10.5061/DRYAD.NN952
Faria, Nuno R.
University of Oxford
Rambaut, Andrew
University of Edinburgh
Suchard, Marc A.
David Geffen School of Medicine at UCLA
Baele, Guy
Rega Institute for Medical Research
Bedford, Trevor
Fred Hutchinson Cancer Research Center
Ward, Melissa J.
University of Edinburgh
Tatem, Andrew J.
Fogarty International Center
Sousa, João D.
Rega Institute for Medical Research
Arinaminpathy, Nimalan
University of Oxford
Pépin, Jacques
Université de Sherbrooke
Posada, David
University of Vigo
Peeters, Martine
University of Montpellier
Pybus, Oliver P.
University of Oxford
Lemey, Philippe
Rega Institute for Medical Research
Data from: The early spread and epidemic ignition of HIV-1 in human populations
Dryad
dataset
2015
20th century
Human Immunodeficiency Virus Type 1
Phylodynamics
2015-07-24T00:00:00Z
2015-07-24T00:00:00Z
en
https://doi.org/10.1126/science.1256739
70066544 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 AnalysisContains (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
DContains (1) table with accession numbers, isolate names, sampling years,
country/location of sampling and (2) nexus format sequence
alignments.Sequence data details and alignments.zipPhylogeographic models
and empirical tree distributions for data sets A to DContains (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.zipExponential-logistic coalescent model, robust counting
and randomisation procedureContains (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
Central Africa
Southern Africa and USA