SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal.

Background: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods: By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. Results: We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions: Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.

Discriminating Between Premigration and Postmigration HIV Acquisition Using Surveillance Data.

BACKGROUND: Migrant populations are overrepresented among persons diagnosed with HIV in the European Union and the European Economic Area. Understanding the timing of HIV acquisition (premigration or postmigration) is crucial for developing public health interventions and for producing reliable estimates of HIV incidence and the number of people living with undiagnosed HIV infection. We summarize a recently proposed method for determining the timing of HIV acquisition and apply it to both real and simulated data. METHODS: The considered method combines estimates from a mixed model, applied to data from a large seroconverters' cohort, with biomarker measurements and individual characteristics to derive probabilities of premigration HIV acquisition within a Bayesian framework. The method is applied to a subset of data from the European Surveillance System (TESSy) and simulated data. FINDINGS: Simulation study results showed good performance with the probabilities of correctly classifying a premigration case or a postmigration case being 87.4% and 80.4%, respectively. Applying the method to TESSy data, we estimated the proportions of migrants who acquired HIV in the destination country were 31.9%, 37.1%, 45.3%, and 45.2% for those originating from Africa, Europe, Asia, and other regions, respectively. CONCLUSIONS: Although the considered method was initially developed for cases with multiple biomarkers' measurements, its performance, when applied to data where only one CD4 count per individual is available, remains satisfactory. Application of the method to TESSy data, estimated that a substantial proportion of HIV acquisition among migrants occurs in destination countries, having important implications for public health policy and programs.

Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal.

Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.

Trends in human immunodeficiency virus diagnoses among men who have sex with men in North America, Western Europe, and Australia, 2000-2014.

PURPOSE: The aim of the article was to investigate recent trends in human immunodeficiency virus (HIV) diagnosis rates among men who have sex with men (MSM) in high-income countries in North America, Western Europe, and Australia. METHODS: Data on annual rates of HIV diagnoses among MSM aged 15 to 65 years from 2000 to 2014 were collected from 13 high-income countries. Joinpoint regression software was used to empirically determine country-specific trend periods. Trends in HIV diagnosis rates and in the proportion of diagnoses occurring in young MSM aged 15 to 24 years were analyzed using Poisson regression and log-binomial regression, respectively. RESULTS: Six countries experienced an increasing trend from 2000 to 2007-08 followed by either a stable or declining trend through 2014. Five countries had recently increasing trends, and two countries had one stable trend from 2000 to 2014. All 13 countries experienced increases in the proportion of diagnoses occurring in young MSM. CONCLUSIONS: Since 2008, half of the 13 high-income countries examined experienced stable or decreasing trends. Still, some countries continue to experience increasing HIV trends, and young MSM are increasingly represented among new diagnoses. Efforts to support early sexual health promotion, reduce barriers to pre-exposure prophylaxis, and improve care engagement for young MSM are critical to addressing current HIV trends.

Molecular characterization of hepatitis C virus for determination of subtypes and detection of resistance mutations to protease inhibitors in a group of intravenous drug users co-infected with HIV.

Modifications in therapeutic regimens for the treatment of hepatitis C virus (HCV) have been observed since the approval of viral protease inhibitors (PI), and the selection of natural drug-resistant variants has been also reported. Thus, it becomes crucial to be aware of consequences of new therapeutic approaches and make available tools for monitoring the infection. The study aimed to apply an "in-house" method for amplification and sequencing of the NS3 region which is the target of PI, and allowing simultaneously the classification of viral subtypes and identification of resistance mutations. Forty-seven samples collected from HIV injecting drug users and drug naive for HCV protease inhibitors were tested for anti-HCV antibodies, 93.6% of them had a positive result and in 70.5% was determined HCV active infection. High frequency of subtype 1a (46.2%), followed by an equal proportion of subtypes 3a, 4a, and 4d (15.4%) was obtained. Two potential recombinants, RF1_2k/1b (3.8%) and 2q/2k (3.8%) were identified. Substitutions V36L/P, T54A, I72L/N/T/V, Q80K/G, S122R/T, D168Q, and I170L/V were observed in 65.4% of the samples. The T54A and Q80K mutations, and the combination V36L + T54A were also identified. Polymorphisms were observed exclusively associated with specific genotypes, particularly, I72L and D168Q with genotype 3, and S122T with genotype 4. The V36L substitution was identified in 92.8% of sequences of non-genotype 1 denoting that this amino acid substitution is a natural polymorphism associated with non-genotype 1 strains. Although no major PI resistance mutations were detected, a more extensive study is needed to evaluate the impact of mutations identified in efficacy of PI treatment.

Improving data management practices in the Portuguese HIV/AIDS surveillance system during a time of public sector austerity.

In a climate of public sector austerity, the demand for accurate information about disease epidemiology rises as health program managers try to align spending to health needs. A policy of case re-notification to improve HIV information quality resulted in a nine-fold increase in the number of case reports received in 2013 by the Portuguese HIV surveillance office. We used value stream mapping to introduce improvements to data processing practices, identify and reduce waste. Two cycles of improvement were trialled. Before intervention, processing time was nine minutes and 28 seconds (95%CI 8:53-10:58) per report. Two months post intervention, it was six minutes and 34 seconds (95% CI 6:25-6:43). One year after the start of the project, processing time was five minutes and 20 seconds (95% CI 1:46-8:52).

[Assessment of Hepatitis C Virus Diversity in Addition to the Frequency of Genotypes in Samples Analyzed Between 2009 and 2014 at the Reference Laboratory of National Health Institute Dr. Ricardo Jorge]. / Conhecer a Diversidade do Vírus da Hepatite C para Além da Frequência dos Genótipos em Amostras Analisadas entre 2009 e 2014 no Laboratório de Referência do Instituto Nacional de Saúde Dr. Ricardo Jorge.

INTRODUCTION: The identification of genotypes was essential for the prognosis and treatment of hepatitis C virus chronic patients in recent years. The aims of the study were to know the frequency of genotypes diagnosed in the last six years at the laboratory, and reveal the contribution of an in-house assay for molecular characterization of viruses. MATERIAL AND METHODS: The genotyping of hepatitis C virus by LiPA was performed in 923 samples, mostly from male individuals. The subtyping of hepatitis C virus by an in-house assay to target regions in the Core/E1 and/or NS5B was performed in 112 samples. RESULTS: We observed a high prevalence of genotype 1 (56.6%), with a frequency of subtype 1a four times higher compared to 1b. All cases of genotype 3 (27.5%) were subtype 3a. For the cases of genotype 4 (12.9%), it were identified subtypes 4a (65.5%), 4d (31%), 4b (1.7%) and 4c (1.7%). Recombinants intragenotype 2, the RF1_2k/1b, and mixed infections, were also identified. DISCUSSION: The most prevalent subtypes (1a and 3a) obtained are usually described in injecting drug users. Although most of the samples analysed match to inmates (78.4%), we cannot exclude any possible risk behaviors associated with illicit drug use. CONCLUSIONS: The high prevalence of subtype 1a, the frequency and diversity of genotype 4, and the identification of recombined virus suggest modification of the molecular pattern of hepatitis C virus infection described in the past. The in-house assay proved to be useful for the correct classification of hepatitis C virus and improving knowledge about the diversity of virus circulating in the country.

Introdução: A identificação dos genótipos do vírus da hepatite C foi essencial para o prognóstico e tratamento dos doentes crónicos durante os últimos anos. Foram objetivos deste estudo conhecer a frequência de genótipos do vírus da hepatite C nos últimos seis anos, e revelar o contributo de um ensaio in-house para caracterização molecular do vírus. Material e Métodos: A genotipagem do vírus da hepatite C por LiPA foi realizada em 923 amostras, maioritariamente provenientes de indivíduos do sexo masculino. A subtipagem do vírus da hepatite C pelo ensaio in-house com alvo nas regiões Core/E1 e/ou NS5B foi efetuada em 112 amostras. Resultados: Observámos elevada prevalência do genótipo 1 (56,6%), sendo a frequência do subtipo 1a quatro vezes superior ao subtipo 1b. Todos os casos de genótipo 3 (27,5%) foram classificados em subtipo 3a. Nas infeções pelo genótipo 4 (12,9%), identificaram-se os subtipos 4a (65,5%), 4d (31%), 4b (1,7%) e 4c (1,7%). Foram identificadas a RF1_2k/1b, recombinantes intragenótipo 2 e potenciais infeções mistas na população analisada. Discussão: Os subtipos mais prevalentes, 1a e 3a, estão descritos como comuns em utilizadores de drogas injetáveis. Apesar da maioria das amostras analisadas corresponder a reclusos (78,4%), não podemos excluir eventuais comportamentos de risco associados ao consumo de drogas ilícitas. Conclusões: A prevalência elevada do subtipo 1a, a frequência e diversidade do genótipo 4 e a identificação de vírus geneticamente recombinados, sugerem alteração do padrão molecular vírus da hepatite C descrito no passado. O ensaio in-house implementado revelou ser útil para a correta classificação do vírus da hepatite C e melhoria do conhecimento sobre a diversidade do vírus em circulação no país.

Characteristics of late presentation of HIV infection in MSM and heterosexual adults in Portugal 2011-2013.

INTRODUCTION: It is estimated that over half of newly diagnosed HIV infections in Europe present late. An HIV positive individual presenting late to care represents a missed opportunity to benefit from treatment, increasing the risk of morbidity and mortality at an individual level, and onward disease transmission at population level. Reducing late presentation is a strategic priority of the Portuguese HIV/AIDS program. We set out to describe the characteristics of late presentation in the two largest transmission risk groups currently in Portugal to inform HIV prevention and treatment. METHODS: We extracted details of all notified cases from individuals over 15 years with a laboratory confirmed HIV diagnosis made between January 2011 and December 2013 from the Portuguese HIV surveillance database and selected cases from heterosexuals and men who have sex with men (MSM). We defined late presentation as an initial CD4 count <350 cells/mm(3) or presence of AIDS-defining disease at time of HIV diagnosis. We calculated adjusted odds ratios (aOR) with 95% confidence intervals (CI) for characteristics associated with late presentation in separate logistic regression for heterosexuals and MSM. RESULTS: Of 4219 HIV positive cases notified, 2589 (61%) were heterosexuals and 1220 (29%) were MSM. A total of 1586 (38%) cases presented late of which 1037 (40%) were heterosexual and 328 (27%) were MSM. The median age at late presentation was 40 in heterosexual women, 46 in heterosexual men and 35 in MSM. A total of 1446 (55%) of heterosexual HIV positive adults were unaware of having had a high risk sexual contact. Late presentation among heterosexuals was associated with being male (aOR=1.58 95% CI 1.29-1.93), not knowing a partners' HIV status (OR=1.59 95% CI 1.35-1.87) and age, increasing the odds of late presentation by a factor of 1.02 per year (95% CI 1.01-1.03). Among MSM, only age was associated with late presentation, increasing by 1.04 (95% CI 1.03-1.05) per year. CONCLUSIONS: Portuguese HIV prevention programs need to increase the risk awareness of heterosexuals, particularly men, to reduce missed opportunities for early diagnosis. As half of all cases presenting late are aged 40 and over, we recommend that general HIV outreach services and specialist services for MSM review their accessibility and acceptability to both middle and older-aged clients.