Browsing by Author "Sampaio, Daniel Ataíde"
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- Influenza A(H3) whole genome analysis: searching causes for vaccine failure in 2011/2012Publication . Pechirra, Pedro; Maia, Ana Carina; Sampaio, Daniel Ataíde; Borges, Vítor; Gomes, João Paulo; Guiomar, RaquelBackground: The 2011/2012 season in Portugal, was characterized by an excess mortality and influenza vaccine failures. Predominant influenza A(H3) viruses with new antigenic properties were associated with potential host immune evasion. The aim of this study was to determine possible viral genetic causes that may be associated with cases of vaccine failure by performing a whole genome-based comparison of viruses detected in vaccinated (vacc) and unvaccinated (unvacc) individuals in 2011/2012 season. Methods: In 2011/12 season, 678 nasopharyngeal swabs from ILI cases were analyzed by the Portuguese NIC. Were detected 260 influenza A(H3) and 6 B/Yamagata viruses. For whole genome sequencing (WGS) 25 A(H3) positive samples, 20 from vacc and 5 from unvacc individuals, were selected. Each of the influenza genomic segments was submitted to standard or multiplex PCR amplification. WGS was performed on a MiSeq platform. Multiple alignments, phylogenetic and mutational analysis were performed using MEGA software 6.0. Results: Influenza A(H3) viruses clustered into different genetic clades, reflecting the clades circulating in Portugal, in2011/2012. 20 viruses belonged to clade 6 (reference strain A/Iowa/19/2010) and 5 viruses have clustered in the clade 3: 1 from clade 3A (A/Stockholm/18/2011), a second from clade 3B (A/England/259/2011) and 3 viruses from clade 3C (A/Victoria/361/2011). Viral genomes were highly similar at nucleotide level, ranging 98.2% – 100.0% of similarity. Matrix and nucleoprotein genomic segments were the most conserved, whereas the highest number of substitutions leading to amino acid changes was observed in hemagglutinin and neuraminidase segments (comparisons performed against the vaccine strain A/Perth/16/2009). The deduced amino acid sequences of viral proteins did not reveal any particular feature assigned to the group of vacc or unvacc individuals. Conclusions: In all 8 genomic segments of studied viruses no particular amino acid substitution was found to be associated with the vacc or unvacc cases. The observed differences were associated with the genetic distances between the clades to which viruses belong rather than with vaccine failure. Still, WGS in influenza surveillance is a powerful tool for monitoring the overall evolution of viral genome and establishment of molecular markers for, disease severity and drug resistance. This study points that a full evaluation of influenza vaccine failures should integrate not only data on virus characteristics, but also on host genetic polymorphisms related to immunity and serosurveys in order to better evaluate interindividual variation in influenza vaccine-induced immune responses.
- Molecular epidemiology of aspergillosis in Magellanic penguins and susceptibility patterns of clinical isolatesPublication . Melo, Aryse Martins; Poester, Vanice Rodrigues; Canabarro, Paula Lima; Sampaio, Daniel Ataíde; Stevens, David A; Veríssimo, Cristina; Sabino, Raquel; Xavier, Melissa OrzechowskiAspergillus section Fumigati is reported in up to 99% of aspergillosis cases in penguins. So far, no data regarding molecular epidemiology and azole resistance are available for A. fumigatus isolates collected from Magellanic penguins. The aim of this work was to perform molecular identification of Aspergillus section Fumigati at species level, to genotype those isolates using microsatellite markers, to evaluate the in vitro susceptibility patterns of A. fumigatus sensu stricto, and to characterize the cyp51A gene in clinical A. fumigatus strains isolated from Magellanic penguins with proven aspergillosis. All 34 isolates included in the study were identified as A. fumigatus sensu stricto. Analyzing the genetic diversity of the isolates of A. fumigatus sensu stricto, we identified two possible outbreaks in the rehabilitation center and we also observed the maintenance of clonal strains through the years. One A. fumigatus sensu stricto isolate was resistant to posaconazole, but the mutations found in the cyp51A gene of this isolate have not been described as conferring phenotypic resistance, suggesting that other mechanisms of resistance could be involved in the resistance of this isolate. With this study, we were able to understand the molecular diversity of Aspergillus fumigatus isolates collected from Magellanic penguins, to characterize them and to associate them with the described global population of Aspergillus fumigatus.