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- Molecular epidemiology of Respiratory Syncytial Virus between 2010-2015, in PortugalPublication . Guiomar, Raquel; Cristóvão, Paula; Conde, Patrícia; Pechirra, PedroBackground: Respiratory syncytial virus is one of the major causes of respiratory infection and complications in younger children and elderly. This study has, for the first time, investigated the genetic diversity of RSV A and RSV B detected since 2010, in influenza like illness (ILI) cases reported in the scope of the Portuguese Influenza Surveillance Programme (NISP). Methods: During 2010-2015, nasopharyngeal swabs (NPS) sent to the National Influenza Reference Laboratory from sentinel and non-sentinel network were tested for RSV A and RSV B by real time multiplex RT-PCR. Nucleotide sequence of a fragment of the hypervariable C-terminal region of the G protein gene and the phylogenetic analysis was performed for an half of detected RSV. Results: Over the study period were detected 114 (5.2%) RSV in 2187 tested NPS. Of these 67 (59%) were from subtype A and 47 (41%) from subtype B. Circulation of RSV preceded or was coincident with the influenza epidemic period. RSV A was predominant in each winter with exception for 2014/2015 winter when RSV B was predominantly detected. Of the RSV positive samples, 58 (51%) were successfully sequenced and genetically characterized: 26 (45%) RSV A and 32 (55%) RSV B. RSV A clustered in two genotypes. A majority (n= 22; 85%) belonged to ON1 genotype and 4 (15%) viruses belonged to NA1 genotype. Only ON1 genotype was detected after 2012/2013 season. RSV B clustered in two genotypes: a majority (n=22; 67%) belonged to BA9 genotype and 11 (33%) clustered in BA10 genotype. BA9 genotype was detected over all the study period, although BA10 was only detected in 2012/2013, and 2014/2015 seasons. Conclusion: Our study highlights the importance of RSV in ILI cases, showing a seasonal circulation each winter season during influenza epidemic. RSV accounted for 5.2% of the cases reported in the scope of influenza surveillance, assuming a huge importance in young children and older ones. Molecular data for RSVA revealed co circulation of NA1 and ON1 till 2012, and after this period ON1 was exclusively detected suggesting a strain replacement by this antigenically advantageous genotype. Globally ON1 is also predominantly detected. For RSVB subtype was observed a co circulation of the BA9 and BA10 genotypes. BA derived genotypes, first identified in 1999 in Buenos Aires are predominant in many countries since then.
- 2014/2015 Influenza season in an inland portuguese regionPublication . Almeida, Sofia; Rodrigues, Débora; Gouveia, Paula; Paulo, Sandra; Faria, Conceição; Pechirra, Pedro; Costa, Inês; Cristóvão, Paula; Guiomar, RaquelInfluenza surveillance is an important tool to identify emerging/reemerging strains, and defining seasonality of the circulating strains. The aim of this work is to compare the circulating strains detected by Centro Hospitalar da Cova da Beira, EPE,(CHCB) from an inland north region of Portugal, with the strains circulating among Europe during2014/2015 Influenza season. In the present review, 249 nasofaringeal swabs received in were analized by real time PCR techniques, designed to amplify Influenza A and Influenza B virus. All the positive samples were sent to the Portuguese reference Laboratory in order to subtype influenza A virus and to perform genetic and antigenic characterization of the detected viruses. During 2014/2015 season, a total of 109 positive cases (62 Influenza A and 47 Influenza B) - were detected in the studied region. In the present season, all seasonal types/subtypes of influenza virus circulated, inspite of low level circulation of the Influenza A(H1)pdm strain (~5%of the positive samples, circulating between 6/2015-9/2015 weeks). A(H3) and B strains co-circulated between weeks 1/2015 and 11/2015 with peak activity in weeks 6 and 7/2015. Influenza A, excluding A(H1)pdm, was responsible for 47% of positive cases, mainly in the last 6 weeks. Influenza B strains were responsible for 42% of positive Influenza cases, mainly in the first 7 weeks of the year. All influenza B strains characterized by the Portuguese National Laboratory were from B/Yamagata lineage. 19% of influenza B strains wereselected for genetic characterization, all were similar to B/Phuket/3073/2013 (clade 3). At the date of submission of the abstract, only 8 Influenza A strains were genetically characterized, 5 belonged to genetic subgroup 3C.2a, represented by A/Hong Kong/5738/2014, dissimilar to the current A(H3N2) vaccine strain and 3 belonged to A/Samara/73/2013 (genetic group 3C.3), antigenically similar to the current A(H3N2) vaccine The co-circulation of influenza types/subtypes was similar to the one described in Europe, but in this Portuguese region, the Influenza B circulated in first part of the epidemic period, followed by A(H3) virus at the end of epidemic period.. The genetic characterization observed in Portugal was similar to the one from ECDC data for Influenza B. Relatively to Influenza A, the majority of detected viruses were dissimilar to the 2014/2015 A(H3) vaccine virus, being a higher proportion than the observed in Europe, but more data is needed to achieve any conclusion.