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For: Gräf T, Bello G, Venas TMM, Pereira EC, Paixão ACD, Appolinario LR, Lopes RS, Mendonça ACDF, da Rocha ASB, Motta FC, Gregianini TS, Salvato RS, Fernandes SB, Rovaris DB, Cavalcanti AC, Leite AB, Riediger I, Debur MDC, Bernardes AFL, Ribeiro-Rodrigues R, Grinsztejn B, Alves do Nascimento V, de Souza VC, Gonçalves L, da Costa CF, Mattos T, Dezordi FZ, Wallau GL, Naveca FG, Delatorre E, Siqueira MM, Resende PC. Identification of a novel SARS-CoV-2 P.1 sub-lineage in Brazil provides new insights about the mechanisms of emergence of variants of concern. Virus Evol 2022;7:veab091. [PMID: 35039782 PMCID: PMC8754780 DOI: 10.1093/ve/veab091] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/25/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
dos Santos MC, Fintelman-Rodrigues N, da Silva ADPD, Silva RLN, Seixas VC, Batista-da-Silva AA, Ferreira MA, Bozza PT, Bozza FA, Souza TML. Does viral circulation in slums have a global impact? The lesson learned from SARS-CoV-2 circulation in Complexo de favelas da Maré, Rio de Janeiro, Brazil. Front Microbiol 2025;16:1483895. [PMID: 40012790 PMCID: PMC11861056 DOI: 10.3389/fmicb.2025.1483895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 01/13/2025] [Indexed: 02/28/2025]  Open
2
Alemán GV, Cerpas C, Juarez JG, Moreira H, Arguello S, Coloma J, Harris E, Gordon A, Bennett SN, Balmaseda Á. Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 pandemic. Sci Rep 2025;15:4817. [PMID: 39924561 PMCID: PMC11808107 DOI: 10.1038/s41598-024-84113-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 12/19/2024] [Indexed: 02/11/2025]  Open
3
Rustagi V, Gupta SRR, Talwar C, Singh A, Xiao ZZ, Jamwal R, Bala K, Bhaskar AK, Nagar S, Singh IK. SARS-CoV-2 pathophysiology and post-vaccination severity: a systematic review. Immunol Res 2024;73:17. [PMID: 39692912 DOI: 10.1007/s12026-024-09553-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 12/02/2024] [Indexed: 12/19/2024]
4
Simoes MP, Hodcroft EB, Simmonds P, Albert J, Alidjinou EK, Ambert-Balay K, Andrés C, Antón A, Auvray C, Bailly JL, Baldanti F, Bastings C, Beard S, Berengua C, Berginc N, Bloemen M, Blomqvist S, Bosma F, Böttcher S, Bubba L, Buderus S, Cabrerizo M, Calvo C, Celma C, Ceriotti F, Clark G, Costa I, Coste-Burel M, Couderé K, Cremer J, del Cuerpo Casas M, Daehne T, de Beer J, de Ceano-Vivas M, De Gascun C, de Rougemont A, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dillner L, Dorenberg DH, Ducancelle A, Dudman S, Dyrdak R, Eis-Huebinger AM, Falces-Romero I, Farkas A, Feeney S, Fernandez-Garcia MD, Flipse J, Franck KT, Galli C, Garrigue I, Geeraedts F, Georgieva I, Giardina F, Guiomar R, Hauzenberger E, Heikens E, Henquell C, Hober D, Hönemann M, Howson-Wells H, Hruškar Ž, Ikonen N, Imbert B, Jansz AR, Jeannoël M, Jiřincová H, Josset L, Keeren K, Kramer-Lindhout N, Krokstad S, Lazrek M, Le Guillou-Guillemette H, Lefeuvre C, Lind A, Lunar MM, Maier M, Marque-Juillet S, McClure CP, McKenna J, Meijer A, Menasalvas Ruiz A, Mengual-Chuliá B, Midgley S, Mirand A, Molenkamp R, Montes M, Moreno-Docón A, Morley U, Murk JL, Navascués-Ortega A, Nijhuis R, Nikolaeva-Glomb L, Nordbø SA, Numanovic S, Oggioni M, Oñate Vergara E, et alSimoes MP, Hodcroft EB, Simmonds P, Albert J, Alidjinou EK, Ambert-Balay K, Andrés C, Antón A, Auvray C, Bailly JL, Baldanti F, Bastings C, Beard S, Berengua C, Berginc N, Bloemen M, Blomqvist S, Bosma F, Böttcher S, Bubba L, Buderus S, Cabrerizo M, Calvo C, Celma C, Ceriotti F, Clark G, Costa I, Coste-Burel M, Couderé K, Cremer J, del Cuerpo Casas M, Daehne T, de Beer J, de Ceano-Vivas M, De Gascun C, de Rougemont A, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dillner L, Dorenberg DH, Ducancelle A, Dudman S, Dyrdak R, Eis-Huebinger AM, Falces-Romero I, Farkas A, Feeney S, Fernandez-Garcia MD, Flipse J, Franck KT, Galli C, Garrigue I, Geeraedts F, Georgieva I, Giardina F, Guiomar R, Hauzenberger E, Heikens E, Henquell C, Hober D, Hönemann M, Howson-Wells H, Hruškar Ž, Ikonen N, Imbert B, Jansz AR, Jeannoël M, Jiřincová H, Josset L, Keeren K, Kramer-Lindhout N, Krokstad S, Lazrek M, Le Guillou-Guillemette H, Lefeuvre C, Lind A, Lunar MM, Maier M, Marque-Juillet S, McClure CP, McKenna J, Meijer A, Menasalvas Ruiz A, Mengual-Chuliá B, Midgley S, Mirand A, Molenkamp R, Montes M, Moreno-Docón A, Morley U, Murk JL, Navascués-Ortega A, Nijhuis R, Nikolaeva-Glomb L, Nordbø SA, Numanovic S, Oggioni M, Oñate Vergara E, Pacaud J, Pacreau ML, Panning M, Pariani E, Pekova L, Pellegrinelli L, Petrovec M, Pietsch C, Pilorge L, Piñeiro L, Piralla A, Poljak M, Prochazka B, Rabella N, Rahamat-Langendoen JC, Rainetova P, Reynders M, Riezebos-Brilman A, Roorda L, Savolainen-Kopra C, Schuffenecker I, Smeets LC, Stoyanova A, Stefic K, Swanink C, Tabain I, Tjhie J, Thouault L, Tumiotto C, Uceda Renteria S, Uršič T, Vallet S, Van Ranst M, Van Wunnik P, Verweij JJ, Vila J, Wintermans B, Wollants E, Wolthers KC, Xavier López-Labrador F, Fischer TK, Harvala H, Benschop KSM. Epidemiological and Clinical Insights into the Enterovirus D68 Upsurge in Europe 2021-2022 and Emergence of Novel B3-Derived Lineages, ENPEN Multicentre Study. J Infect Dis 2024;230:e917-e928. [PMID: 38547499 PMCID: PMC11481312 DOI: 10.1093/infdis/jiae154] [Show More Authors] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 03/27/2024] [Indexed: 10/17/2024]  Open
5
Alemán GV, Cerpas C, Juarez JG, Moreira H, Arguello S, Coloma J, Harris E, Gordon A, Bennett SN, Balmaseda Á. Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 Pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.596876. [PMID: 38895444 PMCID: PMC11185506 DOI: 10.1101/2024.06.03.596876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
6
Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024;52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
7
Puenpa J, Chansaenroj J, Suwannakarn K, Poovorawan Y. Genomic epidemiology and evolutionary analysis during XBB.1.16-predominant periods of SARS-CoV-2 omicron variant in Bangkok, Thailand: December 2022-August 2023. Sci Rep 2024;14:645. [PMID: 38182705 PMCID: PMC10770311 DOI: 10.1038/s41598-023-50856-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]  Open
8
Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024;26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
9
Tay JH, Baele G, Duchene S. Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models. Mol Biol Evol 2023;40:msad212. [PMID: 37738550 PMCID: PMC10560005 DOI: 10.1093/molbev/msad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023]  Open
10
Scheuermann SE, Goff K, Rowe LA, Beddingfield BJ, Maness NJ. Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles. Viruses 2023;15:1937. [PMID: 37766343 PMCID: PMC10537736 DOI: 10.3390/v15091937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]  Open
11
Justo Arevalo S, Uribe Calampa CS, Jimenez Silva C, Quiñones Aguilar M, Bouckaert R, Rebello Pinho JR. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. Nat Commun 2023;14:3557. [PMID: 37322028 PMCID: PMC10272135 DOI: 10.1038/s41467-023-39216-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]  Open
12
Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
13
Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023;21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 551] [Impact Index Per Article: 275.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
14
Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023;4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
15
Neverov AD, Fedonin G, Popova A, Bykova D, Bazykin G. Coordinated evolution at amino acid sites of SARS-CoV-2 spike. eLife 2023;12:e82516. [PMID: 36752391 PMCID: PMC9908078 DOI: 10.7554/elife.82516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/15/2023] [Indexed: 02/05/2023]  Open
16
Wang Q, Ye S, Zhou Z, Song A, Zhu X, Peng J, Liang R, Yang C, Yu X, Huang X, Yu J, Qiu Y, Ge X. Key mutations in the spike protein of SARS-CoV-2 affecting neutralization resistance and viral internalization. J Med Virol 2023;95:e28407. [PMID: 36519597 PMCID: PMC9877909 DOI: 10.1002/jmv.28407] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
17
Alves HJ, de Araújo JLF, Fonseca PLC, Moreira FRR, Bonfim DM, Queiroz DC, Miguita L, de Souza RM, Geddes VEV, Costa WC, de Oliveira JS, Medeiros ELA, de Souza CSA, Saliba JW, Menezes AL, de Oliveira ES, Adelino TER, Guimaraes NR, Ribeiro AA, Moreira RG, Zauli DAG, Silva JDP, Malta FSV, Ferreira ACDS, Silva AVFG, Alfenas-Zerbini P, de Souza FO, Sabino ADP, Xavier LDA, Carobin NV, de Carvalho AF, Lourenço KL, Teixeira SMR, Fernandes APSM, da Fonseca FG, Abrahão JS, Iani FCDM, Rodrigues RAL, de Souza RP, Aguiar RS. Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study. Viruses 2022;14:v14122747. [PMID: 36560750 PMCID: PMC9781153 DOI: 10.3390/v14122747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]  Open
18
SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022;14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022]  Open
19
Almagro JC, Mellado-Sánchez G, Pedraza-Escalona M, Pérez-Tapia SM. Evolution of Anti-SARS-CoV-2 Therapeutic Antibodies. Int J Mol Sci 2022;23:ijms23179763. [PMID: 36077159 PMCID: PMC9456190 DOI: 10.3390/ijms23179763] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 01/17/2023]  Open
20
Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone JT, O’Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay WS, Barrett JC, Chand M, Connor T, Goodfellow I, Gupta RK, Harrison EM, Loman N, Myers R, Robertson DL, Pybus OG, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol 2022;8:veac080. [PMID: 36533153 PMCID: PMC9752794 DOI: 10.1093/ve/veac080] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 01/06/2023]  Open
21
Patel RS, Agrawal B. Heterologous immunity induced by 1st generation COVID-19 vaccines and its role in developing a pan-coronavirus vaccine. Front Immunol 2022;13:952229. [PMID: 36045689 PMCID: PMC9420909 DOI: 10.3389/fimmu.2022.952229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022]  Open
22
Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Yale SARS-CoV-2 Genomic Surveillance Initiative, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
23
Callaway E. How months-long COVID infections could seed dangerous new variants. Nature 2022;606:452-455. [PMID: 35705825 DOI: 10.1038/d41586-022-01613-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
24
Tay JH, Porter AF, Wirth W, Duchene S. The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate. Mol Biol Evol 2022;39:msac013. [PMID: 35038741 PMCID: PMC8807201 DOI: 10.1093/molbev/msac013] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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