Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2015 |
| Outros Autores: | , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| DOI: | 10.1371/journal.pone.0117176 |
| Texto Completo: | https://doi.org/10.1371/journal.pone.0117176 |
Resumo: | PMID: 25671421 WOS:000349545300039 |
| id |
RCAP_2ac73d030ee18b35a923bbbf53fa1d82 |
|---|---|
| oai_identifier_str |
oai:run.unl.pt:10362/36921 |
| network_acronym_str |
RCAP |
| network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository_id_str |
7160 |
| spelling |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in CubaAgricultural and Biological Sciences(all)Biochemistry, Genetics and Molecular Biology(all)Medicine(all)SDG 3 - Good Health and Well-beingPMID: 25671421 WOS:000349545300039As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7%to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the inhouse procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.Instituto de Higiene e Medicina Tropical (IHMT)TB, HIV and opportunistic diseases and pathogens (THOP)Global Health and Tropical Medicine (GHTM)RUNAlemán, YoanVinken, LoreKourí, VivianPérez, LissetteÁlvarez, AlinaAbrahantes, YeisselFonseca, CarlosPérez, JorgeCorrea, ConsueloSoto, YudiraSchrooten, YoeriVandamme, Anne MiekeVan Laethem, Kristel2018-05-14T22:01:18Z2015-02-112015-02-11T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.1371/journal.pone.0117176eng1932-6203PURE: 1224568http://www.scopus.com/inward/record.url?scp=84923036608&partnerID=8YFLogxKhttps://doi.org/10.1371/journal.pone.0117176info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-05-22T17:32:49Zoai:run.unl.pt:10362/36921Portal AgregadorONGhttps://www.rcaap.pt/oai/openairemluisa.alvim@gmail.comopendoar:71602024-05-22T17:32:49Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| title |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| spellingShingle |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba Alemán, Yoan Agricultural and Biological Sciences(all) Biochemistry, Genetics and Molecular Biology(all) Medicine(all) SDG 3 - Good Health and Well-being Alemán, Yoan Agricultural and Biological Sciences(all) Biochemistry, Genetics and Molecular Biology(all) Medicine(all) SDG 3 - Good Health and Well-being |
| title_short |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| title_full |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| title_fullStr |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| title_full_unstemmed |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| title_sort |
Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba |
| author |
Alemán, Yoan |
| author_facet |
Alemán, Yoan Alemán, Yoan Vinken, Lore Kourí, Vivian Pérez, Lissette Álvarez, Alina Abrahantes, Yeissel Fonseca, Carlos Pérez, Jorge Correa, Consuelo Soto, Yudira Schrooten, Yoeri Vandamme, Anne Mieke Van Laethem, Kristel Vinken, Lore Kourí, Vivian Pérez, Lissette Álvarez, Alina Abrahantes, Yeissel Fonseca, Carlos Pérez, Jorge Correa, Consuelo Soto, Yudira Schrooten, Yoeri Vandamme, Anne Mieke Van Laethem, Kristel |
| author_role |
author |
| author2 |
Vinken, Lore Kourí, Vivian Pérez, Lissette Álvarez, Alina Abrahantes, Yeissel Fonseca, Carlos Pérez, Jorge Correa, Consuelo Soto, Yudira Schrooten, Yoeri Vandamme, Anne Mieke Van Laethem, Kristel |
| author2_role |
author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Instituto de Higiene e Medicina Tropical (IHMT) TB, HIV and opportunistic diseases and pathogens (THOP) Global Health and Tropical Medicine (GHTM) RUN |
| dc.contributor.author.fl_str_mv |
Alemán, Yoan Vinken, Lore Kourí, Vivian Pérez, Lissette Álvarez, Alina Abrahantes, Yeissel Fonseca, Carlos Pérez, Jorge Correa, Consuelo Soto, Yudira Schrooten, Yoeri Vandamme, Anne Mieke Van Laethem, Kristel |
| dc.subject.por.fl_str_mv |
Agricultural and Biological Sciences(all) Biochemistry, Genetics and Molecular Biology(all) Medicine(all) SDG 3 - Good Health and Well-being |
| topic |
Agricultural and Biological Sciences(all) Biochemistry, Genetics and Molecular Biology(all) Medicine(all) SDG 3 - Good Health and Well-being |
| description |
PMID: 25671421 WOS:000349545300039 |
| publishDate |
2015 |
| dc.date.none.fl_str_mv |
2015-02-11 2015-02-11T00:00:00Z 2018-05-14T22:01:18Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
| dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
https://doi.org/10.1371/journal.pone.0117176 |
| url |
https://doi.org/10.1371/journal.pone.0117176 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
1932-6203 PURE: 1224568 http://www.scopus.com/inward/record.url?scp=84923036608&partnerID=8YFLogxK https://doi.org/10.1371/journal.pone.0117176 |
| dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
| instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| instacron_str |
RCAAP |
| institution |
RCAAP |
| reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| repository.mail.fl_str_mv |
mluisa.alvim@gmail.com |
| _version_ |
1822181944059756544 |
| dc.identifier.doi.none.fl_str_mv |
10.1371/journal.pone.0117176 |