Not logged in Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models Sianga-Mete, Rita; Hartnady, Penelope; Mandikumba, Wimbai Caroline; Rutherford, Kayleigh; Currin, Christopher Brian; Phelanyane, Florence; Stefan, Sabina; Weaver, Steven; Kosakovsky Pond, Sergei L.; Martin, Darren P. Share Save
Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage Kekana, Dikeledi; Ntozini, Buhle; Hisner, Ryan; Yousif, Mukhlid; Ntuli, Phindile; Ndlovu, Nkosenhle; McCarthy, Kerrigan; Mnguni, Anele; Mahlangu, Boitshoko; Nzimande, Ayanda; Stock, Nadine; Tegally, Houriiyah; Davis, Mary-Ann; Moir, Monika; Wilkinson, Eduan; Baxter, Cheryl; Bhiman, Jinal; Cohen, Cheryl; Walaza, Sibongile; Von Gottberg, Anne; De Oliveira, Tulio; Wolter, Nicole; Martin, Darren Share Save
Increase of niche filling with increase of host richness for plant-infecting mastreviruses Ben Chehida, Selim; Devi Bunwaree, Heemee; Hoareau, Murielle; Moubset, Oumaima; Julian, Charlotte; Blondin, Laurence; Filloux, Denis; Lavergne, Christophe; Roumagnac, Philippe; Varsani, Arvind; Martin, Darren P.; Lett, Jean-Michel; Lefeuvre, Pierre Share Save
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana Choga, Wonderful T.; Gustani-Buss, Emanuele; Tegally, Houriiyah; Maruapula, Dorcas; Yu, Xiaoyu; Moir, Monika; Zuze, Boitumelo J. L.; James, San Emmanuel; Ndlovu, Nokuthula S.; Seru, Kedumetse; Motshosi, Patience; Blenkinsop, Alexandra; Gobe, Irene; Baxter, Cheryl; Manasa, Justen; Lockman, Shahin; Shapiro, Roger; Makhema, Joseph; Wilkinson, Eduan; Blackard, Jason T.; Lemey, Phillipe; Lessells, Richard J.; Martin, Darren P.; de Oliveira, Tulio; Gaseitsiwe, Simani; Moyo, Sikhulile Share Save
Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours Godwe, Celestin; Goni, Oumarou H.; San, James E.; Sonela, Nelson; Tchakoute, Merime; Nanfack, Aubin; Koro, Francioli K.; Butel, Christelle; Vidal, Nicole; Duerr, Ralf; Martin, Darren P.; de Oliveira, Tulio; Peeters, Martine; Altfeld, Marcus; Ayouba, Ahidjo; Ndung'u, Thumbi; Tongo, Marcel Share Save
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Virome release of an invasive exotic plant species in southern France Moubset, Oumaima; Filloux, Denis; Fontes, Hugo; Julian, Charlotte; Fernandez, Emmanuel; Galzi, Serge; Blondin, Laurence; Chehida, Selim Ben; Lett, Jean-Michel; Mesleard, Francois; Kraberger, Simona; Custer, Joy M.; Salywon, Andrew; Makings, Elizabeth; Marais, Armelle; Chiroleu, Frederic; Lefeuvre, Pierre; Martin, Darren P.; Candresse, Thierry; Varsani, Arvind; Ravigne, Virginie; Roumagnac, Philippe Share Save
Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus Van Borm, Steven; Dellicour, Simon; Martin, Darren P.; Lemey, Philippe; Agianniotaki, Eirini I.; Chondrokouki, Eleni D.; Vidanovic, Dejan; Vaskovic, Nikola; Petrovic, Tamas; Lazic, Sava; Koleci, Xhelil; Vodica, Ani; Djadjovski, Igor; Krstevski, Kiril; Vandenbussche, Frank; Haegeman, Andy; De Clercq, Kris; Mathijs, Elisabeth Share Save
Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance Francisco, Ngiambudulu M.; van Wyk, Stephanie; Moir, Monika; San, James Emmanuel; Sebastiao, Cruz S.; Tegally, Houriiyah; Xavier, Joicymara; Maharaj, Akhil; Neto, Zoraima; Afonso, Pedro; Jandondo, Domingos; Paixao, Joana; Miranda, Julio; David, Kumbelembe; Ingles, Luzia; Pereira, Amilton; Paulo, Agostinho; Carralero, Raisa Rivas; Freitas, Helga Reis; Mufinda, Franco; Lutucuta, Silvia; Ghafari, Mahan; Giovanetti, Marta; Giandhari, Jennifer; Pillay, Sureshnee; Naidoo, Yeshnee; Singh, Lavanya; Tshiabuila, Derek; Martin, Darren Patrick; Chabuka, Lucious; Choga, Wonderful; Wanjohi, Dorcas; Mwangi, Sarah; Pillay, Yusasha; Kebede, Yenew; Shumba, Edwin; Ondoa, Pascale; Baxter, Cheryl; Wilkinson, Eduan; Tessema, Sofonias Kifle; Katzourakis, Aris; Lessells, Richard; de Oliveira, Tulio; Morais, Joana Share Save
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Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein Butkovic, Anamarija; Kraberger, Simona; Smeele, Zoe; Martin, Darren P.; Schmidlin, Kara; Fontenele, Rafaela S.; Shero, Michelle R.; Beltran, Roxanne S.; Kirkham, Amy L.; Aleamotu'a, Maketalena; Burns, Jennifer M.; Koonin, Eugene, V; Varsani, Arvind; Krupovic, Mart Share Save
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic Roshdy, Wael H.; Khalifa, Mohamed K.; San, James Emmanuel; Tegally, Houriiyah; Wilkinson, Eduan; Showky, Shymaa; Martin, Darren Patrick; Moir, Monika; Naguib, Amel; Elguindy, Nancy; Gomaa, Mokhtar R.; Fahim, Manal; Abu Elsood, Hanaa; Mohsen, Amira; Galal, Ramy; Hassany, Mohamed; Lessells, Richard J.; Al-Karmalawy, Ahmed A.; EL-Shesheny, Rabeh; Kandeil, Ahmed M.; Ali, Mohamed A.; de Oliveira, Tulio Share Save
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy Kemp, Steven A.; Charles, Oscar J.; Derache, Anne; Smidt, Werner; Martin, Darren P.; Iwuji, Collins; Adamson, John; Govender, Katya; de Oliveira, Tulio; Dabis, Francois; Pillay, Deenan; Goldstein, Richard A.; Gupta, Ravindra K. Share Save
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa Tegally, Houriiyah; Moir, Monika; Everatt, Josie; Giovanetti, Marta; Scheepers, Cathrine; Wilkinson, Eduan; Subramoney, Kathleen; Makatini, Zinhle; Moyo, Sikhulile; Amoako, Daniel G.; Baxter, Cheryl; Althaus, Christian L.; Anyaneji, Ugochukwu J.; Kekana, Dikeledi; Viana, Raquel; Giandhari, Jennifer; Lessells, Richard J.; Maponga, Tongai; Maruapula, Dorcas; Choga, Wonderful; Matshaba, Mogomotsi; Mbulawa, Mpaphi B.; Msomi, Nokukhanya; Naidoo, Yeshnee; Pillay, Sureshnee; Sanko, Tomasz Janusz; San, James E.; Scott, Lesley; Singh, Lavanya; Magini, Nonkululeko A.; Smith-Lawrence, Pamela; Stevens, Wendy; Dor, Graeme; Tshiabuila, Derek; Wolter, Nicole; Preiser, Wolfgang; Treurnicht, Florette K.; Venter, Marietjie; Chiloane, Georginah; McIntyre, Caitlyn; O'Toole, Aine; Ruis, Christopher; Peacock, Thomas P.; Roemer, Cornelius; Kosakovsky Pond, Sergei L.; Williamson, Carolyn; Pybus, Oliver G.; Bhiman, Jinal N.; Glass, Allison; Martin, Darren P.; Jackson, Ben; Rambaut, Andrew; Laguda-Akingba, Oluwakemi; Gaseitsiwe, Simani; von Gottberg, Anne; de Oliveira, Tulio; Bester, Armand Phillip; Claassen, Mathilda; Doolabh, Deelan; Mudau, Innocent; Mbhele, Nokuzola; Engelbrecht, Susan; Goedhals, Dominique; Hardie, Diana; Hsiao, Nei-Yuan; Iranzadeh, Arash; Ismail, Arshad; Joseph, Rageema; Maharaj, Arisha; Mahlangu, Boitshoko; Mahlakwane, Kamela; Davis, Ashlyn; Marais, Gert; Mlisana, Koleka; Mnguni, Anele; Mohale, Thabo; Motsatsi, Gerald; Mwangi, Peter; Ntuli, Noxolo; Nyaga, Martin; Olubayo, Luicer; Radibe, Botshelo; Ramphal, Yajna; Ramphal, Upasana; Strasheim, Wilhelmina; Tebeila, Naume; van Wyk, Stephanie; Wilson, Shannon; Lucaci, Alexander G.; Weaver, Steven; Maharaj, Akhil; Pillay, Yusasha; Davids, Michaela; Mendes, Adriano; Mayaphi, Simnikiwe Share Save
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City Wertheim, Joel O.; Wang, Jade C.; Leelawong, Mindy; Martin, Darren P.; Havens, Jennifer L.; Chowdhury, Moinuddin A.; Pekar, Jonathan E.; Amin, Helly; Arroyo, Anthony; Awandare, Gordon A.; Chow, Hoi Yan; Gonzalez, Edimarlyn; Luoma, Elizabeth; Morang'a, Collins M.; Nekrutenko, Anton; Shank, Stephen D.; Silver, Stefan; Quashie, Peter K.; Rakeman, Jennifer L.; Ruiz, Victoria; Torian, Lucia, V; Vasylyeva, Tetyana, I; Pond, Sergei L. Kosakovsky; Hughes, Scott Share Save
Conserved recombination patterns across coronavirus subgenera de Klerk, Arne; Swanepoel, Phillip; Lourens, Rentia; Zondo, Mpumelelo; Abodunran, Isaac; Lytras, Spyros; MacLean, Oscar A.; Robertson, David; Kosakovsky Pond, Sergei L.; Zehr, Jordan D.; Kumar, Venkatesh; Stanhope, Michael J.; Harkins, Gordon; Murrell, Ben; Martin, Darren P. Share Save
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Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage Scheepers, Cathrine; Everatt, Josie; Amoako, Daniel G.; Tegally, Houriiyah; Wibmer, Constantinos Kurt; Mnguni, Anele; Ismail, Arshad; Mahlangu, Boitshoko; Lambson, Bronwen E.; Martin, Darren P.; Wilkinson, Eduan; San, James Emmanuel; Giandhari, Jennifer; Manamela, Nelia; Ntuli, Noxolo; Kgagudi, Prudence; Cele, Sandile; Richardson, Simone, I; Pillay, Sureshnee; Mohale, Thabo; Ramphal, Upasana; Naidoo, Yeshnee; Khumalo, Zamantungwa T.; Kwatra, Gaurav; Gray, Glenda; Bekker, Linda-Gail; Madhi, Shabir A.; Baillie, Vicky; Van Voorhis, Wesley C.; Treurnicht, Florette K.; Venter, Marietjie; Mlisana, Koleka; Wolter, Nicole; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; Msomi, Nokukhanya; Maponga, Tongai; Preiser, Wolfgang; Makatini, Zinhle; Lessells, Richard; Moore, Penny L.; de Oliveira, Tulio; von Gottberg, Anne; Bhiman, Jinal N. Share Save
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function Martin, Darren P.; Lytras, Spyros; Lucaci, Alexander G.; Maier, Wolfgang; Gruening, Bjoern; Shank, Stephen D.; Weaver, Steven; MacLean, Oscar A.; Orton, Richard J.; Lemey, Philippe; Boni, Maciej F.; Tegally, Houriiyah; Harkins, Gordon W.; Scheepers, Cathrine; Bhiman, Jinal N.; Everatt, Josie; Amoako, Daniel G.; San, James Emmanuel; Giandhari, Jennifer; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; von Gottberg, Anne; De Klerk, Arne; Shafer, Robert W.; Robertson, David L.; Wilkinson, Robert J.; Sewell, B. Trevor; Lessells, Richard; Nekrutenko, Anton; Greaney, Allison J.; Starr, Tyler N.; Bloom, Jesse D.; Murrell, Ben; Wilkinson, Eduan; Gupta, Ravindra K.; de Oliveira, Tulio; Kosakovsky Pond, Sergei L. Share Save
Targeted Sanger sequencing to recover key mutations in SARS- CoV-2 variant genome assemblies produced by next-generation sequencing Singh, Lavanya; San, James E.; Tegally, Houriiyah; Brzoska, Pius M.; Anyaneji, Ugochukwu J.; Wilkinson, Eduan; Clark, Lindsay; Giandhari, Jennifer; Pillay, Sureshnee; Lessells, Richard J.; Martin, Darren Patrick; Furtado, Manohar; Kiran, Anmol M.; de Oliveira, Tulio Share Save
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