Browsing by Author "Oliveira, Ana"
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- Clinical Performance of the CLART Human Papillomavirus 2 Assay Compared With the Hybrid Capture 2 TestPublication . Pista, Angela; Verdasca, Nuno; Oliveira, AnaPersistent infection by high-risk human papillomavirus (HR-HPV) is a cause of cervical cancer. The use of HPV detection in cervical screening programs may improve the ability to identify women at risk of cervical cancer. Therefore, the development of appropriate methods for the detection of HR-HPV is essential. The aim of this study was to evaluate the clinical performance of the CLART Human Papillomavirus 2 assay (CLART) in comparison with the Hybrid Capture 2 test (HC2), using a clinical cut-off of cervical intraepithelial neoplasia grade 2 or worse. Discrepant results were analyzed further by the PapilloCheck HPV genotyping system. In the 425 studied women, HR-HPV positivity rates were similar by both tests (CLART-13 HR-HPV: 63.1%; CLART-17 HR-HPV: 64.7%; HC2: 64.5%). Agreement between CLART-13 HR-HPV (k¼ 0.969; concordance level 98.6%), CLART-17 HR-HPV (k¼ 0.974; concordance level 98.8%), and HC2 were very good. When 13 HR-HPV types were considered, the two tests showed a clinical sensitivity of 96% (95% CI: 92.6–97.9). The clinical specificity of CLART-13 HR-HPV was 73.6% (95% CI: 66.7–79.5) for cervical intraepithelial neoplasia grade 2 or worse, which was comparable to HC2 (71.4%; 95% CI: 64.3–77.5). When all 17 HR-HPV types were considered, CLART showed a clinical sensitivity of 96.9% (95% CI: 93.8–98.5) and a clinical specificity of 71.9% (95% CI: 64.9–78.0). In conclusion, the CLART assay is efficient, sensitive, reproducible, and has a similar performance to HC2 for cervical intraepithelial neoplasia grade 2 or worse. Furthermore, this assay has the advantage of detecting and genotyping 35 HPV types by a single test, which can provide additional information on the predictive value of infection with HR-HPV
- Indicadores de Prognóstico da Carcinogénese do Colo do Útero Associada à Infeção por Vírus do Papiloma HumanoPublication . Oliveira, Ana; Delgado, Candida; Verdasca, Nuno; Pista, Angela[PT] Introdução/Objetivos: A infeção persistente pelo Vírus do Papiloma Humano de alto risco (HPVar) é considerada como a causa necessária, embora não suficiente, para o desenvolvimento do cancro do colo do útero, sugerindo que outros fatores estarão envolvidos no processo de carcinogénese. Este estudo pretendeu avaliar indicadores de prognóstico da persistência da infeção por HPV, nomeadamente o estado físico e a carga viral dos HPV 16 e 18 e a superexpressão dos transcritos do RNAm dos HPV 16, 18, 31, 33 e 45, num grupo de mulheres com ou sem sintomatologia clínica e citopatológica. Material e Métodos: Foram estudadas 378 alíquotas de células epiteliais congeladas pertencentes a utentes dos centros de saúde do Serviço Nacional de Saúde e de clínicas privadas, referenciadas para teste HPV, entre Janeiro de 2007 e Dezembro de 2010. De acordo com o diagnóstico citopatológico, foram definidos cinco grupos: normal, ASCUS, LSIL, HSIL e carcinoma invasivo do colo do útero. Para a determinação do estado físico do DNA e da carga viral dos HPV 16 e 18 foi utilizada metodologia de PCR em tempo real, e para a superexpressão dos transcritos dos oncogenes E6 e E7 o sistema comercial NucliSENS EasyQ HPV. Os indicadores foram analisados em associação com os tipos de lesão do colo do útero. Para a análise estatística foi utilizado o o programa informático SPSS versão 16.0 e o teste de Chi-Quadrado. Resultados: Os resultados mostraram ausência de associação estatisticamente significativa entre a gravidade da lesão e o estado físico do DNA dos HPV 16 e 18. A superexpressão dos transcritos do RNAm E6/E7 e a carga viral dos HPV 16 e 18 aumentaram significativamente em função do grau da lesão. Conclusões: Os resultados obtidos sugerem que a determinação do estado físico do DNA dos HPV 16 e 18, isoladamente, não constitui um indicador de prognóstico para o desenvolvimento e progressão das lesões. A superexpressão dos transcritos dos oncogenes E6 e E7 está associada à progressão das lesões do colo do útero e apresenta maior especificidade no diagnóstico precoce das lesões pré-malignas. A quantificação do DNA dos HPVar pode ser um indicador promissor de prognóstico das lesões pré-neoplásicas do colo do útero.
- Indicadores de Prognóstico da Carcinogénese do Colo do Útero Associada à Infeção por Vírus do Papiloma HumanoPublication . Oliveira, Ana; Delgado, Candida; Verdasca, Nuno; Pista, AngelaIntrodução/Objetivos: A infeção persistente pelo Vírus do Papiloma Humano de alto risco (HPVar) é considerada como a causa ne¬cessária, embora não suficiente, para o desenvolvimento do cancro do colo do útero, sugerindo que outros fatores estarão envolvidos no processo de carcinogénese. Este estudo pretendeu avaliar indicadores de prognóstico da persistência da infeção por HPV, nome¬adamente o estado físico e a carga viral dos HPV 16 e 18 e a superexpressão dos transcritos do RNAm dos HPV 16, 18, 31, 33 e 45, num grupo de mulheres com ou sem sintomatologia clínica e citopatológica. Material e Métodos: Foram estudadas 378 alíquotas de células epiteliais congeladas pertencentes a utentes dos centros de saúde do Serviço Nacional de Saúde e de clínicas privadas, referenciadas para teste HPV, entre Janeiro de 2007 e Dezembro de 2010. De acordo com o diagnóstico citopatológico, foram definidos cinco grupos: normal, ASCUS, LSIL, HSIL e carcinoma invasivo do colo do útero. Para a determinação do estado físico do DNA e da carga viral dos HPV 16 e 18 foi utilizada metodologia de PCR em tempo real, e para a superexpressão dos transcritos dos oncogenes E6 e E7 o sistema comercial NucliSENS EasyQ HPV®. Os indicadores foram analisados em associação com os tipos de lesão do colo do útero. Para a análise estatística foi utilizado o o programa informático SPSS versão 16.0 e o teste de Chi-Quadrado. Resultados: Os resultados mostraram ausência de associação estatisticamente significativa entre a gravidade da lesão e o estado físico do DNA dos HPV 16 e 18. A superexpressão dos transcritos do RNAm E6/E7 e a carga viral dos HPV 16 e 18 aumentaram significativamente em função do grau da lesão. Conclusões: Os resultados obtidos sugerem que a determinação do estado físico do DNA dos HPV 16 e 18, isoladamente, não con¬stitui um indicador de prognóstico para o desenvolvimento e progressão das lesões. A superexpressão dos transcritos dos oncogenes E6 e E7 está associada à progressão das lesões do colo do útero e apresenta maior especificidade no diagnóstico precoce das lesões pré-malignas. A quantificação do DNA dos HPVar pode ser um indicador promissor de prognóstico das lesões pré-neoplásicas do colo do útero.
- Massive dissemination of a SARS-CoV-2 Spike Y839 variant in PortugalPublication . Borges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Leite, Ricardo; Gordo, Isabel; Caetano, Constantino P.; Nunes, Baltazar; Sá, Regina; Oliveira, Ana; Guiomar, Raquel; Portuguese network for SARS-CoV-2 genomics; Gomes, João PauloGenomic 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.
- Molecular Epidemiology of Hepatitis A Virus in a Group of Portuguese Citizens Living in Lisbon AreaPublication . Rodrigues, Luisa; Pista, Angela; Oliveira, Ana; Água-Doce, Ivone; Manita, Carla; Paixão, TeresaHepatitis A virus (HAV) is the most important cause of acute infectious hepatitis worldwide. In Portugal, due to improvements in sanitation epidemic outbreaks of HAV infection have become less frequent. This report is the first, to our knowledge that characterized HAV in Portugal. For the detection and molecular characterization of HAV cases in a group of Portuguese individuals in the Lisbon area, 31 serum samples were tested: 8 from symptomatic children from an acute hepatitis A outbreak in a Roma (Gipsies) community (2004–2005), and 22 from patients with acuteHAV from sporadic cases (2005–2006). A sample of CSF involved in a case of meningitis was also included. IgM anti-HAV detection and nested reverse transcription (RT-PCR), with primers located at the VP1-P2a region, was undertaken to detect HAV genome. In positive samples, molecular characterization was followed by phylogenetic analysis. All samples (n¼31) were positive for IgM anti-HAV. HAV RNA was found in 96.7% of cases. All isolates were classified as genotype I: 22 belonged to sub-genotype IA (73.3%), and 8 to sub-genotype IB (26.7%). All strains obtained from an acute HAV outbreak had sub-genotype IA, in which seven isolates (87.5%) had identical sequences. In HAV sporadic cases sub-genotypes IA and IB were identified, and this may reflect the co-circulation of these two subgenotypes in Portugal. Molecular epidemiology of HAV infection in this group of Portuguese appears to be similar to other European countries. HAV phylogenetic studies can provide important information for the design of appropriate public health measures.
- Molecular Variants of Human Papillomavirus Type 16 and 18 and Risk for Cervical Neoplasia in PortugalPublication . Pista, Angela; Oliveira, Ana; Barateiro, Andreia; Costa, Helena; Verdasca, Nuno; Paixão, TeresaPersistent high-risk human papillomavirus (HPV) infection is considered as the central cause of invasive cervical cancer. Specific HPV 16 and 18 sequence variations were associated with an increased risk for progression. The purpose of this study was to analyze intratypic variations of HPV 16 and 18 within the E6 gene, MY09/11 and LCR regions, and to evaluate the risk of these variants for cervical neoplasia among Portuguese women. Cervical samples from 187 HPV 16-positive and 41 HPV 18-positive women with normal epithelium, cervical intraepithelial neoplasia, or invasive cervical cancer were amplified by type-specific PCR, followed by sequence and phylogenetic analysis. Sixteen new HPV 16 and 18 patterns are described in this paper. European HPV 16 variants were the most frequent (74.3%), particularly Ep-T350 (44.4%), followed by African (16.1%), and Asian-American (9.6%). Non- European HPV 16 variants were more frequent in pre-invasive lesions than in normal tissue and low-grade lesions. However, when analyzed separately, only African variants were associated significantly with an increased risk for cervical cancer. For HPV 18, the AsAi variant showed a trend, which was not statistically significant to an enhanced oncogenicity. European variants seemed to be significantly associated with a lower risk for cervical cancer development. The distribution of HPV 16 and 18 variants was not related to age or race among women living in the same geographical region. Knowledge of variants will be important for risk determination as well as for designing primers or probes for HPV detection methods, and for appropriate cervical cancer prevention strategies.
- Single and multiple human papillomavirus infections in cervical abnormalities in Portuguese womenPublication . Pista, Ângela; Oliveira, Ana; Verdasca, Nuno; Ribeiro, FátimaPersistent infection with high-risk (HR) human papillomavirus (HPV) types is necessary for cervical cancer development. However, little is known about the influence of multiple HPV infections on cervical lesion risk. The aim of this study was to evaluate the frequency of single and multiple HPV infections in Portuguese women, and to assess the frequency of multiple infections in cervical intraepithelial neoplasia (CIN). HPV prevalence, type-specific prevalence and extent of multiple infections were assessed in 1057 cervical samples. The Clinical Array HPV assay was used to detect 35 HPV types. According to histological diagnosis, 425 samples were normal, 375 were CIN1, and 257 were CIN2+. HPV status was studied in relation to age and lesion severity. The prevalence of HPV infection was 52.7%; 25.4%, 67.2% and 76.7% were positive for any HPV type in the normal, CIN1 and CIN2+ cases, respectively. Among HPV-positive cases, 32.0% were associated with multiple infections. Among multiple infections, 96.1% harboured HR HPV types and 38.2% HR-low risk (LR) HPV types. Overall, 33 different HPV types (18 HR and 15 LR) were detected. HR HPV types (44.1%) were significantly more prevalent than LR HPV types (8.6%). The most frequent genotype was HPV 16 (25.5%), followed by HPV 31, 53, 66, 58, and 51. Multiple infections showed a significant increase (p 0.005) according to severity of neoplasia, particularly for HR-HR HPV infections (p 0.003). No association between age and multiple HPV infections was observed (p 0.812). However, multiple HR HPV infections were more frequent in women under 30 years of age (35.3%).
- Use of the NucliSENS EasyQ HPV Assay in the Management of Cervical Intraepithelial NeoplasiaPublication . Oliveira, Ana; Verdasca, Nuno; Pista, ÂngelaPersistent infection by high-risk human papillomavirus is a necessary cause for cervical cancer. DNA-based human papillomavirus (HPV) assays show high sensitivity but poor specificity in detecting high-grade cervical lesions. Assays detecting mRNA of the oncoproteins E6 and E7 show higher specificity but lack either detection of all high-risk genotypes or the ability to specify the detected genotypes. The aim of this study was to evaluate the clinical performance of the NucliSENS EasyQ HPV assay in comparison with the Hybrid Capture 2 test (HC2) and the CLART Human Papillomavirus 2 assay (CLART), using a clinical cut-off of cervical intraepithelial neoplasia grade 2 or worse. In the 554 studied women, the lowest HPV positivity rate was detected for NucliSENS EasyQ HPV assay (55.1%), while HC2 and CLART showed similar results (HC2: 77.4%; CLART: 78.0%). In comparison with the other tests, the NucliSENS EasyQ HPV assay showed a lower clinical sensitivity (79.3% vs. 96.4% for HC2 and 95.9% for CLART) but a higher clinical specificity (72.6% vs. 42.8% for HC2 and 42.5% for CLART). Detection of E6/E7 mRNA transcripts may provide a higher specificity for cervical intraepithelial neoplasia grade 2 lesions or worse, since the oncogenic potential of HPV infection depends on the over-expression of these two oncoproteins.