Episodic sexual transmission of HIV revealed by molecular phylodynamics. by Fraser Lewis, Gareth J Hughes, Andrew Rambaut, Anton Pozniak, Andrew J Leigh Brown

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The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. by John Archer, Andrew Rambaut, Bruce E Taillon, P Richard Harrigan, Marilyn Lewis, David L Robertson

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Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. by Kathryn Campbell, Robert J Gifford, Joshua Singer, Verity Hill, Aine O'Toole, Andrew Rambaut, Katie Hampson, Kirstyn Brunker

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Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. by Gareth J Hughes, Esther Fearnhill, David Dunn, Samantha J Lycett, Andrew Rambaut, Andrew J Leigh Brown, UK HIV Drug Resistance Collaboration

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Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. by Philippe Lemey, Andrew Rambaut, Trevor Bedford, Nuno Faria, Filip Bielejec, Guy Baele, Colin A Russell, Derek J Smith, Oliver G Pybus, Dirk Brockmann, Marc A Suchard

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Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. by Hervé Bourhy, Emmanuel Nakouné, Matthew Hall, Pierre Nouvellet, Anthony Lepelletier, Chiraz Talbi, Laurence Watier, Edward C Holmes, Simon Cauchemez, Philippe Lemey, Christl A Donnelly, Andrew Rambaut

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Spatial dynamics of human-origin H1 influenza A virus in North American swine. by Martha I Nelson, Philippe Lemey, Yi Tan, Amy Vincent, Tommy Tsan-Yuk Lam, Susan Detmer, Cécile Viboud, Marc A Suchard, Andrew Rambaut, Edward C Holmes, Marie Gramer

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APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon. by Andrew E Armitage, Koen Deforche, Chih-Hao Chang, Edmund Wee, Beatrice Kramer, John J Welch, Jan Gerstoft, Lars Fugger, Andrew McMichael, Andrew Rambaut, Astrid K N Iversen

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Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. by Jayna Raghwani, Andrew Rambaut, Edward C Holmes, Vu Ty Hang, Tran Tinh Hien, Jeremy Farrar, Bridget Wills, Niall J Lennon, Bruce W Birren, Matthew R Henn, Cameron P Simmons

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Phylodynamics and human-mediated dispersal of a zoonotic virus. by Chiraz Talbi, Philippe Lemey, Marc A Suchard, Elbia Abdelatif, Mehdi Elharrak, Jalal Nourlil, Abdellah Faouzi, Juan E Echevarría, Sonia Vazquez Morón, Andrew Rambaut, Nicholas Campiz, Andrew J Tatem, Edward C Holmes, Hervé Bourhy

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Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore by Yvonne C.F. Su, Michael A. Zeller, Peter Cronin, Rong Zhang, Yan Zhuang, Jordan Ma, Foong Ying Wong, Giselle G.K. Ng, Áine O’Toole, Andrew Rambaut, Jenny G. Low, Gavin J.D. Smith

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Genomics-informed outbreak investigations of SARS-CoV-2 using civet. by Áine O'Toole, Verity Hill, Ben Jackson, Rebecca Dewar, Nikita Sahadeo, Rachel Colquhoun, Stefan Rooke, J T McCrone, Kate Duggan, Martin P McHugh, Samuel M Nicholls, Radoslaw Poplawski, COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), David Aanensen, Matt Holden, Tom Connor, Nick Loman, Ian Goodfellow, Christine V F Carrington, Kate Templeton, Andrew Rambaut

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Clade Ia Monkeypox Virus Linked to Sexual Transmission, Democratic Republic of the Congo, August 2024 by Jean-Claude Makangara-Cigolo, Kelly-Michel Kenye, Lygie Lunyanga, Daan Jansen, Eddy Kinganda-Lusamaki, Sifa Kavira, Adrienne Amuri-Aziza, Emile Malembi, Yvon Anta, Prince Akil-Bandali, Emmanuel Lokilo-Lofiko, Emmanuel Hasivirwe Vakaniaki, Sabin Sabiti Nundu, Elisabeth Pukuta-Simbu, Princesse Paku-Tshambu, Rilia Ola-Mpumbe, Raphael Lumembe-Numbi, Gabriel Kabamba-Lungenyi, Gradi Luakanda, Cris Kacita, Robert Shongo-Lushima, Dieudonné Mwamba, Áine O’Toole, Sydney Merritt, Megan Halbrook, Daniel Mukadi-Bamuleka, Nicole A. Hoff, Nicola Low, Isaac Bogoch, Muge Cevik, Gregg Gonsalves, Souradet Shaw, Lorenzo Subissi, Laurens Liesenborghs, Ahidjo Ayouba, Martine Peeters, Eric Delaporte, Sofonias Tessema, Anne W. Rimoin, Jean-Jacques Muyembe-Tamfum, Andrew Rambaut, Koen Vercauteren, Steve Ahuka-Mundeke, Jason Kindrachuk, Tony Wawina-Bokalanga, Placide Mbala-Kingebeni

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