Browsing by Author "Melidou, Angeliki"
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- Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021Publication . Funk, Tjede; Pharris, Anastasia; Spiteri, Gianfranco; Bundle, Nick; Melidou, Angeliki; Carr, Michael; Gonzalez, Gabriel; Garcia-Leon, Alejandro; Crispie, Fiona; O’Connor, Lois; Murphy, Niamh; Mossong, Joël; Vergison, Anne; Wienecke-Baldacchino, Anke K.; Abdelrahman, Tamir; Riccardo, Flavia; Stefanelli, Paola; Di Martino, Angela; Bella, Antonino; Lo Presti, Alessandra; Casaca, Pedro; Moreno, Joana; Borges, Vítor; Isidro, Joana; Ferreira, Rita; Gomes, João Paulo; Dotsenko, Liidia; Suija, Heleene; Epstein, Jevgenia; Sadikova, Olga; Sepp, Hanna; Ikonen, Niina; Savolainen-Kopra, Carita; Blomqvist, Soile; Möttönen, Teemu; Helve, Otto; Gomes-Dias, Joana; Adlhoch, CorneliaWe compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).
- Dominant influenza A(H3N2) and B/Yamagata virus circulation in EU/EEA, 2016/17 and 2017/18 seasons, respectivelyPublication . Adlhoch, Cornelia; Snacken, René; Melidou, Angeliki; Ionescu, Silviu; Penttinen, Pasi; The European Influenza Surveillance NetworkThe yearly influenza epidemics during each winter season vary in burden and severity. During the 2016/17 and 2017/18 seasons, all-cause excess mortality was observed during periods of high influenza virus circulation. Our aim is to describe and compare the pattern of influenza virus circulation and related disease severity by number of patients and fatal cases in intensive care units (ICUs) across European Union/European Economic Area (EU/EEA) countries for the seasons 2016/17 and 2017/18. As influenza circulation progressed from a west to east direction across Europe in 2017/18, a better understanding of the current epidemiological situation might help to prepare countries in the eastern part of the World Health Organization (WHO) European Region for high influenza activity and severity.
- Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020Publication . Alm, Erik; Broberg, Eeva K; Connor, Thomas; Hodcroft, Emma B; Komissarov, Andrey B; Maurer-Stroh, Sebastian; Melidou, Angeliki; Neher, Richard A; O’Toole, Áine; Pereyaslov, Dmitriy; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV groupWe show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
- Predominance of influenza A(H1N1)pdm09 virus genetic subclade 6B.1 and influenza B/Victoria lineage viruses at the start of the 2015/16 influenza season in EuropePublication . Broberg, Eeva; Melidou, Angeliki; Prosenc, Katarina; Bragstad, Karoline; Hungnes, Olav; WHO European Region and the European Influenza Surveillance Network members of the reporting countriesInfluenza A(H1N1)pdm09 viruses predominated in the European influenza 2015/16 season. Most analysed viruses clustered in a new genetic subclade 6B.1, antigenically similar to the northern hemisphere vaccine component A/California/7/2009. The predominant influenza B lineage was Victoria compared with Yamagata in the previous season. It remains to be evaluated at the end of the season if these changes affected the effectiveness of the vaccine for the 2015/16 season.
- Predominance of influenza A(H3N2) virus genetic subclade 3C.2a1 during an early 2016/17 influenza season in Europe - Contribution of surveillance data from World Health Organization (WHO) European Region to the WHO vaccine composition consultation for northern hemisphere 2017/18Publication . Melidou, Angeliki; Broberg, Eeva; European region influenza surveillance networkDuring the European 2016/17 influenza season, A(H3N2) viruses have predominated and the majority clustered in genetic subclade 3C.2a1. Genetic analyses showed that circulating viruses have undergone considerable genetic diversification of the haemagglutinin gene from the current vaccine virus A/Hong Kong/4801/2014 (clade 3C.2a), but the antigenic data that is limited by the challenges with the antigenic characterisation of currently circulating A(H3N2) viruses, showed no clear evidence of antigenic change. The recommended A(H3N2) vaccine component for the northern hemisphere 2017/18 influenza season remained unchanged. However, early and mid-season vaccine effectiveness (VE) estimates were suggestive of reduced VE against A(H3N2) viruses.
- Predominance of influenza virus A(H3N2) 3C.2a1b and A(H1N1)pdm09 6B.1A5A genetic subclades in the WHO European Region, 2018–2019Publication . Melidou, Angeliki; Hungnes, Olav; Pereyaslov, Dmitriy; Adlhoch, Cornelia; Segaloff, Hannah; Robesyn, Emmanuel; Penttinen, Pasi; Olsen, Sonja J.; Redlberger-Fritz, Monika; Popow-Kraupp, Therese; Hasibra, Iris; Simaku, Artan; Thomas, Isabelle; Barbezange, Cyril; Dedeić-Ljubović, Amela; Rodić-Vukmir, Nina; Korsun, Neli; Angenova, Svetla; Draženović, Vladimir; Koliou, Maria; Pieridou, Despo; Havlickova, Martina; Nagy, Alexander; Trebbien, Ramona; Galiano, Monica; Thompson, Catherine; Ikonen, Niina; Haveri, Anu; Behillil, Sylvie; Enouf, Vincent; Valette, Martine; Lina, Bruno; Gavashelidze, Mari; Machablishvili, Ann; Gioula, Georgia; Exindari, Maria; Kossyvakis, Athanasios; Mentis, Andreas; Dürrwald, Ralf; Zsuzsanna, Molnar; Monika, Rozsa; Löve, Arthur; Erna, Gudrun; Dunford, Linda; Fitzpatrick, Sarah; Castrucci, Maria Rita; Puzelli, Simona; Sagymbay, Altynay; Nussupbayeva, Gaukhar; Zamjatina, Natalija; Pakarna, Gatis; Griskevičius, Algirdas; Skrickiene, Asta; Fournier, Guillaume; Mossong, Joel; Melillo, Jackie; Zahra, Graziella; Meijer, Adam; Fouchier, Ron; McCaughey, Conall; O'Doherty, Mark; Bragstad, Karoline; Guiomar, Raquel; Pechirra, Pedro; Apostol, Mariana; Alina, Druc; Lazar, Mihaela; Maria, Cherciu Carmen; Komissarov, Andrey; Burtseva, Elena; Gunson, Rory N.; Shepherd, Samantha; Tichá, Elena; Staronova, Edita; Prosenc, Katarina; Berginc, Nataša; Pozo, Francisco; Casas, Inmaculada; Brytting, Mia; Wiman, Åsa; Gonçalves, Ana Rita; Demchyshyna, Iryna; Mironenko, Alla; Moore, Catherine; Cottrell, Simon; European Region influenza surveillance networkBackground: The 2018/2019 influenza season in the WHO European Region was dominated by influenza A (H1N1)pdm09 and (H3N2) viruses, with very few influenza B viruses detected. Methods: Countries in the European Region reported virus characterization data to The European Surveillance System for weeks 40/2018 to 20/2019. These virus antigenic and genetic characterization and haemagglutinin (HA) sequence data were analysed to describe and assess circulating viruses relative to the 2018/2019 vaccine virus components for the northern hemisphere. Results: Thirty countries reported 4776 viruses characterized genetically and 3311 viruses antigenically. All genetically characterized A(H1N1)pdm09 viruses fell in subclade 6B.1A, of which 90% carried the amino acid substitution S183P in the HA gene. Antigenic data indicated that circulating A(H1N1)pdm09 viruses were similar to the 2018/2019 vaccine virus. Genetic data showed that A(H3N2) viruses mostly fell in clade 3C.2a (75%) and 90% of which were subclade 3C.2a1b. A lower proportion fell in clade 3C.3a (23%) and were antigenically distinct from the vaccine virus. All B/Victoria viruses belonged to clade 1A; 30% carried a double amino acid deletion in HA and were genetically and antigenically similar to the vaccine virus component, while 55% carried a triple amino acid deletion or no deletion in HA; these were antigenically distinct from each other and from the vaccine component. All B/Yamagata viruses belonged to clade 3 and were antigenically similar to the virus component in the quadrivalent vaccine for 2018/2019. Conclusions: A simultaneous circulation of genetically and antigenically diverse A(H3N2) and B/Victoria viruses was observed and represented a challenge to vaccine strain selection.
- Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data SetsPublication . Brinkmann, Annika; Andrusch, Andreas; Belka, Ariane; Wylezich, Claudia; Höper, Dirk; Pohlmann, Anne; Nordahl Petersen, Thomas; Lucas, Pierrick; Blanchard, Yannick; Papa, Anna; Melidou, Angeliki; Oude Munnink, Bas B.; Matthijnssens, Jelle; Deboutte, Ward; Ellis, Richard J.; Hansmann, Florian; Baumgärtner, Wolfgang; van der Vries, Erhard; Osterhaus, Albert; Camma, Cesare; Mangone, Iolanda; Lorusso, Alessio; Marcacci, Maurilia; Nunes, Alexandra; Pinto, Miguel; Borges, Vítor; Kroneman, Annelies; Schmitz, Dennis; Corman, Victor Max; Drosten, Christian; Jones, Terry C.; Hendriksen, Rene S.; Aarestrup, Frank M.; Koopmans, Marion; Beer, Martin; Nitsche, AndreasQuality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.