title: The global transmission network of HIV-1.
abstract: Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of the properties and dynamics of this network is essential for surveillance, prevention, and eventual eradication of HIV. Here, we apply a simple and computationally efficient network-based approach to all publicly available HIV polymerase sequences in the global database, revealing a contemporary picture of the spread of HIV-1 within and between countries. This approach automatically recovered well-characterized transmission clusters and extended other clusters thought to be contained within a single country across international borders. In addition, previously undescribed transmission clusters were discovered. Together, these clusters represent all known modes of HIV transmission. The extent of international linkage revealed by our comprehensive approach demonstrates the need to consider the global diversity of HIV, even when describing local epidemics. Finally, the speed of this method allows for near-real-time surveillance of the pandemic's progression.
authors.affiliation: Department of Pathology.
authors.forename: Joel O
authors.initials: JO
authors.lastname: Wertheim
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Leigh Brown
authors.forename: N Lance
authors.initials: NL
authors.lastname: Hepler
authors.forename: Sanjay R
authors.initials: SR
authors.lastname: Mehta
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D018562:Disease Transmission, Infectious; D014644:Genetic Variation; D014943:Global Health; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D017720:Molecular Epidemiology; D058873:Pandemics
keywords: human immunodeficiency virus; molecular epidemiology; transmission network