Browsing by Author "Rocha, Raquel"
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- An Overview of Monkeypox Virus Detection in Different Clinical Samples and Analysis of Temporal Viral Load DynamicsPublication . Cordeiro, Rita; Pelerito, Ana; de Carvalho, Isabel Lopes; Lopo, Sílvia; Neves, Raquel; Rocha, Raquel; Palminha, Paula; Verdasca, Nuno; Palhinhas, Cláudia; Borrego, Maria José; Manita, Carla; Ferreira, Idalina; Bettencourt, Célia; Vieira, Patrícia; Silva, Sónia; Água-Doce, Ivone; Roque, Carla; Cordeiro, Dora; Brondani, Greice; Santos, João Almeida; Martins, Susana; Rodrigues, Irene; Ribeiro, Carlos; Núncio, Maria Sofia; Gomes, João Paulo; Batista, Fernando da ConceiçãoMpox is a zoonotic disease caused by the Monkeypox virus (MPXV), and since May 2022, tens of thousands of cases have been reported in non-endemic countries. We aimed to evaluate the suitability of different sample types for mpox diagnostic and assess the temporal dynamics of viral load. We evaluated 1914 samples from 953 laboratory-confirmed cases. The positivity rate was higher for lesion (91.3%) and rectal swabs (86.1%) when compared with oropharyngeal swabs (69.5%) and urines (41.2%), indicating higher viral loads for the former. Supporting this, lesion and rectal swabs showed lower median PCR C values (C = 23 and C = 24), compared to oropharyngeal swabs and urines (C = 31). Stable MPXV loads were observed in swabs from lesions up to 30 days after symptoms onset, contrasting with a considerable decrease in viral load in rectal and oropharyngeal swabs. Overall, these results point to lesion swabs as the most suitable samples for detecting MPXV in the 2022-2023 multicountry outbreak and show comparable accuracy to rectal swabs up to 8 days after symptoms onset. These findings, together with the observation that about 5% of patients were diagnosed through oropharyngeal swabs while having negative lesions, suggest that multisite testing should be performed to increase diagnostic sensitivity.
- BabA-mediated adherence of pediatric ulcerogenic H. pylori strains to gastric mucins at neutral and acidic pHPublication . Quintana-Hayashi, Macarena P.; Rocha, Raquel; Padra, Médea; Thorell, Anders; Jin, Chunsheng; Karlsson, Niclas G.; Roxo-Rosa, Mónica; Oleastro, Mónica; Lindén, Sara K.Helicobacter pylori infection can result in non-ulcer dyspepsia (NUD), peptic ulcer disease (PUD), adenocarcinoma, and gastric lymphoma. H. pylori reside within the gastric mucus layer, mainly composed of mucins carrying an array of glycan structures that can serve as bacterial adhesion epitopes. The aim of the present study was to characterize the binding ability, adhesion modes, and growth of H. pylori strains from pediatric patients with NUD and PUD to gastric mucins. Our results showed an increased adhesion capacity of pediatric PUD H. pylori strains to human and rhesus monkey gastric mucins compared to the NUD strains both at neutral and acidic pH, regardless if the mucins were positive for Lewis b (Leb), Sialyl-Lewis x (SLex) or LacdiNAc. In addition to babA positive strains being more common among PUD associated strains, H. pylori babA positive strains bound more avidly to gastric mucins than NUD babA positive strains at acidic pH. Binding to Leb was higher among babA positive PUD H. pylori strains compared to NUD strains at neutral, but not acidic, pH. PUD derived babA-knockout mutants had attenuated binding to mucins and Leb at acidic and neutral pH, and to SLex and DNA at acidic pH. The results highlight the role of BabA-mediated adherence of pediatric ulcerogenic H. pylori strains, and points to a role for BabA in adhesion to charged structures at acidic pH, separate from its specific blood group binding activity.
- Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with Nonulcer Dyspepsia and Peptic Ulcer DiseasePublication . Nunes, Alexandra; Rocha, Raquel; Vale, Filipa F.; Vieira, Luís; Sampaio, Daniel A.; Dias, Ricardo; Gomes, João Paulo; Oleastro, MónicaWe present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from children. This will be important for future studies of comparative genomics in order to better understand the virulence determinants underlying peptic ulcer disease.
- Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical originsPublication . Vale, Filipa F.; Nunes, Alexandra; Oleastro, Mónica; Gomes, João P.; Sampaio, Daniel A.; Rocha, Raquel; Vítor, Jorge M. B.; Engstrand, Lars; Pascoe, Ben; Berthenet, Elvire; Sheppard, Samuel K.; Hitchings, Matthew D.; Mégraud, Francis; Vadivelu, Jamuna; Lehours, PhilippeHelicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3' end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.
- Genotipagem do HPV por Multiplex Real Time PCRPublication . Verdasca, Nuno; Rocha, Raquel; Gradíssimo, Ana
- High Risk Human Papillomavirus in a Group of Portuguese WomenPublication . Rocha, Raquel; Verdasca, NunoHuman Papillomavirus (HPV) is the etiological agent for cervical cancer and genital warts. Worldwide, cervical cancer is the fourth most common cancer in women and the high risk HPV (HR-HPV), namely HPV 16 and 18 are responsible for the most of the cases. The objective was to analyze the HR-HPV frequency in a group of women referred for HR-HPV testing. Clinical samples from 3117 women were perform by Cobas® HPV test (Roche Molecular Systems, CA, USA), this assay detected HPV 16 and HPV 18 and ‘Other HR-HPV’ (-31,-33,-35,-39,-45,-51,-52,-56,-58,-59,-66 and 68). Positive samples for ‘Other HR-HPV’ were sequenced for genotyping using MY09/11 primer´s. HR-HPV frequency was 20.8% (649/3117). Among the positive samples, ‘Other HR-HPV’ was the most common (72.8%; 473/649). HPV 16 and 18 were detected only in 22.8% (148/649) and 7.4% (48/649) of the cases, respectively. 7.4% (48/649) of the positive women were infected with more than one HPV (34 with ‘Other HR-HPV’ + HPV 16; 8 with ‘Other HR-HPV’ + HPV 18; 5 with ‘Other HR-HPV’ + HPV 16 + HPV 18 and 1 with HPV 16 + HPV 18). Sequencing of ‘Other HR-HPV’ is ongoing and preliminary results shown the majority frequency for HPV 31 (11.7%) followed by HPV 56 (9.1%) and 8.9% for the HPV 66. The HR-HPV frequency is high (20.8%), 30.4 % of these women were infected with HPV 16 or HPV 18 which is a high frequency. This study reveals the importance of the implementation of screening programs, and the use of HPV detection.
- Population genetic structure of Helicobacter pylori strains from Portuguese-speaking countriesPublication . Oleastro, Mónica; Rocha, Raquel; Vale, Filipa F.The human gastric colonizer Helicobacter pylori is useful to track human migrations given the agreement between the bacterium phylogeographic distribution and human migrations. As Portugal was an African and Brazilian colonizer for over 400 years, we hypothesized that Portuguese isolates were likely genetically closer with those from countries colonized by Portuguese in the past. We aimed to characterize the population structure of several Portuguese-speaking countries, including Portugal, Brazil, Angola, and Cape Verde.
- Portuguese National Serological Survey to Coronavirus Disease 19 - ISNCOVID-19Publication . Kislaya, Irina; Gómez, Verónica; Garcia, Ana Cristina; Machado, Ausenda; Torres, Ana Rita; Roquette, Rita; Sousa-Uva, Mafalda; Matias Dias, Carlos; Nunes, Baltazar; Costa, Inês; Gonçalves, Paulo; Matos, Rita; Machado, Jorge; Manita, Carla; Martins, Fátima; Santos, João; de Sousa, Rita; Soeiro, Sofia; Rocha, Raquel; Roque, Carla; Verdasca, Nuno; Guiomar, Raquel; Rodrigues, Ana Paula; ISNCOVID-19 study teamThe objective of this seroepidemiological survey was to estimate seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) specific antibodies (IgM and/or IgG) in Portugal in May-July 2020. The seroprevalence of SARS-Cov-2 infection (positive for IgM and/or IgG) was 2.9% (CI95: 2.0 - 4.2%). Our results support extend limited extent of infection by SARS-CoV-2 in Portugal due to early lockdown measures implementation.
- Primeiro estudo em Portugal sobre a identificação dos genótipos do vírus do papiloma humano (HPV) numa população feminina vacinada com atividade sexual ativaPublication . Rocha, Raquel; Grupo de Estudo da Vacina do HPV; Verdasca, NunoA infeção por HPV é responsável por 99,7% dos casos de cancro de colo do útero a nível mundial. De modo a prevenir e a minimizar o impacto da infeção por HPV na saúde das mulheres foram desenvolvidas vacinas. A vacina tetravalente está incluída no Plano Nacional de Vacinação (PNV) desde 2008. Com o objetivo de se conhecer a distribuição dos genótipos HPV estudaram-se 152 amostras clínicas de mulheres jovens vacinas com atividade sexual ativa. As amostras clínicas foram colhidas por cytobrush, procedeu-se à deteção e tipificação do HPV pela técnica de microarrays. Das mulheres estudadas, 28,3% apresentaram infeção por genótipos HPV, dos quais 58,1% corresponderam a genótipos de alto risco, sendo mais frequente o HPV 51 (15,2%) seguido do HPV 59 e HPV 58 com 7,6% e 6,1%, respetivamente. Foram também detetados dois casos de infeção por HPV 16, que é um dos genótipos incluído na vacina. Genótipos de baixo risco foram detetados em 25,6% de infeções, sendo o HPV42 o mais frequente com 9,1% dos casos. A história vacinal demonstrou que 83,1% das mulheres foram vacinadas ao abrigo do PNV e iniciaram atividade sexual após administração da vacina, e que 53,6% das mulheres vacinadas fora do PNV iniciaram atividade sexual antes da administração da vacina. Portugal apresenta uma taxa de cobertura vacinal elevada. Estes primeiros resultados reforçam a importância da administração da vacina antes do início da atividade sexual e de se manter o rastreio do cancro do colo do útero.
- The expression of Helicobacter pylori tfs plasticity zone cluster is regulated by pH and adherence, and its composition is associated with differential gastric IL-8 secretionPublication . Silva, Bruno; Nunes, Alexandra; Vale, Filipa F; Rocha, Raquel; Gomes, João Paulo; Dias, Ricardo; Oleastro, MónicaBackground: Helicobacter pylori virulence is associated with different clinical outcomes. The existence of an intact dupA gene from tfs4b cluster has been suggested as a predictor for duodenal ulcer development. However, the role of tfs plasticity zone clusters in the development of ulcers remains unclear. We studied several H. pylori strains to characterize the gene arrangement of tfs3 and tfs4 clusters and their impact in the inflammatory response by infected gastric cells. Methods: The genome of 14 H. pylori strains isolated from Western patients, pediatric (n=10) and adult (n=4), was fully sequenced using the Illumina platform MiSeq, in addition to eight pediatric strains previously sequenced. These strains were used to infect human gastric cells, and the secreted interleukin-8 (IL-8) was quantified by ELISA. The expression of virB2, dupA, virB8, virB10, and virB6 was assessed by quantitative PCR in adherent and nonadherent fractions of H. pylori during in vitro co-infection, at different pH values. Results: We have found that cagA-positive H. pylori strains harboring a complete tfs plasticity zone cluster significantly induce increased production of IL-8 from gastric cells. We have also found that the region spanning from virB2 to virB10 genes constitutes an operon, whose expression is increased in the adherent fraction of bacteria during infection, as well as in both adherent and nonadherent fractions at acidic conditions. Conclusions: A complete tfs plasticity zone cluster is a virulence factor that may be important for the colonization of H. pylori and to the development of severe outcomes of the infection with cagA-positive strains.