Investigating the sequence variation in the influenza A matrix genes during the 2017-2018 and 2018-2019 seasons in samples from a local population in London

Abstract

Recent publications have highlighted the emergence of mutations in the M1 gene of both influenza A H1N1pdm09 and H3N2 subtypes affecting the performance of commercial RT-PCR assays. Respiratory samples from the 2018/2019 season positive by our in-house RT-PCR for influenza A were analysed for the prevalence and impact of any M1 gene mutations. Sequence information was used to re-design primers for our routine assay and their performance assessed. Forty-five samples, consisting of 11 H1N1pdm09 and 34 H3N2 subtypes, together with the NIBSC H1N1 control were sequenced. All samples displayed the core mutations for H1N1 M1(C154T; G174A and G238A) and for H3N2 M1(C153T; C163T and G189T); three of the H1N1pdm09 viruses also showed a small number of point mutations. None of the mutations appeared to affect either the sensitivity or efficiency of the RT-PCR when compared to the re-designed primers. Although the mutations we found agreed with those in the publications cited we did not encounter any problems with our routine diagnostic assay and no improvements were found when the primers were modified to suit those mutations. However, it is likely that the influenza A virus M1 gene will accumulate further mutations that could impact RT-PCR assays and, therefore, it would be prudent to implement routine sequencing of samples during the influenza seasons to ensure no loss in assay performance.