Methods combining genomic and epidemiological data in the reconstruction of transmission trees: a systematic review
H Duault, B Durand, L Canini - Pathogens, 2022 - mdpi.com
In order to better understand transmission dynamics and appropriately target control and
preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks …
preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks …
A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism
We present 109 near full-length HIV genomes amplified from blood serum samples obtained
during early 1986 from across Uganda, which to our knowledge is the earliest and largest …
during early 1986 from across Uganda, which to our knowledge is the earliest and largest …
MicrobeTrace: Retooling molecular epidemiology for rapid public health response
EM Campbell, A Boyles, A Shankar, J Kim… - PLoS computational …, 2021 - journals.plos.org
Outbreak investigations use data from interviews, healthcare providers, laboratories and
surveillance systems. However, integrated use of data from multiple sources requires a …
surveillance systems. However, integrated use of data from multiple sources requires a …
Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters
V Novitsky, JA Steingrimsson, M Howison, FS Gillani… - Scientific reports, 2020 - nature.com
Public health interventions guided by clustering of HIV-1 molecular sequences may be
impacted by choices of analytical approaches. We identified commonly-used clustering …
impacted by choices of analytical approaches. We identified commonly-used clustering …
Detection of HIV-1 transmission clusters from dried blood spots within a universal test-and-treat trial in East Africa
E Pujol-Hodge, JF Salazar-Gonzalez, D Ssemwanga… - Viruses, 2022 - mdpi.com
The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal
test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 …
test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 …
Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study
Background In the last decade, universally available antiretroviral therapy (ART) has led to
greatly improved health and survival of people living with HIV in sub-Saharan Africa, but …
greatly improved health and survival of people living with HIV in sub-Saharan Africa, but …
Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models
Pathogen deep-sequencing is an increasingly routinely used technology in infectious
disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit …
disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit …
Nonstudent young men put students at high risk of HIV acquisition in Guangxi, China: a phylogenetic analysis of surveillance data
H Jiang, G Lan, Q Zhu, S Liang, J Li… - Open Forum …, 2022 - academic.oup.com
Background We sought to identify students and their sexual partners in a molecular
transmission network. Methods We obtained 5996 HIV protease and reverse transcriptase …
transmission network. Methods We obtained 5996 HIV protease and reverse transcriptase …
Phylogenetic networks and parameters inferred from HIV nucleotide sequences of high-risk and general population groups in Uganda: Implications for epidemic …
N Bbosa, D Ssemwanga, RN Nsubuga, N Kiwanuka… - Viruses, 2021 - mdpi.com
Phylogenetic inference is useful in characterising HIV transmission networks and assessing
where prevention is likely to have the greatest impact. However, estimating parameters that …
where prevention is likely to have the greatest impact. However, estimating parameters that …
Demographics of people who transmit HIV-1 in Zambia: a molecular epidemiology analysis in the HPTN-071 PopART study
Background In the last decade, universally available antiretroviral therapy (ART) has led to
greatly improved health and survival of people living with HIV in sub-Saharan Africa, and …
greatly improved health and survival of people living with HIV in sub-Saharan Africa, and …