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To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
This article was published in the following journal.
Name: Nature communications
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Monitoring of information sources of potential value in detecting an emerging epidemic, whether naturally occurring or the result of bioterrorism.
Animate or inanimate sources which normally harbor disease-causing organisms and thus serve as potential sources of disease outbreaks. Reservoirs are distinguished from vectors (DISEASE VECTORS) and carriers, which are agents of disease transmission rather than continuing sources of potential disease outbreaks.
A species of gram-negative, aerobic bacteria that is the etiologic agent of epidemic typhus fever acquired through contact with lice (TYPHUS, EPIDEMIC LOUSE-BORNE) as well as Brill's disease.
A republic in southern Africa, the southernmost part of Africa. It has three capitals: Pretoria (administrative), Cape Town (legislative), and Bloemfontein (judicial). Officially the Republic of South Africa since 1960, it was called the Union of South Africa 1910-1960.
A highly contagious disease characterized by subconjunctival hemorrhage, sudden swelling of the eyelids and congestion, redness, and pain in the eye. Epidemic conjunctivitis caused by Enterovirus 70 (EV-70) was first described in Africa in 1969. It is caused also by Coxsackievirus A24 variant (CA24v). Epidemics by this organism have appeared most frequently in Asia.
Human Immuno Deficiency Virus (HIV)
Human Immunodeficiency Virus (HIV), the causative agent of AIDS. The Human Immunodeficiency Virus, more commonly known as HIV, is a member of the lentivirus sub-set of the retrovirus family of pathogens. It causes AIDS, or Acquired Immuno Deficiency Sy...