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Article ; Online: Determinants of Late HIV Presentation at Ndlavela Health Center in Mozambique.

Chone, Jeremias Salomão / Abecasis, Ana Barroso / Varandas, Luís

International journal of environmental research and public health

2022 Volume 19, Issue 8

Abstract: Background: There has been tremendous progress in the fight against HIV worldwide; however, challenges persist in the control of HIV infection. These challenges include the high prevalence of late presenters. There are many disadvantages of late ... ...

Abstract	Background: There has been tremendous progress in the fight against HIV worldwide; however, challenges persist in the control of HIV infection. These challenges include the high prevalence of late presenters. There are many disadvantages of late presentation-from reduced survival of the infected person to the risk of transmitting the infection. This research aims to analyze the factors that influence the late presentation in patients attending Ndlavela Health Center in Mozambique. Methodology: A retrospective cross-sectional study was carried out at Ndlavela Health Center including patients diagnosed with HIV between 2015 and 2020. The European Late Presenter Consensus working group definitions were used, and univariate and multivariate logistic regression were used to identify factors associated with late presentation. Results: In total, 519 participants were included in the study, of which nearly 47% were classified as late presenters. The male gender (AOR = 2.41), clinical suspicious test (AOR = 4.03), initiated by the health professional (AOR = 2.1,9), and fear of stigma (AOR = 2.80) were the main risk factors for late HIV presentation. Conclusion: Factors that are potentially determinant for late HIV presentation were identified. Actions are needed to focus on risk factors that are most likely to delay presentation.
MeSH term(s)	CD4 Lymphocyte Count ; Cross-Sectional Studies ; HIV Infections/diagnosis ; HIV Infections/epidemiology ; Humans ; Male ; Mozambique/epidemiology ; Retrospective Studies ; Risk Factors
Language	English
Publishing date	2022-04-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph19084568
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Article ; Online: Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G.

Palma, Ana Carolina / Abecasis, Ana Barroso / Vercauteren, Jurgen / Carvalho, Ana Patricia / Cabanas, Joaquim / Vandamme, Anne-Mieke / Camacho, Ricardo Jorge

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2010 Volume 10, Issue 3, Page(s) 373–379

Abstract: Europe is currently observing a significant rise in non-B subtypes. Consequently, the effect of genetic variability on therapy response or genotypic resistance interpretation algorithms is an emerging concern. The purpose of this study is to investigate ... ...

Abstract	Europe is currently observing a significant rise in non-B subtypes. Consequently, the effect of genetic variability on therapy response or genotypic resistance interpretation algorithms is an emerging concern. The purpose of this study is to investigate the amino acid substitutions selected under drug pressure in the protease of human immunodeficiency virus type 1 (HIV-1) subtypes B and G, and determine if there are any significant differences. We investigated therapy-related and subtype-related substitutions in the protease, considering subtype, overall protease inhibitor treatment and individual drug exposure. Many mutations were significantly related to protease inhibitor (PI) therapy, with mutations exclusive to subtype B or subtype G. Some mutations are at positions related to resistance in both subtypes, but the amino acid substitution is different. Other mutations were significantly associated with subtype and PI selective pressure (p<0.05), pointing towards a differential selective pressure in both subtypes. We confirmed previous reports on the subtype-dependent selection of D30N and 89I, and identified a new mutation with such differential selective pressure: 37D was preferentially selected by lopinavir in subtype B. Other novel mutations found under therapy pressure were 13A, 35N, K55R, I66F, I72L/T, T74S, 82M and 89I/V. Our study indicates that even though in general, drug selective pressure and resistance pathways are relatively similar between subtypes B and G, some differences do occur, leading to subtype-dependent substitutions.
MeSH term(s)	Amino Acid Substitution/drug effects ; Drug Resistance, Viral/genetics ; Genetic Variation ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV Protease/genetics ; HIV Protease Inhibitors/therapeutic use ; HIV-1/drug effects ; HIV-1/genetics ; Humans ; Indinavir/therapeutic use ; Lopinavir ; Phylogeny ; Pyrimidinones/therapeutic use ; Selection, Genetic ; Sequence Analysis, Protein
Chemical Substances	HIV Protease Inhibitors ; Pyrimidinones ; Lopinavir (2494G1JF75) ; Indinavir (5W6YA9PKKH) ; HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-)
Language	English
Publishing date	2010-04
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2009.06.019
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Article ; Online: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools.

Pineda-Peña, Andrea-Clemencia / Faria, Nuno Rodrigues / Imbrechts, Stijn / Libin, Pieter / Abecasis, Ana Barroso / Deforche, Koen / Gómez-López, Arley / Camacho, Ricardo J / de Oliveira, Tulio / Vandamme, Anne-Mieke

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2013 Volume 19, Page(s) 337–348

Abstract: Background: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the ... ...

Abstract	Background: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). Methodology: HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. Results: The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ~99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (~99%) and SCUEAL (~96%). Conclusions: REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
MeSH term(s)	Cluster Analysis ; Computational Biology ; Databases, Genetic ; HIV Infections/epidemiology ; HIV Infections/virology ; HIV-1/classification ; HIV-1/genetics ; Humans ; Molecular Typing/methods ; Phylogeny ; Public Health Surveillance ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2013-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2013.04.032
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Article: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

Infection, genetics, and evolution. 2013 Oct., v. 19

2013

Abstract: BACKGROUND: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the ... ...

Abstract	BACKGROUND: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). METHODOLOGY: HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. RESULTS: The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ∼99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (∼99%) and SCUEAL (∼96%). CONCLUSIONS: REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
Keywords	Human immunodeficiency virus 1 ; data collection ; databases ; drug resistance ; genome ; monitoring ; pathogenesis ; patients ; phylogeny
Language	English
Dates of publication	2013-10
Size	p. 337-348.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2013.04.032
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.

Nunes, Marcio Roberto Teixeira / Faria, Nuno Rodrigues / Vasconcelos, Helena Baldez / Medeiros, Daniele Barbosa de Almeida / Silva de Lima, Clayton Pereira / Carvalho, Valéria Lima / Pinto da Silva, Eliana Vieira / Cardoso, Jedson Ferreira / Sousa, Edivaldo Costa / Nunes, Keley Nascimento Barbosa / Rodrigues, Sueli Guerreiro / Abecasis, Ana Barroso / Suchard, Marc A / Lemey, Philippe / Vasconcelos, Pedro Fernando da Costa

Emerging infectious diseases

2012 Volume 18, Issue 11, Page(s) 1858–1864

Abstract: Dengue virus serotype 4 (DENV-4) reemerged in Roraima State, Brazil, 28 years after it was last detected in the country in 1982. To study the origin and evolution of this reemergence, full-length sequences were obtained for 16 DENV-4 isolates from ... ...

Abstract	Dengue virus serotype 4 (DENV-4) reemerged in Roraima State, Brazil, 28 years after it was last detected in the country in 1982. To study the origin and evolution of this reemergence, full-length sequences were obtained for 16 DENV-4 isolates from northern (Roraima, Amazonas, Pará States) and northeastern (Bahia State) Brazil during the 2010 and 2011 dengue virus seasons and for an isolate from the 1982 epidemic in Roraima. Spatiotemporal dynamics of DENV-4 introductions in Brazil were applied to envelope genes and full genomes by using Bayesian phylogeographic analyses. An introduction of genotype I into Brazil from Southeast Asia was confirmed, and full genome phylogeographic analyses revealed multiple introductions of DENV-4 genotype II in Brazil, providing evidence for >3 introductions of this genotype within the last decade: 2 from Venezuela to Roraima and 1 from Colombia to Amazonas. The phylogeographic analysis of full genome data has demonstrated the origins of DENV-4 throughout Brazil.
MeSH term(s)	Animals ; Brazil/epidemiology ; Dengue/epidemiology ; Dengue Virus/classification ; Dengue Virus/genetics ; Genome, Viral ; Genotype ; Humans ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Serotyping ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics
Chemical Substances	Viral Envelope Proteins
Language	English
Publishing date	2012-10-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid1811.120217
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Article: Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G.

Abecasis, Ana Barroso / Deforche, Koen / Snoeck, Joke / Bacheler, Lee T / McKenna, Paula / Carvalho, Ana Patrícia / Gomes, Perpétua / Camacho, Ricardo Jorge / Vandamme, Anne-Mieke

AIDS (London, England)

2005 Volume 19, Issue 16, Page(s) 1799–1806

Abstract: Objective: To investigate whether and how mutations at position 89 of HIV-1 protease were associated with protease inhibitor (PI) failure, and what is the impact of the HIV-1 subtype.: Methods: In a database containing pol nucleotide sequences and ... ...

Abstract	Objective: To investigate whether and how mutations at position 89 of HIV-1 protease were associated with protease inhibitor (PI) failure, and what is the impact of the HIV-1 subtype. Methods: In a database containing pol nucleotide sequences and treatment history, the correlation between PI experience and mutations at codon 89 was determined separately for subtype B and several non-B subtypes. A Bayesian network model was used to map the resistance pathways in which M89I/V is involved for subtype G. The phenotypic effect of M89I/V for several PIs was also measured. Results: The analysis showed that for the subtypes C, F and G in which the wild-type codon at 89 was M compared to L for subtype B, M89I/V was significantly more frequently observed in PI-treated patients displaying major resistance mutations to PIs than in drug-naive patients. M89I/V was strongly associated with PI resistance mutations at codons 71, 74 and 90. Phenotypically, M89I/V alone did not confer a reduced susceptibility to PIs. However, when combined with L90M, a significantly reduced susceptibility to nelfinavir was observed (P < 0.05) in comparison with strains with L90M alone. Conclusions: The results of the present study show that M89I/V is associated with PI experience in subtypes C, F and G but not in subtype B. M89I/V should be considered a secondary PI mutation with an important effect on nelfinavir susceptibility in the presence of L90M.
MeSH term(s)	Adult ; Amino Acid Sequence ; Bayes Theorem ; Drug Resistance, Multiple, Viral/genetics ; Female ; Genotype ; HIV Infections/drug therapy ; HIV Infections/genetics ; HIV Protease/genetics ; HIV Protease Inhibitors/therapeutic use ; HIV-1/genetics ; Humans ; Male ; Mutation/genetics ; Phenotype ; Treatment Failure ; Viral Load
Chemical Substances	HIV Protease Inhibitors ; HIV Protease (EC 3.4.23.-)
Language	English
Publishing date	2005-07-20
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	639076-6
ISSN	1473-5571 ; 0269-9370 ; 1350-2840
ISSN (online)	1473-5571
ISSN	0269-9370 ; 1350-2840
DOI	10.1097/01.aids.0000188422.95162.b7
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Article: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

Pineda-Peña, Andrea-Clemencia / Faria, Nuno Rodrigues / Imbrechts, Stijn / Libin, Pieter / Abecasis, Ana Barroso / Deforche, Koen / Gómez-López, Arley / Camacho, Ricardo J. / de Oliveira, Tulio / Vandamme, Anne-Mieke

Infection, genetics, and evolution

Volume v. 19

Abstract	BACKGROUND: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). METHODOLOGY: HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. RESULTS: The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ∼99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (∼99%) and SCUEAL (∼96%). CONCLUSIONS: REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
Keywords	data collection ; patients ; monitoring ; phylogeny ; databases ; Human immunodeficiency virus 1 ; drug resistance ; pathogenesis ; genome
Language	English
Document type	Article
ISSN	1567-1348
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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Article ; Online: Determinants of Late HIV Presentation at Ndlavela Health Center in Mozambique.

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Article ; Online: Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G.

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Article ; Online: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools.

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Article: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

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Article ; Online: Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.

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Article: Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G.

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Article: Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

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