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1.

The origins of SARS-CoV-2: A critical review.

Holmes, Edward C; Goldstein, Stephen A; Rasmussen, Angela L; Robertson, David L; Crits-Christoph, Alexander; Wertheim, Joel O; Anthony, Simon J; Barclay, Wendy S; Boni, Maciej F; Doherty, Peter C; Farrar, Jeremy; Geoghegan, Jemma L; Jiang, Xiaowei; Leibowitz, Julian L; Neil, Stuart J D; Skern, Tim; Weiss, Susan R; Worobey, Michael; Andersen, Kristian G; Garry, Robert F; Rambaut, Andrew.

Cell ; 184(19): 4848-4856, 2021 09 16.

Artículo Inglés | MEDLINE | ID: mdl-34480864

2.

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.

Jackson, Ben; Boni, Maciej F; Bull, Matthew J; Colleran, Amy; Colquhoun, Rachel M; Darby, Alistair C; Haldenby, Sam; Hill, Verity; Lucaci, Anita; McCrone, John T; Nicholls, Samuel M; O'Toole, Áine; Pacchiarini, Nicole; Poplawski, Radoslaw; Scher, Emily; Todd, Flora; Webster, Hermione J; Whitehead, Mark; Wierzbicki, Claudia; Loman, Nicholas J; Connor, Thomas R; Robertson, David L; Pybus, Oliver G; Rambaut, Andrew.

Cell ; 184(20): 5179-5188.e8, 2021 09 30.

Artículo Inglés | MEDLINE | ID: mdl-34499854

3.

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Volz, Erik; Hill, Verity; McCrone, John T; Price, Anna; Jorgensen, David; O'Toole, Áine; Southgate, Joel; Johnson, Robert; Jackson, Ben; Nascimento, Fabricia F; Rey, Sara M; Nicholls, Samuel M; Colquhoun, Rachel M; da Silva Filipe, Ana; Shepherd, James; Pascall, David J; Shah, Rajiv; Jesudason, Natasha; Li, Kathy; Jarrett, Ruth; Pacchiarini, Nicole; Bull, Matthew; Geidelberg, Lily; Siveroni, Igor; Goodfellow, Ian; Loman, Nicholas J; Pybus, Oliver G; Robertson, David L; Thomson, Emma C; Rambaut, Andrew; Connor, Thomas R.

Cell ; 184(1): 64-75.e11, 2021 01 07.

Artículo Inglés | MEDLINE | ID: mdl-33275900

4.

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.

Thomson, Emma C; Rosen, Laura E; Shepherd, James G; Spreafico, Roberto; da Silva Filipe, Ana; Wojcechowskyj, Jason A; Davis, Chris; Piccoli, Luca; Pascall, David J; Dillen, Josh; Lytras, Spyros; Czudnochowski, Nadine; Shah, Rajiv; Meury, Marcel; Jesudason, Natasha; De Marco, Anna; Li, Kathy; Bassi, Jessica; O'Toole, Aine; Pinto, Dora; Colquhoun, Rachel M; Culap, Katja; Jackson, Ben; Zatta, Fabrizia; Rambaut, Andrew; Jaconi, Stefano; Sreenu, Vattipally B; Nix, Jay; Zhang, Ivy; Jarrett, Ruth F; Glass, William G; Beltramello, Martina; Nomikou, Kyriaki; Pizzuto, Matteo; Tong, Lily; Cameroni, Elisabetta; Croll, Tristan I; Johnson, Natasha; Di Iulio, Julia; Wickenhagen, Arthur; Ceschi, Alessandro; Harbison, Aoife M; Mair, Daniel; Ferrari, Paolo; Smollett, Katherine; Sallusto, Federica; Carmichael, Stephen; Garzoni, Christian; Nichols, Jenna; Galli, Massimo.

Cell ; 184(5): 1171-1187.e20, 2021 03 04.

Artículo Inglés | MEDLINE | ID: mdl-33621484

5.

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.

Lu, Jing; du Plessis, Louis; Liu, Zhe; Hill, Verity; Kang, Min; Lin, Huifang; Sun, Jiufeng; François, Sarah; Kraemer, Moritz U G; Faria, Nuno R; McCrone, John T; Peng, Jinju; Xiong, Qianling; Yuan, Runyu; Zeng, Lilian; Zhou, Pingping; Liang, Chumin; Yi, Lina; Liu, Jun; Xiao, Jianpeng; Hu, Jianxiong; Liu, Tao; Ma, Wenjun; Li, Wei; Su, Juan; Zheng, Huanying; Peng, Bo; Fang, Shisong; Su, Wenzhe; Li, Kuibiao; Sun, Ruilin; Bai, Ru; Tang, Xi; Liang, Minfeng; Quick, Josh; Song, Tie; Rambaut, Andrew; Loman, Nick; Raghwani, Jayna; Pybus, Oliver G; Ke, Changwen.

Cell ; 181(5): 997-1003.e9, 2020 05 28.

Artículo Inglés | MEDLINE | ID: mdl-32359424

6.

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic.

Diehl, William E; Lin, Aaron E; Grubaugh, Nathan D; Carvalho, Luiz Max; Kim, Kyusik; Kyawe, Pyae Phyo; McCauley, Sean M; Donnard, Elisa; Kucukural, Alper; McDonel, Patrick; Schaffner, Stephen F; Garber, Manuel; Rambaut, Andrew; Andersen, Kristian G; Sabeti, Pardis C; Luban, Jeremy.

Cell ; 167(4): 1088-1098.e6, 2016 11 03.

Artículo Inglés | MEDLINE | ID: mdl-27814506

7.

Context-specific emergence and growth of the SARS-CoV-2 Delta variant.

McCrone, John T; Hill, Verity; Bajaj, Sumali; Pena, Rosario Evans; Lambert, Ben C; Inward, Rhys; Bhatt, Samir; Volz, Erik; Ruis, Christopher; Dellicour, Simon; Baele, Guy; Zarebski, Alexander E; Sadilek, Adam; Wu, Neo; Schneider, Aaron; Ji, Xiang; Raghwani, Jayna; Jackson, Ben; Colquhoun, Rachel; O'Toole, Áine; Peacock, Thomas P; Twohig, Kate; Thelwall, Simon; Dabrera, Gavin; Myers, Richard; Faria, Nuno R; Huber, Carmen; Bogoch, Isaac I; Khan, Kamran; du Plessis, Louis; Barrett, Jeffrey C; Aanensen, David M; Barclay, Wendy S; Chand, Meera; Connor, Thomas; Loman, Nicholas J; Suchard, Marc A; Pybus, Oliver G; Rambaut, Andrew; Kraemer, Moritz U G.

Nature ; 610(7930): 154-160, 2022 10.

Artículo Inglés | MEDLINE | ID: mdl-35952712

8.

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

Volz, Erik; Mishra, Swapnil; Chand, Meera; Barrett, Jeffrey C; Johnson, Robert; Geidelberg, Lily; Hinsley, Wes R; Laydon, Daniel J; Dabrera, Gavin; O'Toole, Áine; Amato, Robert; Ragonnet-Cronin, Manon; Harrison, Ian; Jackson, Ben; Ariani, Cristina V; Boyd, Olivia; Loman, Nicholas J; McCrone, John T; Gonçalves, Sónia; Jorgensen, David; Myers, Richard; Hill, Verity; Jackson, David K; Gaythorpe, Katy; Groves, Natalie; Sillitoe, John; Kwiatkowski, Dominic P; Flaxman, Seth; Ratmann, Oliver; Bhatt, Samir; Hopkins, Susan; Gandy, Axel; Rambaut, Andrew; Ferguson, Neil M.

Nature ; 593(7858): 266-269, 2021 05.

Artículo Inglés | MEDLINE | ID: mdl-33767447

9.

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks.

Keita, Alpha Kabinet; Koundouno, Fara R; Faye, Martin; Düx, Ariane; Hinzmann, Julia; Diallo, Haby; Ayouba, Ahidjo; Le Marcis, Frederic; Soropogui, Barré; Ifono, Kékoura; Diagne, Moussa M; Sow, Mamadou S; Bore, Joseph A; Calvignac-Spencer, Sebastien; Vidal, Nicole; Camara, Jacob; Keita, Mamadou B; Renevey, Annick; Diallo, Amadou; Soumah, Abdoul K; Millimono, Saa L; Mari-Saez, Almudena; Diop, Mamadou; Doré, Ahmadou; Soumah, Fodé Y; Kourouma, Kaka; Vielle, Nathalie J; Loucoubar, Cheikh; Camara, Ibrahima; Kourouma, Karifa; Annibaldis, Giuditta; Bah, Assaïtou; Thielebein, Anke; Pahlmann, Meike; Pullan, Steven T; Carroll, Miles W; Quick, Joshua; Formenty, Pierre; Legand, Anais; Pietro, Karla; Wiley, Michael R; Tordo, Noel; Peyrefitte, Christophe; McCrone, John T; Rambaut, Andrew; Sidibé, Youssouf; Barry, Mamadou D; Kourouma, Madeleine; Saouromou, Cé D; Condé, Mamadou.

Nature ; 597(7877): 539-543, 2021 09.

Artículo Inglés | MEDLINE | ID: mdl-34526718

10.

Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression.

Featherstone, Leo A; Rambaut, Andrew; Duchene, Sebastian; Wirth, Wytamma.

Syst Biol ; 2024 Feb 17.

Artículo Inglés | MEDLINE | ID: mdl-38366939

11.

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.

Happi, Christian; Adetifa, Ifedayo; Mbala, Placide; Njouom, Richard; Nakoune, Emmanuel; Happi, Anise; Ndodo, Nnaemeka; Ayansola, Oyeronke; Mboowa, Gerald; Bedford, Trevor; Neher, Richard A; Roemer, Cornelius; Hodcroft, Emma; Tegally, Houriiyah; O'Toole, Áine; Rambaut, Andrew; Pybus, Oliver; Kraemer, Moritz U G; Wilkinson, Eduan; Isidro, Joana; Borges, Vítor; Pinto, Miguel; Gomes, João Paulo; Freitas, Lucas; Resende, Paola C; Lee, Raphael T C; Maurer-Stroh, Sebastian; Baxter, Cheryl; Lessells, Richard; Ogwell, Ahmed E; Kebede, Yenew; Tessema, Sofonias K; de Oliveira, Tulio.

PLoS Biol ; 20(8): e3001769, 2022 08.

Artículo Inglés | MEDLINE | ID: mdl-35998195

12.

Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease.

Mbala-Kingebeni, Placide; Pratt, Catherine; Mutafali-Ruffin, Mbusa; Pauthner, Matthias G; Bile, Faustin; Nkuba-Ndaye, Antoine; Black, Allison; Kinganda-Lusamaki, Eddy; Faye, Martin; Aziza, Amuri; Diagne, Moussa M; Mukadi, Daniel; White, Bailey; Hadfield, James; Gangavarapu, Karthik; Bisento, Nella; Kazadi, Donatien; Nsunda, Bibiche; Akonga, Marceline; Tshiani, Olivier; Misasi, John; Ploquin, Aurelie; Epaso, Victor; Sana-Paka, Emilia; N'kasar, Yannick Tutu Tshia; Mambu, Fabrice; Edidi, Francois; Matondo, Meris; Bula Bula, Junior; Diallo, Boubacar; Keita, Mory; Belizaire, Marie R D; Fall, Ibrahima S; Yam, Abdoulaye; Mulangu, Sabue; Rimoin, Anne W; Salfati, Elias; Torkamani, Ali; Suchard, Marc A; Crozier, Ian; Hensley, Lisa; Rambaut, Andrew; Faye, Ousmane; Sall, Amadou; Sullivan, Nancy J; Bedford, Trevor; Andersen, Kristian G; Wiley, Michael R; Ahuka-Mundeke, Steve; Muyembe Tamfum, Jean-Jacques.

N Engl J Med ; 384(13): 1240-1247, 2021 04 01.

Artículo Inglés | MEDLINE | ID: mdl-33789012

13.

SCORPIO: a utility for defining and classifying mutation constellations of virus genomes.

Colquhoun, Rachel; Jackson, Ben; O'Toole, Áine; Rambaut, Andrew.

Bioinformatics ; 39(10)2023 10 03.

Artículo Inglés | MEDLINE | ID: mdl-37713452

14.

Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.

Campbell, Kathryn; Gifford, Robert J; Singer, Joshua; Hill, Verity; O'Toole, Aine; Rambaut, Andrew; Hampson, Katie; Brunker, Kirstyn.

PLoS Pathog ; 18(5): e1010023, 2022 05.

Artículo Inglés | MEDLINE | ID: mdl-35500026

15.

Zika virus evolution and spread in the Americas.

Metsky, Hayden C; Matranga, Christian B; Wohl, Shirlee; Schaffner, Stephen F; Freije, Catherine A; Winnicki, Sarah M; West, Kendra; Qu, James; Baniecki, Mary Lynn; Gladden-Young, Adrianne; Lin, Aaron E; Tomkins-Tinch, Christopher H; Ye, Simon H; Park, Daniel J; Luo, Cynthia Y; Barnes, Kayla G; Shah, Rickey R; Chak, Bridget; Barbosa-Lima, Giselle; Delatorre, Edson; Vieira, Yasmine R; Paul, Lauren M; Tan, Amanda L; Barcellona, Carolyn M; Porcelli, Mario C; Vasquez, Chalmers; Cannons, Andrew C; Cone, Marshall R; Hogan, Kelly N; Kopp, Edgar W; Anzinger, Joshua J; Garcia, Kimberly F; Parham, Leda A; Ramírez, Rosa M Gélvez; Montoya, Maria C Miranda; Rojas, Diana P; Brown, Catherine M; Hennigan, Scott; Sabina, Brandon; Scotland, Sarah; Gangavarapu, Karthik; Grubaugh, Nathan D; Oliveira, Glenn; Robles-Sikisaka, Refugio; Rambaut, Andrew; Gehrke, Lee; Smole, Sandra; Halloran, M Elizabeth; Villar, Luis; Mattar, Salim.

Nature ; 546(7658): 411-415, 2017 06 15.

Artículo Inglés | MEDLINE | ID: mdl-28538734

16.

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.

O'Toole, Áine; Pybus, Oliver G; Abram, Michael E; Kelly, Elizabeth J; Rambaut, Andrew.

BMC Genomics ; 23(1): 121, 2022 Feb 11.

Artículo Inglés | MEDLINE | ID: mdl-35148677

17.

Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST.

Dellicour, Simon; Gill, Mandev S; Faria, Nuno R; Rambaut, Andrew; Pybus, Oliver G; Suchard, Marc A; Lemey, Philippe.

Mol Biol Evol ; 38(8): 3486-3493, 2021 07 29.

Artículo Inglés | MEDLINE | ID: mdl-33528560

18.

The evolution of Ebola virus: Insights from the 2013-2016 epidemic.

Holmes, Edward C; Dudas, Gytis; Rambaut, Andrew; Andersen, Kristian G.

Nature ; 538(7624): 193-200, 2016 10 13.

Artículo Inglés | MEDLINE | ID: mdl-27734858

19.

Persistent HIV-1 replication maintains the tissue reservoir during therapy.

Lorenzo-Redondo, Ramon; Fryer, Helen R; Bedford, Trevor; Kim, Eun-Young; Archer, John; Pond, Sergei L Kosakovsky; Chung, Yoon-Seok; Penugonda, Sudhir; Chipman, Jeffrey; Fletcher, Courtney V; Schacker, Timothy W; Malim, Michael H; Rambaut, Andrew; Haase, Ashley T; McLean, Angela R; Wolinsky, Steven M.

Nature ; 530(7588): 51-56, 2016 Feb 04.

Artículo Inglés | MEDLINE | ID: mdl-26814962

20.

Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction.

Gill, Mandev S; Lemey, Philippe; Suchard, Marc A; Rambaut, Andrew; Baele, Guy.

Mol Biol Evol ; 37(6): 1832-1842, 2020 06 01.

Artículo Inglés | MEDLINE | ID: mdl-32101295

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