Background: Recent years reports in Guangxi showed that CRF01_AE had dominated in the central city Nanning and the eastern city Liuzhou, and there may be more than one introductions of CRF01_AE in Guangxi.To gain a deeper understanding on the evolution of the HIV-1 epidemic and genetic characterization of CRF01_AE in Guangxi, we recruited 349 HIV/AIDS patients from the cities all over Guangxi.Methods: Full-length gag, pol genes and partial env gene were amplified and analyzed using phylogenetic, recombinart, intersubject diversity, signature pattern, and sequence logo approaches.Results: The distribution of HIV-1 genotypes based on gag, pol and partial env sequences (n=349) was as follows: CRF01_AE (66.5%), CRF08_BC (19.2%), CRF07_BC (7.2%), URF (4.6%), subtype B (1.7%), and subtype B (0.9%).CRF01_AE predominated in all geographical regions and risk populations and there were multiple introductions of CRF01_ AE strains in Guangxi.We found a peculiar CRF01_AE monophyletic lineage distinct from other CRF01_AE viruses, and we designated it "CRF01_AE-v" for convenience.CRF01_ AE-v circulating in both heterosexuals and injecting drug users (IDUs) had accounted for 39.7% of CRF01_AE.It showed a selective advantage in the Guangxi population and formed its own characteristic compared with all the CRF01_AE references.Conclusions: Our results suggested that CRF01_AE-v was a new variant of CRF0 1_AE and it might lead to a new epidemic in Guangxi.