Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

08:00 EDT 29th March 2019 | BioPortfolio

Summary of "Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis."

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.


Journal Details

This article was published in the following journal.

Name: Nature communications
ISSN: 2041-1723
Pages: 1411


DeepDyve research library

PubMed Articles [10243 Associated PubMed Articles listed on BioPortfolio]

Interaction between epidemic spread and collective behavior in scale-free networks with community structure.

Many real-world networks exhibit community structure: the connections within each community are dense, while connections between communities are sparser. Moreover, there is a common but non-negligible...

The impact of water crises and climate changes on the transmission of protozoan parasites in Africa.

Waterborne protozoa (WBP) are important cause of several outbreaks all over the world. The report system of WBP in Africa is weak. More than one third of African countries (21/54) reported WBP with ab...

Estimating under-observation and the full size of the 2016 Zika epidemic in Rio de Janeiro.

The 2015-16 Zika epidemic spread quickly from north to south in Brazil. Two striking features were the much higher incidence in young adult women due to sexual transmission, and the serious congenital...

Sexual transmission and the probability of an end of the Ebola virus disease epidemic.

The criteria of zero Ebola cases defined by the World Health Organization did not explicitly account for the sexual transmission and led to multiple recrudescent events in West Africa from 2015-2016, ...

Incorporating media data into a model of infectious disease transmission.

Understanding the effect of media on disease spread can help improve epidemic forecasting and uncover preventive measures to slow the spread of disease. Most previously introduced models have approxim...

Clinical Trials [3439 Associated Clinical Trials listed on BioPortfolio]

Simian Foamy Virus Transmission to Humans

About three quarters of the viral agents that have emerged recently in humans are considered to originate from other animals. These viruses have often evolved and spread into the human pop...

Public Health Targeting of PrEP at HIV Positives' Bridging Networks

This developmental research grant award (R21) requests funds to explore the feasibility and impact of a public health system PrEP intervention in a recently emerging HIV epidemic in Athens...

Efficacy of ART to Interrupt HIV Transmission Networks

The investigators are conducting a study to learn more about the spread of HIV infection within different geographic regions and populations in San Diego County, with the goal of demonstra...

A Prospective Household Observational Cohort Study of Influenza, Respiratory Syncytial Virus and Other Respiratory Pathogens Community Burden and Transmission Dynamics in South Africa

Title: A Prospective Household observational cohort study of Influenza, Respiratory Syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Afri...

Neonatal Vaccination Against Hepatitis B in Africa - Sero-survey in Senegal

Chronic infection with hepatitis B virus (HBV) is a leading cause of death in adults in sub-Saharan Africa (SSA). Prior to the introduction of the hepatitis B vaccine, main modes of transm...

Medical and Biotech [MESH] Definitions

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.

Quick Search


DeepDyve research library

Relevant Topic

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...

Searches Linking to this Article