Molecular epidemiology and genetic characterization of influenza B virus in Lebanon during 2016–2018

Influenza B viruses are a major cause of serious acute respiratory infections in humans. Nasopharyngeal swabs were collected from subjects with influenza-like illness during October 2016–June 2018 and screened for influenza A and B. The hemagglutinin (HA) and neuraminidase (NA) genes of the Lebanese influenza B specimens were sequenced and phylogenetically compared with the vaccine strains and specimens from the Eastern Mediterranean Region and Europe. Influenza A and B viruses co-circulated between October and May and peaked between January and March. During the 2016–2017 season, A/H3N2 (33.4%) and B/Yamagata (29.7%) were the predominantly circulating viruses followed by B/Victoria and A/H1N1pdm09 viruses. During the 2017–2018 season, A/H3N2 (31.5%) and A/H1Npdm09 (29.3%) were most prevalent with co-circulation of B/Yamagata and to a lesser extent B/Victoria viruses. The B/Yamagata specimens belonged to clade-3 while the B/Victoria belonged to clade-1A. None of the analyzed specimens had a mutation known to confer resistance to NA inhibitors (NAIs). Multiple subtypes of influenza co-circulate each year in Lebanon with a peak between January and March. The trivalent vaccine included a B/Victoria strain which mismatched the B/Yamagata lineage that predominated during the study period, highlighting the importance of quadrivalent vaccines. •Multiple influenza types/subtypes circulation in Lebanon during 2016–2018.•No resistant markers of neuraminidase inhibitors were detected among influenza B.•Circulation of B/Yamagata clade-3 and B/Victoria clade-1A viruses in Lebanon.•Flu B trivalent vaccine strain was mismatched to the dominantly circulating one.