Ana Abecasis

Institute of Hygiene and Tropical Medicine | IHMT · Department of Public Health

Objectives: Surveillance drug resistance mutations (SDRMs) in drug-naive patients are typically used to survey HIV-1-transmitted drug resistance (TDR). We test here how SDRMs in patients failing treatment, the original source of TDR, contribute to assessing TDR, transmissibility and transmission source of SDRMs. Design: This is a retrospective o...

Background: Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes. Results: We investigated the subtype distribution of HIV-1 in Europe and Israel in a rep...

Human immunodeficiency virus type 1 (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide distribution, this classification system is widely used in fields as diverse as vaccine develo...

Bacterial endospores are the most resistant cell type known to humans, as they are able to withstand extremes of temperature, pressure, chemical injury, and time. They are also of interest because the endospore is the infective particle in a variety of human and livestock diseases. Endosporulation is characterized by the morphogenesis of an endospo...

Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic,...

Background: Investigating the role of late presenters (LP) on HIV-1 transmission is important, as they can contribute to the onward spread of HIV-1 virus in the long period before diagnosis, when they are not aware of their HIV status Objective: To describe the clinical and socio-demographic characteristics of HIV-1 infected individuals followed in...

Emerging infectious diseases are one of the main threats to public health, with the potential to cause a pandemic when the infectious agent manages to spread globally. The first major pandemic to appear in the 20th century was the influenza pandemic of 1918, caused by the influenza A H1N1 strain that is characterized by a high fatality rate. Anothe...

Ritonavir-boosted atazanavir is an option for second-line therapy in low- and middle-income countries (LMICs). We analyzed publicly available HIV-1 protease sequences from previously PI-naïve patients with virological failure (VF) following treatment with atazanavir. Overall, 1497 patient sequences were identified, including 740 reported in 27 publ...

Background The increased use of antiretroviral therapy (ART) has decreased mortality and morbidity of HIV-1 infected people but increasing levels of HIV drug resistance threatens the success of ART regimens. Conversely, late presentation can impact treatment outcomes, health costs, and potential transmission of HIV. Objective To describe the patte...

The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveilla...

Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, numerous new sequences, even in organisms other than mosquitos, have been identified and characteriz...

The analysis of the viruses allocated to the recently established Brevihamaparvovirus genus (Parvoviridae family), which includes all previously known brevidensoviruses, has not yet been carried out on an extensive basis. As a result, no detailed genetic lineage characterization has ever been performed for this group of insect-specific viruses. Usi...

Objective: To investigate the dynamics of phylogenetic transmission clusters involving immigrants of Portuguese Speaking Countries living in Portugal. Design/methods: We included genomic sequences, socio-demographic and clinical data from 772 HIV migrants followed in Portugal between 2001 and 2017. To reconstruct HIV-1 Transmission Clusters (TCs...

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 (HBV/A) was t...

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 anal...

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 determi...

The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range. In this study, we i...

Schistosomiasis is a chronic neglected tropical disease saddling millions of people in the world, mainly children living in poor rural areas. Praziquantel (PZQ) is currently the only drug used for the treatment and control of this disease. However, the extensive use of this drug has brought concern about the emergence of PZQ-resistance/tolerance by...

Background: Undiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters for HIV care may help to identify characteristics of such patients. Objective: The present study aims to identify factors associated with late presentation (LP) and late presentation with advanced disease (LPAD) based on a population...

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 Port...

HIV and tuberculosis (TB) are among the global deadliest diseases. Migrant populations are particularly vulnerable to these infections. Yet, literature is still scarce on the epidemiology of HIV-TB co-infection among migrants. In this study, we characterized native and migrant HIV patients followed in Portuguese hospitals, who were diagnosed with T...

Background: Undiagnosed HIV-1 patients still account for 25% of worldwide HIV patients. Studying late presenters for HIV care may help to identify characteristics of such patients. Objective: The present study aims to identify factors associated with late presentation (LP) and late presentation with advanced disease (LPAD) based on a population of...

Background Treatment for all recommendations has allowed access to antiretroviral (ARV) treatment to an increasing number of patients. This minimizes transmission of infection but can potentiate the risk for development of transmitted drug resistance (TDR) and acquired drug resistance (ADR). Objective To study the trends of TDR and ADR in patients...

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 re...

One of the cornerstones in combating the HIV pandemic is the ability to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. We first present a method to learn e...

Background Tuberculosis (TB) is one of the main causes of death worldwide. In 2017, the proportion of TB cases among foreign-born individuals in Portugal was of 19%, and this proportion has been increasing. TB control among migrant populations largely depends on the role of the healthcare providers and their close contact with the patients. We aime...

One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. To that end, we firstly present a met...

Background Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines....

Despite the rapid spread of the Zika virus throughout the Americas in 2015, its phylogenetic classification is limited to either an African or Asian genotype. This classification no longer reflects the present genetic diversity of circulating strains and their geographic reach. Using 414 publicly available Zika virus genomes from 40 different count...

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 mosqu...

Background Portugal has one of the most severe HIV-1 epidemic in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines....

Viral pathogens causing global disease burdens are often characterised by high rates of evolutionary changes, facilitating escape from therapeutic or immune selective pressure. Extensive viral diversity at baseline can shorten the time to resistance emergence and alter mutational pathways, but the impact of genotypic background on the genetic barri...

Background : Viral pathogens causing global disease burdens are often characterised by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be diffic...

HIV-1 subtypes associate with differences in transmission and disease progression. Thus, the existence of geographic hotspots of subtype diversity deepens the complexity of HIV-1/AIDS control. The already high subtype diversity in Portugal seems to be increasing due to infections with sub-subtype A1 virus. We performed phylogenetic analysis of 65 A...

In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an effic...

The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the continental territory and the islands of São Miguel...

Background Tuberculosis (TB) is still a major global health problem. The increasing number of cases observed among foreign-born populations contrasts with the decreasing trends observed in later years in some high-income countries. Healthcare providers are key interveners in the control of TB and HIV-TB infections. In this study, we aimed to explor...

Since HIV-1 treatment is increasingly considered an effective preventionstrategy, it is important to study local HIV-1 epidemics to formulate tailored preventionpolicies. The prevalence of HIV-1 in Cyprus was historically low until 2005. To investigatethe shift in epidemiological trends, we studied the transmission dynamics of HIV-1 in Cyprususing...

When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local variation. This can be done by using a heritability model and fitting it to a local set-point viral load distribu...

Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit for these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codo...

Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit for these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codo...

Objectives: A 4 years 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 the transmission event...

Background: Together with Treponema pallidum ssp. pertenue, Haemophilus ducreyi is a major cause of exudative cutaneous ulcers (CU) 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:...

Since HIV-1 treatment is increasingly considered an effective preventionstrategy, it is important to study local HIV-1 epidemics to formulate tailored preventionpolicies. The prevalence of HIV-1 in Cyprus was historically low until 2005. To investigatethe shift in epidemiological trends, we studied the transmission dynamics of HIV-1 in Cyprususing...

The adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. T...

The adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. T...

: Because HIV is a fast-evolving virus, HIV genomic sequences of several individuals can be used to investigate whether they belong to a transmission network. Since the infamous 'Florida dentist case' in the beginning of the 90 s, phylogenetic analyses has been recurrently used in court settings as a forensic tool in HIV transmission investigations...

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 i...

HCV viral load (VL) comparison between HCV monoinfected and co-infected patients with genotype 1b. Statistical analysis was performed with Mann-Whitney test, p value < 0.05 was considered significant. (TIF)

Background International human migration has been rapidly growing. Migrants coming from low and middle income countries continue to be considerably vulnerable and at higher risk for infectious diseases, namely HIV (Human Immunodeficiency Virus) and tuberculosis (TB). In Europe, the number of patients with HIV-TB co-infection has been increasing and...

Database searches. (DOCX)

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of...

The Zika Pandemic and the threat of the introduction of Vector Borne Diseases in Europe Ana Abecasis, Ricardo Parreira, Henrique Silveira, Patrícia Salgueiro, João Pinto, Carla Sousa Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal Background: Zika virus (ZIKV) is a mosquit...

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....

BEST HOPE is a project to construct a cohort of newly diagnosed HIV patients in Portugal: BEST HOPE aims are: 1) to analyze the prevalence and characteristics of TDR in newly diagnosed HIV patients, and 2) to describe and analyze risk factors associated with HIV infection and transmission of drug resistance in Portugal.