Incidence of matrix genes mutations affecting PCR tests among influenza H3N2 clades circulating during the 2014/15 season.

Influenza circulating during the 2014/15 season was associated with significant drift and the emergence of new H3N2 subgroups. It was also known that mutations were accumulating in the WHO-recommended amplification region of the M1 gene, affecting the performance of many commercial polymerase chain reaction assays. However, the prevalence of M1 target mutations was unknown. To investigate this, isolates from the GISAID database from Australia (n=100), Europe (n=473), and the USA (n=1175) were analyzed. The predominate clade was 3C.2a (75%), with a higher representation among USA isolates (81%). The M1 target demonstrated four primary sequence patterns, designated A-D. Pattern D was most often observed (84%). Some clades correlated with M1 target patterns, as seen between subclades 3C.2a and 3C.3a and patterns D and C, respectively. 3C.3 isolates were more diverse, with three patterns represented. Among the 3C.3b isolates, pattern B predominated in non-USA viruses, while pattern D predominated among USA isolates.