Influenza-like illness outbreaks in nursing homes in Corsica, France, 2014–2015: epidemiological and molecular characterization

Masse, S.; Minodier, L.; Heuze, G.; Blanchon, T.; Capai, L.; Falchi, A.

A(H3N2) viral specimens with a cycle threshold <30 were processed and submitted to haemagglutinin (HA) sequencing. The HA sequences of A(H3N2) from seven Weekly number of ILI residents declared by Nursing Homes and weekly number of ILI residents swabbed NH residents and one NH HCW were amplified by RT-PCR using primer sets for human A(H3N2) (nucleic acids 48-1642) (Minodier et al. 2014 ). Twenty-one sequences detected in patients enrolled by GPs in the Corsican Sentinelles Network during the 2014-2015 influenza season were also included. Double-stranded sequencing of the purified PCR products (primer sequences are available on request) was performed using an Applied Biosystems Sequencer (ABI 3700, PerkinElmer). Phylogenetic trees were constructed using a neighbour-joining method based on Kimura's two-parameter genetic distances matrix with 1000 bootstrap replicates (n = 1000) using the MEGA 6.0 program. The nucleotide sequence data from this study were deposited into GenBank at the National Center for Biotechnology Information (NCBI) (GenBank KU289606-KU289637) (http://www.ncbi.nlm.nih.gov).