Phylogenomics of human immunodeficiency virus type 1 (HIV-1)

HIV-1 belongs to the family of Retroviridae and to the genus of Lentivirus. Its high mutation and recombination rates and high cell turnover result in high levels of genetic diversity. HIV-1 has four different groups (M, N, O and P). However, the HIV-1 world pandemic is caused only by HIV-1 group M. Within HIV-1 group M, the phylogenetic analysis reveals three types of categories, based on the clustering and distances in the phylogenetic tree and on the recombination patterns: subtypes, sub-subtypes and Circulating Recombinant Forms (CRFs). The early use of Sanger sequencing to diagnose HIV-1 drug resistance has resulted in large availability of HIV-1 genomes worldwide. Herein, we describe methods for genotyping HIV-1, bioinformatics tools and databases for HIV phylogenomics, as well as the application of clinical and epidemiological phylogenomic investigations.