Replication Data for: HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya

A two-way strategy was used to obtain HIV genetic data from Mombasa, Nairobi and Kisumu. Firstly, we retrieved HIV genetic data that is freely available in the public domain, and assigned characteristics by gender, age, date of collection, region of origin and risk group (MSM, FSW, HET). Secondly, we generated additional HIV genetic data from samples requested from our partners running well-characterized HIV studies from Mombasa, Nairobi and Kisumu. These sequences (N=4058) were analysed to describe HIV genotypes, transmission clusters and evolutionary dynamics in HIV-1 transmission using a phylogenetic approach. Nucleotide sequences were deposited in GenBank under the following accession numbers: MT084914 - MT085076.