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For: MacLean OA, Lytras S, Weaver S, Singer JB, Boni MF, Lemey P, Kosakovsky Pond SL, Robertson DL. Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biol 2021;19:e3001115. [PMID: 33711012 PMCID: PMC7990310 DOI: 10.1371/journal.pbio.3001115] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/24/2021] [Accepted: 01/25/2021] [Indexed: 02/08/2023]  Open
Number Cited by Other Article(s)
1
Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Wang Y, Ji X, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Rambaut A, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. Cell 2025:S0092-8674(25)00353-8. [PMID: 40339581 DOI: 10.1016/j.cell.2025.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 11/21/2024] [Accepted: 03/19/2025] [Indexed: 05/10/2025]
2
Guillebaud J, Ou TP, Hul V, Hoem T, Meng C, Nuon S, Hoem S, Lim R, Khun L, Furey NM, Cappelle J, Duong V, Chevalier V. Study of coronavirus diversity in wildlife in Northern Cambodia suggests continuous circulation of SARS-CoV-2-related viruses in bats. Sci Rep 2025;15:12628. [PMID: 40221475 PMCID: PMC11993651 DOI: 10.1038/s41598-025-92475-x] [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: 09/20/2024] [Accepted: 02/27/2025] [Indexed: 04/14/2025]  Open
3
Case JB, Jain S, Suthar MS, Diamond MS. SARS-CoV-2: The Interplay Between Evolution and Host Immunity. Annu Rev Immunol 2025;43:29-55. [PMID: 39705164 DOI: 10.1146/annurev-immunol-083122-043054] [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] [Indexed: 12/22/2024]
4
Álvarez-Herrera M, Ruiz-Rodriguez P, Navarro-Domínguez B, Zulaica J, Grau B, Bracho MA, Guerreiro M, Aguilar‐Gallardo C, González-Candelas F, Comas I, Geller R, Coscollá M. Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein. Virus Evol 2025;11:veaf015. [PMID: 40308784 PMCID: PMC12041916 DOI: 10.1093/ve/veaf015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 02/20/2025] [Accepted: 03/11/2025] [Indexed: 05/02/2025]  Open
5
Havens JL, Kosakovsky Pond SL, Zehr JD, Pekar JE, Parker E, Worobey M, Andersen KG, Wertheim JO. Dynamics of natural selection preceding human viral epidemics and pandemics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.26.640439. [PMID: 40060453 PMCID: PMC11888428 DOI: 10.1101/2025.02.26.640439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
6
Zehr JD, Kosakovsky Pond SL, Shank SD, McQueary H, Grenier JK, Whittaker GR, Stanhope MJ, Goodman LB. Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus. Microbiol Spectr 2024;12:e0086724. [PMID: 39373506 PMCID: PMC11542594 DOI: 10.1128/spectrum.00867-24] [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: 05/09/2024] [Accepted: 08/24/2024] [Indexed: 10/08/2024]  Open
7
Xia X. How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank? Microorganisms 2024;12:2187. [PMID: 39597576 PMCID: PMC11596409 DOI: 10.3390/microorganisms12112187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 10/27/2024] [Accepted: 10/27/2024] [Indexed: 11/29/2024]  Open
8
Yao Z, Ramachandran S, Huang S, Kim E, Jami-Alahmadi Y, Kaushal P, Bouhaddou M, Wohlschlegel JA, Li MM. Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production. EMBO J 2024;43:4625-4655. [PMID: 39261662 PMCID: PMC11480453 DOI: 10.1038/s44318-024-00193-3] [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: 09/22/2023] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 09/13/2024]  Open
9
Li JY, Wang HY, Cheng YX, Ji C, Weng S, Han N, Yang R, Zhou HY, Wu A. Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic. Virus Evol 2024;10:veae074. [PMID: 39399153 PMCID: PMC11470760 DOI: 10.1093/ve/veae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 08/24/2024] [Accepted: 09/02/2024] [Indexed: 10/15/2024]  Open
10
Holmes EC. The Emergence and Evolution of SARS-CoV-2. Annu Rev Virol 2024;11:21-42. [PMID: 38631919 DOI: 10.1146/annurev-virology-093022-013037] [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] [Indexed: 04/19/2024]
11
Misra S, Gilbride E, Ramasamy S, Pond SLK, Kuchipudi SV. Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.606826. [PMID: 39229076 PMCID: PMC11370473 DOI: 10.1101/2024.08.19.606826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
12
Cereghino C, Michalak K, DiGiuseppe S, Guerra J, Yu D, Faraji A, Sharp AK, Brown AM, Kang L, Weger-Lucarelli J, Michalak P. Evolution at Spike protein position 519 in SARS-CoV-2 facilitated adaptation to humans. NPJ VIRUSES 2024;2:29. [PMID: 40295673 PMCID: PMC11721114 DOI: 10.1038/s44298-024-00036-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/25/2024] [Indexed: 04/30/2025]
13
Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024;20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]  Open
14
Salamango DJ. Finally neutralizing the threat? A novel SARS-CoV-2 vaccine platform that elicits enhanced neutralizing antibody responses. mBio 2024;15:e0006724. [PMID: 38407097 PMCID: PMC11005347 DOI: 10.1128/mbio.00067-24] [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] [Indexed: 02/27/2024]  Open
15
Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024;16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]  Open
16
Rubio A, de Toro M, Pérez-Pulido AJ. The most exposed regions of SARS-CoV-2 structural proteins are subject to strong positive selection and gene overlap may locally modify this behavior. mSystems 2024;9:e0071323. [PMID: 38095866 PMCID: PMC10804949 DOI: 10.1128/msystems.00713-23] [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: 07/10/2023] [Accepted: 11/10/2023] [Indexed: 12/22/2023]  Open
17
Anderson TK, Medina RA, Nelson MI. The Evolution of SARS-CoV-2 and Influenza A Virus at the Human–Animal Interface. GENETICS AND EVOLUTION OF INFECTIOUS DISEASES 2024:549-572. [DOI: 10.1016/b978-0-443-28818-0.00016-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
18
Forni D, Pozzoli U, Cagliani R, Clerici M, Sironi M. Dinucleotide biases in RNA viruses that infect vertebrates or invertebrates. Microbiol Spectr 2023;11:e0252923. [PMID: 37800906 PMCID: PMC10714974 DOI: 10.1128/spectrum.02529-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/12/2023] [Indexed: 10/07/2023]  Open
19
Volz E. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet 2023;24:724-734. [PMID: 37328556 DOI: 10.1038/s41576-023-00610-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 06/18/2023]
20
Wu X, Shan K, Zan F, Tang X, Qian Z, Lu J. Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023;10:e2205445. [PMID: 37267926 PMCID: PMC10427376 DOI: 10.1002/advs.202205445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/08/2023] [Indexed: 06/04/2023]
21
Lucaci AG, Zehr JD, Enard D, Thornton JW, Kosakovsky Pond SL. Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses. Mol Biol Evol 2023;40:msad150. [PMID: 37395787 PMCID: PMC10336034 DOI: 10.1093/molbev/msad150] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]  Open
22
Lambrechts L. Does arbovirus emergence in humans require adaptation to domestic mosquitoes? Curr Opin Virol 2023;60:101315. [PMID: 36996522 DOI: 10.1016/j.coviro.2023.101315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/01/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
23
Rezaei Z, Asaei S, Sepehrpour S, Jamalidoust M, Namayandeh M, Norouzi F, Pourabbas B. SARS-CoV-2 variants circulating in the Fars province, southern Iran, December 2020-March 2021: A cross-sectional study. Health Sci Rep 2023;6:e1373. [PMID: 37383927 PMCID: PMC10293940 DOI: 10.1002/hsr2.1373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023]  Open
24
Yao Z, Ramachandran S, Huang S, Jami-Alahmadi Y, Wohlschlegel JA, Li MMH. Chikungunya virus glycoproteins transform macrophages into productive viral dissemination vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542714. [PMID: 37398144 PMCID: PMC10312455 DOI: 10.1101/2023.05.29.542714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
25
Pamornchainavakul N, Paploski IAD, Makau DN, Kikuti M, Rovira A, Lycett S, Corzo CA, VanderWaal K. Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography. Pathogens 2023;12:740. [PMID: 37242410 PMCID: PMC10222675 DOI: 10.3390/pathogens12050740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]  Open
26
Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023;19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]  Open
27
Cristina Diaconu C, Madalina Pitica I, Chivu-Economescu M, Georgiana Necula L, Botezatu A, Virginia Iancu I, Iulia Neagu A, L. Radu E, Matei L, Maria Ruta S, Bleotu C. SARS-CoV-2 Variant Surveillance in Genomic Medicine Era. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]  Open
28
Shapira G, Patalon T, Gazit S, Shomron N. Immunosuppression as a Hub for SARS-CoV-2 Mutational Drift. Viruses 2023;15:v15040855. [PMID: 37112835 PMCID: PMC10145566 DOI: 10.3390/v15040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]  Open
29
Chakraborty C, Saha A, Bhattacharya M, Dhama K, Agoramoorthy G. Natural selection of the D614G mutation in SARS-CoV-2 Omicron (B.1.1.529) variant and its subvariants. MOLECULAR THERAPY. NUCLEIC ACIDS 2023;31:437-439. [PMID: 36817724 PMCID: PMC9923361 DOI: 10.1016/j.omtn.2023.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
30
Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023;13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023]  Open
31
Sun Q, Zeng J, Tang K, Long H, Zhang C, Zhang J, Tang J, Xin Y, Zheng J, Sun L, Liu S, Du X. Variation in synonymous evolutionary rates in the SARS-CoV-2 genome. Front Microbiol 2023;14:1136386. [PMID: 36970680 PMCID: PMC10034387 DOI: 10.3389/fmicb.2023.1136386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 03/11/2023]  Open
32
Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time. Viruses 2023;15:v15030684. [PMID: 36992393 PMCID: PMC10057463 DOI: 10.3390/v15030684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]  Open
33
Colston JM, Hinson P, Nguyen NLH, Chen YT, Badr HS, Kerr GH, Gardner LM, Martin DN, Quispe AM, Schiaffino F, Kosek MN, Zaitchik BF. Effects of hydrometeorological and other factors on SARS-CoV-2 reproduction number in three contiguous countries of tropical Andean South America: a spatiotemporally disaggregated time series analysis. IJID REGIONS 2023;6:29-41. [PMID: 36437857 PMCID: PMC9675637 DOI: 10.1016/j.ijregi.2022.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 06/09/2023]
34
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023;21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 410] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
35
Surya K, Gardner JD, Organ CL. Detecting punctuated evolution in SARS-CoV-2 over the first year of the pandemic. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2023.1066147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
36
Taylor MK, Williams EP, Xue Y, Jenjaroenpun P, Wongsurawat T, Smith AP, Smith AM, Parvathareddy J, Kong Y, Vogel P, Cao X, Reichard W, Spruill-Harrell B, Samarasinghe AE, Nookaew I, Fitzpatrick EA, Smith MD, Aranha M, Smith JC, Jonsson CB. Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants. Viruses 2023;15:611. [PMID: 36992320 PMCID: PMC10059853 DOI: 10.3390/v15030611] [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: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023]  Open
37
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
38
White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Proc Natl Acad Sci U S A 2023;120:e2215067120. [PMID: 36719912 PMCID: PMC9963525 DOI: 10.1073/pnas.2215067120] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
39
Escalera-Zamudio M, Kosakovsky Pond SL, de la Viña NM, Gutiérrez B, Inward RPD, Thézé J, van Dorp L, Castelán-Sánchez HG, Bowden TA, Pybus OG, Hulswit RJG. Identification of evolutionary trajectories shared across human betacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2021.05.24.445313. [PMID: 34075377 PMCID: PMC8168386 DOI: 10.1101/2021.05.24.445313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
40
Pal S, Mehta P, Pandey A, Ara A, Ghoshal U, Ghoshal UC, Pandey R, Tripathi RK, Yadav PN, Ravishankar R, Kundu TK, Rajender S. Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India. Front Microbiol 2023;14:986729. [PMID: 36819024 PMCID: PMC9929466 DOI: 10.3389/fmicb.2023.986729] [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: 07/05/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023]  Open
41
Arruda HR, Lima TM, Alvim RG, Victorio FB, Abreu DP, Marsili FF, Cruz KD, Marques MA, Sosa-Acosta P, Quinones-Vega M, de S. Guedes J, Nogueira FC, Silva JL, Castilho LR, de Oliveira GA. Conformational stability of SARS-CoV-2 glycoprotein spike variants. iScience 2023;26:105696. [PMID: 36465857 PMCID: PMC9710096 DOI: 10.1016/j.isci.2022.105696] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/18/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]  Open
42
Zhang D, Wang Y, Chen X, He Y, Zhao M, Lu X, Lu J, Ji L, Shen Q, Wang X, Yang S, Zhang W. Diversity of viral communities in faecal samples of farmed red foxes. Heliyon 2023;9:e12826. [PMID: 36685457 PMCID: PMC9850053 DOI: 10.1016/j.heliyon.2023.e12826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]  Open
43
Lamkiewicz K, Esquivel Gomez LR, Kühnert D, Marz M. Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2. Curr Top Microbiol Immunol 2023;439:305-339. [PMID: 36592250 DOI: 10.1007/978-3-031-15640-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
44
Cholleti H, de Jong J, Blomström AL, Berg M. Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats. Pathogens 2022;12:pathogens12010012. [PMID: 36678360 PMCID: PMC9861107 DOI: 10.3390/pathogens12010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]  Open
45
Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022;15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]  Open
46
Domingo JL. An updated review of the scientific literature on the origin of SARS-CoV-2. ENVIRONMENTAL RESEARCH 2022;215:114131. [PMID: 36037920 PMCID: PMC9420317 DOI: 10.1016/j.envres.2022.114131] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 05/03/2023]
47
Amendola A, Canuti M, Bianchi S, Kumar S, Fappani C, Gori M, Colzani D, Kosakovsky Pond SL, Miura S, Baggieri M, Marchi A, Borghi E, Zuccotti G, Raviglione MC, Magurano F, Tanzi E. Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. ENVIRONMENTAL RESEARCH 2022;215:113979. [PMID: 36029839 PMCID: PMC9404229 DOI: 10.1016/j.envres.2022.113979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 05/12/2023]
48
Alhaji NB, Odetokun IA, Lawan MK, Adeiza AM, Nafarnda WD, Salihu MJ. Risk assessment and preventive health behaviours toward COVID-19 amongst bushmeat handlers in Nigerian wildlife markets: Drivers and One Health challenge. Acta Trop 2022;235:106621. [PMID: 35908578 PMCID: PMC9329136 DOI: 10.1016/j.actatropica.2022.106621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/08/2022]
49
Kurpas MK, Jaksik R, Kuś P, Kimmel M. Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution. Viruses 2022;14:2375. [PMID: 36366473 PMCID: PMC9695218 DOI: 10.3390/v14112375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 01/31/2023]  Open
50
Cantoni D, Murray MJ, Kalemera MD, Dicken SJ, Stejskal L, Brown G, Lytras S, Coey JD, McKenna J, Bridgett S, Simpson D, Fairley D, Thorne LG, Reuschl A, Forrest C, Ganeshalingham M, Muir L, Palor M, Jarvis L, Willett B, Power UF, McCoy LE, Jolly C, Towers GJ, Doores KJ, Robertson DL, Shepherd AJ, Reeves MB, Bamford CGG, Grove J. Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Rep 2022;23:e54322. [PMID: 35999696 PMCID: PMC9535765 DOI: 10.15252/embr.202154322] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022]  Open
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