 38 reported long-term care facilities. Genome showed most outbreak pairs identified by using were highly related. Inclusion surveillance demonstrated sources likely introductions broader circulating lineages. Pairwise distance majority hemagglutinin-specific genes enabled identification thresholds discrimination within between pairs; area under curve ranged 0.93–0.95. Routine defining facilities unlikely to add significantly definition. Sequencing may prove useful investigating introductions.