Browsing by Author "Correia, Vanessa"
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- Antiviral drug profile of seasonal influenza viruses circulating in Portugal from 2004/2005 to 2008/2009 winter seasonPublication . Correia, Vanessa; Rebelo-de-Andrade, Helena; Santos, Luís A.; Lackanby, Angie; Zambon, MariaA research project on antiviral drug resistance of influenza viruses circulating in Portugal has been carried out since 2007. Here, the first results obtained regarding the evaluation of susceptibility to amantadine and oseltamivir are presented. Information about antiviral prescription and exposure was available through the National Influenza Surveillance Programme. Amantadine susceptibility was evaluated by pyrosequencing for known resistance markers on 178 influenza A strains from 2004/2005 to 2006/2007. Susceptibility to oseltamivir was evaluated by 50% inhibitory concentration determination on 340 virus strains from 2004/2005 to 2008/2009, 134 of which were further analyzed by sequencing of the neuraminidase gene. This study revealed that influenza antiviral drugs were rarely prescribed at national level. Resistance to amantadine was observed on only A(H3N2) strain isolated during 2005/2006 and on 38 (74.5%) of the 51 A(H3N2) strains from 2006/2007, all carrying the mutation S31N in theirM2sequence. Oseltamivir resistance was observed in 6 (20.7%) of the 29 A(H1N1) strains from 2007/2008 and in all strains from 2008/2009, which exhibited extremely high IC50 values and carrying the mutation H275Y in their neuraminidase sequence. The national data generated and analyzed in this study may contribute to increase the knowledge on influenza antiviral drug resistance which is a problem of global concern.
- Antiviral drug profile of seasonal influenza viruses circulating in Portugal from 2004/2005 to 2008/2009 winter seasonsPublication . Correia, Vanessa; Andrade, Helena Rebelo de; Santos, Luís A.; Lackenby, Angie; Zambon, MariaA research project on antiviral drug resistance of influenza viruses circulating in Portugal has been carried out since 2007. Here, the first results obtained regarding the evaluation of susceptibility to amantadine and oseltamivir are presented. Information about antiviral prescription and exposure was available through the National Influenza Surveillance Programme. Amantadine susceptibility was evaluated by pyrosequencing for known resistance markers on 178 influenza A strains from 2004/2005 to 2006/2007. Susceptibility to oseltamivir was evaluated by 50% inhibitory concentration determination on 340 virus strains from 2004/2005 to 2008/2009, 134 of which were further analyzed by sequencing of the neuraminidase gene. This study revealed that influenza antiviral drugs were rarely prescribed at national level. Resistance to amantadine was observed on only A(H3N2) strain isolated during 2005/2006 and on 38 (74.5%) of the 51 A(H3N2) strains from 2006/2007, all carrying the mutation S31N in their M2 sequence. Oseltamivir resistance was observed in 6 (20.7%) of the 29 A(H1N1) strains from 2007/2008 and in all strains from 2008/2009, which exhibited extremely high IC(50) values and carrying the mutation H275Y in their neuraminidase sequence. The national data generated and analyzed in this study may contribute to increase the knowledge on influenza antiviral drug resistance which is a problem of global concern.
- A cost-efficient solution: reagent comparison guide for neuraminidase inhibition assayPublication . Louro, João; Correia, Vanessa; Rebelo de Andrade, HelenaObjectives: Compare available alternative reagents for Neuraminidase Activity Assay and Neuraminidase Inhibition Assay; Assess the phenotypic susceptibility profiles of influenza viruses from different (sub)types to the new Neuraminidase Inhibitors: laninamivir and peramivir.
- How to dissect viral infections and their interplay with the host-proteome by immunoaffinity and mass spectrometry: A tutorialPublication . Santos, Hugo M.; Carvalho, Luís B.; Lodeiro, Carlos; Martins, Gonçalo; Gomes, Inês L.; Antunes, Wilson D.T.; Correia, Vanessa; Almeida-Santos, Maria M.; Rebelo-de-Andrade, Helena; Matos, António P.A.; Capelo, J.L.The capabilities of bioanalytical mass spectrometry to (i) detect and differentiate viruses at the peptide level whilst maintaining high sample throughput and (ii) to provide diagnosis and prognosis for infected patients are presented as a tutorial in this work to aid analytical chemists and physicians to gain insights into the possibilities offered by current high-resolution mass spectrometry technology and bioinformatics. From (i) sampling to sample treatment; (ii) Matrix-Assisted Laser Desorption Ionization- to Electrospray Ionization -based mass spectrometry; and (iii) from clustering to peptide sequencing; a detailed step-by-step guide is provided and exemplified using SARS-CoV-2 Spike Y839 variant and the variant of concern SARS-CoV-2 Alpha (B.1.1.7 lineage), Influenza B, and Influenza A subtypes AH1N1pdm09 and AH3N2.
- Molecular footprints of selective pressure in the neuraminidase gene of currently circulating human influenza subtypes and lineagesPublication . Correia, Vanessa; Abecasis, Ana B.; Rebelo-de-Andrade, HelenaInfluenza neuraminidase (NA) is under selective pressure (SP) of both host immune system and drug use. Here, we assembled large datasets of NA sequences of worldwide circulating viruses to estimate the global and site-specific SP acting on all current subtypes/lineages of human influenza NA. An overall negative SP of similar magnitude and a prevalence of negatively selected sites were observed for all subtypes/lineages. Positively selected sites varied according to the subtype/lineage, including N1-NA sites 247 and 275, N2-NA sites 148 and 151, and B/Victoria-NA site 395 associated with drug-resistance or reduced susceptibility. These results evidenced a potential role of positive selection in the low-level spread of A(H1N1)pdm09-H275Y drug-resistant viruses, and alerted for a potential higher risk of spread of a synergistic A(H1N1)pdm09 drug-resistant variant (H275Y/S247N). The positive selection detected at N2-NA sites 148 and 151 was probably an artefact from cell-culture. Overall mapping revealed six potential new druggable regions.
- NS1 protein as a novel anti-influenza target: Map-and-mutate antiviral rationale reveals new putative druggable hot spots with an important role on viral replicationPublication . Trigueiro-Louro, João; Santos, Luís A.; Almeida, Filipe; Correia, Vanessa; Brito, Rui M.M.; Rebelo-de-Andrade, HelenaInfluenza NS1 is a promising anti-influenza target, considering its conserved and druggable structure, and key function in influenza replication and pathogenesis. Notwithstanding, target identification and validation, strengthened by experimental data, are lacking. Here, we further explored our previously designed structure-based antiviral rationale directed to highly conserved druggable NS1 regions across a broad spectrum of influenza A viruses. We aimed to identify NS1-mutated viruses exhibiting a reduced growth phenotype and/or an altered cell apoptosis profile. We found that NS1 mutations Y171A, K175A (consensus druggable pocket 1), W102A (consensus druggable pocket 3), Q121A and G184P (multiple consensus druggable pockets) - located at hot spots amenable for pharmacological modulation - significantly impaired A(H1N1)pdm09 virus replication, in vitro. This is the first time that NS1-K175A, -W102A, and -Q121A mutations are characterized. Our map-and-mutate strategy provides the basis to establish the NS1 as a promising target using a rationale with a higher resilience to resistance development.
- Perfil de suscetibilidade do vírus influenza aos antivirais específicos para a gripe de 2004 a 2011Publication . Correia, Vanessa; Santos, Luis André; Andrade, Helena Rebelo de
- To hit or not to hit: large-scale sequence analysis and structure characterization of influenza A NS1 unlocks new antiviral target potentialPublication . Trigueiro-Louro, João M.; Correia, Vanessa; Santos, Luís A.; Guedes, Rita C.; Brito, Rui M.M.; Rebelo-de-Andrade, HelenaInfluenza NS1 protein is among the most promising novel druggable anti-influenza target, based on its structure; multiple interactions; and global function in influenza replication and pathogenesis. Notwithstanding, drug development guidance based on NS1 structural biology is lacking. Here, we design a promising strategy directed to highly conserved druggable regions as a result of an exhaustive large-scale sequence analysis and structure characterization of NS1 protein across human-infecting influenza A subtypes, over the past 100 years. We have identified 3 druggable pockets and 8 new potential hot spot residues in the NS1 protein, not described before, additionally to other 16 sites previously identified, which represent attractive targets for pharmacological modulation. This study provides a rationale towards structure-function studies of NS1 druggable sites, which have the potential to accelerate the NS1 target validation. This research also contributes to a deeper comprehension and insight into the evolutionary dynamics of influenza A NS1 protein.
- Uncovering the role of positive selection in the evolutionary pathways to influenza virus resistance or reduced inhibition by neuraminidase inhibitorsPublication . Correia, Vanessa; Abecasis, Ana; Rebelo de Andrade, HelenaThis study aimed at estimating the site-specific SP on the NA gene of currently circulating human influenza viruses, in order to infer the SP acting specifically on the sites associated with (H)RI by NAIs and on further sites contacting directly or indirectly with the drug (active site). The frequency of drug-resistant and (H)RI variants was determined as a secondary objective, prompted by the need of determining the entire amino acid composition of the sites to understand SP data
- Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV SpikePublication . Trigueiro-Louro, João; Correia, Vanessa; Figueiredo-Nunes, Inês; Gíria, Marta; Rebelo-de-Andrade, HelenaThere are no approved target therapeutics against SARS-CoV-2 or other beta-CoVs. The beta-CoV Spike protein is a promising target considering the critical role in viral infection and pathogenesis and its surface exposed features. We performed a structure-based strategy targeting highly conserved druggable regions resulting from a comprehensive large-scale sequence analysis and structural characterization of Spike domains across SARSr- and MERSr-CoVs. We have disclosed 28 main consensus druggable pockets within the Spike. The RBD and SD1 (S1 subunit); and the CR, HR1 and CH (S2 subunit) represent the most promising conserved druggable regions. Additionally, we have identified 181 new potential hot spot residues for the hSARSr-CoVs and 72 new hot spot residues for the SARSr- and MERSr-CoVs, which have not been described before in the literature. These sites/residues exhibit advantageous structural features for targeted molecular and pharmacological modulation. This study establishes the Spike as a promising anti-CoV target using an approach with a potential higher resilience to resistance development and directed to a broad spectrum of Beta-CoVs, including the new SARS-CoV-2 responsible for COVID-19. This research also provides a structure-based rationale for the design and discovery of chemical inhibitors, antibodies or other therapeutic modalities successfully targeting the Beta-CoV Spike protein.