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. 2015 Dec 15;5:18147. doi: 10.1038/srep18147

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Copyright © 2015, Macmillan Publishers Limited

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(A) Bootscanning plot analysis. Analyses were performed using CRF01_AE (90TH.CM240) and subtype B (83FR.HXB2) as parental subtypes, and subtype C (95IN21068) as the reference strain with a moving window of 350 nt and a step of 50 nt. (B) The deduced subtype structure. Black = subtype B (of US-European origin); gray = CRF01_AE; blank = sequence data not available. (C) Subgenomic phylogenies estimated using the neighbor-joining method from alignments representing regions I, III and V (CRF01_AE), and Regions II and IV (subtype B). Bootstrap scores greater than 70% are indicated at corresponding nodes. “01TH” = Thai CRF01_AE; “01AF” = African CRF01_AE; clusters 1 and 2 = CRF01_AE variants associated with transmission among MSM in China (An et al.; Kondo et al. JV).