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For: Stern A, Bianco S, Yeh MT, Wright C, Butcher K, Tang C, Nielsen R, Andino R. Costs and benefits of mutational robustness in RNA viruses. Cell Rep 2014;8:1026-36. [PMID: 25127138 DOI: 10.1016/j.celrep.2014.07.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 05/18/2014] [Accepted: 07/11/2014] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Pauciullo S, Zulian V, La Frazia S, Paci P, Garbuglia AR. Spillover: Mechanisms, Genetic Barriers, and the Role of Reservoirs in Emerging Pathogens. Microorganisms 2024;12:2191. [PMID: 39597581 PMCID: PMC11596118 DOI: 10.3390/microorganisms12112191] [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: 09/20/2024] [Revised: 10/16/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]  Open
2
Illingworth CJR, Guerra-Assuncao JA, Gregg S, Charles O, Pang J, Roy S, Abdelnabi R, Neyts J, Breuer J. Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evol 2024;10:veae001. [PMID: 38486802 PMCID: PMC10939363 DOI: 10.1093/ve/veae001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/23/2023] [Accepted: 01/03/2024] [Indexed: 03/17/2024]  Open
3
Catching A, Te Yeh M, Bianco S, Capponi S, Andino R. A tradeoff between enterovirus A71 particle stability and cell entry. Nat Commun 2023;14:7450. [PMID: 37978288 PMCID: PMC10656440 DOI: 10.1038/s41467-023-43029-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/26/2023] [Indexed: 11/19/2023]  Open
4
Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023;11:308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023]  Open
5
Strobel HM, Stuart EC, Meyer JR. A Trait-Based Approach to Predicting Viral Host-Range Evolvability. Annu Rev Virol 2022;9:139-156. [PMID: 36173699 DOI: 10.1146/annurev-virology-091919-092003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
6
Diaz Arenas C, Ardaševa A, Miller J, Mikheyev AS, Yokobayashi Y. Ribozyme Mutagenic Evolution: Mechanisms of Survival. ORIGINS LIFE EVOL B 2022;51:321-339. [PMID: 34994918 DOI: 10.1007/s11084-021-09617-0] [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: 04/18/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
7
Suryawanshi YR, Nace RA, Russell SJ, Schulze AJ. MicroRNA-detargeting proves more effective than leader gene deletion for improving safety of oncolytic Mengovirus in a nude mouse model. Mol Ther Oncolytics 2021;23:1-13. [PMID: 34589580 PMCID: PMC8455367 DOI: 10.1016/j.omto.2021.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]  Open
8
Van Eyndhoven LC, Singh A, Tel J. Decoding the dynamics of multilayered stochastic antiviral IFN-I responses. Trends Immunol 2021;42:824-839. [PMID: 34364820 DOI: 10.1016/j.it.2021.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 12/11/2022]
9
Merleau NSC, Pénisson S, Gerrish PJ, Elena SF, Smerlak M. Why are viral genomes so fragile? The bottleneck hypothesis. PLoS Comput Biol 2021;17:e1009128. [PMID: 34237053 PMCID: PMC8291636 DOI: 10.1371/journal.pcbi.1009128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/20/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]  Open
10
Singhal S, Turner PE. Effects of historical co-infection on host shift abilities of exploitative and competitive viruses. Evolution 2021;75:1878-1888. [PMID: 33969482 PMCID: PMC12058955 DOI: 10.1111/evo.14263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 12/29/2022]
11
Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs. Sci Rep 2021;11:9986. [PMID: 33976241 PMCID: PMC8113533 DOI: 10.1038/s41598-021-88132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023]  Open
12
Novelli G, Biancolella M, Mehrian-Shai R, Colona VL, Brito AF, Grubaugh ND, Vasiliou V, Luzzatto L, Reichardt JKV. COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy. Hum Genomics 2021;15:27. [PMID: 33966626 PMCID: PMC8107019 DOI: 10.1186/s40246-021-00326-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022]  Open
13
Barlukova A, Rouzine IM. The evolutionary origin of the universal distribution of mutation fitness effect. PLoS Comput Biol 2021;17:e1008822. [PMID: 33684109 PMCID: PMC7971868 DOI: 10.1371/journal.pcbi.1008822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/18/2021] [Accepted: 02/19/2021] [Indexed: 01/27/2023]  Open
14
Sarkar R, Mitra S, Chandra P, Saha P, Banerjee A, Dutta S, Chawla-Sarkar M. Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations. Arch Virol 2021;166:801-812. [PMID: 33464421 PMCID: PMC7814186 DOI: 10.1007/s00705-020-04911-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 01/24/2023]
15
Rouzine IM. An Evolutionary Model of Progression to AIDS. Microorganisms 2020;8:microorganisms8111714. [PMID: 33142907 PMCID: PMC7692852 DOI: 10.3390/microorganisms8111714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]  Open
16
Butković A, González R, Cobo I, Elena SF. Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness. Virus Evol 2020;6:veaa041. [PMID: 32782826 PMCID: PMC7409916 DOI: 10.1093/ve/veaa041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
17
Sexton NR, Ebel GD. Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns. Viruses 2019;11:v11070643. [PMID: 31336898 PMCID: PMC6669465 DOI: 10.3390/v11070643] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022]  Open
18
McCarthy C, Jayawardena N, Burga LN, Bostina M. Developing Picornaviruses for Cancer Therapy. Cancers (Basel) 2019;11:E685. [PMID: 31100962 PMCID: PMC6562951 DOI: 10.3390/cancers11050685] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 12/24/2022]  Open
19
Drayman N, Patel P, Vistain L, Tay S. HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 2019;8:e46339. [PMID: 31090537 PMCID: PMC6570482 DOI: 10.7554/elife.46339] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022]  Open
20
Zhao L, Abbasi AB, Illingworth CJR. Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evol 2019;5:vez008. [PMID: 31024738 PMCID: PMC6476161 DOI: 10.1093/ve/vez008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
21
Zinger T, Gelbart M, Miller D, Pennings PS, Stern A. Inferring population genetics parameters of evolving viruses using time-series data. Virus Evol 2019;5:vez011. [PMID: 31191979 PMCID: PMC6555871 DOI: 10.1093/ve/vez011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
22
Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018;5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
23
Dolan PT, Whitfield ZJ, Andino R. Mapping the Evolutionary Potential of RNA Viruses. Cell Host Microbe 2018;23:435-446. [PMID: 29649440 PMCID: PMC5908228 DOI: 10.1016/j.chom.2018.03.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
24
Emergency Services of Viral RNAs: Repair and Remodeling. Microbiol Mol Biol Rev 2018. [PMID: 29540453 DOI: 10.1128/mmbr.00067-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
25
Drayman N, Karin O, Mayo A, Danon T, Shapira L, Rafael D, Zimmer A, Bren A, Kobiler O, Alon U. Dynamic Proteomics of Herpes Simplex Virus Infection. mBio 2017;8:e01612-17. [PMID: 29114028 PMCID: PMC5676043 DOI: 10.1128/mbio.01612-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 10/06/2017] [Indexed: 12/28/2022]  Open
26
Jerison ER, Kryazhimskiy S, Mitchell JK, Bloom JS, Kruglyak L, Desai MM. Genetic variation in adaptability and pleiotropy in budding yeast. eLife 2017;6:27167. [PMID: 28826486 PMCID: PMC5580887 DOI: 10.7554/elife.27167] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/14/2017] [Indexed: 12/25/2022]  Open
27
Stern A, Yeh MT, Zinger T, Smith M, Wright C, Ling G, Nielsen R, Macadam A, Andino R. The Evolutionary Pathway to Virulence of an RNA Virus. Cell 2017;169:35-46.e19. [PMID: 28340348 DOI: 10.1016/j.cell.2017.03.013] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 12/31/2022]
28
Moratorio G, Henningsson R, Barbezange C, Carrau L, Bordería AV, Blanc H, Beaucourt S, Poirier EZ, Vallet T, Boussier J, Mounce BC, Fontes M, Vignuzzi M. Attenuation of RNA viruses by redirecting their evolution in sequence space. Nat Microbiol 2017;2:17088. [PMID: 28581455 PMCID: PMC7098180 DOI: 10.1038/nmicrobiol.2017.88] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 04/27/2017] [Indexed: 12/18/2022]
29
Variation in Recombination Rate: Adaptive or Not? Trends Genet 2017;33:364-374. [DOI: 10.1016/j.tig.2017.03.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 01/30/2023]
30
Minicka J, Elena SF, Borodynko-Filas N, Rubiś B, Hasiów-Jaroszewska B. Strain-dependent mutational effects for Pepino mosaic virus in a natural host. BMC Evol Biol 2017;17:67. [PMID: 28264646 PMCID: PMC5339997 DOI: 10.1186/s12862-017-0920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/20/2017] [Indexed: 11/10/2022]  Open
31
Xiao Y, Rouzine IM, Bianco S, Acevedo A, Goldstein EF, Farkov M, Brodsky L, Andino R. RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell Host Microbe 2016;19:493-503. [PMID: 27078068 DOI: 10.1016/j.chom.2016.03.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/13/2016] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
32
Dynamics of West Nile virus evolution in mosquito vectors. Curr Opin Virol 2016;21:132-138. [PMID: 27788400 DOI: 10.1016/j.coviro.2016.09.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/09/2016] [Accepted: 09/12/2016] [Indexed: 01/24/2023]
33
Grubaugh ND, Weger-Lucarelli J, Murrieta RA, Fauver JR, Garcia-Luna SM, Prasad AN, Black WC, Ebel GD. Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching. Cell Host Microbe 2016;19:481-92. [PMID: 27049584 DOI: 10.1016/j.chom.2016.03.002] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/19/2016] [Accepted: 03/07/2016] [Indexed: 11/30/2022]
34
Barr J, Fearns R. Genetic Instability of RNA Viruses. GENOME STABILITY 2016. [PMCID: PMC7149711 DOI: 10.1016/b978-0-12-803309-8.00002-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
35
Stern A, Andino R. Viral Evolution. VIRAL PATHOGENESIS 2016. [PMCID: PMC7149360 DOI: 10.1016/b978-0-12-800964-2.00017-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
36
Jones BA, Lessler J, Bianco S, Kaufman JH. Statistical Mechanics and Thermodynamics of Viral Evolution. PLoS One 2015;10:e0137482. [PMID: 26422205 PMCID: PMC4589373 DOI: 10.1371/journal.pone.0137482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/16/2015] [Indexed: 11/18/2022]  Open
37
Peck KM, Burch CL, Heise MT, Baric RS. Coronavirus Host Range Expansion and Middle East Respiratory Syndrome Coronavirus Emergence: Biochemical Mechanisms and Evolutionary Perspectives. Annu Rev Virol 2015;2:95-117. [PMID: 26958908 DOI: 10.1146/annurev-virology-100114-055029] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
38
Grubaugh ND, Smith DR, Brackney DE, Bosco-Lauth AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD. Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness. PLoS Pathog 2015;11:e1004874. [PMID: 25993022 PMCID: PMC4439088 DOI: 10.1371/journal.ppat.1004874] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/12/2015] [Indexed: 01/13/2023]  Open
39
Bank C, Hietpas RT, Jensen JD, Bolon DNA. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol 2014;32:229-38. [PMID: 25371431 DOI: 10.1093/molbev/msu301] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
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