Full-length sequence analysis of HIV-1 isolate CM237: a CRF01_AE/B intersubtype recombinant from Thailand

The Walter Reed Army Institute of Research (WRAIR) has assembled a panel of human immunodeficiency virus type 1 (HIV-1) isolates designed to assess performance of viral load assays. In most cases, subtype was assigned based on limited sequence information from gag and/or env regions of the genome. Since HIV-1 quantitative assays target different regions of the genome, gag p24 (gag), pol integrase (polIN), and env gp41 immunodominant (IDR) regions were sequenced. For isolate CM237 from Thailand, previously designated as subtype B, gag p24 and IDR sequences clustered with HIV-1 group M subtype B, whereas pol integrase (IN) was derived from circulating recombinant form CRF01_AE. Therefore, we determined the full-length sequence of CM237 to characterize its genomic organization. This analysis confirmed that CM237 is a CRF01_AE/B mosaic with the majority of the genome derived from subtype B and the 3' end of reverse transcriptase through integrase from CRF01_AE.