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1.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.

Martin, Darren P; Weaver, Steven; Tegally, Houriiyah; San, James Emmanuel; Shank, Stephen D; Wilkinson, Eduan; Lucaci, Alexander G; Giandhari, Jennifer; Naidoo, Sureshnee; Pillay, Yeshnee; Singh, Lavanya; Lessells, Richard J; Gupta, Ravindra K; Wertheim, Joel O; Nekturenko, Anton; Murrell, Ben; Harkins, Gordon W; Lemey, Philippe; MacLean, Oscar A; Robertson, David L; de Oliveira, Tulio; Kosakovsky Pond, Sergei L.

Cell; 184(20): 5189-5200.e7, 2021 09 30.

Artículo en Inglés | MEDLINE | ID: mdl-34537136

2.

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.

Viana, Raquel; Moyo, Sikhulile; Amoako, Daniel G; Tegally, Houriiyah; Scheepers, Cathrine; Althaus, Christian L; Anyaneji, Ugochukwu J; Bester, Phillip A; Boni, Maciej F; Chand, Mohammed; Choga, Wonderful T; Colquhoun, Rachel; Davids, Michaela; Deforche, Koen; Doolabh, Deelan; du Plessis, Louis; Engelbrecht, Susan; Everatt, Josie; Giandhari, Jennifer; Giovanetti, Marta; Hardie, Diana; Hill, Verity; Hsiao, Nei-Yuan; Iranzadeh, Arash; Ismail, Arshad; Joseph, Charity; Joseph, Rageema; Koopile, Legodile; Kosakovsky Pond, Sergei L; Kraemer, Moritz U G; Kuate-Lere, Lesego; Laguda-Akingba, Oluwakemi; Lesetedi-Mafoko, Onalethatha; Lessells, Richard J; Lockman, Shahin; Lucaci, Alexander G; Maharaj, Arisha; Mahlangu, Boitshoko; Maponga, Tongai; Mahlakwane, Kamela; Makatini, Zinhle; Marais, Gert; Maruapula, Dorcas; Masupu, Kereng; Matshaba, Mogomotsi; Mayaphi, Simnikiwe; Mbhele, Nokuzola; Mbulawa, Mpaphi B; Mendes, Adriano; Mlisana, Koleka.

Nature; 603(7902): 679-686, 2022 03.

Artículo en Inglés | MEDLINE | ID: mdl-35042229

3.

The biological and clinical significance of emerging SARS-CoV-2 variants.

Tao, Kaiming; Tzou, Philip L; Nouhin, Janin; Gupta, Ravindra K; de Oliveira, Tulio; Kosakovsky Pond, Sergei L; Fera, Daniela; Shafer, Robert W.

Nat Rev Genet; 22(12): 757-773, 2021 12.

Artículo en Inglés | MEDLINE | ID: mdl-34535792

4.

Detection of a SARS-CoV-2 variant of concern in South Africa.

Tegally, Houriiyah; Wilkinson, Eduan; Giovanetti, Marta; Iranzadeh, Arash; Fonseca, Vagner; Giandhari, Jennifer; Doolabh, Deelan; Pillay, Sureshnee; San, Emmanuel James; Msomi, Nokukhanya; Mlisana, Koleka; von Gottberg, Anne; Walaza, Sibongile; Allam, Mushal; Ismail, Arshad; Mohale, Thabo; Glass, Allison J; Engelbrecht, Susan; Van Zyl, Gert; Preiser, Wolfgang; Petruccione, Francesco; Sigal, Alex; Hardie, Diana; Marais, Gert; Hsiao, Nei-Yuan; Korsman, Stephen; Davies, Mary-Ann; Tyers, Lynn; Mudau, Innocent; York, Denis; Maslo, Caroline; Goedhals, Dominique; Abrahams, Shareef; Laguda-Akingba, Oluwakemi; Alisoltani-Dehkordi, Arghavan; Godzik, Adam; Wibmer, Constantinos Kurt; Sewell, Bryan Trevor; Lourenço, José; Alcantara, Luiz Carlos Junior; Kosakovsky Pond, Sergei L; Weaver, Steven; Martin, Darren; Lessells, Richard J; Bhiman, Jinal N; Williamson, Carolyn; de Oliveira, Tulio.

Nature; 592(7854): 438-443, 2021 04.

Artículo en Inglés | MEDLINE | ID: mdl-33690265

5.

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.

Joyce, Collin; Murrell, Sasha; Murrell, Ben; Omorodion, Oluwarotimi; Ver, Lorena S; Carrico, Nancy; Bastidas, Raiza; Nedellec, Rebecca; Bick, Michael; Woehl, Jordan; Zhao, Fangzhu; Burns, Alison; Barman, Shawn; Appel, Michael; Ramos, Alejandra; Wickramasinghe, Lalinda; Eren, Kemal; Vollbrecht, Thomas; Smith, Davey M; Kosakovsky Pond, Sergei L; McBride, Ryan; Worth, Charli; Batista, Facundo; Sok, Devin; Poignard, Pascal; Briney, Bryan; Wilson, Ian A; Landais, Elise; Burton, Dennis R.

PLoS Pathog; 19(6): e1011416, 2023 Jun.

Artículo en Inglés | MEDLINE | ID: mdl-37384622

6.

Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch.

MacLeod, Daniel T; Choi, Nancy M; Briney, Bryan; Garces, Fernando; Ver, Lorena S; Landais, Elise; Murrell, Ben; Wrin, Terri; Kilembe, William; Liang, Chi-Hui; Ramos, Alejandra; Bian, Chaoran B; Wickramasinghe, Lalinda; Kong, Leopold; Eren, Kemal; Wu, Chung-Yi; Wong, Chi-Huey; Kosakovsky Pond, Sergei L; Wilson, Ian A; Burton, Dennis R; Poignard, Pascal.

Immunity; 44(5): 1215-26, 2016 05 17.

Artículo en Inglés | MEDLINE | ID: mdl-27192579

7.

Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.

Lucaci, Alexander G; Zehr, Jordan D; Enard, David; Thornton, Joseph W; Kosakovsky Pond, Sergei L.

Mol Biol Evol; 40(7)2023 07 05.

Artículo en Inglés | MEDLINE | ID: mdl-37395787

8.

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

MacLean, Oscar A; Lytras, Spyros; Weaver, Steven; Singer, Joshua B; Boni, Maciej F; Lemey, Philippe; Kosakovsky Pond, Sergei L; Robertson, David L.

PLoS Biol; 19(3): e3001115, 2021 03.

Artículo en Inglés | MEDLINE | ID: mdl-33711012

9.

Anti-COVID drug accelerates viral evolution.

Kosakovsky Pond, Sergei L; Martin, Darren.

Nature; 623(7987): 486-487, 2023 Nov.

Artículo en Inglés | MEDLINE | ID: mdl-37875683

10.

Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria.

Rahman, Shakibur; Kosakovsky Pond, Sergei L; Webb, Andrew; Hey, Jody.

Proc Natl Acad Sci U S A; 118(20)2021 05 18.

Artículo en Inglés | MEDLINE | ID: mdl-33972434

11.

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; Grüning, Björn; 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.

Mol Biol Evol; 39(4)2022 04 11.

Artículo en Inglés | MEDLINE | ID: mdl-35325204

12.

Recommendations on data sharing in HIV drug resistance research.

Inzaule, Seth C; Siedner, Mark J; Little, Susan J; Avila-Rios, Santiago; Ayitewala, Alisen; Bosch, Ronald J; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Charpentier, Charlotte; Descamps, Diane; Eshleman, Susan H; Fokam, Joseph; Frenkel, Lisa M; Gupta, Ravindra K; Ioannidis, John P A; Kaleebu, Pontiano; Kantor, Rami; Kassaye, Seble G; Kosakovsky Pond, Sergei L; Kouamou, Vinie; Kouyos, Roger D; Kuritzkes, Daniel R; Lessells, Richard; Marcelin, Anne-Genevieve; Mbuagbaw, Lawrence; Minalga, Brian; Ndembi, Nicaise; Neher, Richard A; Paredes, Roger; Pillay, Deenan; Raizes, Elliot G; Rhee, Soo-Yon; Richman, Douglas D; Ruxrungtham, Kiat; Sabeti, Pardis C; Schapiro, Jonathan M; Sirivichayakul, Sunee; Steegen, Kim; Sugiura, Wataru; van Zyl, Gert U; Vandamme, Anne-Mieke; Wensing, Annemarie M J; Wertheim, Joel O; Gunthard, Huldrych F; Jordan, Michael R; Shafer, Robert W.

PLoS Med; 20(9): e1004293, 2023 Sep.

Artículo en Inglés | MEDLINE | ID: mdl-37738247

13.

Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches.

Kosakovsky Pond, Sergei L; Wisotsky, Sadie R; Escalante, Ananias; Magalis, Brittany Rife; Weaver, Steven.

Mol Biol Evol; 38(3): 1184-1198, 2021 03 09.

Artículo en Inglés | MEDLINE | ID: mdl-33064823

14.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.

Amendola, Antonella; Canuti, Marta; Bianchi, Silvia; Kumar, Sudhir; Fappani, Clara; Gori, Maria; Colzani, Daniela; Kosakovsky Pond, Sergei L; Miura, Sayaka; Baggieri, Melissa; Marchi, Antonella; Borghi, Elisa; Zuccotti, Gianvincenzo; Raviglione, Mario C; Magurano, Fabio; Tanzi, Elisabetta.

Environ Res; 215(Pt 1): 113979, 2022 12.

Artículo en Inglés | MEDLINE | ID: mdl-36029839

15.

A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex.

Avanzato, Victoria A; Oguntuyo, Kasopefoluwa Y; Escalera-Zamudio, Marina; Gutierrez, Bernardo; Golden, Michael; Kosakovsky Pond, Sergei L; Pryce, Rhys; Walter, Thomas S; Seow, Jeffrey; Doores, Katie J; Pybus, Oliver G; Munster, Vincent J; Lee, Benhur; Bowden, Thomas A.

Proc Natl Acad Sci U S A; 116(50): 25057-25067, 2019 12 10.

Artículo en Inglés | MEDLINE | ID: mdl-31767754

16.

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.

Wisotsky, Sadie R; Kosakovsky Pond, Sergei L; Shank, Stephen D; Muse, Spencer V.

Mol Biol Evol; 37(8): 2430-2439, 2020 08 01.

Artículo en Inglés | MEDLINE | ID: mdl-32068869

17.

Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2.

Pollock, David D; Castoe, Todd A; Perry, Blair W; Lytras, Spyros; Wade, Kristen J; Robertson, David L; Holmes, Edward C; Boni, Maciej F; Kosakovsky Pond, Sergei L; Parry, Rhys; Carlton, Elizabeth J; Wood, James L N; Pennings, Pleuni S; Goldstein, Richard A.

Mol Biol Evol; 37(9): 2706-2710, 2020 09 01.

Artículo en Inglés | MEDLINE | ID: mdl-32658964

18.

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.

Kosakovsky Pond, Sergei L; Poon, Art F Y; Velazquez, Ryan; Weaver, Steven; Hepler, N Lance; Murrell, Ben; Shank, Stephen D; Magalis, Brittany Rife; Bouvier, Dave; Nekrutenko, Anton; Wisotsky, Sadie; Spielman, Stephanie J; Frost, Simon D W; Muse, Spencer V.

Mol Biol Evol; 37(1): 295-299, 2020 Jan 01.

Artículo en Inglés | MEDLINE | ID: mdl-31504749

19.

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis.

Council, Olivia D; Zhou, Shuntai; McCann, Chase D; Hoffman, Irving; Tegha, Gerald; Kamwendo, Deborah; Matoga, Mitch; Kosakovsky Pond, Sergei L; Cohen, Myron S; Swanstrom, Ronald.

J Virol; 94(12)2020 06 01.

Artículo en Inglés | MEDLINE | ID: mdl-32269129

20.

Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago.

Cui, Rongfeng; Tyers, Alexandra M; Malubhoy, Zahabiya Juzar; Wisotsky, Sadie; Valdesalici, Stefano; Henriette, Elvina; Kosakovsky Pond, Sergei L; Valenzano, Dario Riccardo.

Mol Ecol; 30(14): 3610-3623, 2021 07.

Artículo en Inglés | MEDLINE | ID: mdl-33998095

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