Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch

Autores
Fernández, María Florencia; Distefano, Maximiliano Ezequiel; Mangano, Andrea María Mercedes; Sen, Luisa; Aulicino, Paula
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
HIV-1 infection through vertical transmission provides a good model to evaluate intra-host viral evolution and allows to gain insight into the dynamics of viral populations. Our aim was to assess the diversity and dynamics of X4- and R5-using HIV-1 variants in vertically infected children who presented a switch in SI/ NSI phenotype in MT-2 cell assays during chronic infection. Through molecular cloning and next generation sequencing of the C2-V5 env fragment, we investigated HIV-1 evolution and co-receptor usage based on V3 loop prediction bioinformatic tools of longitudinal samples obtained from 4 children. In all cases, the phylogenetic relationships were assessed by Maximum-Likelihood trees constructed with MEGA 6.0. In two cases, V3 loop sequences predicted exclusively R5-using and or X4-using strains, while in another two a higher degree of concordance was observed between the phenotypic and genotypic characteristics. In 3 of the 4 cases, C2-V5 env sequences from different time points were intermingled in phylogenetic trees, with no segregation neither by time or tropism. In only one case monophyletic clustering defined groups of sequences with different co-receptor usage. Comparison of amino acid frequency between isolates with SI and NSI phenotype allowed the identification of 9 possible genetic determinants in subtype F C2-V5 region of env associated to SI/ NSI phenotype in these patients, one of which had previously been reported for subtype B. Overall, we found a low degree of correlation between phenotypic and genotypic properties of HIV-1 quasispecies in patients under chronic infection. Whether HIV-1 subtype or other factors influence the evolution of HIV-1 in vivo will require further research.
Fil: Fernández, María Florencia. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Distefano, Maximiliano Ezequiel. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina
Fil: Mangano, Andrea María Mercedes. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Sen, Luisa. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aulicino, Paula. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
HIV-1
INTRA-HOST DYNAMICS
PHENOTYPE
TROPISM
VERTICAL TRANSMISSION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/174879
Acceder
id CONICETDig_a54ab40dfbe38a36fcb2617d1782af08
oai_identifier_str oai:ri.conicet.gov.ar:11336/174879
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switchFernández, María FlorenciaDistefano, Maximiliano EzequielMangano, Andrea María MercedesSen, LuisaAulicino, PaulaHIV-1INTRA-HOST DYNAMICSPHENOTYPETROPISMVERTICAL TRANSMISSIONhttps://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3HIV-1 infection through vertical transmission provides a good model to evaluate intra-host viral evolution and allows to gain insight into the dynamics of viral populations. Our aim was to assess the diversity and dynamics of X4- and R5-using HIV-1 variants in vertically infected children who presented a switch in SI/ NSI phenotype in MT-2 cell assays during chronic infection. Through molecular cloning and next generation sequencing of the C2-V5 env fragment, we investigated HIV-1 evolution and co-receptor usage based on V3 loop prediction bioinformatic tools of longitudinal samples obtained from 4 children. In all cases, the phylogenetic relationships were assessed by Maximum-Likelihood trees constructed with MEGA 6.0. In two cases, V3 loop sequences predicted exclusively R5-using and or X4-using strains, while in another two a higher degree of concordance was observed between the phenotypic and genotypic characteristics. In 3 of the 4 cases, C2-V5 env sequences from different time points were intermingled in phylogenetic trees, with no segregation neither by time or tropism. In only one case monophyletic clustering defined groups of sequences with different co-receptor usage. Comparison of amino acid frequency between isolates with SI and NSI phenotype allowed the identification of 9 possible genetic determinants in subtype F C2-V5 region of env associated to SI/ NSI phenotype in these patients, one of which had previously been reported for subtype B. Overall, we found a low degree of correlation between phenotypic and genotypic properties of HIV-1 quasispecies in patients under chronic infection. Whether HIV-1 subtype or other factors influence the evolution of HIV-1 in vivo will require further research.Fil: Fernández, María Florencia. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Distefano, Maximiliano Ezequiel. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; ArgentinaFil: Mangano, Andrea María Mercedes. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sen, Luisa. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Aulicino, Paula. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaElsevier Science2019-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/174879Fernández, María Florencia; Distefano, Maximiliano Ezequiel; Mangano, Andrea María Mercedes; Sen, Luisa; Aulicino, Paula; Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch; Elsevier Science; Infection, Genetics and Evolution; 78; 11-2019; 1-321567-1348CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.meegid.2019.104066info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/abs/pii/S1567134819302928info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:06:22Zoai:ri.conicet.gov.ar:11336/174879instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:06:22.791CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
title Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
spellingShingle Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
Fernández, María Florencia
HIV-1
INTRA-HOST DYNAMICS
PHENOTYPE
TROPISM
VERTICAL TRANSMISSION
title_short Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
title_full Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
title_fullStr Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
title_full_unstemmed Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
title_sort Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch
dc.creator.none.fl_str_mv Fernández, María Florencia
Distefano, Maximiliano Ezequiel
Mangano, Andrea María Mercedes
Sen, Luisa
Aulicino, Paula
author Fernández, María Florencia
author_facet Fernández, María Florencia
Distefano, Maximiliano Ezequiel
Mangano, Andrea María Mercedes
Sen, Luisa
Aulicino, Paula
author_role author
author2 Distefano, Maximiliano Ezequiel
Mangano, Andrea María Mercedes
Sen, Luisa
Aulicino, Paula
author2_role author
author
author
author
dc.subject.none.fl_str_mv HIV-1
INTRA-HOST DYNAMICS
PHENOTYPE
TROPISM
VERTICAL TRANSMISSION
topic HIV-1
INTRA-HOST DYNAMICS
PHENOTYPE
TROPISM
VERTICAL TRANSMISSION
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv HIV-1 infection through vertical transmission provides a good model to evaluate intra-host viral evolution and allows to gain insight into the dynamics of viral populations. Our aim was to assess the diversity and dynamics of X4- and R5-using HIV-1 variants in vertically infected children who presented a switch in SI/ NSI phenotype in MT-2 cell assays during chronic infection. Through molecular cloning and next generation sequencing of the C2-V5 env fragment, we investigated HIV-1 evolution and co-receptor usage based on V3 loop prediction bioinformatic tools of longitudinal samples obtained from 4 children. In all cases, the phylogenetic relationships were assessed by Maximum-Likelihood trees constructed with MEGA 6.0. In two cases, V3 loop sequences predicted exclusively R5-using and or X4-using strains, while in another two a higher degree of concordance was observed between the phenotypic and genotypic characteristics. In 3 of the 4 cases, C2-V5 env sequences from different time points were intermingled in phylogenetic trees, with no segregation neither by time or tropism. In only one case monophyletic clustering defined groups of sequences with different co-receptor usage. Comparison of amino acid frequency between isolates with SI and NSI phenotype allowed the identification of 9 possible genetic determinants in subtype F C2-V5 region of env associated to SI/ NSI phenotype in these patients, one of which had previously been reported for subtype B. Overall, we found a low degree of correlation between phenotypic and genotypic properties of HIV-1 quasispecies in patients under chronic infection. Whether HIV-1 subtype or other factors influence the evolution of HIV-1 in vivo will require further research.
Fil: Fernández, María Florencia. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Distefano, Maximiliano Ezequiel. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina
Fil: Mangano, Andrea María Mercedes. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Sen, Luisa. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aulicino, Paula. Gobierno de la Ciudad de Buenos Aires. Hospital de Pediatría "Juan P. Garrahan"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description HIV-1 infection through vertical transmission provides a good model to evaluate intra-host viral evolution and allows to gain insight into the dynamics of viral populations. Our aim was to assess the diversity and dynamics of X4- and R5-using HIV-1 variants in vertically infected children who presented a switch in SI/ NSI phenotype in MT-2 cell assays during chronic infection. Through molecular cloning and next generation sequencing of the C2-V5 env fragment, we investigated HIV-1 evolution and co-receptor usage based on V3 loop prediction bioinformatic tools of longitudinal samples obtained from 4 children. In all cases, the phylogenetic relationships were assessed by Maximum-Likelihood trees constructed with MEGA 6.0. In two cases, V3 loop sequences predicted exclusively R5-using and or X4-using strains, while in another two a higher degree of concordance was observed between the phenotypic and genotypic characteristics. In 3 of the 4 cases, C2-V5 env sequences from different time points were intermingled in phylogenetic trees, with no segregation neither by time or tropism. In only one case monophyletic clustering defined groups of sequences with different co-receptor usage. Comparison of amino acid frequency between isolates with SI and NSI phenotype allowed the identification of 9 possible genetic determinants in subtype F C2-V5 region of env associated to SI/ NSI phenotype in these patients, one of which had previously been reported for subtype B. Overall, we found a low degree of correlation between phenotypic and genotypic properties of HIV-1 quasispecies in patients under chronic infection. Whether HIV-1 subtype or other factors influence the evolution of HIV-1 in vivo will require further research.
publishDate 2019
dc.date.none.fl_str_mv 2019-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/174879
Fernández, María Florencia; Distefano, Maximiliano Ezequiel; Mangano, Andrea María Mercedes; Sen, Luisa; Aulicino, Paula; Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch; Elsevier Science; Infection, Genetics and Evolution; 78; 11-2019; 1-32
1567-1348
CONICET Digital
CONICET
url http://hdl.handle.net/11336/174879
identifier_str_mv Fernández, María Florencia; Distefano, Maximiliano Ezequiel; Mangano, Andrea María Mercedes; Sen, Luisa; Aulicino, Paula; Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch; Elsevier Science; Infection, Genetics and Evolution; 78; 11-2019; 1-32
1567-1348
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.meegid.2019.104066
info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/abs/pii/S1567134819302928
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier Science
publisher.none.fl_str_mv Elsevier Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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