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For: Tzou PL, Kosakovsky Pond SL, Avila-Rios S, Holmes SP, Kantor R, Shafer RW. Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. PLoS One 2020;15:e0225352. [PMID: 32102090 DOI: 10.1371/journal.pone.0225352] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/30/2020] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Alidjinou EK, Coulon P, Tetart M, Guigon A, Diarra A, Aissi E, Bazus H, Derdour V, Meybeck A, Viget N, Hober D, Bocket L, Robineau O. Defective HIV-1 DNA pol sequences are not associated with HIV-1 DNA levels and drive most APOBEC-context drug resistance mutations. J Antimicrob Chemother 2025;80:941-946. [PMID: 39849847 DOI: 10.1093/jac/dkaf016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 01/08/2025] [Indexed: 01/25/2025]  Open
2
Taramasso L, Bonora S, Cingolani A, Di Biagio A, Gianotti N, Guaraldi G, Lo Caputo S, Madeddu G, Maggi P, Marchetti G, Nozza S, Rusconi S, Maggiolo F. Question and answers on long-acting therapy with cabotegravir and rilpivirine in people with HIV. J Antimicrob Chemother 2025;80:610-623. [PMID: 39888371 DOI: 10.1093/jac/dkaf025] [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] [Indexed: 02/01/2025]  Open
3
Alagaratnam J, Kelly N, Dustan S, Naous N, Nwanbila M, Byrne R, Girometti N, Asboe D, Taylor GP, Boffito M. Proviral HIV DNA sequencing to inform suitability for long-acting injectable cabotegravir/rilpivirine. AIDS 2025;39:95-98. [PMID: 39639724 PMCID: PMC11627323 DOI: 10.1097/qad.0000000000004040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 10/04/2024] [Accepted: 10/08/2024] [Indexed: 12/07/2024]
4
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
5
Zhou Y, Ouyang F, Liu X, Lu J, Hu H, Sun Q, Yang H. A Sensitivity and Consistency Comparison Between Next-Generation Sequencing and Sanger Sequencing in HIV-1 Pretreatment Drug Resistance Testing. Viruses 2024;16:1713. [PMID: 39599828 PMCID: PMC11599105 DOI: 10.3390/v16111713] [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: 09/29/2024] [Revised: 10/26/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024]  Open
6
Campagna R, Nonne C, Antonelli G, Turriziani O. Archived HIV-1 Drug Resistance Mutations: Role of Proviral HIV-1 DNA Genotype for the Management of Virological Responder People Living with HIV. Viruses 2024;16:1697. [PMID: 39599811 PMCID: PMC11599110 DOI: 10.3390/v16111697] [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: 08/31/2024] [Revised: 10/28/2024] [Accepted: 10/29/2024] [Indexed: 11/29/2024]  Open
7
Zeeb M, Frischknecht P, Huber M, Schenkel CD, Neumann K, Leeman C, Notter J, Rauch A, Stöckle M, Cavassini M, Bernasconi E, Braun DL, Günthard HF, Metzner KJ, Kouyos RD. Genetic Diversity From Proviral DNA as a Proxy for Time Since HIV-1 Infection. J Infect Dis 2024;230:e631-e636. [PMID: 38507572 PMCID: PMC11420808 DOI: 10.1093/infdis/jiae149] [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: 11/17/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]  Open
8
Armenia D, Carioti L, Micheli V, Bon I, Allice T, Bonura C, Bruzzone B, Bracchitta F, Cerutti F, Giammanco GM, Stefanelli F, Bonifacio MA, Bertoli A, Vatteroni M, Ibba G, Novazzi F, Lipsi MR, Cuomo N, Vicenti I, Ceccherini-Silberstein F, Rossetti B, Bezenchek A, Saladini F, Zazzi M, Santoro MM. Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy. Viruses 2024;16:1422. [PMID: 39339898 PMCID: PMC11437420 DOI: 10.3390/v16091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024]  Open
9
Armenia D, Spagnuolo V, Bellocchi MC, Galli L, Duca L, Marchegiani G, Clemente T, Carioti L, Lolatto R, Calza L, Celesia BM, Cascio A, Francisci D, Saracino A, Torti C, Zazzi M, Castagna A, Santoro MM. Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry. J Antimicrob Chemother 2024;79:2354-2363. [PMID: 39004997 DOI: 10.1093/jac/dkae236] [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: 02/12/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024]  Open
10
Moore HP, Palumbo PJ, Notarte KI, Fogel JM, Cummings V, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Remien RH, Beyrer C, Hudelson SE, Eshleman SH, for the HPTN 078 study. Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase. J Clin Microbiol 2024;62:e0013624. [PMID: 38727213 PMCID: PMC11237527 DOI: 10.1128/jcm.00136-24] [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: 01/26/2024] [Accepted: 04/15/2024] [Indexed: 06/13/2024]  Open
11
Ode H, Matsuda M, Shigemi U, Mori M, Yamamura Y, Nakata Y, Okazaki R, Kubota M, Setoyama Y, Imahashi M, Yokomaku Y, Iwatani Y. Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations. Sci Rep 2024;14:12099. [PMID: 38802662 PMCID: PMC11130118 DOI: 10.1038/s41598-024-63054-3] [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: 04/12/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]  Open
12
Sun X, Zhang H, Kong X, Li N, Zhang T, An M, Ding H, Shang H, Han X. Low-level viremia episodes appear to affect the provirus composition of the circulating cellular HIV reservoir during antiretroviral therapy. Front Microbiol 2024;15:1376144. [PMID: 38841056 PMCID: PMC11150674 DOI: 10.3389/fmicb.2024.1376144] [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: 01/25/2024] [Accepted: 04/12/2024] [Indexed: 06/07/2024]  Open
13
Andre-Garnier E, Bocket L, Bourlet T, Hocqueloux L, Lepiller Q, Maillard A, Reigadas S, Barriere G, Durand F, Montes B, Stefic K, Marcelin AG. Use of genotypic HIV DNA testing: a DELPHI-type consensus. J Antimicrob Chemother 2024;79:578-588. [PMID: 38269616 PMCID: PMC10904721 DOI: 10.1093/jac/dkae007] [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: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]  Open
14
Ouyang F, Yuan D, Zhai W, Liu S, Zhou Y, Yang H. HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis. Viruses 2024;16:239. [PMID: 38400015 PMCID: PMC10893194 DOI: 10.3390/v16020239] [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: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024]  Open
15
Ka’e AC, Nanfack AJ, Ambada G, Santoro MM, Takou D, Semengue ENJ, Nka AD, Bala MLM, Endougou ON, Elong E, Beloumou G, Djupsa S, Gouissi DH, Fainguem N, Tchouaket MCT, Sosso SM, Kesseng D, Ndongo FA, Sonela N, Kamta ACL, Tchidjou HK, Ndomgue T, Ndiang STM, Nlend AEN, Nkenfou CN, Montesano C, Halle-Ekane GE, Cappelli G, Tiemessen CT, Colizzi V, Ceccherini-Silberstein F, Perno CF, Fokam J. Inflammatory profile of vertically HIV-1 infected adolescents receiving ART in Cameroon: a contribution toward optimal pediatric HIV control strategies. Front Immunol 2023;14:1239877. [PMID: 37646023 PMCID: PMC10461471 DOI: 10.3389/fimmu.2023.1239877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/21/2023] [Indexed: 09/01/2023]  Open
16
Gaitan NC, D’Antoni ML, Acosta RK, Gianella S, Little SJ, Chaillon A. Brief Report: Comparative Analysis of Pre-existing HIV Drug Resistance Mutations in Proviral DNA Using Next-Generation Sequencing and Routine HIV RNA Genotyping. J Acquir Immune Defic Syndr 2023;93:213-218. [PMID: 36961945 PMCID: PMC10272101 DOI: 10.1097/qai.0000000000003195] [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: 10/18/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023]
17
Tao K, Rhee SY, Tzou PL, Osman ZA, Pond SLK, Holmes SP, Shafer RW. HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses 2023;15:992. [PMID: 37112972 PMCID: PMC10143361 DOI: 10.3390/v15040992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]  Open
18
Fokam J, Ngoufack Jagni Semengue E, Molimbou E, Etame NK, Santoro MM, Takou D, Mossiang L, Meledie AP, Chenwi CA, Yagai B, Nka AD, Dambaya B, Teto G, Ka’e AC, Beloumou GA, Ndjeyep SCD, Fainguem N, Abba A, Kengni AMN, Tchouaket MCT, Bouba NP, Billong SC, Djubgang R, Saounde ET, Sosso SM, Kouanfack C, Bissek ACZK, Eben-Moussi E, Colizzi V, Perno CF, Ceccherini-Silberstein F, Ndjolo A. Evaluation of Circulating and Archived HIV-1 Integrase Drug-Resistance Variants among Patients on Third-Line ART in Cameroon: Implications for Dolutegravir-Containing Regimens in Resource-Limited Settings. Microbiol Spectr 2022;10:e0342022. [PMID: 36259973 PMCID: PMC9769697 DOI: 10.1128/spectrum.03420-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 01/10/2023]  Open
19
Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022;35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
20
Tzou PL, Tao K, Sahoo MK, Kosakovsky Pond SL, Pinsky BA, Shafer RW. Sierra SARS-CoV-2 sequence and antiviral resistance analysis program. J Clin Virol 2022;157:105323. [PMID: 36334368 PMCID: PMC9595491 DOI: 10.1016/j.jcv.2022.105323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/11/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
21
Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. PLoS One 2022;17:e0261045. [PMID: 35263335 PMCID: PMC8906623 DOI: 10.1371/journal.pone.0261045] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/22/2022] [Indexed: 11/19/2022]  Open
22
Armenia D, Santoro MM, Bellocchi MC, Carioti L, Galli L, Galli A, Scutari R, Salsi E, Mussini C, Sterrantino G, Calza L, Rossetti B, Zazzi M, Castagna A. Viral resistance burden and APOBEC editing correlate with virological response in heavily treatment-experienced people living with multi-drug resistant HIV. Int J Antimicrob Agents 2021;59:106492. [PMID: 34871747 DOI: 10.1016/j.ijantimicag.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022]
23
Moraka NO, Garcia-Broncano P, Hu Z, Ajibola G, Bareng OT, Pretorius-Holme M, Maswabi K, Maphorisa C, Mohammed T, Gaseitsiwe S, VanZyl GU, Kuritzkes DR, Lichterfeld M, Moyo S, Shapiro RL. Patterns of pretreatment drug resistance mutations of very early diagnosed and treated infants in Botswana. AIDS 2021;35:2413-2421. [PMID: 34324451 PMCID: PMC8631156 DOI: 10.1097/qad.0000000000003041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022]
24
Sarinoglu RC, Sili U, Hasdemir U, Aksu B, Soyletir G, Korten V. Diversity of HIV-1 subtypes and transmitted drug-resistance mutations among minority HIV-1 variants in a Turkish cohort. Curr HIV Res 2021;20:54-62. [PMID: 34802406 DOI: 10.2174/1570162x19666211119111740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/02/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022]
25
Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021;13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022]  Open
26
Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Viruses 2020;12:v12070694. [PMID: 32605062 PMCID: PMC7411816 DOI: 10.3390/v12070694] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]  Open
27
Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses 2020;12:v12060666. [PMID: 32575676 PMCID: PMC7354622 DOI: 10.3390/v12060666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]  Open
28
Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework. Viruses 2020;12:v12060645. [PMID: 32545906 PMCID: PMC7354600 DOI: 10.3390/v12060645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/29/2020] [Accepted: 06/11/2020] [Indexed: 01/24/2023]  Open
29
Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations. Viruses 2020;12:v12060617. [PMID: 32516949 PMCID: PMC7354449 DOI: 10.3390/v12060617] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023]  Open
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