Phylogenetic analysis of the hemagglutinin (HA) gene of A(H3N2) influenza viruses circulating in Northern Italy during the 2016-2017 influenza season

Background A(H3N2) influenza virus predominated in Europe during the 2016-2017 season, characterised by an excess mortality in people >65 years concurrent with A(H3N2) circulation. A molecular and evolutionary characterisation of A(H3N2) detected in Lombardy (Northern Italy) within the Italian Influenza Surveillance Network (InfluNet) during 2016-2017 season was performed. Methods 549 respiratory samples from ILI outpatients (525/549=95.6%) and SARI/ARDS inpatients (24/549=4.4%) were collected in Lombardy from week 46-2016 to week 17-2017. Influenza viruses were typed (A/B) and subtyped (H1pdm09/H3N2) by real-time RT-PCR. A(H3N2) HA complete gene (nt. 1-1778) was phylogenetically analysed. Results Influenza viruses were detected in 52.3% (287/549) specimens; 93.4% (268/287) were A(H3N2). 34% (91/268) was sequenced. All HA sequences clustered in the genetic group 3C, sub-group 3C.2a, which included the vaccine strain A/HongKong/4801/2014 (similarity: 98.3-99.4%). Most (78/91=85.7%) sequences were A/Bolzano/7/2016-like (similarity: 98.7-99.9%) and belonged to sub-clade 3C.2a1, characterised by amino acid (aa) substitutions N171K (in epitope D), I406V and G484E. 41% of these sequences had mutation T135 (loss of a glycosylation site). Two additional sub-clades were identified: 3C.2a2 (7/91=7.7%) and 3C.2a3 (4/91=4.4%), characterised by aa changes N121K/S144K (epitope A/D) and T131K/R142K (epitope A), respectively. 57 mutations in 54 aa positions were identified, many at single sequence level. Most (>80%) aa changes were detected in HA1 subunit and >50% occurred in epitope A or D. No signature substitutions were observed in HA sequences of A(H3N2) strains detected in SARI/ARDS cases or vaccinated individuals. Conclusion The majority of A(H3N2) viruses circulating in 2016-2017 season clustered in sub-clade 3C.2a1, molecularly and antigenically similar to A/HongKong/4801/2014 vaccine strain. Several HA variants were identified. Full-length sequencing will be useful to define the molecular and evolutionary characteristics of these A(H3N2) viruses.