Spatial phylodynamics of HIV-1 epidemic emergence in east Africa.
METHODS
We sought to investigate the evolutionary and historical reasons for the different epidemiological patterns of HIV-1 in the early epidemic. In order to characterize the demographic history of HIV-1 subtypes A and D in east Africa, we examined molecular epidemiology, geographical and historical data.


METHODS
We employed high-resolution phylodynamics to investigate the introduction of HIV-1A and D into east Africa, the geographic trends of viral spread, and the demographic growth of each subtype. We also used geographic information system data to investigate human migration trends, population growth, and human mobility.


RESULTS
HIV-1A and D were introduced into east Africa after 1950 and spread exponentially during the 1970s, concurrent with eastward expansion. Spatiotemporal data failed to explain the establishment and spread of HIV based on urban population growth and migration. The low prevalence of the virus in the Democratic Republic of Congo before and after the emergence of the pandemic was, however, consistent with regional accessibility data, highlighting the difficulty in travel between major population centers in central Africa. In contrast, the strong interconnectivity between population centers across the east African region since colonial times has likely fostered the rapid growth of the epidemic in this locale.


CONCLUSIONS
This study illustrates how phylodynamic analysis of pathogens informed by geospatial data can provide a more holistic and evidence-based interpretation of past epidemics. We advocate that this 'landscape phylodynamics' approach has the potential to provide a framework both to understand epidemics' spread and to design optimal intervention strategies.
Gray
Rebecca R
RR
Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA.
Tatem
Andrew J
AJ
Lamers
Susanna
S
Hou
Wei
W
Laeyendecker
Oliver
O
Serwadda
David
D
Sewankambo
Nelson
N
Gray
Ronald H
RH
Wawer
Maria
M
Quinn
Thomas C
TC
Goodenow
Maureen M
MM
Salemi
Marco
M
D000351:Africa, Eastern / Q000453:epidemiology; D001499:Bayes Theorem; D004196:Disease Outbreaks; D004641:Emigration and Immigration / Q000706:statistics & numerical data / Q000639:trends; D019143:Evolution, Molecular; D040362:Geographic Information Systems; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D011158:Population Growth