Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? (Q35006672)

5 August 2017

title

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? (English)

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5 August 2017

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Paul Kellam

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Túlio de Oliveira

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object named as

Tulio de Oliveira

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Andrew J Leigh Brown

object named as

Andrew L Brown

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3

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Myron S. Cohen

series ordinal

8

object named as

Myron S Cohen

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5 August 2017

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Deenan Pillay

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5 August 2017

2

Joshua T Herbeck

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Christophe Fraser

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5 August 2017

Ann M Dennis

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5 August 2017

language of work or name

English

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publication date

1 October 2014

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Journal of Acquired Immune Deficiency Syndromes

5 August 2017

published in

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5 August 2017

volume

67

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5 August 2017

issue

2

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5 August 2017

page(s)

181-195

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Consolidated Guidelines on the Use of Antiretroviral Drugs for Treating and Preventing HIV Infection: Recommendations for a Public Health Approach

5 August 2017

cites work

1 reference

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Linkage of viral sequences among HIV-infected village residents in Botswana: estimation of linkage rates in the presence of missing data

8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

1 reference

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8 July 2018

1 reference

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8 July 2018

1 reference

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Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees

8 July 2018

1 reference

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Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa

8 July 2018

1 reference

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Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences.

8 July 2018

1 reference

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Stabilizing HIV prevalence masks high HIV incidence rates amongst rural and urban women in KwaZulu-Natal, South Africa

8 July 2018

1 reference

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Prevalence of transmitted HIV drug resistance in Botswana: lessons learned from the HIVDR-Threshold Survey conducted among women presenting for routine antenatal care as part of the 2007 national sentinel survey.

8 July 2018

1 reference

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HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: a molecular epidemiological study

8 July 2018

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8 July 2018

1 reference

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8 July 2018

1 reference

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Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland

8 July 2018

1 reference

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Public database for HIV drug resistance in southern Africa

8 July 2018

1 reference

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Barking up the wrong evidence tree. Comment on Lurie & Rosenthal, "Concurrent partnerships as a driver of the HIV epidemic in sub-Saharan Africa? The evidence is limited".

8 July 2018

1 reference

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Ethical challenges in cluster randomized controlled trials: experiences from public health interventions in Africa and Asia

8 July 2018

1 reference

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Phylodynamics of infectious disease epidemics

8 July 2018

1 reference

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Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom

8 July 2018

1 reference

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Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe

8 July 2018

1 reference

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Spatial phylodynamics of HIV-1 epidemic emergence in east Africa.

8 July 2018

1 reference

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On incomplete sampling under birth-death models and connections to the sampling-based coalescent

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Clinical presentation and diagnosis of primary HIV-1 infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Localized spatial clustering of HIV infections in a widely disseminated rural South African epidemic

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Phylogenetic diversity and low level antiretroviral resistance mutations in HIV type 1 treatment-naive patients from Cape Town, South Africa

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Episodic sexual transmission of HIV revealed by molecular phylodynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

The emergence of HIV/AIDS in the Americas and beyond

8 July 2018

1 reference

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Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

8 July 2018

1 reference

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High rates of forward transmission events after acute/early HIV-1 infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Evaluating the proximate determinants framework for HIV infection in rural Zimbabwe.

8 July 2018

1 reference

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Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups

8 July 2018

1 reference

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Bayesian coalescent inference of past population dynamics from molecular sequences

8 July 2018

1 reference

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Integrating demographic and epidemiological approaches to research on HIV/AIDS: the proximate-determinants framework

8 July 2018

1 reference

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The molecular population genetics of HIV-1 group O

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV transmission risk behavior among men and women living with HIV in 4 cities in the United States

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Acute HIV revisited: new opportunities for treatment and prevention

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Unifying the epidemiological and evolutionary dynamics of pathogens

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Prognosis of HIV-1-infected patients starting highly active antiretroviral therapy: a collaborative analysis of prospective studies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Human immunodeficiency virus. Phylogeny and the origin of HIV-1.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

A cladistic measure of gene flow inferred from the phylogenies of alleles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Molecular epidemiology of HIV transmission in a dental practice

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Population dynamics of HIV-2 in rural West Africa: comparison with HIV-1 and ongoing transmission at the heart of the epidemic

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Evidence of multiple introductions of HIV-1 subtype C in Angola

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Short communication: High prevalence of transmitted antiretroviral drug resistance among newly HIV type 1 diagnosed adults in Mombasa, Kenya

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Prevalence of drug-resistant mutations in newly diagnosed drug-naïve HIV-1-infected individuals in a treatment site in the waterberg district, limpopo province

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV transmissions during seroconversion contribute significantly to new infections in men who have sex with men in Australia

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Epidemiological network analysis in HIV-1 B infected patients diagnosed in Italy between 2000 and 2008.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Combination prevention: a deeper understanding of effective HIV prevention

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Concurrency driving the African HIV epidemics: where is the evidence?

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV-1 genetic diversity and transmitted drug resistance in health care settings in Maputo, Mozambique

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Surprisingly high prevalence of subtype C and specific HIV-1 subtype/CRF distribution in men having sex with men in Senegal

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Genetic characterization of HIV-1 strains in Togo reveals a high genetic complexity and genotypic drug-resistance mutations in ARV naive patients

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naïve individuals

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Resistance mutational analysis of HIV type 1 subtype C among rural South African drug-naive patients prior to large-scale availability of antiretrovirals

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

The WHO public-health approach to antiretroviral treatment against HIV in resource-limited settings.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Molecular testing of multiple HIV-1 transmissions in a criminal case.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Genetic and phylogenetic analyses of HIV-1 corroborate the transmission link hypothesis

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Continuation of high-risk behavior by HIV-positive drug users. Treatment implications.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV-1 nomenclature proposal

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Revealing the history of infectious disease epidemics through phylogenetic trees

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

Subtype Assignment and Phylogenetic Analysis of HIV Type 1 Strains in Patients from Swaziland

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4304655

HIV-1 drug resistance in antiretroviral-naive patients in sub-Saharan Africa

9 December 2018

1 reference

12 December 2020

Phylogenetic Investigation of Transmission Pathways of Drug-Resistant HIV-1 Utilizing Pol Sequences Derived From Resistance Genotyping

1 reference

12 December 2020

Rates of disease progression by baseline CD4 cell count and viral load after initiating triple-drug therapy

1 reference

12 December 2020

Toward a robust monitoring of HIV subtypes distribution worldwide

1 reference

12 December 2020

Transmission networks of HIV-1 among men having sex with men in the Netherlands

1 reference

12 December 2020

Molecular epidemiology of acute hepatitis B in the Netherlands in 2004: nationwide survey

1 reference

12 December 2020

Natural history of HIV-1 infection

1 reference

12 December 2020

10.1097/QAI.0000000000000271

Identifiers

DOI

1 reference

5 August 2017

1 reference

5 August 2017

1 reference