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Bellerba F, Bardeck N, Boehm M, D'Ecclesiis O, Raimondi S, Tomezzoli E, Miranda MS, Alves IM, Alves D, Abecasis A, Gabellone V, Gabrielli E, Vaglio G, Shamsara E, Pfeifer N, Mommo C, Incardona F, Kaiser R, Gandini S. SARS-CoV-2 trends in Italy, Germany and Portugal and school opening during the period of Omicron variant dominance: A quasi experimental study in the EuCARE project. Int J Infect Dis 2024; 138:63-72. [PMID: 37956899 DOI: 10.1016/j.ijid.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/21/2023] Open
Abstract
OBJECTIVES We investigated the impact of school reopening on SARS-CoV-2 transmission in Italy, Germany, and Portugal in autumn 2022 when the Omicron variant was prevalent. METHODS A prospective international study was conducted using the case reproduction number (Rc) calculated with the time parametrization of Omicron. For Germany and Italy, staggered difference-in-differences analysis was employed to explore the causal relationship between school reopening and Rc changes, accounting for varying reopening dates. In Portugal, interrupted time series analysis was used due to simultaneous school reopenings. Multivariable models were adopted to adjust for confounders. RESULTS In Italy and Germany, post-reopening Rc estimates were significantly lower compared to those from regions/states that had not yet reopened at the same time points, both in the student population (overall average treatment effect for the treated subpopulation [O-ATT]: -0.80 [95% CI: -0.94;-0.66] for Italy; O-ATT-0.30 [95% CI: -0.36;-0.23] for Germany) and the adult population (O-ATT: -0.04 [95% CI: -0.07;-0.01] for Italy; O-ATT: -0.07 [95% CI: -0.11;-0.03] for Germany). In Portugal, there was a significant decreasing trend in Rc following school reopenings compared to the pre-reopening period (sustained effect: -0.03 [95% CI: -0.04; -0.03] in students; -0.02 [95% CI: -0.03; -0.02] in adults). CONCLUSIONS We found no evidence of a causal relationship between school reopenings in autumn 2022 and Omicron SARS-CoV-2 transmission.
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Affiliation(s)
- Federica Bellerba
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Nils Bardeck
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Michael Boehm
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Oriana D'Ecclesiis
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Sara Raimondi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elisa Tomezzoli
- Applied Research Division for Cognitive and Psychological Science, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Mafalda Silva Miranda
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT-UNL), Lisbon, Portugal
| | - Inês Martins Alves
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT-UNL), Lisbon, Portugal
| | - Daniela Alves
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT-UNL), Lisbon, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT-UNL), Lisbon, Portugal
| | - Valeria Gabellone
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Elisa Gabrielli
- Specialisation School in Hygiene and Preventive Medicine, University of Bologna, Bologna, Italy
| | - Giulia Vaglio
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Elham Shamsara
- Department of Computer Science, Methods in Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Nico Pfeifer
- Department of Computer Science, Methods in Medical Informatics, University of Tübingen, Tübingen, Germany
| | | | | | - Rolf Kaiser
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Sara Gandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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Joaquim L, Miranda MNS, Pimentel V, Martins MDRO, Nhampossa T, Abecasis A, Pingarilho M. Retention in Care and Virological Failure among Adult HIV-Positive Patients on First-Line Antiretroviral Treatment in Maputo, Mozambique. Viruses 2023; 15:1978. [PMID: 37896757 PMCID: PMC10610786 DOI: 10.3390/v15101978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/29/2023] [Accepted: 08/10/2023] [Indexed: 10/29/2023] Open
Abstract
INTRODUCTION Access to antiretroviral treatment (ART) is increasingly available worldwide; however, the number of patients lost to follow-up and number of treatment failures continue to challenge most African countries. OBJECTIVES To analyse the retention in clinical care and the virological response and their associated factors of HIV-1 patients from the Maputo Military Hospital (MMH). METHODS A cross-sectional observational study was conducted to analyse data from patients who started ART between 2016 and 2018 in the MMH. RESULTS At the end of 12 months, 75.1% of 1247 patients were active on clinical follow-up and 16.8% had suspected virologic failure (VL > 1000 copies/mm3). Patients younger than 40 years old were more likely to be lost to follow-up when compared to those aged >50 years old, as well as patients who were unemployed and patients with a CD4 count < 350 cells/mm3. Patients with haemoglobin levels lower than 10 g/dL and with a CD4 count < 350 cells/mm3 were more likely to have virological failure. CONCLUSIONS We have identified clinical and sociodemographic determinants of loss to follow-up and in the development of virological failure for HIV-positive patients in clinical care in the MMH. Therefore, HIV programs must consider these factors to increase the screening of patients at high risk of poor outcomes and particularly to strengthen adherence counselling programs.
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Affiliation(s)
- Leonid Joaquim
- Centro Integrado de Cuidados e Tratamento, Hospital Militar de Maputo, Maputo P.O. Box 21414368/9, Mozambique
| | - Mafalda N. S. Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (M.N.S.M.); (V.P.); (M.d.R.O.M.); (A.A.); (M.P.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (M.N.S.M.); (V.P.); (M.d.R.O.M.); (A.A.); (M.P.)
| | - Maria do Rosario Oliveira Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (M.N.S.M.); (V.P.); (M.d.R.O.M.); (A.A.); (M.P.)
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça, Sede, Manhiça, Rua 12, Maputo 1929, Mozambique;
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (M.N.S.M.); (V.P.); (M.d.R.O.M.); (A.A.); (M.P.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal; (M.N.S.M.); (V.P.); (M.d.R.O.M.); (A.A.); (M.P.)
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Raimondi S, Gandini S, Rubio Quintanares GH, Abecasis A, Lopalco PL, D’Ecclesiis O, Chiocca S, Tomezzoli E, Cutica I, Mazzoni D, Amparo N, Pingarilho M, Carmagnola D, Dellavia C, Zuccotti G, Ronchini C, Bellerba F, Dewald F, Kaiser R, Incardona F. Correction: European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection. BMC Infect Dis 2023; 23:96. [PMID: 36797690 PMCID: PMC9933008 DOI: 10.1186/s12879-023-08065-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Affiliation(s)
- Sara Raimondi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Sara Gandini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gibran Horemheb Rubio Quintanares
- Institute of Virology, University Clinics of Cologne, Cologne, Germany. .,Paul Ehrlich Institut, Langen, Germany. .,Infectious Diseases Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - Ana Abecasis
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Pier Luigi Lopalco
- grid.9906.60000 0001 2289 7785Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Oriana D’Ecclesiis
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Susanna Chiocca
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elisa Tomezzoli
- grid.15667.330000 0004 1757 0843Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ilaria Cutica
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Davide Mazzoni
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nuno Amparo
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal ,Public Health Clusters’ Public Health Unit of Central Alentejo, Lisbon, Portugal
| | - Marta Pingarilho
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Daniela Carmagnola
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Claudia Dellavia
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Gianvincenzo Zuccotti
- grid.414189.10000 0004 1772 7935Pediatric Department, Vittore Buzzi” Children’s Hospital, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| | - Chiara Ronchini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Bellerba
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Felix Dewald
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
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Raimondi S, Gandini S, Rubio Quintanares GH, Abecasis A, Lopalco PL, D’Ecclesiis O, Chiocca S, Tomezzoli E, Cutica I, Mazzoni D, Amparo N, Pingarilho M, Carmagnola D, Dallavia C, Zuccotti G, Ronchini C, Bellerba F, Dewald F, Kaiser R, Incardona F. European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection. BMC Infect Dis 2023; 23:1. [PMID: 36597074 PMCID: PMC9808677 DOI: 10.1186/s12879-022-07947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/13/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Contradictory results were reported on the role of school closure/reopening on the overall SARS-CoV-2 transmission rate, as well as on which kind and level of mitigation measures implemented in schools may be effective in limiting its diffusion. Some recent studies were reassuring, showing that opening did not increase the community spread, although teachers and families are worried about the high class density. On the other hand, distance learning was associated with a negative impact on learning, sociability and psychological health, especially in vulnerable children. As it becomes clear that the SARS-CoV-2 pandemic will last for a long time, there is a high need for studies and solutions to support safe schools opening based on scientific evidence of harms and benefits. The Lolli-Methode (LM) is a strategy for epidemiological surveillance and early intervention aiming at SARS-CoV-2 outbreaks' reduction in schools, relying on polymerase chain reaction analysis of saliva samples. METHODS In this cluster randomised trial protocol, we aim to determine whether the LM is useful to support schools opening and to reduce clusters and attack rates in schools, compared with the standard of care (SoC) surveillance by public health departments. This multicenter study will enrol 440 classes (around 8800 students, teachers and other personnel) from two countries, cluster randomised to LM or SoC. The samples from the pools will be collected and tested using PCR-based techniques. Test results will be combined with questionnaires filled in by children, parents, schoolteachers, and principals, concerning ongoing mitigation measures, their perceived psychological impact and other health and socio-economic information. An ancillary observational study will be carried out to study the prevalence of SARS-CoV-2 in schools, frequencies and size of clusters and attack rates, to compare the effectiveness of the different preventive measures adopted and to evaluate psychological issues in students and teachers in relation to the pandemic's containment measures. DISCUSSION By the end of this study, we will have defined and characterised the applicability of the LM for SARS-CoV-2 surveillance, as well as the impact of pandemic preventive measures on children and teachers. Trial registration International Standard Randomised Controlled Trial Number: NCT05396040, 27.05.2022.
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Affiliation(s)
- Sara Raimondi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Sara Gandini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gibran Horemheb Rubio Quintanares
- Institute of Virology, University Clinics of Cologne, Cologne, Germany. .,Paul Ehrlich Institut, Langen, Germany. .,Infectious Diseases Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
| | - Ana Abecasis
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Pier Luigi Lopalco
- grid.9906.60000 0001 2289 7785Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Oriana D’Ecclesiis
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Susanna Chiocca
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elisa Tomezzoli
- grid.15667.330000 0004 1757 0843Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ilaria Cutica
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Davide Mazzoni
- grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nuno Amparo
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal ,Public Health Clusters’ Public Health Unit of Central Alentejo, Lisbon, Portugal
| | - Marta Pingarilho
- grid.10772.330000000121511713Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - Daniela Carmagnola
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Claudia Dallavia
- grid.4708.b0000 0004 1757 2822Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Gianvincenzo Zuccotti
- grid.414189.10000 0004 1772 7935Pediatric Department, “Vittore Buzzi” Children’s Hospital, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| | - Chiara Ronchini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Bellerba
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Felix Dewald
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Clinics of Cologne, Cologne, Germany
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Pirkl M, Büch J, Devaux C, Böhm M, Sönnerborg A, Incardona F, Abecasis A, Vandamme AM, Zazzi M, Kaiser R, Lengauer T, The EuResist Network Study Group. Analysis of mutational history of multidrug-resistant genotypes with a mutagenetic tree model. J Med Virol 2023; 95:e28389. [PMID: 36484375 DOI: 10.1002/jmv.28389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) can develop resistance to all antiretroviral drugs. Multidrug resistance, however, is a rare event in modern HIV treatment, but can be life-threatening, particular in patients with very long therapy histories and in areas with limited access to novel drugs. To understand the evolution of multidrug resistance, we analyzed the EuResist database to uncover the accumulation of mutations over time. We hypothesize that the accumulation of resistance mutations is not acquired simultaneously and randomly across viral genotypes but rather tends to follow a predetermined order. The knowledge of this order might help to elucidate potential mechanisms of multidrug resistance. Our evolutionary model shows an almost monotonic increase of resistance with each acquired mutation, including less well-known nucleoside reverse transcriptase (RT) inhibitor-related mutations like K223Q, L228H, and Q242H. Mutations within the integrase (IN) (T97A, E138A/K G140S, Q148H, N155H) indicate high probability of multidrug resistance. Hence, these IN mutations also tend to be observed together with mutations in the protease (PR) and RT. We followed up with an analysis of the mutation-specific error rates of our model given the data. We identified several mutations with unusual rates (PR: M41L, L33F, IN: G140S). This could imply the existence of previously unknown virus variants in the viral quasispecies. In conclusion, our bioinformatics model supports the analysis and understanding of multidrug resistance.
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Affiliation(s)
- Martin Pirkl
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Joachim Büch
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Carole Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Michael Böhm
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Solna, Sweden
| | | | - Ana Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Institute for the Future, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rolf Kaiser
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Institute of Virology, University Hospital Cologne, University of Cologne, Cologne, Germany
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Marcelino R, Ezeonwumelu IJ, Janeiro A, Mimoso P, Matos S, Briz V, Pimentel V, Pingarilho M, Tato Marinho R, Maria Marcelino J, Taveira N, Abecasis A. Phylogeography of hepatitis B virus: The role of Portugal in the early dissemination of HBV worldwide. PLoS One 2022; 17:e0276618. [PMID: 36548381 PMCID: PMC9778982 DOI: 10.1371/journal.pone.0276618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
In Portugal, the genetic diversity, origin of HBV and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A was the most prevalent (n = 54, 41.5%), followed by D (n = 44, 33.8%), and E (n = 32, 24.6%). Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV subgenotype D4 was the first to be introduced in Portugal around 1857 (HPD 95% 1699-1931) followed by D3 and A2 a few decades later. HBV genotype E and subgenotype A1 were introduced in Portugal later, almost simultaneously. Our results indicate a very important role of Portugal in the exportation of subgenotypes D4 and A2 to Brazil and Cape Verde, respectively, in the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and provides new insights in the early and global epidemic history of this virus.
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Affiliation(s)
- Rute Marcelino
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
- * E-mail:
| | - Ifeanyi Jude Ezeonwumelu
- AIDS Research Institute-IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - André Janeiro
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Paula Mimoso
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Sónia Matos
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Veronica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Rui Tato Marinho
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Medical School of Universidade de Lisboa, Portugal
| | - José Maria Marcelino
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Nuno Taveira
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
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7
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O. Martins MR, Shaaban AN, Abecasis A, Muggli Z, Amado R, Vaz D, Dias SS, Silva AC, Fronteira I. Are immigrants more vulnerable to the socioeconomic impact of COVID-19? A cross-sectional study in Amadora Municipality, Lisbon metropolitan area. Front Public Health 2022; 10:920308. [PMID: 35979471 PMCID: PMC9376589 DOI: 10.3389/fpubh.2022.920308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Immigrants carry an extra burden of morbidities and mortalities since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. Pre-existing inequalities among immigrants may threaten their economic wellbeing during the pandemic. This study analyzed the socioeconomic impact of COVID-19 on immigrants and natives living in Amadora, Metropolitan Region of Lisbon and the extent to which preexisting inequalities had been exacerbated during the pandemic. Materials and methods This cross-sectional study was conducted in Amadora Municipality, Lisbon Region, through phone interviews and using a structured questionnaire. Data collected in July 2020, included information on a cohort of 420 households, of which 51% were immigrants. To evaluate the socioeconomic position and economic wellbeing changes occurring during the pandemic we estimate crude and adjusted odds ratio (OR) and 95% CI, using Portuguese natives as the reference group. Results Overall, 287 (70%) participants responded to the questionnaire, of which 47% are immigrants. Preexisting socioeconomic inequalities were exacerbated during the pandemic. Compared with natives, immigrants were more likely to experience job loss, temporary lay-off, and income loss during the COVID-19 pandemic. Immigrants were also more likely to face several kinds of financial hardship during the pandemic, such as difficulties in buying food, hygiene products, and paying bills. Conclusion To the best of our knowledge, this study is the first to capture the direct socioeconomic impact of COVID-19 among immigrants and natives in Portugal. It highlights the bidirectional relation between inequalities deeply rooted among immigrants and COVID-19. Socioeconomic inequalities affect local patterns of COVID-19 burden, as confirmed in previous studies, but COVID-19 also has an impact on the economic wellbeing of Amadora immigrants during the pandemic. Urgent policies must be implemented to mitigate the economic burden of COVID-19 among immigrants, namely in Amadora, Lisbon Region.
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Affiliation(s)
- Maria Rosario O. Martins
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
- *Correspondence: Maria Rosario O. Martins
| | - Ahmed Nabil Shaaban
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
| | - Zelia Muggli
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
| | - Regina Amado
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
| | - Dora Vaz
- Amadora Primary Care Health Centers Group, Regional Health Administration of Lisbon and Tagus Valley, Lisbon, Portugal
| | - Sara S. Dias
- ciTechCare—Center for Innovative Care and Health Technology, Polytechnic of Leiria, Leiria, Portugal
- School of Health Sciences, Polytechnic Institute of Leiria, Leiria, Portugal
| | - Antonio C. Silva
- Public Health Department, Regional Health Administration of Lisbon and Tagus Valley, Ministry of Health, Lisbon, Portugal
- AJPAS—Associação de Intervenção Comunitária, Desenvolvimento Social e de Saúde, Amadora, Portugal
| | - Ines Fronteira
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine (IHMT), NOVA University of Lisbon, Lisbon, Portugal
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Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
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Pingarilho M, Pimentel V, Miranda MNS, Silva AR, Diniz A, Ascenção BB, Piñeiro C, Koch C, Rodrigues C, Caldas C, Morais C, Faria D, da Silva EG, Teófilo E, Monteiro F, Roxo F, Maltez F, Rodrigues F, Gaião G, Ramos H, Costa I, Germano I, Simões J, Oliveira J, Ferreira J, Poças J, da Cunha JS, Soares J, Henriques J, Mansinho K, Pedro L, Aleixo MJ, Gonçalves MJ, Manata MJ, Mouro M, Serrado M, Caixeiro M, Marques N, Costa O, Pacheco P, Proença P, Rodrigues P, Pinho R, Tavares R, de Abreu RC, Côrte-Real R, Serrão R, Castro RSE, Nunes S, Faria T, Baptista T, Martins MRO, Gomes P, Mendão L, Simões D, Abecasis A. HIV-1-Transmitted Drug Resistance and Transmission Clusters in Newly Diagnosed Patients in Portugal Between 2014 and 2019. Front Microbiol 2022; 13:823208. [PMID: 35558119 PMCID: PMC9090520 DOI: 10.3389/fmicb.2022.823208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To describe and analyze transmitted drug resistance (TDR) between 2014 and 2019 in newly infected patients with HIV-1 in Portugal and to characterize its transmission networks. Methods Clinical, socioepidemiological, and risk behavior data were collected from 820 newly diagnosed patients in Portugal between September 2014 and December 2019. The sequences obtained from drug resistance testing were used for subtyping, TDR determination, and transmission cluster (TC) analyses. Results In Portugal, the overall prevalence of TDR between 2014 and 2019 was 11.0%. TDR presented a decreasing trend from 16.7% in 2014 to 9.2% in 2016 (p for-trend = 0.114). Multivariate analysis indicated that TDR was significantly associated with transmission route (MSM presented a lower probability of presenting TDR when compared to heterosexual contact) and with subtype (subtype C presented significantly more TDR when compared to subtype B). TC analysis corroborated that the heterosexual risk group presented a higher proportion of TDR in TCs when compared to MSMs. Among subtype A1, TDR reached 16.6% in heterosexuals, followed by 14.2% in patients infected with subtype B and 9.4% in patients infected with subtype G. Conclusion Our molecular epidemiology approach indicates that the HIV-1 epidemic in Portugal is changing among risk group populations, with heterosexuals showing increasing levels of HIV-1 transmission and TDR. Prevention measures for this subpopulation should be reinforced.
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Affiliation(s)
- Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Mafalda N S Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Ana Rita Silva
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - António Diniz
- Unidade de Imunodeficiência, Centro Hospitalar Universitário Lisboa Norte - HPV, Lisbon, Portugal
| | | | - Carmela Piñeiro
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Carmo Koch
- Centro de Biologia Molecular, Serviço de Imunohemoterapia do Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Catarina Rodrigues
- Serviço de Medicina, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Cátia Caldas
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Célia Morais
- Serviço de Patologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Domitília Faria
- Serviço de Medicina, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | | | - Eugénio Teófilo
- Serviço de Medicina, Hospital de Santo António dos Capuchos, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Fátima Monteiro
- Centro de Biologia Molecular, Serviço de Imunohemoterapia do Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Fausto Roxo
- Hospital de Dia de Doenças Infeciosas, Hospital Distrital de Santarém, Santarém, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Fernando Rodrigues
- Serviço de Patologia Clínica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Guilhermina Gaião
- Serviço de Patologia Clínica, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - Helena Ramos
- Serviço de Patologia Clínica, Centro Hospitalar do Porto, Porto, Portugal
| | - Inês Costa
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
| | - Isabel Germano
- Serviço de Medicina, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Joana Simões
- Serviço de Medicina, Hospital de São José, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Joaquim Oliveira
- Serviço de Doenças, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - José Ferreira
- Serviço de Medicina, Hospital de Faro, Centro Hospitalar Universitário do Algarve, Faro, Portugal
| | - José Poças
- Serviço de Infeciologia, Centro Hospitalar de Setúbal, Setúbal, Portugal
| | | | - Jorge Soares
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Júlia Henriques
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Liliana Pedro
- Serviço de Medicina, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | | | | | - Maria José Manata
- Serviço de Doenças Infeciosas, Hospital de Curry Cabral, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Margarida Mouro
- Serviço de Infeciologia, Hospital de Aveiro, Centro Hospitalar Baixo Vouga, Aveiro, Portugal
| | - Margarida Serrado
- Unidade de Imunodeficiência, Centro Hospitalar Universitário Lisboa Norte - HPV, Lisbon, Portugal
| | - Micaela Caixeiro
- Serviço de Infeciologia, Hospital Professor Doutor Fernando da Fonseca, Amadora, Portugal
| | - Nuno Marques
- Serviço de Infeciologia, Hospital Garcia da Orta, Almada, Portugal
| | - Olga Costa
- Serviço de Patologia Clínica, Biologia Molecular, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Patrícia Pacheco
- Serviço de Infeciologia, Hospital Professor Doutor Fernando da Fonseca, Amadora, Portugal
| | - Paula Proença
- Serviço de Infeciologia, Hospital de Faro, Centro Hospitalar Universitário do Algarve, Faro, Portugal
| | - Paulo Rodrigues
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - Raquel Pinho
- Serviço de Medicina, Hospital de Portimão, Centro Hospitalar Universitário do Algarve, Portimão, Portugal
| | - Raquel Tavares
- Serviço de Infeciologia, Hospital Beatriz Ângelo, Loures, Portugal
| | - Ricardo Correia de Abreu
- Serviço de Infeciologia, Unidade de Local de Saúde de Matosinhos, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Rita Côrte-Real
- Serviço de Patologia Clínica, Biologia Molecular, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Rosário Serrão
- Serviço de Doenças Infeciosas, Centro Hospitalar Universitário de São João, Porto, Portugal
| | | | - Sofia Nunes
- Serviço de Infeciologia, Hospital de Aveiro, Centro Hospitalar Baixo Vouga, Aveiro, Portugal
| | - Telo Faria
- Unidade Local de Saúde do Baixo Alentejo, Hospital José Joaquim Fernandes, Beja, Portugal
| | - Teresa Baptista
- Serviço de Doenças Infeciosas, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Maria Rosário O Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Costa da Caparica, Portugal
| | - Luís Mendão
- Grupo de Ativistas em Tratamentos (GAT), Lisbon, Portugal
| | - Daniel Simões
- Grupo de Ativistas em Tratamentos (GAT), Lisbon, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
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Morais P, Trovão N, Abecasis A, Parreira R. Insect-specific viruses in the Parvoviridae family: genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus. Virus Res 2022; 313:198728. [DOI: 10.1016/j.virusres.2022.198728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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Morais P, Trovão N, Abecasis A, Parreira R. Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences. Virus Res 2022; 313:198727. [DOI: 10.1016/j.virusres.2022.198727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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12
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Rossetti B, Fabbiani M, Di Carlo D, Incardona F, Abecasis A, Gomes P, Geretti AM, Seguin-Devaux C, Garcia F, Kaiser R, Modica S, Shallvari A, Sönnerborg A, Zazzi M. Effectiveness of integrase strand transfer inhibitors in HIV-infected treatment-experienced individuals across Europe. HIV Med 2022; 23:774-789. [PMID: 35199909 DOI: 10.1111/hiv.13262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To explore the effectiveness and durability of integrase strand transfer inhibitor (INSTI)-based regimens in pre-treated subjects. METHODS Treatment-experienced individuals starting an INSTI-based regimen during 2012-2019 were selected from the INTEGRATE collaborative study. The time to virological failure [VF: one measurement of viral load (VL) ≥ 1000 copies/mL or two ≥ 50 copies/ml or one VL measurement ≥ 50 copies/mL followed by treatment change] and to INSTI discontinuation were evaluated. RESULTS Of 13 560 treatments analysed, 4284 were from INSTI-naïve, non-viraemic (IN-NV) individuals, 1465 were from INSTI-naïve, viraemic (IN-V) individuals, 6016 were from INSTI-experienced, non-viraemic (IE-NV) individuals and 1795 were from INSTI-experienced, viraemic (IE-V) individuals. Major INSTI drug resistance mutations (DRMs) were previously detected in 4/519 (0.8%) IN-NV, 3/394 (0.8%) IN-V, 7/1510 (0.5%) IE-NV and 25/935 (2.7%) IE-V individuals. The 1-year estimated probabilities of VF were 3.1% [95% confidence interval (CI): 2.5-3.8] in IN-NV, 18.4% (95% CI: 15.8-21.2) in IN-V, 4.2% (95% CI: 3.6-4.9) in IE-NV and 23.9% (95% CI: 20.9-26.9) in IE-V subjects. The 1-year estimated probabilities of INSTI discontinuation were 12.1% (95% CI: 11.1-13.0) in IN-NV, 19.6% (95% CI: 17.5-21.6) in IN-V, 10.8% (95% CI: 10.0-11.6) in IE-NV and 21.7% (95% CI: 19.7-23.5) in IE-V subjects. CONCLUSIONS Both VF and INSTI discontinuation occur at substantial rates in viraemic subjects. Detection of DRMs in a proportion of INSTI-experienced individuals makes INSTI resistance testing mandatory after failure.
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Affiliation(s)
- Barbara Rossetti
- Infectious Diseases Unit, University Hospital of Siena, Siena, Italy
| | | | | | | | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical - Universidade Nova de Lisboa, Lisbon, Portugal
| | - Perpetua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
| | - Anna Maria Geretti
- Department of Infectious Disease, University of Rome Tor Vergata, Rome, Italy.,Department of Infectious Diseases, King's College London, London, UK
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Federico Garcia
- Hospital Universitario San Cecilio, Granada, Spain.,Instituto de Investigación IBS., Granada, Spain.,Ciber de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | | | - Sara Modica
- Infectious Diseases Unit, University Hospital of Siena, Siena, Italy
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Miranda AC, Miranda M, Pingarilho M, Pimentel V, Torres J, Peres S, Baptista Alberto T, Gomes P, Abecasis A, Mansinho K. Determinants of HIV-1 Late Presentation in a Cohort of Portuguese HIV-1 Patients. AIDS Res Hum Retroviruses 2021; 37:846-851. [PMID: 33461392 DOI: 10.1089/aid.2020.0175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Undiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters (LPs) for HIV care may help to identify characteristics of such patients. The present study aims to identify factors associated with late presentation and late presentation with advanced disease based on a population of patients followed in a Portuguese hospital between 1984 and 2017. Sociodemographic and clinical data from infected patients with HIV-1 aged 18 years and older, followed in Egas Moniz Hospital, in Portugal were collected. Of the 907 patients included in this study, 68.7% were males and the median age was 37 years (interquartile range 30-47). Four hundred fifty-nine patients (50.6%) were LP and, of these, 284 patients (61.9%) were LPAD. The LP population mostly originated from Portugal and sub-Saharan Africa (64.4% and 28.8%; p = .004) and the HIV exposure category, mainly heterosexuals and men have sex with men (57.0% and 24.9%; p < .001). The stage of disease and viral load at diagnosis were significantly associated with both LP and LPAD (p < .001). Factors associated with LP in the logistic regression included age at diagnosis lower than 30 years (adjusted odds ratio [aOR] 0.34; 0.17-0.68; p = .002) and origin from sub-Saharan Africa (aOR 2.24; 1.44-3.50; p < .001). Late presentation is a major obstacle to halt the HIV epidemic. In this population, the majority of newly diagnosed HIV-infected individuals were LPs. Our results characterize vulnerable populations that should be frequently tested for HIV.
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Affiliation(s)
- Ana Cláudia Miranda
- Department of Infectious Diseases, Hospital Center Lisboa Ocidental, Egas Moniz Hospital, Lisbon, Portugal
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine/New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine/New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine/New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - João Torres
- Department of Infectious Diseases, Hospital Center Lisboa Ocidental, Egas Moniz Hospital, Lisbon, Portugal
| | - Susana Peres
- Department of Infectious Diseases, Hospital Center Lisboa Ocidental, Egas Moniz Hospital, Lisbon, Portugal
| | - Teresa Baptista Alberto
- Department of Infectious Diseases, Hospital Center Lisboa Ocidental, Egas Moniz Hospital, Lisbon, Portugal
| | - Perpetua Gomes
- Laboratory of Molecular Biology (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
- Egas Moniz Interdisciplinary Research Center (CiiEM), Egas Moniz University Institute, Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine/New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Kamal Mansinho
- Department of Infectious Diseases, Hospital Center Lisboa Ocidental, Egas Moniz Hospital, Lisbon, Portugal
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Rossetti B, Fabbiani M, Di Carlo D, Incardona F, Abecasis A, Gomes P, Geretti AM, Seguin-Devaux C, Garcia F, Kaiser R, Modica S, Shallvari A, Sönnerborg A, Zazzi M. Effectiveness of integrase strand transfer inhibitor-based regimens in HIV-infected treatment-naive individuals: results from a European multi-cohort study. J Antimicrob Chemother 2021; 76:2394-2399. [PMID: 34212176 DOI: 10.1093/jac/dkab200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/16/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND INSTIs have become a pillar of first-line ART. Real-world data are needed to assess their effectiveness in routine care. OBJECTIVES We analysed ART-naive patients who started INSTI-based regimens in 2012-19 whose data were collected by INTEGRATE, a European collaborative study including seven national cohorts. METHODS Kaplan-Meier analyses assessed time to virological failure (VF), defined as one viral load (VL) ≥1000 copies/mL, two consecutive VLs ≥50 copies/mL, or one VL ≥50 copies/mL followed by treatment change after ≥24 weeks of follow-up, and time to INSTIs discontinuation (INSTI-DC) for any reason. Factors associated with VF and INSTI-DC were explored by logistic regression analysis. RESULTS Of 2976 regimens started, 1901 (63.9%) contained dolutegravir, 631 (21.2%) elvitegravir and 444 (14.9%) raltegravir. The 1 year estimated probabilities of VF and INSTI-DC were 5.6% (95% CI 4.5-6.7) and 16.2% (95% CI 14.9-17.6), respectively, and were higher for raltegravir versus both elvitegravir and dolutegravir. A baseline VL ≥100 000 copies/mL [adjusted HR (aHR) 2.17, 95% CI 1.55-3.04, P < 0.001] increased the risk of VF, while a pre-treatment CD4 count ≥200 cells/mm3 reduced the risk (aHR 0.52, 95% CI 0.37-0.74, P < 0.001). Predictors of INSTI-DC included use of raltegravir versus dolutegravir (aHR 3.03, 95% CI 2.34-3.92, P < 0.001), use of >3 drugs versus 3 drugs (aHR 2.73, 95% CI 1.55-4.79, P < 0.001) and starting ART following availability of dolutegravir (aHR 0.64, 95% CI 0.48-0.83, P = 0.001). Major INSTI mutations indicative of transmitted drug resistance occurred in 2/1114 (0.2%) individuals. CONCLUSIONS This large multi-cohort study indicates high effectiveness of elvitegravir- or dolutegravir-based first-line ART in routine practice across Europe.
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Affiliation(s)
- Barbara Rossetti
- Infectious Diseases Unit, University Hospital of Siena, Siena, Italy
| | | | | | | | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical-Universidade Nova de Lisboa, Lisbon, Portugal
| | - Perpetua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
| | | | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
| | | | | | - Sara Modica
- Infectious Diseases Unit, University Hospital of Siena, Siena, Italy
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Miranda MNS, Pingarilho M, Pimentel V, Martins MDRO, Vandamme AM, Bobkova M, Böhm M, Seguin-Devaux C, Paredes R, Rubio R, Zazzi M, Incardona F, Abecasis A. Determinants of HIV-1 Late Presentation in Patients Followed in Europe. Pathogens 2021; 10:pathogens10070835. [PMID: 34357985 PMCID: PMC8308660 DOI: 10.3390/pathogens10070835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
To control the Human Immunodeficiency Virus (HIV) pandemic, the World Health Organization (WHO) set the 90-90-90 target to be reached by 2020. One major threat to those goals is late presentation, which is defined as an individual presenting a TCD4+ count lower than 350 cells/mm3 or an AIDS-defining event. The present study aims to identify determinants of late presentation in Europe based on the EuResist database with HIV-1 infected patients followed-up between 1981 and 2019. Our study includes clinical and socio-demographic information from 89851 HIV-1 infected patients. Statistical analysis was performed using RStudio and SPSS and a Bayesian network was constructed with the WEKA software to analyze the association between all variables. Among 89,851 HIV-1 infected patients included in the analysis, the median age was 33 (IQR: 27.0-41.0) years and 74.4% were males. Of those, 28,889 patients (50.4%) were late presenters. Older patients (>56), heterosexuals, patients originated from Africa and patients presenting with log VL >4.1 had a higher probability of being late presenters (p < 0.001). Bayesian networks indicated VL, mode of transmission, age and recentness of infection as variables that were directly associated with LP. This study highlights the major determinants associated with late presentation in Europe. This study helps to direct prevention measures for this population.
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Affiliation(s)
- Mafalda N. S. Miranda
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
- Correspondence: ; Tel.: +351-213-652-600
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
| | - Maria do Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
- Laboratory Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, Rega Institute for Medical Research, 3000 Leuven, Belgium
| | - Marina Bobkova
- Gamaleya Research Center of Epidemiology and Microbiology, Department of General Virology, Gamaleya Scientific Research Institute, 123098 Moscow, Russia;
| | - Michael Böhm
- Department of Medicine, Saarland University Hospital, 66421 Homburg, Germany;
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg;
| | - Roger Paredes
- Infectious Diseases Department and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Rafael Rubio
- Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, 28026 Madrid, Spain;
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Francesca Incardona
- IPRO—InformaPRO S.r.l., 98, 00152 Rome, Italy;
- EuResist Network, 98/100, 00152 Rome, Italy
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (M.P.); (V.P.); (M.d.R.O.M.); (A.-M.V.); (A.A.)
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16
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Pingarilho M, Pimentel V, Diogo I, Fernandes S, Miranda M, Pineda-Pena A, Libin P, Theys K, O. Martins MR, Vandamme AM, Camacho R, Gomes P, Abecasis A. Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations. Viruses 2020; 12:E1238. [PMID: 33143301 PMCID: PMC7693025 DOI: 10.3390/v12111238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Treatment for All recommendations have allowed access to antiretroviral (ARV) treatment for an increasing number of patients. This minimizes the transmission of infection but can potentiate the risk of transmitted (TDR) and acquired drug resistance (ADR). OBJECTIVE To study the trends of TDR and ADR in patients followed up in Portuguese hospitals between 2001 and 2017. METHODS In total, 11,911 patients of the Portuguese REGA database were included. TDR was defined as the presence of one or more surveillance drug resistance mutation according to the WHO surveillance list. Genotypic resistance to ARV was evaluated with Stanford HIVdb v7.0. Patterns of TDR, ADR and the prevalence of mutations over time were analyzed using logistic regression. RESULTS AND DISCUSSION The prevalence of TDR increased from 7.9% in 2003 to 13.1% in 2017 (p < 0.001). This was due to a significant increase in both resistance to nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleotide reverse transcriptase inhibitors (NNRTIs), from 5.6% to 6.7% (p = 0.002) and 2.9% to 8.9% (p < 0.001), respectively. TDR was associated with infection with subtype B, and with lower viral load levels (p < 0.05). The prevalence of ADR declined from 86.6% in 2001 to 51.0% in 2017 (p < 0.001), caused by decreasing drug resistance to all antiretroviral (ARV) classes (p < 0.001). CONCLUSIONS While ADR has been decreasing since 2001, TDR has been increasing, reaching a value of 13.1% by the end of 2017. It is urgently necessary to develop public health programs to monitor the levels and patterns of TDR in newly diagnosed patients.
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Affiliation(s)
- Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Andrea Pineda-Pena
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Pieter Libin
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
- Artificial Intelligence Lab, Department of computer science, Vrije Universiteit Brussel, 1000 Brussels, Belgium
- Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, 3500 Hasselt, Belgium
| | - Kristof Theys
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Ricardo Camacho
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
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Pimentel V, Pingarilho M, Alves D, Diogo I, Fernandes S, Miranda M, Pineda-Peña AC, Libin P, Martins MRO, Vandamme AM, Camacho R, Gomes P, Abecasis A. Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017. Viruses 2020; 12:v12030268. [PMID: 32121161 PMCID: PMC7150888 DOI: 10.3390/v12030268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.
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Affiliation(s)
- Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Daniela Alves
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111321, Colombia
| | - Pieter Libin
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
- Artificial Intelligence lab, Department of computer science, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Ricardo Camacho
- KU Leuven, Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisboa, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349-008 Lisboa, Portugal; (V.P.); (M.P.); (D.A.); (M.M.); (A.-C.P.-P.); (M.R.O.M.); (A.-M.V.)
- Correspondence:
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Grant JC, González-Beiras C, Amick KM, Fortney KR, Gangaiah D, Humphreys TL, Mitjà O, Abecasis A, Spinola SM. Multiple Class I and Class II Haemophilus ducreyi Strains Cause Cutaneous Ulcers in Children on an Endemic Island. Clin Infect Dis 2019; 67:1768-1774. [PMID: 29897409 DOI: 10.1093/cid/ciy343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022] Open
Abstract
Background Together with Treponema pallidum subspecies pertenue, Haemophilus ducreyi is a major cause of exudative cutaneous ulcers (CUs) in children. For H. ducreyi, both class I and class II strains, asymptomatic colonization, and environmental reservoirs have been found in endemic regions, but the epidemiology of this infection is unknown. Methods Based on published whole-genome sequences of H. ducreyi CU strains, a single-locus typing system was developed and applied to H. ducreyi-positive CU samples obtained prior to, 1 year after, and 2 years after the initiation of a mass drug administration campaign to eradicate CU on Lihir Island in Papua New Guinea. DNA from the CU samples was amplified with class I and class II dsrA-specific primers and sequenced; the samples were classified into dsrA types, which were geospatially mapped. Selection pressure analysis was performed on the dsrA sequences. Results Thirty-seven samples contained class I sequences, 27 contained class II sequences, and 13 contained both. There were 5 class I and 4 class II types circulating on the island; 3 types accounted for approximately 87% of the strains. The composition and geospatial distribution of the types varied little over time and there was no evidence of selection pressure. Conclusions Multiple strains of H. ducreyi cause CU on an endemic island and coinfections are common. In contrast to recent findings with T. pallidum pertenue, strain composition is not affected by antibiotic pressure, consistent with environmental reservoirs of H. ducreyi. Such reservoirs must be addressed to achieve eradication of H. ducreyi.
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Affiliation(s)
- Jacob C Grant
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | | | - Kristen M Amick
- Department of Biology, Allegheny College, Meadville, Pennsylvania
| | - Kate R Fortney
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | - Dharanesh Gangaiah
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | | | - Oriol Mitjà
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea.,Barcelona Institute for Global Health, Hospital Clinic, University of Barcelona, Spain.,School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby
| | - Ana Abecasis
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
| | - Stanley M Spinola
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis.,Department of Medicine, Indiana University School of Medicine, Indianapolis.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis
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19
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Salgueiro P, Serrano C, Gomes B, Alves J, Sousa CA, Abecasis A, Pinto J. Phylogeography and invasion history of Aedes aegypti, the Dengue and Zika mosquito vector in Cape Verde islands (West Africa). Evol Appl 2019; 12:1797-1811. [PMID: 31548858 PMCID: PMC6752157 DOI: 10.1111/eva.12834] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/14/2019] [Accepted: 06/01/2019] [Indexed: 12/25/2022] Open
Abstract
Aedes-borne arboviruses have spread globally with outbreaks of vast impact on human populations and health systems. The West African archipelago of Cape Verde had its first outbreak of Dengue in 2009, at the time the largest recorded in Africa, and was one of the few African countries affected by the Zika virus epidemic. Aedes aegypti was the mosquito vector involved in both outbreaks. We performed a phylogeographic and population genetics study of A. aegypti in Cape Verde in order to infer the geographic origin and evolutionary history of this mosquito. These results are discussed with respect to the implications for vector control and prevention of future outbreaks. Mosquitoes captured before and after the Dengue outbreak on the islands of Santiago, Brava, and Fogo were analyzed with two mitochondrial genes COI and ND4, 14 microsatellite loci and five kdr mutations. Genetic variability was comparable to other African populations. Our results suggest that A. aegypti invaded Cape Verde at the beginning of the Holocene from West Africa. Given the historic importance of Cape Verde in the transatlantic trade of the 16th-17th centuries, a possible contribution to the genetic pool of the founding populations in the New World cannot be fully discarded. However, contemporary gene flow with the Americas is likely to be infrequent. No kdr mutations associated with pyrethroid resistance were detected. The implications for vector control and prevention of future outbreaks are discussed.
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Affiliation(s)
- Patrícia Salgueiro
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
| | - Célia Serrano
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
| | - Bruno Gomes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
- Oswaldo Cruz Institute (IOC)Fundação Oswaldo Cruz (FIOCRUZ)Rio de JaneiroBrasil
| | - Joana Alves
- Direção Geral de Saúde/Instituto Nacional de Saúde Pública, Ministério da Saúde de Cabo VerdePraiaCabo Verde
| | - Carla A. Sousa
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
| | - João Pinto
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)Universidade Nova de Lisboa (UNL)LisboaPortugal
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Ezeonwumelu I, Bártolo I, Martin F, Abecasis A, Campos T, Romero-Severson EO, Leitner T, Taveira N. Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period. AIDS Res Hum Retroviruses 2018; 34:857-862. [PMID: 30073842 DOI: 10.1089/aid.2018.0060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 4-year-old child born to an HIV-1 seronegative mother was diagnosed with HIV-1, the main risk factor being transmission from the child's father who was seroconverting at the time of the child's birth. In the context of a forensic investigation, we aimed to identify the source of infection of the child and date of the transmission event. Samples were collected from the father and child at two time points about 4 years after the child's birth. Partial segments of three HIV-1 genes (gag, pol, and env) were sequenced and maximum likelihood (ML) and Bayesian methods were used to determine direction and estimate date of transmission. Neutralizing antibodies were determined using a single cycle assay. Bayesian trees displayed a paraphyletic-monophyletic topology in all three genomic regions, with the father's host label at the root, which is consistent with father-to-son transmission. ML trees found similar topologies in gag and pol and a monophyletic-monophyletic topology in env. Analysis of the time of the most recent common ancestor of each HIV-1 gene population indicated that the child was infected shortly after the father. Consistent with the infection history, both father and son developed broad and potent HIV-specific neutralizing antibody responses. In conclusion, the direction of transmission implicated the father as the source of transmission. Transmission occurred during the seroconversion period when the father was unaware of the infection and was likely accidental. This case shows how genetic, phylogenetic, and serological data can contribute for the forensic investigation of HIV transmission.
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Affiliation(s)
- Ifeanyi Ezeonwumelu
- HIV Evolution, Epidemiology and Prevention, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
| | - Inês Bártolo
- HIV Evolution, Epidemiology and Prevention, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Martin
- HIV Evolution, Epidemiology and Prevention, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Teresa Campos
- Departamento de Pediatria, Hospital Prof. Dr. Fernando Fonseca EPE, Amadora, Portugal
| | - Ethan O. Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Nuno Taveira
- HIV Evolution, Epidemiology and Prevention, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
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Tavares A, Garcia A, Abecasis A, Viveiros M, Dias S. 4.10-P12Perspectives of health care providers in Portugal on the provision of care to migrant patients with TB or HIV-TB co-infection. Eur J Public Health 2018. [DOI: 10.1093/eurpub/cky048.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A Tavares
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Portugal
| | - A Garcia
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Portugal
- Departamento de Epidemiologia, Instituto Nacional de Saúde Dr. Ricardo Jorge (INSA), Portugal
| | - A Abecasis
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Portugal
| | - M Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Portugal
| | - S Dias
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Portugal
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Paraschiv S, Banica L, Nicolae I, Niculescu I, Abagiu A, Jipa R, Pineda-Peña AC, Pingarilho M, Neaga E, Theys K, Libin P, Otelea D, Abecasis A. Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users. PLoS One 2017; 12:e0185866. [PMID: 29016621 PMCID: PMC5633171 DOI: 10.1371/journal.pone.0185866] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/20/2017] [Indexed: 12/18/2022] Open
Abstract
Co-infections with HIV and HCV are very frequent among people who inject drugs (PWID). However, very few studies comparatively reconstructed the transmission patterns of both viruses in the same population. We have recruited 117 co-infected PWID during a recent HIV outbreak in Romania. Phylogenetic analyses were performed on HIV and HCV sequences in order to characterize and compare transmission dynamics of the two viruses. Three large HIV clusters (2 subtype F1 and one CRF14_BG) and thirteen smaller HCV transmission networks (genotypes 1a, 1b, 3a, 4a and 4d) were identified. Eighty (65%) patients were both in HIV and HCV transmission chains and 70 of those shared the same HIV and HCV cluster with at least one other patient. Molecular clock analysis indicated that all identified HIV clusters originated around 2006, while the origin of the different HCV clusters ranged between 1980 (genotype 1b) and 2011 (genotypes 3a and 4d). HCV infection preceded HIV infection in 80.3% of cases. Coincidental transmission of HIV and HCV was estimated to be rather low (19.65%) and associated with an outbreak among PWID during detention in the same penitentiary. This study has reconstructed and compared the dispersion of these two viruses in a PWID population.
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Affiliation(s)
- Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- * E-mail:
| | - Leontina Banica
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Ionelia Nicolae
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Iulia Niculescu
- Clinical Department, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
- SMZ Süd—Kaiser-Franz-Josef-Spital, 4. Med. Abteilung, Vienna, Austria
| | - Adrian Abagiu
- Clinical Department, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Raluca Jipa
- Clinical Department, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC) and Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Marta Pingarilho
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Emil Neaga
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Kristof Theys
- KU Leuven—University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Pieter Libin
- KU Leuven—University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Artificial Intelligence lab, Department of computer science, Vrije Universiteit Brussel, Brussels, Belgium
| | - Dan Otelea
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases ‘Matei Bals’, Bucharest, Romania
| | - Ana Abecasis
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- KU Leuven—University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
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Gama A, Abecasis A, Pingarilho M, Mendão L, Martins MO, Barros H, Dias S. Cruising Venues as a Context for HIV Risky Behavior Among Men Who Have Sex With Men. Arch Sex Behav 2017; 46:1061-1068. [PMID: 26987977 DOI: 10.1007/s10508-016-0707-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/01/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
We examined differences in sexual risk behaviors, HIV prevalence, and demographic characteristics between men who have sex with men (MSM) who visit different types of venues to meet sexual partners, and identified correlates of high-risk behaviors. A cross-sectional behavioral survey was conducted with a venue-based sample of 1011 MSM in Portugal. Overall, 36.3 % of MSM usually visit cruising venues to meet sexual partners (63.7 % only visit social gay venues). Cruising venues' visitors reported higher HIV prevalence (14.6 % [95 % CI 11-18 %] vs. 5.5 % [95 % CI 4-7 %]). Visiting cruising venues was more likely among those older, reporting high number of male sexual partners, group sex, and unprotected anal sex with a partner whose HIV status was unknown. Cruising venues play an important role in increasing risk of HIV transmission among MSM who frequent them. Venue-focused behavioral interventions that promote healthy sexual behaviors are needed.
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Affiliation(s)
- Ana Gama
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, n. 100, 1349-008, Lisbon, Portugal.
| | - Ana Abecasis
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, n. 100, 1349-008, Lisbon, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, n. 100, 1349-008, Lisbon, Portugal
| | - Luís Mendão
- Grupo Português de Ativistas sobre Tratamentos de VIH/SIDA, Lisbon, Portugal
| | - Maria O Martins
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, n. 100, 1349-008, Lisbon, Portugal
| | - Henrique Barros
- Institute of Public Health of University of Porto, University of Porto Medical School, Porto, Portugal
| | - Sónia Dias
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, n. 100, 1349-008, Lisbon, Portugal
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24
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Theys K, Abecasis A, Libin P, Gomes PT, Cabanas J, Camacho RJ, Van Laethem K. Discordant predictions of residual activity could impact dolutegravir prescription upon raltegravir failure. J Clin Virol 2015; 70:120-127. [PMID: 26305833 DOI: 10.1016/j.jcv.2015.07.311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/03/2015] [Accepted: 07/25/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Dolutegravir is approved for the treatment of HIV-1 patients exposed to other integrase inhibitors, but the decision to use dolutegravir in this setting should be informed by drug resistance testing. OBJECTIVES This study determined the extent of disagreement in predicted residual dolutegravir activity after raltegravir use, and identified individual mutational patterns for which uncertainty exists among HIV-1 expert systems. STUDY DESIGN Mutation patterns were classified in raltegravir signature pathways including positions 143, 148 and 155, and interpreted into clinically informative resistance levels using genotypic drug resistance interpretation systems ANRS v24, HIVdb v7.0 and Rega v9.1.0, and instructions of dolutegravir use as approved by the Food and Drug Administration and the European Medicines Agency. RESULTS In 216HIV-1 patients failing raltegravir-therapy, 87% patients displayed mutations associated with resistance towards integrase inhibitors. A total of 141 unique mutational patterns were observed, with N155H (25.4%), Q148H (16.2%) and Y143R (8.3%) the most prevalent signature mutations. The Q148 pathway occurred almost exclusively in HIV-1 subtype B viruses. Concordances in predicted dolutegravir susceptibility scores among 5 systems were obtained in 57.8% of patients, and concordant intermediate resistant and concordant resistant scores were only observed in 6.5% and 0.9% of patients, respectively. However, systems individually scored higher levels of dolutegravir intermediate resistance and resistance, ranging from 4.2% to 10.2% and from 14.8% to 22.7% of patients, respectively. A consensus on interpreting the extent of residual activity was lacking in 34.7% of patients and was highly resistance pathway-specific. CONCLUSIONS Dolutegravir may potentially be effective in the majority of HIV-1 patients failing raltegravir, but concern over the uncertainty in predicted residual activity could withhold clinicians from prescribing dolutegravir during its clinical assessment.
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Affiliation(s)
- Kristof Theys
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium.
| | - Ana Abecasis
- Global Health and Tropical Medicine, International Public Health and Biostatistics, Institute for Hygiene and Tropical Medicine, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Pieter Libin
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium; Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Perpe Tua Gomes
- LMCBM, SPC, HEM - Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Joaquim Cabanas
- LMCBM, SPC, HEM - Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Kristel Van Laethem
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium; University Hospitals Leuven, AIDS Reference Laboratory, Herestraat 49, 3000 Leuven, Belgium
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Frentz D, van de Vijver D, Abecasis A, Albert J, Hamouda O, Jørgensen L, Kücherer C, Struck D, Schmit JC, Vercauteren J, Åsjö B, Balotta C, Bergin C, Beshkov D, Camacho R, Clotet B, Griskevicius A, Grossman Z, Horban A, Kolupajeva T, Korn K, Kostrikis L, Linka KLM, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher C, Programme AWOBOTSPREAD. Patterns of transmitted HIV drug resistance in Europe vary by risk group. PLoS One 2014; 9:e94495. [PMID: 24721998 PMCID: PMC3983178 DOI: 10.1371/journal.pone.0094495] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/17/2014] [Indexed: 12/19/2022] Open
Abstract
Background In Europe, a continuous programme (SPREAD) has been in place for ten years to study transmission of drug resistant HIV. We analysed time trends of transmitted drug resistance mutations (TDRM) in relation to the risk behaviour reported. Methods HIV-1 patients newly diagnosed in 27 countries from 2002 through 2007 were included. Inclusion was representative for risk group and geographical distribution in the participating countries in Europe. Trends over time were calculated by logistic regression. Results From the 4317 patients included, the majority was men-having-sex-with-men -MSM (2084, 48%), followed by heterosexuals (1501, 35%) and injection drug users (IDU) (355, 8%). MSM were more often from Western Europe origin, infected with subtype B virus, and recently infected (<1 year) (p<0.001). The prevalence of TDRM was highest in MSM (prevalence of 11.1%), followed by heterosexuals (6.6%) and IDU (5.1%, p<0.001). TDRM was predominantly ascribed to nucleoside reverse transcriptase inhibitors (NRTI) with a prevalence of 6.6% in MSM, 3.3% in heterosexuals and 2.0% in IDU (p = 0.001). A significant increase in resistance to non- nucleoside reverse transcriptase inhibitors (NNRTIs) and a decrease in resistance to protease inhibitors was observed in MSM (p = 0.008 and p = 0.006, respectively), but not in heterosexual patients (p = 0.68 and p = 0.14, respectively). Conclusions MSM showed to have significantly higher TDRM prevalence compared to heterosexuals and IDU. The increasing NNRTI resistance in MSM is likely to negatively influence the therapy response of first-line therapy, as most include NNRTI drugs.
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Affiliation(s)
- Dineke Frentz
- Department of virology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Ana Abecasis
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Daniel Struck
- Laboratory of Retrovirology, CRP-Santé, Luxembourg, Luxembourg
| | - Jean-Claude Schmit
- Laboratory of Retrovirology, CRP-Santé, Luxembourg, Luxembourg
- Centre Hospitalier de Luxembourg, Luxembourg
| | | | - Birgitta Åsjö
- Section for Microbiology and Immunology, The Gade Institute, University of Bergen, Bergen, Norway
| | | | - Colm Bergin
- Department of GU Medicine & Infectious Diseases, St James's Hospital, Dublin, Ireland
| | - Danail Beshkov
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ricardo Camacho
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
- Hospital Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari "Germans Trias i Pujol," Badalona, Spain
| | | | | | - Andrzej Horban
- Warsaw Medical University and Hospital of Infectious Diseases, Warsaw, Poland
| | | | - Klaus Korn
- University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Kirsi Liitsola Marek Linka
- National Institute for Health and Welfare, Helsinki, Finland
- National Institute of Public Health, Prague, Czech Republic
| | | | - Dan Otelea
- Molecular Diagnostics, "Prof Dr Matei Bals" Institute for Infectious Diseases, Bucharest, Romania
| | | | - Roger Paredes
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | | | | | - Charles Boucher
- Department of virology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Annemarie Wensing31* on behalf of the SPREAD Programme
- Department of virology, Erasmus Medical Center, Rotterdam, the Netherlands
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Robert Koch Institute, Berlin, Germany
- Statens Serum Institute, Copenhagen, Denmark
- Laboratory of Retrovirology, CRP-Santé, Luxembourg, Luxembourg
- Centre Hospitalier de Luxembourg, Luxembourg
- Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Section for Microbiology and Immunology, The Gade Institute, University of Bergen, Bergen, Norway
- University of Milan, Milan, Italy
- Department of GU Medicine & Infectious Diseases, St James's Hospital, Dublin, Ireland
- Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
- Hospital Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari "Germans Trias i Pujol," Badalona, Spain
- National Public Health Surveillance Laboratory, Vilnius, Lithuania
- Sheba Medical Center, Tel Hashomer, Israel
- Warsaw Medical University and Hospital of Infectious Diseases, Warsaw, Poland
- Infectology Center of Latvia, Riga, Latvia
- University of Erlangen-Nuremberg, Erlangen, Germany
- University of Cyprus, Nicosia, Cyprus
- National Institute for Health and Welfare, Helsinki, Finland
- National Institute of Public Health, Prague, Czech Republic
- Molecular Diagnostics, "Prof Dr Matei Bals" Institute for Infectious Diseases, Bucharest, Romania
- Medical School, University of Athens, Athens, Greece
- University of Ljubljana, Ljubljana, Slovenia
- Medical University Vienna, Vienna, Austria
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
- Slovak Medical University, Bratislava, Slovakia
- University of Belgrade School of Medicine, Belgrade, Serbia
- Department of Medical Microbiology,University Medical Center Utrecht, Utrecht, the Netherlands
- * E-mail:
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Ferreira DD, Cook S, Lopes Â, de Matos AP, Esteves A, Abecasis A, de Almeida APG, Piedade J, Parreira R. Characterization of an insect-specific flavivirus (OCFVPT) co-isolated from Ochlerotatus caspius collected in southern Portugal along with a putative new Negev-like virus. Virus Genes 2013; 47:532-45. [PMID: 23877720 DOI: 10.1007/s11262-013-0960-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
We describe the isolation and characterization of an insect-specific flavivirus (ISF) from Ochlerotatus caspius (Pallas, 1771) mosquitoes collected in southern Portugal. The RNA genome of this virus, tentatively designated OCFVPT, for O. caspius flavivirus from Portugal, encodes a polyprotein showing all the features expected for a flavivirus. As frequently observed for ISF, the viral genomes seems to encode a putative Fairly Interesting Flavivirus ORF (FIFO)-like product, the synthesis of which would occur as a result of a -1 translation frameshift event. OCFVPT was isolated in the C6/36 Stegomyia albopicta (= Aedes albopictus) cell line where it replicates rapidly, but failed to replicate in Vero cells in common with other ISFs. Unlike some of the latter, however, the OCFVPT genome does not seem to be integrated in the mosquito cells we tested. Phylogenetic analyses based on partial ISF NS5 nucleotide sequences placed OCFVPT among recently published viral strains documented from mosquitoes collected in the Iberian Peninsula, while analyses of ORF/E/NS3/or NS5 amino acid sequences cluster OCFVPT with HANKV (Hanko virus), an ISF recently isolated from O. caspius mosquitoes collected in Finland. Taking into account the genetic relatedness with this virus, OCFVPT is not expected to be overtly cytopathic to C6/36 cells. The cytopathic effects associated with its presence in culture supernatants are postulated to be the result of the replication of a co-isolated putative new Negev-like virus.
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Affiliation(s)
- Daniela Duque Ferreira
- Unidade de Microbiologia Médica, Grupo de Virologia, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, 1349-008, Lisbon, Portugal
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27
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Gomes P, Palma AC, Cabanas J, Abecasis A, Carvalho AP, Ziermann R, Diogo I, Gonçalves F, Lobo CS, Camacho R. Comparison of the COBAS TAQMAN™ HIV-1 HPS with VERSANT HIV-1 RNA 3.0 Assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes. J Virol Methods 2006; 135:223-8. [PMID: 16675034 DOI: 10.1016/j.jviromet.2006.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2005] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 11/28/2022]
Abstract
Quantitation of HIV-1 RNA levels in plasma has an undisputed prognostic value and is extremely important for evaluating response to antiretroviral therapy. The purpose of this study was to evaluate the performance of the real-time PCR COBAS TaqMan 48 analyser, comparing it to the existing VERSANT 3.0 (bDNA) for HIV-1 RNA quantitation in plasma of individuals infected with different HIV-1 subtypes (104 blood samples). A positive linear correlation between the two tests (r2 = 0.88) was found. Quantitation by the COBAS TaqMan assay was approximately 0.32log10 higher than by bDNA. The relationship between the two assays was similar within all subtypes with a Deming regression of <1 and <0 for the Bland-Altman plots. Overall, no significant differences were found in plasma viral load quantitation in different HIV-1 subtypes between both assays; therefore these assays are suitable for viral load quantitation of highly genetically diverse HIV-1 plasma samples.
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Affiliation(s)
- Perpétua Gomes
- Laboratório de Virologia, Serviço de Imuno-Hemoterapia, Hospital Egas Moniz, Rua da Junqueria 126, 1349-019 Lisboa, Portugal.
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28
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Abecasis A, Paraskevis D, Epalanga M, Fonseca M, Burity F, Bartolomeu J, Carvalho AP, Gomes P, Vandamme AM, Camacho R. HIV-1 genetic variants circulation in the North of Angola. Infection, Genetics and Evolution 2005; 5:231-7. [PMID: 15737914 DOI: 10.1016/j.meegid.2004.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 07/07/2004] [Indexed: 11/23/2022]
Abstract
Few molecular epidemiological data on HIV-1 in Angola are available. In this study, we analysed 37 pol sequences from patients originated from Luanda and Cabinda in Angola. It was our objective to investigate the circulation of different HIV-1 subtypes in this country. We found a high HIV-1 genetic diversity. The predominant subtypes were C and F, while subtypes A, D, G and H were also detected. Three sequences were untypable and may possibly belong to new subtypes or recombinants of unknown subtypes. Moreover, 13 recombinant sequences were found, most of them with very complex patterns including untypable fragments.
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Affiliation(s)
- A Abecasis
- Laboratório de Virologia, Serviço de Imuno-hemoterapia, Hospital de Egas Moniz, Rua da Junqueira, 126, 1349-019 Lisboa, Portugal.
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29
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Paraskevis D, Deforche K, Abecasis A, Camacho R, Vandamme AM. Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method. Infect Genet Evol 2005; 5:219-24. [PMID: 15737912 DOI: 10.1016/j.meegid.2004.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 07/01/2004] [Indexed: 11/26/2022]
Abstract
The increased complexity of HIV-1 genetic heterogeneity raises the issue for reliable classification and analysis of these sequences. Until now, bootscanning analysis has been the main method used for the analysis of potential HIV-1 intersubtype recombinants. We show evidence that in some cases of complex recombinants, where three or more segments with discordant phylogenetic signal may exist in protease (PR) and partial reverse transcriptase (RT) region, Bayesian scanning provides a clearer picture than bootscanning plots about the boundaries of potential recombination. Thus, a recently developed Bayesian scanning tool can facilitate the analysis and classification of HIV-1 mosaic sequences.
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Affiliation(s)
- D Paraskevis
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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30
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Affiliation(s)
- Perpétua Gomes
- Laboratório de Virologia, Serviço de Imuno-Hemoterapia, Hospital Egas Moniz, Lisbon,
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