Background: A surge in scarlet fever in 2014-2019 in England coincided with the emergence of a new subclone of emm1 Streptococcus pyogenes, M1UK. The sublineage diverged from the previously dominant pandemic M1T1 strains by 27 single nucleotide polymorphisms (SNPs) and was characterised by a 10-fold increase in expression of the superantigen SpeA. By 2016, M1UK strains accounted for 84% of M1 invasive strains. At the onset of the COVID-19 pandemic in March 2020, the incidence of reported S. pyogenes infections, including invasive disease, fell. We aimed to develop a rapid molecular-diagnostic test to enable lineage assignment, and determine if M1UK has persisted in the population of M1 strains.
Methods: We optimised an allele-specific PCR (AS-PCR) technique capable of distinguishing M1UK from M1global, using primers specific to 3 of 27 SNPs in M1UK (in rofA, gldA and pstB genes). The PCR was validated using genome-sequenced emm1 strains from 2017 and 2018. It was then used to screen all 305 invasive emm1 isolates referred between January 2020 -December 2020 to the national reference laboratory.
Results: AS-PCR successfully identified strains that were known to be M1global and M1UK. AS-PCR also correctly identified intermediate sublineages including M113SNPs and M123SNPs. When applied to all emm1 invasive isolates from 2020, 278/305 (91.14%) invasive M1 isolates were M1UK, with no intermediate isolates identified.
Summary: The AS-PCR provides an economical and easy alternative to genome sequencing for detection of M1UK isolates. Despite the COVID-19 pandemic, and overall reduction in S. pyogenes disease attributable to emm1, M1UK remained dominant in the population of emm1 S. pyogenes in England.