Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal.

BACKGROUND: The global scale-up of antiretroviral treatment (ART) offers significant health benefits by suppressing HIV-1 replication and increasing CD4 cell counts. However, incomplete viral suppression poses a potential threat for the emergence of drug resistance mutations (DRMs), limiting ART options, and increasing HIV transmission. OBJECTIVE: We investigated the patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) among HIV-1 patients in Portugal. METHODS: Data were obtained from 1050 HIV-1 patient samples submitted for HIV drug resistance (HIVDR) testing from January 2022 to June 2023. Evaluation of DRM affecting viral susceptibility to nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase strand transfer inhibitors (INSTIs) was performed using an NGS technology, the Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay. RESULTS: About 71% of patients were ART naïve and 29% were experienced. Overall, 20% presented with any DRM. The prevalence of TDR and ADR was 12.6% and 41.1%, respectively. M184V, T215S, and M41L mutations for NRTI, K103N for NNRTI, and M46I/L for PIs were frequent in naïve and treated patients. E138K and R263K mutations against INSTIs were more frequent in naïve than treated patients. TDR and ADR to INSTIs were 0.3% and 7%, respectively. Patients aged 50 or over (OR: 1.81, p = 0.015), originating from Portuguese-speaking African countries (PALOPs) (OR: 1.55, p = 0.050), HIV-1 subtype G (OR: 1.78, p = 0.010), and with CD4 < 200 cells/mm3 (OR: 1.70, p = 0.043) were more likely to present with DRMs, while the males (OR: 0.63, p = 0.003) with a viral load between 4.1 to 5.0 Log10 (OR: 0.55, p = 0.003) or greater than 5.0 Log10 (OR: 0.52, p < 0.001), had lower chances of presenting with DRMs. CONCLUSIONS: We present the first evidence on TDR and ADR to INSTI regimens in followed up patients presenting for healthcare in Portugal. We observed low levels of TDR to INSTIs among ART-naïve and moderate levels in ART-exposed patients. Regimens containing PIs could be an alternative second line in patients with intermediate or high-level drug resistance, especially against second-generation INSTIs (dolutegravir, bictegravir, and cabotegravir).

Usefulness of the Phalen Test and the Tinel Sign in the Prognosis and the Impact on Quality of Life of Patients with Carpal Tunnel Syndrome Undergoing Classical Open Carpal Tunnel Release.

Objective: To evaluate the usefulness of the Phalen test and the Tinel sign in the prognosis and the impact on quality of life in the clinical course of patients with carpal tunnel syndrome undergoing surgical treatment through the traditional open approach. Methods: The present is a cohort study on prognosis. We included 115 patients with high probability of receiving a clinical diagnosis of carpal tunnel syndrome with indication for surgical treatment. All patients underwent the Phalen test and Tinel sign and answered the Boston Carpal Tunnel Questionnaire before and after the surgical treatment. Results: The estimates for the probability of the time until remission of the Phalen test at 2, 4 and 16 weeks postoperatively were of 3.54% (95% confidence interval [95%CI]: 1.16%-8.17%), 0.88% (95%CI: 0.08%-4.38%) and 0.88% (95%CI: 0.08% to 4.38%) respectively, and, for the Tinel sign, they were of 12.39% (95%CI: 7.13%-19.18% ), 4.42% (95%CI : 1.65%-9.36%) and 2.65% (95%CI : 0.70%-6.94%) respectively. There was a reduction in the postoperative score on the Boston Carpal Tunnel Questionnaire of 1.8 points for symptom severity ( p < 0.001) and of 1.6 points for functional status ( p < 0.001). Conclusion: Phalen test remission was earlier than that of the Tinel sign, but, when performed as of the second postoperative week, they were prognostic factors favorable to the clinical course, with improved quality of life.

Determinants of HIV late presentation among men who have sex with men in Portugal (2014-2019): who's being left behind?

Introduction: HIV late presentation (LP) remains excessive in Europe. We aimed to analyze the factors associated with late presentation in the MSM population newly diagnosed with HIV in Portugal between 2014 and 2019. Methods: We included 391 newly HIV-1 diagnosed Men who have Sex with Men (MSM), from the BESTHOPE project, in 17 countrywide Portuguese hospitals. The data included clinical and socio-behavioral questionnaires and the viral genomic sequence obtained in the drug resistance test before starting antiretrovirals (ARVs). HIV-1 subtypes and epidemiological surveillance mutations were determined using different bioinformatics tools. Logistic regression was used to estimate the association between predictor variables and late presentation (LP). Results: The median age was 31 years, 51% had a current income between 501-1,000 euros, 28% were migrants. 21% had never been tested for HIV before diagnosis, with 42.3% of MSM presenting LP. 60% were infected with subtype B strains. In the multivariate regression, increased age at diagnosis, higher income, lower frequency of screening, STI ever diagnosed and higher viral load were associated with LP. Conclusion: Our study suggests that specific subgroups of the MSM population, such older MSM, with higher income and lower HIV testing frequency, are not being targeted by community and clinical screening services. Overall, targeted public health measures should be strengthened toward these subgroups, through strengthened primary care testing, expanded access to PrEP, information and promotion of HIV self-testing and more inclusive and accessible health services.

Serological screening in a large-scale municipal survey in Cascais, Portugal, during the first waves of the COVID-19 pandemic: lessons for future pandemic preparedness efforts.

Background: Serological surveys for SARS-CoV-2 were used early in the COVID-19 pandemic to assess epidemiological scenarios. In the municipality of Cascais (Portugal), serological testing combined with a comprehensive socio-demographic, clinical and behavioral questionnaire was offered to residents between May 2020 and beginning of 2021. In this study, we analyze the factors associated with adherence to this municipal initiative, as well as the sociodemographic profile and chronic diseases clinical correlates associated to seropositivity. We aim to contribute with relevant information for future pandemic preparedness efforts. Methods: This was a cross-sectional study with non-probabilistic sampling. Citizens residing in Cascais Municipality went voluntarily to blood collection centers to participate in the serological survey. The proportion of participants, stratified by socio-demographic variables, was compared to the census proportions to identify the groups with lower levels of adherence to the survey. Univariate and multivariate logistic regression were used to identify socio-demographic, clinical and behavioral factors associated with seropositivity. Results: From May 2020 to February 2021, 19,608 participants (9.2% of the residents of Cascais) were included in the study. Based on the comparison to census data, groups with lower adherence to this survey were men, the youngest and the oldest age groups, individuals with lower levels of education and unemployed/inactive. Significant predictors of a reactive (positive) serological test were younger age, being employed or a student, and living in larger households. Individuals with chronic diseases generally showed lower seroprevalence. Conclusion: The groups with low adherence to this voluntary study, as well as the socio-economic contexts identified as more at risk of viral transmission, may be targeted in future pandemic situations. We also found that the individuals with chronic diseases, perceiving higher risk of serious illness, adopted protective behaviors that limited infection rates, revealing that health education on preventive measures was effective for these patients.

The Role of Late Presenters in HIV-1 Transmission Clusters in Europe.

BACKGROUND: Investigating the role of late presenters (LPs) in HIV-1 transmission is important, as they can contribute to the onward spread of HIV-1 virus before diagnosis, when they are not aware of their HIV status. OBJECTIVE: To characterize individuals living with HIV-1 followed up in Europe infected with subtypes A, B, and G and to compare transmission clusters (TC) in LP vs. non-late presenter (NLP) populations. METHODS: Information from a convenience sample of 2679 individuals living with HIV-1 was collected from the EuResist Integrated Database between 2008 and 2019. Maximum likelihood (ML) phylogenies were constructed using FastTree. Transmission clusters were identified using Cluster Picker. Statistical analyses were performed using R. RESULTS: 2437 (91.0%) sequences were from subtype B, 168 (6.3%) from subtype A, and 74 (2.8%) from subtype G. The median age was 39 y/o (IQR: 31.0-47.0) and 85.2% of individuals were males. The main transmission route was via homosexual (MSM) contact (60.1%) and 85.0% originated from Western Europe. In total, 54.7% of individuals were classified as LPs and 41.7% of individuals were inside TCs. In subtype A, individuals in TCs were more frequently males and natives with a recent infection. For subtype B, individuals in TCs were more frequently individuals with MSM transmission route and with a recent infection. For subtype G, individuals in TCs were those with a recent infection. When analyzing cluster size, we found that LPs more frequently belonged to small clusters (<8 individuals), particularly dual clusters (2 individuals). CONCLUSION: LP individuals are more present either outside or in small clusters, indicating a limited role of late presentation to HIV-1 transmission.

Retention in Care and Virological Failure among Adult HIV-Positive Patients on First-Line Antiretroviral Treatment in Maputo, Mozambique.

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.

Blood pressure pattern among blood donors exposed to SARS-CoV-2 in Luanda, Angola: A retrospective study.

Background and Aims: SARS-CoV-2 infection is a public health concern. Several aspects related to the pattern of infection remain unclear. This study aimed to investigate the blood pressure pattern among blood donors exposed to SARS-CoV-2 in Luanda, Angola, a sub-Saharan African country. Methods: We performed a retrospective analysis containing 343 blood donors from December 2019 to September 2020. Parametric tests compared means while χ 2 and logistic regression checked features associated with high blood pressure and were considered significant when p < 0.05. Results: The mean age of blood donors was 32.2 ± 8.81 years (ranging from 18 to 61 years) and 93% of the men's gender. Overall, 4.7% of the studied population had been exposed to SARS-CoV-2. High blood pressure prevalence increased from unexposed to exposed SARS-CoV-2 (6.7%-18.8%, p = 0.071). SARS-CoV-2 exposure increase systole (131 ± 12.2 mmHg to 136 ± 14.2 mmHg, p = 0.098), diastole (79.9 ± 9.53 mmHg to 84.2 ± 12.7 mmHg, p = 0.086), pulse in beats per minute (72.0 ± 11.1 to 73.7 ± 8.50, p = 0.553), and decrease donating time (6.31 ± 3.72 min to 5.48 ± 1.61 min, p = 0.371). Chances of having high blood pressure were high [OR: 3.20 (95% confidence interval [CI]: 0.85-12.1), p = 0.086] in exposed SARS-CoV-2. Donors exposed to SARS-CoV-2 with abnormal donation time increased from the donor up to 40 years to over 40 years (from 35.7% to 50%, p = 0.696). The mean systolic, diastolic, and pulse pressure were higher for non-O donors (p > 0.05). A significant link was observed, between the Rhesus factor and blood pressure status (p = 0.032). Conclusion: We showed important variations in blood pressure indices of the Angolan population exposed to SARS-CoV-2. Older age and non-O blood groups appear to be important biological factors for SARS-CoV-2 infection, as well as the risk of developing cardiovascular disease after or during SARS-CoV-2 exposure. Further studies assessing the impact on cardiovascular functions with ongoing or long-term SARS-CoV-2 exposure in individuals from resource-limited countries should be considered.

Demographic characteristics and risk factors related to high blood pressure among healthy blood donors from Luanda, Angola: A retrospective study.

Background and Aims: Hypertension is a public health concern, mainly in resource-limited countries. We investigated the characteristics and risk factors related to high blood pressure in healthy blood donors from, Luanda, the capital city of Angola. Methods: This was a retrospective study that included 343 healthy donors from December 2019 to September 2020. Results: The mean age was 32 ± 9 years. Men represented 93% of the population. Mean systolic blood pressure (SBP) was 131 ± 12.3 mmHg (ranging from 100 to 160 mmHg) and diastolic blood pressure (DBP) was 80.1 ± 9.72 mmHg (from 56.0 to 100 mmHg). DBP was related to age and gender (p < 0.05). About 7.3% of the donors had high-pressure (>140/90 mmHg). Age between 20 and 40 years (odds ratio [OR]: 2.52, p = 0.043), women (OR: 1.87, p = 0.548), nonurbanized areas (OR: 0.39, p = 0.067), high educational level (OR: 0.76, p = 0.637), employed (OR: 0.49, p = 0.491), voluntary donors (OR: 0.87, p = 0.799), blood group B (OR: 2.06, p = 0.346), and Rh- (OR: 0.26, p = 0.104), were potentially related with high-pressure. The high-pressure cases increased from December 2019 (4%) to September 2020 (28%) (p = 0.019). Conclusion: We showed high pressure among the healthy blood donors population. Demographic characteristics, ABO/Rh blood group, and year period are features that should be considered in cardiovascular disease control strategies. Biological and nonbiological features related to blood pressure changes should be considered for further studies in the Angolan population.

Phylogeography of hepatitis B virus: The role of Portugal in the early dissemination of HBV worldwide.

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.

Prevalence of Anatomical Variations in Patients with Carpal Tunnel Syndrome Undergoing Classical Open Carpal Tunnel Release.

Objective To evaluate the prevalence of anatomical variations encountered in patients with carpal tunnel syndrome who underwent carpal tunnel classical open release. Methods A total of 115 patients with a high probability of clinical diagnosis for carpal tunnel syndrome and indication for surgical treatment were included. These patients underwent electroneuromyography and ultrasound for diagnostic confirmation. They underwent surgical treatment by carpal tunnel classical open release, in which a complete inventory of the surgical wound was performed in the search and visualization of anatomical variations intra- and extra-carpal tunnel. Results The total prevalence of anatomical variations intra- and extra-carpal tunnel found in this study was 63.5% (95% confidence interval [CI]: 54.5-72.4). The prevalence of the carpal transverse muscle was 57.4% (95% CI: 47.8-66.6%), of the bifid median nerve associated with the persistent median artery was 1.7% (95% CI: 0.0-4.2%), and the median bifid nerve associated with the persistent median artery and the transverse carpal muscle was 1.7% (95% CI: 0.0-4.2%). Conclusion The most prevalent extra-carpal tunnel anatomical variation was carpal transverse muscle. The most prevalent intra-carpal tunnel anatomical variation was median bifid nerve associated with the persistent median artery. The surgical finding of an extra-carpal tunnel anatomical variation, such as the transverse carpal muscle, may indicate the presence of other associated carpal intra tunnel anatomical variations, such as the bifid median nerve, persistent median artery, and anatomical variations of the recurrent median nerve branch.

Prevalence of Anatomical Variations in Patients with Carpal Tunnel Syndrome Undergoing Classical Open Carpal Tunnel Release / Prevalência de variações anatômicas encontradas em pacientes com síndrome do túnel do carpo submetidos a liberação cirúrgica por via aberta clássica

Abstract Objective To evaluate the prevalence of anatomical variations encountered in patients with carpal tunnel syndrome who underwent carpal tunnel classical open release. Methods A total of 115 patients with a high probability of clinical diagnosis for carpal tunnel syndrome and indication for surgical treatment were included. These patients underwent electroneuromyography and ultrasound for diagnostic confirmation. They underwent surgical treatment by carpal tunnel classical open release, in which a complete inventory of the surgical wound was performed in the search and visualization of anatomical variations intra- and extra-carpal tunnel. Results The total prevalence of anatomical variations intra- and extra-carpal tunnel found in this study was 63.5% (95% confidence interval [CI]: 54.5-72.4). The prevalence of the carpal transverse muscle was 57.4% (95% CI: 47.8-66.6%), of the bifid median nerve associated with the persistent median artery was 1.7% (95% CI: 0.0-4.2%), and the median bifid nerve associated with the persistent median artery and the transverse carpal muscle was 1.7% (95% CI: 0.0-4.2%). Conclusion The most prevalent extra-carpal tunnel anatomical variation was carpal transverse muscle. The most prevalent intra-carpal tunnel anatomical variation was median bifid nerve associated with the persistent median artery. The surgical finding of an extra-carpal tunnel anatomical variation, such as the transverse carpal muscle, may indicate the presence of other associated carpal intra tunnel anatomical variations, such as the bifid median nerve, persistent median artery, and anatomical variations of the recurrent median nerve branch.

Resumo Objetivo Avaliar a prevalência de variações anatômicas encontradas em pacientes com síndrome do túnel do carpo submetidos a liberação cirúrgica por via aberta clássica. Métodos Foram incluídos um total de 115 pacientes com alta probabilidade de diagnóstico clínico de síndrome do túnel do carpo, com indicação para o tratamento cirúrgico. Estes pacientes realizaram eletroneuromiografia e ultrassonografia para confirmação diagnóstica. Foram submetidos ao tratamento cirúrgico por via aberta clássica, no qual foi realizado um inventário completo da ferida operatória na busca e visualização de variações anatômicas intra e extra túnel do carpo. Resultados A prevalência total das variações anatômicas intra e extra túnel do carpo encontradas neste estudo foi de 63,5% (intervalo de confiança [IC]95%: 54,5-72,4%). A prevalência do músculo transverso do carpo foi de 57,4% (IC95%: 47,8-66,6%), do nervo mediano bífido associado à artéria mediana persistente foi de 1,7% (IC95%: 0,0-4,2%) e do nervo mediano bífido associado à artéria mediana persistente e ao músculo transverso do carpo foi de 1,7% (IC95%: 0,0-4,2%). Conclusão A variação anatômica extra túnel do carpo mais prevalente foi o músculo transverso do carpo e a variação anatômica intra túnel do carpo mais prevalente foi o nervo mediano bífido associado à artéria mediana persistente. O achado cirúrgico de uma variação anatômica extra túnel do carpo, como o músculo transverso do carpo, pode nos indicar a presença de outras variações anatômicas intra túnel do carpo associadas, como nervo mediano bífido, artéria mediana persistente e variações anatômicas do ramo recorrente do nervo mediano.

A Tale of Three Recent Pandemics: Influenza, HIV and SARS-CoV-2.

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. Another major pandemic was caused by the human immunodeficiency virus (HIV), that started early in the 20th century and remained undetected until 1981. The ongoing HIV pandemic demonstrated a high mortality and morbidity rate, with discrepant impacts in different regions around the globe. The most recent major pandemic event, is the ongoing pandemic of COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused over 5.7 million deaths since its emergence, 2 years ago. The aim of this work is to highlight the main determinants of the emergence, epidemic response and available countermeasures of these three pandemics, as we argue that such knowledge is paramount to prepare for the next pandemic. We analyse these pandemics' historical and epidemiological contexts and the determinants of their emergence. Furthermore, we compare pharmaceutical and non-pharmaceutical interventions that have been used to slow down these three pandemics and zoom in on the technological advances that were made in the progress. Finally, we discuss the evolution of epidemiological modelling, that has become an essential tool to support public health policy making and discuss it in the context of these three pandemics. While these pandemics are caused by distinct viruses, that ignited in different time periods and in different regions of the globe, our work shows that many of the determinants of their emergence and countermeasures used to halt transmission were common. Therefore, it is important to further improve and optimize such approaches and adapt it to future threatening emerging infectious diseases.

HIV-1-Transmitted Drug Resistance and Transmission Clusters in Newly Diagnosed Patients in Portugal Between 2014 and 2019.

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.

Trends of Transmitted and Acquired Drug Resistance in Europe From 1981 to 2019: A Comparison Between the Populations of Late Presenters and Non-late Presenters.

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 patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in HIV-1 infected patients followed in Europe, to compare its patterns in late presenters (LP) vs non-late presenters (NLP), and to analyze the most prevalent drug resistance mutations among HIV-1 subtypes. Methods: Our study included clinical, socio-demographic, and genotypic information from 26,973 HIV-1 infected patients from the EuResist Integrated Database (EIDB) between 1981 and 2019. Results: Among the 26,973 HIV-1 infected patients in the analysis, 11,581 (42.9%) were ART-naïve patients and 15,392 (57.1%) were ART-experienced. The median age was 37 (IQR: 27.0-45.0) years old and 72.6% were males. The main transmission route was through heterosexual contact (34.9%) and 81.7% of patients originated from Western Europe. 71.9% of patients were infected by subtype B and 54.8% of patients were classified as LP. The overall prevalence of TDR was 12.8% and presented an overall decreasing trend (p for trend < 0.001), the ADR prevalence was 68.5% also with a decreasing trend (p for trend < 0.001). For LP and NLP, the TDR prevalence was 12.3 and 12.6%, respectively, while for ADR, 69.9 and 68.2%, respectively. The most prevalent TDR drug resistance mutations, in both LP and NLP, were K103N/S, T215rev, T215FY, M184I/V, M41I/L, M46I/L, and L90M. Conclusion: Our study showed that the overall TDR (12.8%) and ADR (68.5%) presented decreasing trends during the study time period. For LP, the overall TDR was slightly lower than for NLP (12.3 vs 12.6%, respectively); while this pattern was opposite for ADR (LP slightly higher than NLP). We suggest that these differences, in the case of TDR, can be related to the dynamics of fixation of drug resistance mutations; and in the case of ADR with the more frequent therapeutic failure in LPs.

SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves.

Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.

Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal.

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 surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized 'African' and 'Asian' genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.

Differential patterns of postmigration HIV-1 infection acquisition among Portuguese immigrants of different geographical origins.

OBJECTIVE: To investigate the dynamics of phylogenetic transmission clusters involving immigrants of Portuguese Speaking Countries living in Portugal. DESIGN/METHODS: We included genomic sequences, sociodemographic and clinical data from 772 HIV migrants followed in Portugal between 2001 and 2017. To reconstruct HIV-1 transmission clusters, we applied phylogenetic inference from 16 454 patients: 772 migrants, 2973 Portuguese and 12 709 global controls linked to demographic and clinical data. Transmission clusters were defined using: clusters with SH greater than 90% (phylogenetic support), genetic distance less than 3.5% and clusters that included greater than 66% of patients from one specific geographic origin compared with the total of sequences within the cluster. Logistic regression was performed to assess factors associated with clustering. RESULTS: Three hundred and six (39.6%) of migrants were included in transmission clusters. This proportion differed substantially by region of origin [Brazil 54% vs. Portuguese Speaking African Countries (PALOPs) 36%, P < 0.0001] and HIV-1 infecting subtype (B 52%, 43% subtype G and 32% CRF02_AG, P < 0.001). Belonging to a transmission cluster was independently associated with treatment-naive patients, CD4+ greater than 500, with recent calendar years of sampling, origin from PALOPs and with seroconversion. Among Brazilian migrants - mainly infected with subtype B - 40.6% were infected by Portuguese. Among migrants from PALOPs - mainly infected with subtypes G and CFR02_AG - the transmission occurred predominantly within the migrants' community (53 and 80%, respectively). CONCLUSION: The acquisition of infection among immigrants living in Portugal differs according to the country of origin. These results can contribute to monitor the HIV epidemic and prevent new HIV infections among migrants.

SARS-CoV-2 epidemic in Brazil: how variants displacement have driven distinct epidemic waves

Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID- 19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.

Determinants of HIV-1 Late Presentation in Patients Followed in Europe.

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.

Determinants of HIV-1 Late Presentation in a Cohort of Portuguese HIV-1 Patients.

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.