Serotype M1 group A Streptococcus strains cause epidemic waves of human inf
ections long thought to be mono- or pauciclonal. The gene encoding an extra
cellular group A Streptococcus protein (streptococcal inhibitor of compleme
nt) that inhibits human complement was sequenced in 1,132 M1 strains recove
red from population-based surveillance of infections in Canada, Finland and
the United States. Epidemic waves are composed of strains expressing a rem
arkably heterogeneous array of variants of streptococcal inhibitor of compl
ement that arise very rapidly by natural selection on mucosal surfaces. Thu
s, our results enhance the understanding of pathogen population dynamics in
epidemic waves and infectious disease reemergence.