CRF01_AE accounted for 84% of the recent infections among men-who-have-sex-with-men (MSM) in Liaoning province of northeastern China. CRF01_AE strains were grouped into two distinct clusters (designated clusters 1 and 2) that were also detected in other regions in China. Phylodynamics study revealed that these two CRF01_AE strains were independently introduced into MSM population in China in the early and mid 1990s. Our study elucidated unique features of dynamics and interrelationships of MSM epidemics in China.
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