Early-Transmitted Variants and Their Evolution in a HIV-1 Positive Couple: NGS and Phylogenetic Analyses
We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combine...
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| Veröffentlicht in: | Viruses Jg. 13; H. 3; S. 513 |
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| Abstract | We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies. |
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| AbstractList | We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies. We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies.We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies. |
| Author | Bergna, Annalisa Trabattoni, Daria Lai, Alessia Zuccotti, Gian Vincenzo Zehender, Gianguglielmo Fenizia, Claudio Clerici, Mario Giacomet, Vania |
| AuthorAffiliation | 2 Clinic of Pediatrics, ASST Fatebenefratelli-Sacco, Sacco Clinical Sciences Institute, Via G.B. Grassi 74, 20157 Milan, Italy; vania.giacomet@unimi.it (V.G.); GianVincenzo.Zuccotti@unimi.it (G.V.Z.) 3 Department of Pathophysiology and Transplantation, University of Milan, Via F. Sforza 35, 20122 Milan, Italy; mario.clerici@unimi.it 1 Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; alessia.lai@unimi.it (A.L.); bergna.anna@gmail.com (A.B.); gianguglielmo.zehender@unimi.it (G.Z.); daria.trabattoni@unimi.it (D.T.) 4 IRCCS Fondazione Don Carlo Gnocchi, Via Capecelatro 66, 20148 Milan, Italy |
| AuthorAffiliation_xml | – name: 2 Clinic of Pediatrics, ASST Fatebenefratelli-Sacco, Sacco Clinical Sciences Institute, Via G.B. Grassi 74, 20157 Milan, Italy; vania.giacomet@unimi.it (V.G.); GianVincenzo.Zuccotti@unimi.it (G.V.Z.) – name: 1 Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; alessia.lai@unimi.it (A.L.); bergna.anna@gmail.com (A.B.); gianguglielmo.zehender@unimi.it (G.Z.); daria.trabattoni@unimi.it (D.T.) – name: 3 Department of Pathophysiology and Transplantation, University of Milan, Via F. Sforza 35, 20122 Milan, Italy; mario.clerici@unimi.it – name: 4 IRCCS Fondazione Don Carlo Gnocchi, Via Capecelatro 66, 20148 Milan, Italy |
| Author_xml | – sequence: 1 givenname: Alessia surname: Lai fullname: Lai, Alessia – sequence: 2 givenname: Vania surname: Giacomet fullname: Giacomet, Vania – sequence: 3 givenname: Annalisa surname: Bergna fullname: Bergna, Annalisa – sequence: 4 givenname: Gian Vincenzo orcidid: 0000-0002-2795-9874 surname: Zuccotti fullname: Zuccotti, Gian Vincenzo – sequence: 5 givenname: Gianguglielmo orcidid: 0000-0002-1886-2915 surname: Zehender fullname: Zehender, Gianguglielmo – sequence: 6 givenname: Mario surname: Clerici fullname: Clerici, Mario – sequence: 7 givenname: Daria orcidid: 0000-0001-9535-3359 surname: Trabattoni fullname: Trabattoni, Daria – sequence: 8 givenname: Claudio orcidid: 0000-0003-0735-8331 surname: Fenizia fullname: Fenizia, Claudio |
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| Cites_doi | 10.1038/nrmicro3471 10.1128/JVI.00522-15 10.1086/529206 10.1080/01621459.1995.10476572 10.1093/molbev/msj030 10.1093/ve/vey038 10.1073/pnas.1414926112 10.1089/aid.2011.0245 10.1073/pnas.0802203105 10.1371/journal.ppat.1000890 10.1080/09540121.2019.1668534 10.1126/science.1165706 10.1038/nri700 10.1371/journal.ppat.1000590 10.1038/nrmicro3003 10.1086/511988 10.1186/1471-2148-7-214 10.1371/journal.pbio.1002251 10.1093/infdis/jis503 10.1371/journal.ppat.1004565 10.1136/bmj.l5554 10.1002/jia2.25357 10.1093/ve/vew007 10.1371/journal.pone.0007122 10.1073/pnas.1522675113 10.1093/molbev/msaa015 10.1073/pnas.1103764108 10.1073/pnas.1405194111 10.1089/aid.2007.0115 10.1016/j.semcancer.2013.11.003 10.1128/JVI.73.1.152-160.1999 10.1371/journal.pone.0093428 10.1016/j.jtbi.2009.07.038 10.1093/bioinformatics/bts199 10.1128/JVI.01788-13 10.1093/molbev/msy096 10.1038/nm.2316 10.3390/v3060861 10.1172/jci.insight.132997 10.1128/JVI.02697-10 10.1128/JVI.00056-10 10.1038/nm880 10.1097/OLQ.0000000000001048 10.1038/s41467-019-10884-9 10.1016/S2352-3018(19)30226-7 10.1128/JVI.02132-08 10.1172/JCI135953 10.1038/s41598-018-19783-3 10.1186/s12977-017-0343-8 10.1126/science.1254194 10.1093/infdis/jiz281 10.1093/ve/vew012 10.1038/nm.3932 10.1016/S2352-3018(17)30183-2 10.1093/molbev/msn083 |
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| Keywords | HIV deep phylogenetic NGS analyses HIV evolution HIV quasispecies human immunodeficiency virus (HIV) mucosal bottleneck HIV T/F variants HIV sexual transmission |
| Language | English |
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| SubjectTerms | antiretroviral agents Bayesian theory blood HIV deep phylogenetic NGS analyses HIV evolution HIV quasispecies HIV T/F variants human immunodeficiency virus (HIV) mucosal bottleneck phylogeny sexual behavior therapeutics trees vaccine development |
| Title | Early-Transmitted Variants and Their Evolution in a HIV-1 Positive Couple: NGS and Phylogenetic Analyses |
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