Search Results - "Brown, Andrew Leigh"

The Global Transmission Network of HIV-1 by Wertheim, Joel O., Brown, Andrew J. Leigh, Hepler, N. Lance, Mehta, Sanjay R., Richman, Douglas D., Smith, Davey M., Pond, Sergei L. Kosakovsky

“…Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of…”
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HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens by Kosakovsky Pond, Sergei L, Weaver, Steven, Leigh Brown, Andrew J, Wertheim, Joel O

“…In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens,…”
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Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic by Brown, Andrew J. Leigh, Lycett, Samantha J., Weinert, Lucy, Hughes, Gareth J., Fearnhill, Esther, Dunn, David T.

“…Background. Many studies of sexual behavior have shown that individuals vary greatly in their number of sexual partners over time, but it has proved difficult…”
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Episodic sexual transmission of HIV revealed by molecular phylodynamics by LEWIS, F, HUGHES, G.J, RAMBAUT, A, POZNIAK, A, BROWN, A.J.L

“…The structure of sexual contact networks plays a key role in the epidemiology of sexually transmitted infections, and their reconstruction from interview data…”
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Dynamics of the emergence and establishment of a newly dominant genotype of Japanese encephalitis virus throughout Asia by Schuh, Amy J, Ward, Melissa J, Leigh Brown, Andrew J, Barrett, Alan D T

“…In recent years, genotype I (GI) of Japanese encephalitis virus (JEV) has displaced genotype III (GIII) as the dominant virus genotype throughout Asia. In this…”
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Reassortment patterns of avian influenza virus internal segments among different subtypes by Lu, Lu, Lycett, Samantha J, Leigh Brown, Andrew J

“…The segmented RNA genome of avian Influenza viruses (AIV) allows genetic reassortment between co-infecting viruses, providing an evolutionary pathway to…”
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Phylodynamics of Infectious Disease Epidemics by Volz, Erik M, Kosakovsky Pond, Sergei L, Ward, Melissa J, Leigh Brown, Andrew J, Frost, Simon D. W

“…We present a formalism for unifying the inference of population size from genetic sequences and mathematical models of infectious disease in populations. Virus…”
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Quantifying predictors for the spatial diffusion of avian influenza virus in China by Lu, Lu, Leigh Brown, Andrew J, Lycett, Samantha J

“…Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the…”
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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 by Grant, Heather E, Roy, Sunando, Williams, Rachel, Tutill, Helena, Ferns, Bridget, Cane, Patricia A, Carswell, J Wilson, Ssemwanga, Deogratius, Kaleebu, Pontiano, Breuer, Judith, Leigh Brown, Andrew J

“…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…”
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High-Level Drug-Resistant Mutations among HIV-1 Subtype A6 and CRF02_AG in Kazakhstan by Sanaubarova, Ainur, Pujol-Hodge, Emma, Dzissyuk, Natalya, Lemey, Philippe, Vermund, Sten H, Leigh Brown, Andrew J, Ali, Syed

“…HIV incidence in Kazakhstan increased by 73% between 2010 and 2020, with an estimated 35,000 people living with HIV (PLHIV) in 2020. The development of…”
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Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions by HUE, Stéphane, BROWN, Alison E, LEIGH BROWN, Andrew J, RAGONNET-CRONIN, Manon, LYCETT, Samantha J, DUNN, David T, FEARNHILL, Esther, DOLLING, David I, POZNIAK, Anton, PILLAY, Deenan, DELPECH, Valerie C

“…HIV-1 subtype B infections are associated with MSM in the UK. Yet, around 13% of subtype B infections are found in those reporting heterosexual contact as…”
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Phylogeography of Japanese encephalitis virus: genotype is associated with climate by Schuh, Amy J, Ward, Melissa J, Brown, Andrew J Leigh, Barrett, Alan D T

“…The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and…”
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Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom by Hughes, Gareth J, Fearnhill, Esther, Dunn, David, Lycett, Samantha J, Rambaut, Andrew, Leigh Brown, Andrew J

“…The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network…”
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Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico by Lu, Lu, Lycett, Samantha J, Leigh Brown, Andrew J

“…Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the…”
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A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project by Yebra, Gonzalo, Frampton, Dan, Gallo Cassarino, Tiziano, Raffle, Jade, Hubb, Jonathan, Ferns, R Bridget, Waters, Laura, Tong, C Y William, Kozlakidis, Zisis, Hayward, Andrew, Kellam, Paul, Pillay, Deenan, Clark, Duncan, Nastouli, Eleni, Leigh Brown, Andrew J

“…The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from…”
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Employing phylogenetic tree shape statistics to resolve the underlying host population structure by Kayondo, Hassan W, Ssekagiri, Alfred, Nabakooza, Grace, Bbosa, Nicholas, Ssemwanga, Deogratius, Kaleebu, Pontiano, Mwalili, Samuel, Mango, John M, Leigh Brown, Andrew J, Saenz, Roberto A, Galiwango, Ronald, Kitayimbwa, John M

“…Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal…”
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Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa by Pujol-Hodge, Emma, Salazar-Gonzalez, Jesus F, Ssemwanga, Deogratius, Charlebois, Edwin D, Ayieko, James, Grant, Heather E, Liegler, Teri, Atkins, Katherine E, Kaleebu, Pontiano, Kamya, Moses R, Petersen, Maya, Havlir, Diane V, Leigh Brown, Andrew J

“…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…”
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Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison by Ratmann, Oliver, Hodcroft, Emma B, Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon, Hossain, A S Md Mukarram, Joy, Jeffrey B, Kendall, Michelle, Kühnert, Denise, Leventhal, Gabriel E, Liang, Richard, Plazzotta, Giacomo, Poon, Art F Y, Rasmussen, David A, Stadler, Tanja, Volz, Erik, Weis, Caroline, Leigh Brown, Andrew J, Fraser, Christophe

“…Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far,…”
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The contribution of viral genotype to plasma viral set-point in HIV infection by Hodcroft, Emma, Hadfield, Jarrod D, Fearnhill, Esther, Phillips, Andrew, Dunn, David, O'Shea, Siobhan, Pillay, Deenan, Leigh Brown, Andrew J

“…Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely…”
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An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1 by Kosakovsky Pond, Sergei L, Posada, David, Stawiski, Eric, Chappey, Colombe, Poon, Art F Y, Hughes, Gareth, Fearnhill, Esther, Gravenor, Mike B, Leigh Brown, Andrew J, Frost, Simon D W

“…Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined…”
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