An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay.

•Novel tool for HIV subtyping, which able to identify subtypes B, C, CRF01_AE for Thailand, Southeast Asian countries, India and China.•The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings.•Sensitive enough to capture the recombinant genomes and dual infections in large-scale populations.•Provide an option for molecular surveillance of HIV-1 in the area is vital for vaccine development and evaluation.