Molecular Epidemiology of HIV-1 virus in Egypt: A major change in the circulating subtypes.

Background Human immunodeficiency virus type 1 (HIV-1) is characterized by high genetic diversity due to its high-mutation and recombination rates. Although, there is an increasing prevalence of circulating recombinant forms (CRFs) worldwide. Subtype B is still recognized as the predominant subtype in the Middle East and North Africa (MENA) region. There is a limited sampling of HIV in this region due to its low prevalence. The main purpose of this study is to provide a summary of the current status of the resident HIV subtypes and their distribution among Egyptian patients. Methodology Forty-five HIV-1 patients were included in this study. Partial pol gene covering the protease (PR) and reverse transcriptase (RT) was successfully amplified in 21 HIV patients using nested PCR of cDNA of the viral genomic RNA, then sequenced. The sequence data were used for viral HIV-1 subtyping by 5 online subtyping tools: NCBI viral genotyping tool, Stanford University HIV database (HIVDB) subtyping program, REGA tool, Context-based modeling for expeditious typing (COMET) tool, and Recombinant identification program (RIP) tool. The final subtype assignment was based on molecular phylogenetic analysis. Results Unexpectedly, non-B subtypes are dominating with the most common circulating one is CRF02_AG (57.1%) followed by subtype B (14.3%), subtype BG recombinant (9.5%), CRF35_AD (9.5%), subtype A1 and CRF06_cpx (4.8 % each). Conclusion To the best of our knowledge, this is the first study to tackle HIV-1 subtyping among the group of HIV-1 patients in Egypt. CRF02_AG is the most prevalent subtype in Egypt.