Background: The evolution of influenza viruses causes a decrease in vaccine effectiveness (VE), requiring constant monitoring of mutations and readjustments to the recommended composition of influenza vaccines. We evaluated the VE and the mutations of the viruses present in the Mexican population at the beginning of 2018.

Methods: We diagnosed influenza in outpatients with high-performance Rapid Influenza Diagnostic Test (RIDT) and qRT-PCR. Descriptive statistics were used to describe the study population, while a Xi2 was used to determine clinical variables. VE was analyzed through a negative test design. We sequenced the hemagglutinin (HA) gene, performed a phylogenetic analysis and analyzed the nonsynonymous substitutions both in- and outside antigenic sites.

Results: Of the 240 patients analyzed, 42.5% received the trivalent vaccine, and 37.5% were positive for influenza. The VE for the general population for any influenza virus type or subtype was 37.0%, while the VE for the predominant influenza A(H3N2) subtype was the lowest (19.7%). The phylogenetic analysis of HA showed the co-circulation of clades and subclades 3C.2a1, 3C.2a1b, 3C.2a2, 3C.2a2re, 3C.2a3, and 3C.3a with identities approximately 97%-98% similar to the vaccine composition.

Conclusions: The low VE was related to the co-circulation of multiple clades and subclades of influenza A(H3N2), with sufficient genetic and phenotypic distance to allow for the infection of vaccinated individuals.