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 …

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

HE Grant, S Roy, R Williams, H Tutill, B Ferns, PA Cane… - Retrovirology, 2022 - Springer
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 …

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 …

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 …

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 …

Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study

M Hall, T Golubchik, D Bonsall, L Abeler-Dörner… - The Lancet …, 2024 - thelancet.com
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 …

Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models

X Xi, SEF Spencer, M Hall… - Journal of the Royal …, 2022 - academic.oup.com
Pathogen deep-sequencing is an increasingly routinely used technology in infectious
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 …

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 …

Demographics of people who transmit HIV-1 in Zambia: a molecular epidemiology analysis in the HPTN-071 PopART study

M Hall, T Golubchik, D Bonsall, L Abeler-Dörner… - medRxiv, 2021 - medrxiv.org
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 …