Sílvia Duarte
A5085155561- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Bacteriophages and microbial interactions
- Poxvirus research and outbreaks
- Plant Virus Research Studies
- COVID-19 epidemiological studies
- Reproductive tract infections research
- Bacterial Infections and Vaccines
- Viral Infections and Outbreaks Research
- Vaccine Coverage and Hesitancy
- Genomics and Phylogenetic Studies
- Oral microbiology and periodontitis research
- Influenza Virus Research Studies
- Animal Virus Infections Studies
- Mycobacterium research and diagnosis
- Microbial infections and disease research
- Streptococcal Infections and Treatments
- Evolution and Genetic Dynamics
- Respiratory viral infections research
- Bacillus and Francisella bacterial research
- Pneumonia and Respiratory Infections
- Congenital Anomalies and Fetal Surgery
- COVID-19 diagnosis using AI
- Genital Health and Disease
National Institute of Health Dr. Ricardo Jorge
2015-2025
Universidade Nova de Lisboa
2024
Instituto Politecnico de Setubal
2024
Instituto Nacional de Saúde
2020-2024
Centro Hospitalar Lisboa Norte
2024
Hospital de Santa Maria
2024
Universidade de Brasília
2024
Pontificia Universidad Javeriana
2016-2023
Administracao Central do Sistema de Saude
2023
Ricardo (United Kingdom)
2023
The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified May 2022 (refs.
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
To understand how organisms evolve, it is fundamental to study mutations emerge and establish. Here, we estimated the rate of mutation accumulation SARS-CoV-2 in vitro investigated repeatability its evolution when facing a new cell type but no immune or drug pressures.We performed experimental with two strains SARS-CoV-2, one carrying originally described spike protein (CoV-2-D) another D614G that has spread worldwide (CoV-2-G). After 15 passages Vero cells whole genome sequencing,...
Recent studies have shown that persistent SARS-CoV-2 infections in immunocompromised patients can trigger the accumulation of an unusual high number mutations with potential relevance at both biological and epidemiological levels. Here, we report a case patient (non-Hodgkin lymphoma under immunosuppressive therapy) infection (marked by intermittent positivity) over least 6 months. Viral genome sequencing was performed days 1, 164, 171 to evaluate evolution. Among 15 single-nucleotide...
We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with odds of proportion increasing at an estimated 89% (95% confidence interval: 83–95%) per week until 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track spread, besides failure (SGTF) proxy. SGTL/SGTF samples were associated statistically significant higher viral loads, but not substantial shift age distribution compared non-SGTF/SGTL cases.
Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters investigate their relationships. Here, we combine genomic epidemiological data of the 2022 mpox outbreak better early viral spread, diversification transmission dynamics. By 52% confirmed cases in Portugal, identified virus sublineages with highest impact on case numbers fitted them into a global context, finding evidence that several international probably emerged or spread...
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of early infections, these methods are resource intensive require samples high viral DNA concentrations. Given atypical clinical presentation cases associated uncertainty regarding load across both course infection...
Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well the institutional capacity to provide essential health services. Here, we investigated an outbreak SARS-CoV-2 a “non-COVID-19” hospital ward unveiled by massive testing, which challenged reconstruction transmission chains. The contacts network during 15-day period before screening was investigated, positive RNA samples were...
Abstract We estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 BA.2 lineages against infection disease progression. During April–June 2022, we implemented a case–case cohort study classified using whole-genome sequencing or spike gene target failure. For the study, adjusted odds ratios (aORs) vaccination logistic regression. VE progression penalized observed no reduced for (aOR 1.07 [95% CI 0.93–1.23]) 0.96 0.84–1.09]) infection. Among...
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased knowledge epidemiology this disease. However, due to difficulties associated with growth and isolation fastidious pathogen in culture, availability strains subsequently WGS data still limited. Methods To surpass these constraints, we aimed implement culture-free...
To survey genetic markers of potential antimicrobial resistance (AMR) to macrolides and fluoroquinolones among Chlamydia trachomatis-positive samples from the collection Portuguese National Reference Laboratory for Sexually Transmitted Infections (STIs), explore a multiplex PCR approach coupled with NGS provide complementary information regarding strain's genomic backbone. A total 502 C. samples, mostly anorectal exudates, were subjected sequencing five targets, including loci potentially...
<title>Abstract</title> Probe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance two Illumina probe-based panels, Respiratory Urinary Pathogen ID panels (RPIP UPIP), using 99 clinical samples from 15 different sample types (e.g., cerebrospinal fluid,...
Introduction: Early reports showed that Omicron (BA.1) SARS-CoV-2 could be less severe. However, the magnitude of risk reduction hospitalization and mortality infections compared with Delta (B.1.617.2) is not yet clear. This study compares severe disease among patients infected variant in Portugal.Methods: We conducted a cohort individuals diagnosed infection between 1st 29th December 2021. Cases were positive PCR test notified to national surveillance system. variants classified first by...
Abstract Background In a context of multiple Omicron lineages circulation, it is relevant to clarify the effect vaccination and previous infections on risk infection severe post-infection outcomes. Methods Using electronic health records SARS-CoV-2 laboratory surveillance data, we conducted case-case cohort study covering period BA.2/BA.5 lineage replacement in Portugal, compare vaccine effectiveness complete primary booster dose against infection, COVID-19 hospitalization, mortality....
Abstract Introduction Early reports showed that Omicron (BA.1) SARS-CoV-2 could be less severe. However, the magnitude of risk reduction hospitalization and mortality infections compared with Delta (B.1.617.2) is not yet clear. This study compares severe disease among patients infected variant in Portugal. Methods We conducted a cohort individuals diagnosed infection between 1 st 29 th December 2021. Cases were positive PCR test notified to national surveillance system. variants classified...
Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute Health collaboration with a nationwide consortium >50 hospitals/laboratories. Here, we track geotemporal spread variant mutation (D839Y) potential host-interacting region involving Spike fusion peptide, which is target motif anti-viral drugs that plays key role infectivity. The Y839 most likely imported from Italy mid-late February and massively disseminated during early epidemic, becoming...
Coronavirus disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is mainly transmitted through droplets, but other ways of transmission have been hypothesized. We report a case vertical SARS-CoV-2 in preterm born to an infected mother, confirmed the presence virus neonatal blood, nasopharyngeal and oropharyngeal swabs collected first half hour life. The neonate presented with distress, similar findings severely affected adults. This highlights importance...
Abstract Background and objectives To understand how organisms evolve, it is fundamental to study mutations emerge establish. Here, we estimated the rate of mutation accumulation SARS-CoV-2 in vitro investigated repeatability its evolution when facing a new cell type but no immune or drug pressures. Methodology We performed experimental with two strains SARS-CoV-2, one carrying originally described spike protein (CoV-2-D) another D614G that has spread worldwide (CoV-2-G). After 15 passages...
Background: The validity of the surveys on self-reported smoking status is often questioned because smokers underestimate cigarette use and deny habit.It has been suggested that self-report should be accompanied by cotinine test.This report evaluates usefulness serum test to assess association between periodontal in a study with large sample population used studies other markers epidemiologic medicine researches.Material Methods: 578 patients who were part multicenter blood biomarkers...