Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and non-pandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.
Preliminary Analysis
Contains (1) BEAST XML input file, (2) empirical tree distribution (1,000 trees) (GTR+gamma substitution model, uncorrelated relaxed clock model, skygrid tree prior), and (3) nexus format sequence alignment.
Sequence data details and alignments for data sets A to D
Contains (1) table with accession numbers, isolate names, sampling years, country/location of sampling and (2) nexus format sequence alignments.
Sequence data details and alignments.zip
Phylogeographic models and empirical tree distributions for data sets A to D
Contains (1) the BEAST XML input file used to generate Figure 1; (2) BEAST XML files used to generate the phylogeographic analyses with an asymmetric diffusion model in Tables S2-S5; and (3) empirical tree distributions (2,000 trees) (GTR+gamma substitution model, uncorrelated relaxed clock model, skygrid tree prior).
Phylogeographic models and empirical tree distributions.zip
Exponential-logistic coalescent model, robust counting and randomisation procedure
Contains (1) the BEAST XML input file for the exponential-logistic coalescent model used to estimate the epidemiological transition time, (2) the BEAST XML input file for the robust counting analysis (Fig. 3 and Figs. S5-S6), and (3) the BEAST XML input file corresponding to the randomisation procedure shown in Fig. S4.
Exponential-logistic demographic mode, robust counting and randomisation procedure.zip