42 results on '"Piñana, Maria"'
Search Results
2. Molecular characterization and clinical impact of human bocavirus at a tertiary hospital in Barcelona (Catalonia, Spain) during the 2014–2017 seasons
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Piñana, Maria, Vila, Jorgina, Andrés, Cristina, Saura, Jordi, González-Sánchez, Alejandra, Creus-Costa, Anna, Saubi, Narcís, Esperalba, Juliana, Rando, Ariadna, Iglesias-Cabezas, Manuel Jesús, Quer, Josep, Soriano-Arandes, Antoni, Soler-Palacín, Pere, Pumarola, Tomàs, and Antón, Andrés
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- 2023
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3. The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain
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Piñana, Maria, González-Sánchez, Alejandra, Andrés, Cristina, Abanto, Michel, Vila, Jorgina, Esperalba, Juliana, Moral, Noelia, Espartosa, Elena, Saubi, Narcís, Creus, Anna, Codina, Maria Gema, Folgueira, Dolores, Martinez-Urtaza, Jaime, Pumarola, Tomàs, and Antón, Andrés
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- 2023
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4. Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing
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Andrés, Cristina, del Cuerpo, Margarita, Rabella, Núria, Piñana, Maria, Iglesias-Cabezas, Manuel Jesús, González-Sánchez, Alejandra, Esperalba, Juliana, Rando, Ariadna, Martín, Maria Carmen, Fuentes, Francisco, Rubio, Susana, Saubi, Narcís, Pumarola, Tomàs, and Antón, Andrés
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- 2023
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5. Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion
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Andrés, Cristina, González-Sánchez, Alejandra, Jiménez, Moraima, Márquez-Algaba, Ester, Piñana, Maria, Fernández-Naval, Candela, Esperalba, Juliana, Saubi, Narcís, Quer, Josep, Rando-Segura, Ariadna, Miarons, Marta, Codina, Maria Gema, Ruiz-Camps, Isabel, Pumarola, Tomàs, Abrisqueta, Pau, and Antón, Andrés
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- 2023
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6. Clinical presentation and virological assessment of confirmed human monkeypox virus cases in Spain: a prospective observational cohort study
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Tarín-Vicente, Eloy José, Alemany, Andrea, Agud-Dios, Manuel, Ubals, Maria, Suñer, Clara, Antón, Andrés, Arando, Maider, Arroyo-Andrés, Jorge, Calderón-Lozano, Lorena, Casañ, Cristina, Cabrera, José Miguel, Coll, Pep, Descalzo, Vicente, Folgueira, María Dolores, García-Pérez, Jorge N, Gil-Cruz, Elena, González-Rodríguez, Borja, Gutiérrez-Collar, Christian, Hernández-Rodríguez, Águeda, López-Roa, Paula, de los Ángeles Meléndez, María, Montero-Menárguez, Julia, Muñoz-Gallego, Irene, Palencia-Pérez, Sara Isabel, Paredes, Roger, Pérez-Rivilla, Alfredo, Piñana, María, Prat, Nuria, Ramirez, Aída, Rivero, Ángel, Rubio-Muñiz, Carmen Alejandra, Vall, Martí, Acosta-Velásquez, Kevin Stephen, Wang, An, Galván-Casas, Cristina, Marks, Michael, Ortiz-Romero, Pablo L, and Mitjà, Oriol
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- 2022
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7. The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants
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Campos, Carolina, Colomer-Castell, Sergi, Garcia-Cehic, Damir, Gregori, Josep, Andrés, Cristina, Piñana, Maria, González-Sánchez, Alejandra, Borràs, Blanca, Parés-Badell, Oleguer, Adombi, Caroline Melanie, Ibañez-Lligoña, Marta, Esperalba, Juliana, Codina, Maria Gema, Rando-Segura, Ariadna, Saubí, Narcis, Esteban, Juan Ignacio, Rodriguez-Frías, Francisco, Pumarola, Tomàs, Antón, Andrés, and Quer, Josep
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- 2022
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8. Insights into immune evasion of human metapneumovirus: novel 180- and 111-nucleotide duplications within viral G gene throughout 2014-2017 seasons in Barcelona, Spain
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Piñana, Maria, Vila, Jorgina, Maldonado, Carolina, Galano-Frutos, Juan José, Valls, Maria, Sancho, Javier, Nuvials, Francesc Xavier, Andrés, Cristina, Martín-Gómez, María Teresa, Esperalba, Juliana, Codina, Maria Gema, Pumarola, Tomàs, and Antón, Andrés
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- 2020
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9. Novel tp0548 Sequence-Type of Treponema pallidum Identified in Barcelona, Spain
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Fernández-Naval, Candela, Arando, Maider, Espasa, Mateu, Antón, Andrés, Gimferrer, Laura, Piñana, Maria, Fernández-Huerta, Miguel, González-López, Juan José, Serra-Pladevall, Judit, Pumarola, Tomàs, Vall-Mayans, Martí, and Esperalba, Juliana
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- 2019
10. Surveillance of enteroviruses from paediatric patients attended at a tertiary hospital in Catalonia from 2014 to 2017
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Andrés, Cristina, Vila, Jorgina, Gimferrer, Laura, Piñana, Maria, Esperalba, Juliana, Codina, Maria Gema, Barnés, Meritxell, Martín, Maria Carmen, Fuentes, Francisco, Rubio, Susana, Alcubilla, Pilar, Rodrigo, Carlos, Pumarola, Tomàs, and Antón, Andrés
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- 2019
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11. Evaluation of Seegene Allplex Respiratory Panel 1 kit for the detection of influenza virus and human respiratory syncytial virus
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Gimferrer, Laura, Andrés, Cristina, Rando, Ariadna, Piñana, Maria, Codina, Maria Gema, Martin, Maria del Carmen, Fuentes, Francisco, Rubio, Susana, Alcubilla, Pilar, Pumarola, Tomàs, and Antón, Andrés
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- 2018
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12. In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications.
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Gregori, Josep, Colomer-Castell, Sergi, Ibañez-Lligoña, Marta, Garcia-Cehic, Damir, Campos, Carolina, Buti, Maria, Riveiro-Barciela, Mar, Andrés, Cristina, Piñana, Maria, González-Sánchez, Alejandra, Rodriguez-Frias, Francisco, Cortese, Maria Francesca, Tabernero, David, Rando-Segura, Ariadna, Pumarola, Tomás, Esteban, Juan Ignacio, Antón, Andrés, and Quer, Josep
- Subjects
MUTAGENS ,HEPATITIS E ,NUCLEOTIDE sequencing ,ENTEROVIRUSES ,RESPIRATORY syncytial virus ,PHENOTYPES ,HAPLOTYPES - Abstract
The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial role beyond single point mutations. Quasispecies structured in a flat-like manner (referred to as flat-like) are considered to possess high average fitness, occupy a significant fraction of the functional genetic space of the virus, and exhibit a high capacity to evade specific or mutagenic treatments. In this paper, we studied HEV and HCV samples using high-depth next-generation sequencing (NGS), with indices scoring the different properties describing flat-like quasispecies. The significance of these indices was demonstrated by comparing the values obtained from these samples with those from acute infections caused by respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). Our results revealed that flat-like quasispecies in HEV and HCV chronic infections without RAS are characterized by numerous low-frequency haplotypes with no dominant one. Surprisingly, these low-frequency haplotypes (at the nucleotide level) exhibited a high level of synonymity, resulting in much lower diversity at the phenotypic level. Currently, clinical approaches for managing flat-like quasispecies are lacking. Here, we propose methods to identifying flat-like quasispecies, which represents an essential initial step towards exploring alternative treatment protocols for viruses resistant to conventional therapies. [ABSTRACT FROM AUTHOR]
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- 2024
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13. Unraveling the effects of the COVID‐19 pandemic on the hospital burden of respiratory syncytial virus
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Perramon‐Malavez, Aida, primary, López de Rioja, Victor, additional, Creus‐Costa, Anna, additional, Andrés, Cristina, additional, Montañola‐Sales, Cristina, additional, Vila, Jorgina, additional, Lera, Esther, additional, Antón, Andrés, additional, Worner, Núria, additional, Balcells, Joan, additional, Piñana, Maria, additional, Soler‐Palacin, Pere, additional, Prats, Clara, additional, and Soriano‐Arandes, Antoni, additional
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- 2023
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14. Unraveling the effects of the COVID-19 pandemic on the hospital burden of respiratory syncytial virus
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Universitat Politècnica de Catalunya. Doctorat en Física Computacional i Aplicada, Universitat Politècnica de Catalunya. Departament de Física, Universitat Politècnica de Catalunya. BIOCOM-SC - Biologia Computacional i Sistemes Complexos, Perramon Malavez, Aida, López de Rioja, Víctor, Montañola Sales, Cristina, Vila, Jorgina, Antón, Andrés, Piñana, Maria, Soler-Palacín, Pere, Prats Soler, Clara, Soriano-Arandes, Antoni, Creus Costa, Anna, Andrés Vergés, Cristina, Lera Carballo, Esther, Wörner Tomasa, Núria, Balcells Ramírez, Joan, Universitat Politècnica de Catalunya. Doctorat en Física Computacional i Aplicada, Universitat Politècnica de Catalunya. Departament de Física, Universitat Politècnica de Catalunya. BIOCOM-SC - Biologia Computacional i Sistemes Complexos, Perramon Malavez, Aida, López de Rioja, Víctor, Montañola Sales, Cristina, Vila, Jorgina, Antón, Andrés, Piñana, Maria, Soler-Palacín, Pere, Prats Soler, Clara, Soriano-Arandes, Antoni, Creus Costa, Anna, Andrés Vergés, Cristina, Lera Carballo, Esther, Wörner Tomasa, Núria, and Balcells Ramírez, Joan
- Abstract
The research leading to these results received funding from Fundació La Marató TV3 under Grant Agreement No 202134‐30‐31., Peer Reviewed, Objectius de Desenvolupament Sostenible::3 - Salut i Benestar, Postprint (published version)
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- 2023
15. Suspected case of monkeypox reinfection versus reactivation in a immunocompetent patient, Barcelona, 2022
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Álvarez-López, Patricia, primary, Borras-Bermejo, Blanca, additional, López Pérez, Luis, additional, Antón, Andrés, additional, Piñana, Maria, additional, García-Pérez, Jorge, additional, Descalzo, Vicente, additional, Monforte, Arnau, additional, Martínez-Gómez, Xavier, additional, Falcó, Vicenç, additional, and Arando, Maider, additional
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- 2023
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16. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses
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Ibañez-Lligoña, Marta, primary, Colomer-Castell, Sergi, additional, González-Sánchez, Alejandra, additional, Gregori, Josep, additional, Campos, Carolina, additional, Garcia-Cehic, Damir, additional, Andrés, Cristina, additional, Piñana, Maria, additional, Pumarola, Tomàs, additional, Rodríguez-Frias, Francisco, additional, Antón, Andrés, additional, and Quer, Josep, additional
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- 2023
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17. The burden of non‐SARS‐CoV2 viral lower respiratory tract infections in hospitalized children in Barcelona (Spain): A long‐term, clinical, epidemiologic and economic study
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Vila, Jorgina, primary, Lera, Esther, additional, Andrés, Cristina, additional, Piñana, Maria, additional, Rello‐Saltor, Victoria, additional, Tobeña‐Rué, Marc, additional, Balcells, Joan, additional, Benítez‐Díaz, Zaira, additional, Aller, Marta Beatriz, additional, Muñoz, Rosario, additional, Vázquez, Ana, additional, Rodrigo, Carlos, additional, Soler‐Palacín, Pere, additional, and Antón, Andrés, additional
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- 2022
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18. Molecular characterization and clinical impact of human bocavirus at a tertiary hospital in Barcelona (Catalonia, Spain) during the 2014–2017 seasons
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Piñana, Maria, primary, Vila, Jorgina, additional, Andrés, Cristina, additional, Saura, Jordi, additional, González-Sánchez, Alejandra, additional, Creus-Costa, Anna, additional, Saubi, Narcís, additional, Esperalba, Juliana, additional, Rando, Ariadna, additional, Iglesias-Cabezas, Manuel Jesús, additional, Quer, Josep, additional, Soriano-Arandes, Antoni, additional, Soler-Palacín, Pere, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional
- Published
- 2022
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19. The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants
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Campos, Carolina, primary, Colomer-Castell, Sergi, additional, Garcia-Cehic, Damir, additional, Gregori, Josep, additional, Andrés, Cristina, additional, Piñana, Maria, additional, González-Sánchez, Alejandra, additional, Borràs, Blanca, additional, Parés-Badell, Oleguer, additional, Adombi, Caroline Melanie, additional, Ibañez, Marta, additional, Esperalba, Juliana, additional, Codina, Maria Gema, additional, Rando, Ariadna, additional, Saubí, Narcis, additional, Esteban, Juan Ignacio, additional, Rodriguez-Frías, Francisco, additional, Pumarola, Tomàs, additional, Antón, Andrés, additional, and Quer, Josep, additional
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- 2022
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20. Enterovirus D68 in Hospitalized Children, Barcelona, Spain, 2014–2021
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Andrés, Cristina, primary, Vila, Jorgina, additional, Creus-Costa, Anna, additional, Piñana, Maria, additional, González-Sánchez, Alejandra, additional, Esperalba, Juliana, additional, Codina, Maria Gema, additional, Castillo, Carla, additional, Martín, Maria Carmen, additional, Fuentes, Francisco, additional, Rubio, Susana, additional, García-Comuñas, Karen, additional, Vásquez-Mercado, Rodrigo, additional, Saubi, Narcís, additional, Rodrigo, Carlos, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional
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- 2022
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21. Next-Generation Sequencing for Confronting Virus Pandemics
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Quer, Josep, Colomer-Castell, Sergi, Campos, Carolina, Andrés, Cristina, Piñana, Maria, Cortese, Maria Francesca, González-Sánchez, Alejandra, Garcia-Cehic, Damir, Ibáñez, Marta, Pumarola Suñé, Tomàs, Rodriguez-Frias, Francisco, Antón, Andrés, Tabernero, David, Quer, Josep, Colomer-Castell, Sergi, Campos, Carolina, Andrés, Cristina, Piñana, Maria, Cortese, Maria Francesca, González-Sánchez, Alejandra, Garcia-Cehic, Damir, Ibáñez, Marta, Pumarola Suñé, Tomàs, Rodriguez-Frias, Francisco, Antón, Andrés, and Tabernero, David
- Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission
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- 2022
22. Characteristics of 24 SARS-CoV-2-Sequenced Reinfection Cases in a Tertiary Hospital in Spain
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Borras-Bermejo, Blanca, primary, Piñana, Maria, additional, Andrés, Cristina, additional, Zules, Ricardo, additional, González-Sánchez, Alejandra, additional, Esperalba, Juliana, additional, Parés-Badell, Oleguer, additional, García-Cehic, Damir, additional, Rando, Ariadna, additional, Campos, Carolina, additional, Codina, Maria Gema, additional, Martín, Maria Carmen, additional, Castillo, Carla, additional, García-Comuñas, Karen, additional, Vásquez-Mercado, Rodrigo, additional, Martins-Martins, Reginald, additional, Colomer-Castell, Sergi, additional, Pumarola, Tomàs, additional, Campins, Magda, additional, Quer, Josep, additional, and Antón, Andrés, additional
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- 2022
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23. Viral populations of SARS-CoV-2 in upper respiratory tract, placenta, amniotic fluid and umbilical cord blood support viral replication in placenta
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Piñana, Maria, Abril, Josep F., Andrés, Cristina, Silgado, Aroa, Navarro, Alexandra, Suy, Anna, Sulleiro, Elena, Pumarola, Tomàs, Quer, Josep, and Antón, Andrés
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- 2021
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24. Next-Generation Sequencing for Confronting Virus Pandemics
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Quer, Josep, primary, Colomer-Castell, Sergi, additional, Campos, Carolina, additional, Andrés, Cristina, additional, Piñana, Maria, additional, Cortese, Maria Francesca, additional, González-Sánchez, Alejandra, additional, Garcia-Cehic, Damir, additional, Ibáñez, Marta, additional, Pumarola, Tomàs, additional, Rodríguez-Frías, Francisco, additional, Antón, Andrés, additional, and Tabernero, David, additional
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- 2022
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25. A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)
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Andrés, Cristina, primary, Piñana, Maria, additional, Borràs-Bermejo, Blanca, additional, González-Sánchez, Alejandra, additional, García-Cehic, Damir, additional, Esperalba, Juliana, additional, Rando, Ariadna, additional, Zules-Oña, Ricardo-Gabriel, additional, Campos, Carolina, additional, Codina, Maria Gema, additional, Blanco-Grau, Albert, additional, Colomer-Castell, Sergi, additional, Martín, Maria Carmen, additional, Castillo, Carla, additional, García-Comuñas, Karen, additional, Vásquez-Mercado, Rodrigo, additional, Martins-Martins, Reginaldo, additional, Saubi, Narcís, additional, Campins-Martí, Magda, additional, Pumarola, Tomàs, additional, Quer, Josep, additional, and Antón, Andrés, additional
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- 2022
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26. Clinical evaluation of the Procleix SARS-CoV-2 assay, a sensitive, high-throughput test that runs on an automated system
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Sauleda, Silvia, primary, Palacios, Lourdes, additional, Brès, Vanessa, additional, Piñana, Maria, additional, Alonso-Hernandez, Lorena, additional, Bes, Marta, additional, Piron, Maria, additional, Entrena, Edurne, additional, Minguez-Micolau, Antonio M., additional, Marimón, Jose Maria, additional, Gurrola, Adrian, additional, Soria, Gloria, additional, Puig, Lluís, additional, Antón, Andrés, additional, Pumarola, Tomás, additional, and Linnen, Jeffrey M., additional
- Published
- 2022
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27. The burden of non‐SARS‐CoV2 viral lower respiratory tract infections in hospitalized children in Barcelona (Spain): A long‐term, clinical, epidemiologic and economic study.
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Vila, Jorgina, Lera, Esther, Andrés, Cristina, Piñana, Maria, Rello‐Saltor, Victoria, Tobeña‐Rué, Marc, Balcells, Joan, Benítez‐Díaz, Zaira, Aller, Marta Beatriz, Muñoz, Rosario, Vázquez, Ana, Rodrigo, Carlos, Soler‐Palacín, Pere, and Antón, Andrés
- Subjects
RESPIRATORY infections ,HOSPITAL care of children ,PARAINFLUENZA viruses ,PEDIATRIC intensive care ,RESPIRATORY syncytial virus ,INTENSIVE care units ,PLANT viruses - Abstract
Background: Viral lower respiratory tract infections (LRTI) are the leading cause of hospitalization in children. In Catalonia (Spain), information is scarce about the burden of viral LRTIs in paediatric hospitalizations. The aim of this study is to describe epidemiological, clinical, virological and economic features of paediatric hospitalizations due to viral LRTI. Methods: From October 2012 to December 2020, children aged <16 years admitted to a tertiary paediatric hospital in Catalonia (Spain) with confirmed viral LRTI were included in the study. Virus seasonality, prevalence, age and sex distribution, clinical characteristics, hospital costs and bed occupancy rates were determined. Results: A total of 3,325 children were included (57.17% male, 9.44% with comorbidities) accounting for 4056 hospitalizations (32.47% ≤ 12 months): 53.87% with wheezing/asthma, 37.85% with bronchiolitis and 8.28% with pneumonia. The most common virus was respiratory syncytial virus (RSV) (52.59%). Influenza A was associated with pneumonia (odds ratio [OR] 7.75) and caused longer hospitalizations (7 ± 31.58 days), while RSV was associated with bronchiolitis (OR 6.62) and was the most frequent reason for admission to the paediatric intensive care unit (PICU) (11.23%) and for respiratory support (78.76%). Male sex, age ≤12 months, chronic conditions and bronchiolitis significantly increased the odds of PICU admission. From October to May, viral LRTIs accounted for 12.36% of overall hospital bed days. The total hospitalization cost during the study period was €16,603,415. Conclusions: Viral LRTIs are an important cause of morbidity, hospitalization and PICU admission in children. The clinical burden is associated with significant bed occupancy and health‐care costs, especially during seasonal periods. [ABSTRACT FROM AUTHOR]
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- 2023
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28. Severe SARS-CoV-2 placenta infection can impact neonatal outcome in the absence of vertical transmission
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Cribiù, Fulvia Milena, primary, Erra, Roberta, additional, Pugni, Lorenza, additional, Rubio-Perez, Carlota, additional, Alonso, Lidia, additional, Simonetti, Sara, additional, Croci, Giorgio Alberto, additional, Serna, Garazi, additional, Ronchi, Andrea, additional, Pietrasanta, Carlo, additional, Lunghi, Giovanna, additional, Fagnani, Anna Maria, additional, Piñana, Maria, additional, Matter, Matthias, additional, Tzankov, Alexandar, additional, Terracciano, Luigi, additional, Anton, Andres, additional, Ferrazzi, Enrico, additional, Ferrero, Stefano, additional, Iurlaro, Enrico, additional, Seoane, Joan, additional, and Nuciforo, Paolo, additional
- Published
- 2021
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29. Host-dependent editing of SARS-CoV-2 in COVID-19 patients
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Gregori, Josep, primary, Cortese, Maria Francesca, additional, Piñana, Maria, additional, Campos, Carolina, additional, Garcia-Cehic, Damir, additional, Andrés, Cristina, additional, Abril, Josep Francesc, additional, Codina, Maria Gema, additional, Rando, Ariadna, additional, Esperalba, Juliana, additional, Sulleiro, Elena, additional, Joseph, Joan, additional, Saubí, Narcís, additional, Colomer-Castell, Sergi, additional, Martin, Mari Carmen, additional, Castillo, Carla, additional, Esteban, Juan Ignacio, additional, Pumarola, Tomas, additional, Rodriguez-Frias, Francisco, additional, Antón, Andrés, additional, and Quer, Josep, additional
- Published
- 2021
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30. The high genetic similarity between rhinoviruses and enteroviruses remains as a pitfall for molecular diagnostic tools: A three-year overview
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Andrés, Cristina, Piñana, Maria, Vila, Jorgina, Esperalba, Juliana, Trejo-Zahínos, Jesús, Codina, Maria Gema, Martín, Maria Carmen, Fuentes, Francisco, Rubio, Susana, Pumarola, Tomàs, and Antón, Andrés
- Published
- 2019
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31. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
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Andres, Cristina, primary, Garcia-Cehic, Damir, additional, Gregori, Josep, additional, Piñana, Maria, additional, Rodriguez-Frias, Francisco, additional, Guerrero-Murillo, Mercedes, additional, Esperalba, Juliana, additional, Rando, Ariadna, additional, Goterris, Lidia, additional, Codina, Maria Gema, additional, Quer, Susanna, additional, Martín, Maria Carmen, additional, Campins, Magda, additional, Ferrer, Ricard, additional, Almirante, Benito, additional, Esteban, Juan Ignacio, additional, Pumarola, Tomás, additional, Antón, Andrés, additional, and Quer, Josep, additional
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- 2020
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32. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
- Author
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Andrés, Cristina, Garcia-Cehic, D., Gregori, Josep, Piñana, Maria, Rodriguez-Frias, Francisco, Guerrero-Murillo, Mercedes, Esperalba, Juliana, Rando, Adriana, Goterris, Lidia, Codina, Gema, Quer, Susanna, Martín, Maria Carmen, Campins Martí, Magda, Ferrer, Ricard, Almirante, Benito, Esteban Mur, Juan Ignacio, Pumarola, Tomás, Antón, Andrés, Quer, Josep, Andrés, Cristina, Garcia-Cehic, D., Gregori, Josep, Piñana, Maria, Rodriguez-Frias, Francisco, Guerrero-Murillo, Mercedes, Esperalba, Juliana, Rando, Adriana, Goterris, Lidia, Codina, Gema, Quer, Susanna, Martín, Maria Carmen, Campins Martí, Magda, Ferrer, Ricard, Almirante, Benito, Esteban Mur, Juan Ignacio, Pumarola, Tomás, Antón, Andrés, and Quer, Josep
- Abstract
The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.
- Published
- 2020
33. Molecular influenza surveillance at a tertiary university hospital during four consecutive seasons (2012–2016) in Catalonia, Spain
- Author
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Andrés, Cristina, primary, Peremiquel-Trillas, Paula, additional, Gimferrer, Laura, additional, Piñana, Maria, additional, Codina, Maria Gema, additional, Rodrigo-Pendás, José Ángel, additional, Campins-Martí, Magda, additional, Carmen Martín, María, additional, Fuentes, Francisco, additional, Rubio, Susana, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional
- Published
- 2019
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34. Molecular influenza surveillance at a tertiary university hospital during four consecutive seasons (2012-2016) in Catalonia, Spain
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Andrés, Cristina, Peremiquel-Trillas, Paula, Gimferrer Arriaga, Laura, Piñana, Maria, Codina, Maria Gema, Rodrigo-Pendás, José Ángel, Campins-Martí, Magda, Carmen Martín, María, Fuentes, Francisco, Rubio, Susana, Pumarola Suñé, Tomàs, Antón, Andrés, Andrés, Cristina, Peremiquel-Trillas, Paula, Gimferrer Arriaga, Laura, Piñana, Maria, Codina, Maria Gema, Rodrigo-Pendás, José Ángel, Campins-Martí, Magda, Carmen Martín, María, Fuentes, Francisco, Rubio, Susana, Pumarola Suñé, Tomàs, and Antón, Andrés
- Abstract
Influenza viruses (FLUV) are continuously evolving, which explain the occurrence of seasonal influenza epidemics and the need to review the vaccine strain composition annually. The aim is to describe the genetic diversity and clinical outcomes of FLUV detected at a tertiary university hospital in Barcelona (Spain) during the 2012-2016 seasons. The detection of FLUV from patients attended at the Emergency Department or admitted to the hospital was performed by either immunofluorescence or PCR-based assays. A specific real-time one-step multiplex RT-PCR was performed for influenza A (FLUAV) subtyping. The complete coding haemagglutinin domain 1 (HA1) and neuraminidase (NA) (2015-2016) protein sequences from a representative sampling were molecular characterised. A total 1774 (66.1%) FLUAV and 910 (33.9%) influenza B (FLUBV) cases were laboratory-confirmed. The hospitalisation rate was different between seasons, being the highest (81.4%) during the 2014-2015 season. FLUV were genetically close to vaccine strains except to the 2014-2015, in which most characterised A(H3N2) viruses belonged to a genetic group different from the vaccine strain. During the 2015-2016 season, B/Victoria-like viruses were the most predominant, but this component was not included in the trivalent vaccine used. Mutations D222G or D222N in HA1-domain were found in 3 A(H1N1)pdm09 strains from ICU-admitted cases. Three A(H1N1)pdm09 strains carried the NA H275Y (2) and S247N (1) mutations, respectively related to resistance or decreased susceptibility to oseltamivir. The circulation of drifted A(H3N2) strains during the 2014-2015 season was related to the high hospitalisation rate due to the mismatch with the vaccine strains. The predominance of a FLUBV lineage not included in the trivalent influenza vaccine during the 2015-2016 season highlights the need to use a tetravalent influenza vaccine. Virological surveillance of viral variants carrying protein changes that alter tropism and susceptibility
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- 2019
35. Virological surveillance of human respiratory syncytial virus A and B at a tertiary hospital in Catalonia (Spain) during five consecutive seasons (2013–2018)
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Gimferrer, Laura, primary, Vila, Jorgina, additional, Piñana, Maria, additional, Andrés, Cristina, additional, Rodrigo-Pendás, José A, additional, Peremiquel-Trillas, Paula, additional, Codina, María G, additional, C Martín, María del, additional, Esperalba, Juliana, additional, Fuentes, Francisco, additional, Rubio, Susana, additional, Campins-Martí, Magda, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional
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- 2019
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36. Genetic diversity of rhinoviruses detected at a tertiary hospital in Catalonia (Spain) during the 2014–2017 seasons
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Andrés, Cristina, primary, Peremiquel-Trillas, Paula, additional, Gimferrer, Laura, additional, Isern, Anna, additional, Piñana, Maria, additional, Rodrigo-Pendás, José Ángel, additional, Codina, Maria Gema, additional, Martín, María del Carmen, additional, Fuentes, Francisco, additional, Rubio, Susana, additional, Campins-Martí, Magda, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional
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- 2018
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37. Recombinant CV-A6 Strains Related to Hand-Foot-Mouth Disease and Herpangina at Primary Care Centers (Barcelona, Spain)
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Andrés, Cristina, Guasch, Eulàlia, Piñana, Maria, Fernandes, Paula, Gimferrer, Laura, Esso, Diego Van, Codina, Maria Gema, Esperalba, Juliana, Vila, Jorgina, Rodrigo, Carlos, Martín, Maria Carmen, Fuentes, Francisco, Rubio, Susana, Pumarola, Tomàs, and Antón, Andrés
- Abstract
Aim:To describe the genetic diversity of enteroviruses (EV) causing hand, foot and mouth disease (HFMD) and herpangina, especially of coxsackievirus (CV)-A6, from patients attended at pediatric primary care centers during the 2017–2018 season. Methods:Phylogenetic analysis of partial VP1 region was performed for genetic characterization. The complete VP1 and 3Dpol proteins were sequenced for lineage determination and detection of recombination events. Results:An 80% of samples were EV laboratory-confirmed. CV-A6 was the most detected (70%) and associated with atypical HFMD (78%). The comparison of VP1 and 3Dpol phylogenies showed evidence of recombination in three strains, in which two shifted to CV-A16 3Dpol. Conclusion:The study provides recent information regarding the nonrecombinant and recombinant EVs related to HFMD at primary care centers.
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- 2019
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38. Genetic variability of human metapneumovirus A strain circulating in Catalonia during the 2014–2015 and 2015–2016 seasons: A 180-nucleotide G gene duplication reported
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Piñana, María, Vila, Jorgina, Gimferrer, Laura, Valls, María, Andrés, Cristina, Ramón, Javier, Codina, María Gema, Martín, María del Carmen, Fuentes, Francisco, Saiz, Rosario, Alcubilla, Pilar, Rodrigo, Carlos, Pumarola, Tomàs, and Antón, Andrés
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- 2016
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39. Molecular epidemiology of circulating human coronaviruses in children at a tertiary hospital in Catalonia (Spain) from 2014 to 2016
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Ramón, Javier, Vila, Jorgina, Andrés, Cristina, Castillo, Cintia, Gimferrer, Laura, Piñana, María, Codina, María Gema, Fuentes, Francisco, Martín, María del Carmen, Saiz, Rosario, Alcubilla, Pilar, Rodrigo, Carlos, Pumarola, Tomàs, and Antón, Andrés
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- 2016
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40. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
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Alm E., Broberg E.K., Connor T., Hodcroft E.B., Komissarov A.B., Maurer-Stroh S., Melidou A., Neher R.A., O'Toole A., Pereyaslov D., Beerenwinkel N., Posada-Cespedes S., Jablonski K.P., Ferreira P.F., Topolsky I., Avsic-Zupanc T., Korva M., Poljak M., Zakotnik S., Zorec T.M., Bragstad K., Hungnes O., Stene-Johansen K., Reusken C., Meijer A., Vennema H., Ruiz-Roldan L., Bracho M.A., Garcia-Gonzalez N., Chiner-Oms A., Cancino-Munoz I., Comas I., Goig G.A., Torres-Puente M., Lopez M.G., Martinez-Priego L., D'Auria G., Ruiz-Hueso P., Ferrus-Abad L., de Marco G., Galan-Vendrell I., Carbo-Ramirez S., Ruiz-Rodriguez P., Coscolla M., Polackova K., Kramna L., Cinek O., Richter J., Krashias G., Tryfonos C., Bashiardes S., Koptides D., Christodoulou C., Bartolini B., Gruber C.E., Di Caro A., Castilletti C., Stefani F., Rimoldi S.G., Romeri F., Salerno F., Polesello S., Nagy A., Jirincova H., Vecerova J., Novakova L., Cordey S., Murtskhvaladze M., Kotaria N., Schar T., Beisel C., Vugrek O., Rokic F., Trgovec-Greif L., Jurak I., Rukavina T., Sucic N., Schonning K., Karst S.M., Kirkegaard R.H., Michaelsen T.Y., Sorensen E.A., Knutson S., Brandt J., Le-Quy V., Sorensen T., Petersen C., Pedersen M.S., Larsen S.L., Skov M.N., Rasmussen M., Fonager J., Fomsgaard A., Maksyutov R.A., Gavrilova E.V., Pyankov O.V., Bodnev S.A., Tregubchak T.V., Shvalov A.N., Antonets D.V., Resende P.C., Goya S., Perrin A., Lee R.T., Yadahalli S., Han A.X., Russell C.A., Schmutz S., Zaheri M., Kufner V., Huber M., Trkola A., Antwerpen M., Walter M.C., van der Werf S., Gambaro F., Behillil S., Enouf V., Donati F., Ustinova M., Rovite V., Klovins J., Savicka O., Wienecke-Baldacchino A.K., Ragimbeau C., Fournier G., Mossong J., Aberle S.W., Haukland M., Enkirch T., Advani A., Karlberg M.L., Lindsjo O.K., Broddesson S., Slavikova M., Lickova M., Klempa B., Staronova E., Ticha E., Szemes T., Rusnakova D., Stadler T., Quer J., Anton A., Andres C., Pinana M., Garcia-Cehic D., Pumarola T., Izopet J., Gioula G., Exindari M., Papa A., Chatzidimitriou D., Metallidis S., Pappa S., Macek M., Geryk J., Broz P., Briksi A., Hubacek P., Drevinek P., Zajac M., Kvapil P., Holub M., Kvapilova K., Novotny A., Kasny M., Klempt P., Vapalahti O., Smura T., Sironen T., Selhorst P., Anthony C., Arien K., Simon-Loriere E., Rabalski L., Bienkowska-Szewczyk K., Borges V., Isidro J., Gomes J.P., Guiomar R., Pechirra P., Costa I., Duarte S., Vieira L., Pyrc K., Zuckerman N.S., Turdikulova S., Abdullaev A., Dalimova D., Abdurakhimov A., Tagliabracci A., Alessandrini F., Melchionda F., Onofri V., Turchi C., Bagnarelli P., Menzo S., Caucci S., Di Sante L., Popa A., Genger J.-W., Agerer B., Lercher A., Endler L., Smyth M., Penz T., Schuster M., Senekowitsch M., Laine J., Bock C., Bergthaler A., Shevtsov A., Kalendar R., Ramanculov Y., Graf A., Muenchhoff M., Keppler O.T., Krebs S., Blum H., Marcello A., Licastro D., D'Agaro P., Laubscher F., Vidanovic D., Tesovic B., Volkening J., Clementi N., Mancini N., Rupnik M., Mahnic A., Walker A., Houwaart T., Wienemann T., Vasconcelos M.K., Strelow D., Jensen B.-E.O., Senff T., Hulse L., Adams O., Andree M., Hauka S., Feldt T., Keitel V., Kindgen-Milles D., Timm J., Pfeffer K., Dilthey A.T., Moore C., Ozdarendeli A., Pavel S.T.I., Yetiskin H., Aydin G., Holyavkin C., Uygut M.A., Cevik C., Shchetinin A., Gushchin V., Dinler-Doganay G., Doganay L., Kizilboga-Akgun T., Karacan I., Pancer K., Maes P., Marti-Carreras J., Wawina-Bokalanga T., Vanmechelen B., Thurmer A., Wedde M., Durrwald R., von Kleist M., Drechsel O., Wolff T., Fuchs S., Kmiecinski R., Michel J., Nitsche A., Casas I., Caballero M.I., Zaballos A., Jimenez P., Jimenez M., Fernandez S.M., Fernandez S.V., de la Plaza I.C., Fadeev A., Ivanova A., Sergeeva M., Stefanelli P., Estee Torok M., Hall G., da Silva Filipe A., Turtle L., Afifi S., McCluggage K., Beer R., Ledesma J., Maksimovic J., Spellman K., Hamilton W.L., Marchbank A., Southgate J.A., Underwood A., Taylor B., Yeats C., Abudahab K., Gemmell M.R., Eccles R., Lucaci A., Nelson C.A., Rainbow L., Whitehead M., Gregory R., Haldenby S., Paterson S., Hughes M.A., Curran M.D., Baker D., Tucker R., Green L.R., Feltwell T., Halstead F.D., Wyles M., Jahun A.S., Ahmad S.S.Y., Georgana I., Goodfellow I., Yakovleva A., Meredith L.W., Gavriil A., Awan A.R., Fisher C., Edgeworth J., Lynch J., Moore N., Williams R., Kidd S.P., Cortes N., Brunker K., McCrone J.T., Quick J., Duckworth N., Walsh S., Sloan T., Ludden C., George R.P., Eltringham G., Brown J.R., Aranday-Cortes E., Shepherd J.G., Hughes J., Li K.K., Williams T.C., Johnson N., Jesudason N., Mair D., Thomson E., Shah R., Parr Y.A., Carmichael S., Robertson D.L., Nomikou K., Broos A., Niebel M., Smollett K., Tong L., Miah S., Wittner A., Phillips N., Payne B., Dewar R., Holmes A., Bolt F., Price J.R., Mookerjee S., Sethi D.K., Potter W., Stanley R., Prakash R., Dervisevic S., Graham J.C., Nelson A., Smith D., Young G.R., Yew W.C., Todd J.A., Trebes A., Andersson M., Bull M., Watkins J., Birchley A., Gatica-Wilcox B., Gilbert L., Kumziene-Summerhayes S., Rey S., Chauhan A., Butcher E., Bicknell K., Elliott S., Glaysher S., Lackenby A., Bibby D., Platt S., Mohamed H., Machin N.W., Mbisa J.L., Evans J., Perry M., Pacchiarini N., Corden S., Adams A.G., Gaskin A., Coombs J., Graham L.J., Cottrell S., Morgan M., Gifford L., Kolyva A., Rudder S.J., Trotter A.J., Mather A.E., Aydin A., Page A.J., Kay G.L., de Oliveira Martins L., Yasir M., Alikhan N.-F., Thomson N.M., Gilroy R., Kingsley R.A., O'Grady J., Gutierrez A.V., Diaz M., Viet T.L., Tedim A.P., Adriaenssens E.M., Patrick Mcclure C., Sang F., Clark G., Howson-Wells H.C., Debebe J., Ball J., Chappell J., Khakh M., Carlile M., Loose M., Lister M.M., Holmes N., Tsoleridis T., Fleming V.M., Wright V., Smith W., Gallagher M.D., Parker M., Partridge D.G., Evans C., Baker P., Essex S., Liggett S., Keeley A.J., Bashton M., Rooke S., Dervisavic S., Meader E.J., Lopez C.E.B., Angyal A., Kristiansen M., Tutill H.J., Findlay J., Mestek-Boukhibar L., Forrest L., Dyal P., Williams R.J., Panchbhaya Y., Williams C.A., Roy S., Pandey S., Stockton J., Loman N.J., Poplawski R., Nicholls S., Rowe W.P.M., Khokhar F., Pinckert M.L., Hosmillo M., Chaudhry Y., Caller L.G., Davidson R.K., Griffith L., Rambaut A., Jackson B., Colquhoun R., Hill V., Nichols J., Asamaphan P., Darby A., Jackson K.A., Iturriza-Gomara M., Vamos E.E., Green A., Aanensen D., Bonsall D., Buck D., Macintyre-Cockett G., de Cesare M., Pybus O., Golubchik T., Scarlett G., Loveson K.F., Robson S.C., Beckett A., Lindsey B., Groves D.C., Parsons P.J., McHugh M.P., Barnes J.D., Manso C.F., Grammatopoulos D., Menger K.E., Harrison E., Gunson R., Peacock S.J., Gonzalez G., Carr M., Mihaela L., Popovici O., Brytting M., Bresner C., Fuller W., Workman T., Mentis A.F., Kossyvakis A., Karamitros T., Pogka V., Kalliaropoulos A., Horefti E., Kontou A., Martinez-Gonzalez B., Labropoulou V., Voulgari-Kokota A., Evangelidou M., Bizta P., Belimezi M., Lambrechts L., Doymaz M.Z., Yazici M.K., Cetin N.S., Karaaslan E., Kallio-Kokko H., Virtanen J., Suvanto M., Nguyen P.T., Ellonen P., Hannula S., Kangas H., Sreenu V.B., Burian K., Terhes G., Gombos K., Gyenesei A., Urban P., Herczeg R., Jakab F., Kemenesi G., Toth G.E., Somogyi B., Zana B., Zeghbib S., Kuczmog A., Foldes F., Lanszki Z., Madai M., Papp H., Pereszlenyi C.I., Babinszky G.C., Dudas G., Csoma E., Abou Tayoun A.N., Alsheikh-Ali A.A., Loney T., Nowotny N., Abdul-Wahab O., Gonzalez-Candelas F., Andersen M.H., Taylor S., MARTI CARRERAS, Joan, Vanmechelen, Bert, Wawina, Tony, Medical Microbiology and Infection Prevention, AII - Infectious diseases, WHO European Region Sequencing Lab, GISAID EpiCoV Grp, Erik, Alm, Eeva K, Broberg, Thomas, Connor, Emma B, Hodcroft, Andrey B, Komissarov, Sebastian, Maurer-Stroh, Angeliki, Melidou, Richard A, Neher, Áine, O’Toole, Dmitriy, Pereyaslov, WHO European Region sequencing laboratories and GISAID EpiCoV group (Niko Beerenwinkel, The, Posada-Céspedes, Susana, Philipp, Kim, Jablonski, Falé Ferreira, Pedro, Topolsky, Ivan, Avšičžupanc, Tatjana, Korva, Miša, Poljak, Mario, Zakotnik, Samo, Tomaž, Zorec, Mark, Bragstad, Karoline, Hungnes, Olav, Stene-Johansen, Kathrine, Reusken, Chantal, Meijer, Adam, Vennema, Harry, Ruiz-Roldán, Lidia, Alma Bracho, María, García-González, Neri, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, A Goig, Galo, Torres-Puente, Manuela, G López, Mariana, Martínez-Priego, Llúcia, D’Auria, Giuseppe, LoretoFerrús-Abad, de Marco, Griselda, Galan-Vendrell, Inmaculada, Carbó-Ramirez, Sandra, Ruíz-Hueso, Paula, Coscollá, Mireia, Polackova, Katerina, Kramna, Lenka, Cinek, Ondrej, Richter, Jan, Krashias, George, Tryfonos, Christina, Bashiardes, Stavro, Koptides, Dana, Christodoulou, Christina, Bartolini, Barbara, Em Gruber, Cesare, Di Caro, Antonino, Castilletti, Concetta, Stefani, Fabrizio, Giordana Rimoldi, Sara, Romeri, Francesca, Salerno, Franco, Polesello, Stefano, Nagy, Alexander, Jirincova, Helena, Vecerova, Jaromira, Novakova, Ludmila, Cordey, Samuel, Murtskhvaladze, Marine, Kotaria, Nato, Schär, Tobia, Beisel, Christian, Vugrek, Oliver, Rokić, Filip, Trgovecgreif, Lovro, Jurak, Igor, Rukavina, Tomislav, Sučić, Neven, Schønning, Kristian, M Karst, Søren, H Kirkegaard, Rasmu, Y Michaelsen, Thoma, Aa Sørensen, Emil, Knutson, Simon, Brandt, Jakob, Le-Quy, Vang, Sørensen, Trine, Petersen, Celine, Schou Pedersen, Martin, Løkkegaard Larsen, Sanne, Nielsine Skov, Marianne, Rasmussen, Morten, Fonager, Jannik, Fomsgaard, Ander, Amirovich Maksyutov, Rinat, Vasil’Evna Gavrilova, Elena, Victorovich Pyankov, Oleg, Alexandrovich Bodnev, Sergey, Vladimirovna Tregubchak, Tatyana, Nikolayevich Shvalov, Alexander, Victorovich Antonets, Deni, Cristina Resende, Paola, Goya, Stephanie, Perrin, Amandine, Tc Lee, Raphael, Yadahalli, Shilpa, X Han, Alvin, A Russell, Colin, Schmutz, Stefan, Zaheri, Maryam, Kufner, Verena, Huber, Michael, Trkola, Alexandra, Antwerpen, Marku, C Walter, Mathia, van der Werf, Sylvie, Gambaro, Fabiana, Behillil, Sylvie, Enouf, Vincent, Donati, Flora, Ustinova, Monta, Rovite, Vita, Klovins, Jani, Savicka, Oksana, K Wienecke-Baldacchino, Anke, Ragimbeau, Catherine, Fournier, Guillaume, Mossong, Joël, W Aberle, Stephan, Haukland, Mattia, Enkirch, Theresa, Advani, Abdolreza, Lind Karlberg, Maria, Karlsson Lindsjö, Oskar, Broddesson, Sandra, Sláviková, Monika, Ličková, Martina, Klempa, Bori, Staroňová, Edita, Tichá, Elena, Szemes, Tomáš, Rusňáková, Diana, Stadler, Tanja, Quer, Josep, Anton, Andre, Andres, Cristina, Piñana, Maria, Garcia-Cehic, Damir, Pumarola, Toma, Izopet, Jacque, Gioula, Georgia, Exindari, Maria, Papa, Anna, Chatzidimitriou, Dimitrio, Metallidis, Symeon, Pappa, Stella, Macek Jr, Milan, Geryk, Jan, Brož, Petr, Briksí, Aleš, Hubáček, Petr, Dřevínek, Pavel, Zajac, Miroslav, Kvapil, Petr, Holub, Michal, Kvapilová, Kateřina, Novotný, Adam, Kašný, Martin, Klempt, Petr, Vapalahti, Olli, Smura, Teemu, Sironen, Tarja, Selhorst, Philippe, Anthony, Colin, Ariën, Kevin, Simon-Loriere, Etienne, Rabalski, Lukasz, Bienkowska-Szewczyk, Krystyna, Borges, Vítor, Isidro, Joana, Paulo Gomes, João, Guiomar, Raquel, Pechirra, Pedro, Costa, Inê, Duarte, Sílvia, Vieira, Luí, Pyrc, Krzysztof, S Zuckerman, Neta, Turdikulova, Shahlo, Abdullaev, Alisher, Dalimova, Dilbar, Abdurakhimov, Abror, Tagliabracci, Adriano, Alessandrini, Federica, Melchionda, Filomena, Onofri, Valerio, Turchi, Chiara, Bagnarelli, Patrizia, Menzo, Stefano, Caucci, Sara, Di Sante, Laura, Popa, Alexandra, Genger, Jakob-Wendelin, Agerer, Benedikt, Lercher, Alexander, Endler, Luka, Smyth, Mark, Penz, Thoma, Schuster, Michael, Senekowitsch, Martin, Laine, Jan, Bock, Christoph, Bergthaler, Andrea, Shevtsov, Alexandr, Kalendar, Ruslan, Ramanculov, Yerlan, Graf, Alexander, Muenchhoff, Maximilian, T Keppler, Oliver, Krebs, Stefan, Blum, Helmut, Marcello, Alessandro, Licastro, Danilo, D’Agaro, Pierlanfranco, Laubscher, Florian, Vidanovic, Dejan, Tesovic, Bojana, Volkening, Jeremy, Clementi, Nicola, Mancini, Nicasio, Rupnik, Maja, Mahnic, Aleksander, Walker, Andrea, Houwaart, Torsten, Wienemann, Tobia, Kohns Vasconcelos, Malte, Strelow, Daniel, Ole Jensen, Björn-Erik, Senff, Tina, Hülse, Lisanna, Adams, Ortwin, Andree, Marcel, Hauka, Sandra, Feldt, Torsten, Keitel, Verena, Kindgen-Milles, Detlef, Timm, Jörg, Pfeffer, Klau, T Dilthey, Alexander, Moore, Catherine, Ozdarendeli, Aykut, Terkis Islam Pavel, Shaikh, Yetiskin, Hazel, Aydin, Gunsu, Holyavkin, Can, Ali Uygut, Muhammet, Cevik, Ceren, Shchetinin, Alexey, Gushchin, Vladimir, Dinler-Doganay, Gizem, Doganay, Levent, Kizilboga-Akgun, Tugba, Karacan, Ilker, Pancer, Katarzyna, Maes, Piet, Martí-Carreras, Joan, Wawina-Bokalanga, Tony, Thürmer, Andrea, Wedde, Marianne, Dürrwald, Ralf, Von Kleist, Max, Drechsel, Oliver, Wolff, Thorsten, Fuchs, Stephan, Kmiecinski, Rene, Michel, Janine, Nitsche, Andrea, Casas, Inmaculada, Iglesias Caballero, María, Zaballos, Ángel, Jiménez, Pilar, Jiménez, Mercede, Monzón Fernández, Sara, Varona Fernández, Sarai, Cuesta De La Plaza, Isabel, Fadeev, Artem, Ivanova, Anna, Sergeeva, Mariia, Stefanelli, Paola, Estee Torok, M, Hall, Grant, da Silva Filipe, Ana, Turtle, Lance, Afifi, Safiah, Mccluggage, Kathryn, Beer, Robert, Ledesma, Juan, Maksimovic, Joshua, Spellman, Karla, L Hamilton, William, Marchbank, Angela, Alexander Southgate, Joel, Underwood, Anthony, Taylor, Ben, Yeats, Corin, Abudahab, Khalil, R Gemmell, Matthew, Eccles, Richard, Lucaci, Anita, Abigail Nelson, Charlotte, Rainbow, Lucille, Whitehead, Mark, Gregory, Richard, Haldenby, Sam, Paterson, Steve, A Hughes, Margaret, D Curran, Martin, Baker, David, Tucker, Rachel, R Green, Luke, Feltwell, Theresa, D Halstead, Fenella, Wyles, Matthew, S Jahun, Aminu, Y Ahmad, Shazaad S, Georgana, Iliana, Goodfellow, Ian, Yakovleva, Anna, W Meredith, Luke, Gavriil, Artemi, Raza Awan, Ali, Fisher, Chloe, Jonathan, European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Cardiff University, Public Health Wales [Cardiff, Royaume uni], University of Basel (Unibas), Research Institute of Influenza, St. Petersburg, Russia, Agency for science, technology and research [Singapore] (A*STAR), National University of Singapore (NUS), University of Edinburgh, WHO Regional Office for Europe [Copenhagen], We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible, The WHO European Region sequencing laboratories and GISAID EpiCoV group*: Niko Beerenwinkel, Susana Posada-Céspedes, Kim Philipp Jablonski, Pedro Falé Ferreira, Ivan Topolsky, Tatjana Avšič-Županc, Miša Korva, Mario Poljak, Samo Zakotnik, Tomaž Mark Zorec, Karoline Bragstad, Olav Hungnes, Kathrine Stene-Johansen, Chantal Reusken, Adam Meijer, Harry Vennema, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Álvaro Chiner-Oms, Irving Cancino-Muñoz, Iñaki Comas, Galo A Goig, Manuela Torres-Puente, Mariana G López, Llúcia Martínez-Priego, Giuseppe D'Auria, Paula Ruíz-Hueso, Loreto Ferrús-Abad, Griselda de Marco, Inmaculada Galan-Vendrell, Sandra Carbó-Ramirez, Paula Ruiz-Rodriguez, Mireia Coscollá, Katerina Polackova, Lenka Kramna, Ondrej Cinek, Jan Richter, George Krashias, Christina Tryfonos, Stavros Bashiardes, Dana Koptides, Christina Christodoulou, Barbara Bartolini, Cesare Em Gruber, Antonino Di Caro, Concetta Castilletti, Fabrizio Stefani, Sara Giordana Rimoldi, Francesca Romeri, Franco Salerno, Stefano Polesello, Alexander Nagy, Helena Jirincova, Jaromira Vecerova, Ludmila Novakova, Samuel Cordey, Marine Murtskhvaladze, Nato Kotaria, Tobias Schär, Christian Beisel, Oliver Vugrek, Filip Rokić, Lovro Trgovec-Greif, Igor Jurak, Tomislav Rukavina, Neven Sučić, Kristian Schønning, Søren M Karst, Rasmus H Kirkegaard, Thomas Y Michaelsen, Emil Aa Sørensen, Simon Knutson, Jakob Brandt, Vang Le-Quy, Trine Sørensen, Celine Petersen, Martin Schou Pedersen, Sanne Løkkegaard Larsen, Marianne Nielsine Skov, Morten Rasmussen, Jannik Fonager, Anders Fomsgaard, Rinat Amirovich Maksyutov, Elena Vasil'Evna Gavrilova, Oleg Victorovich Pyankov, Sergey Alexandrovich Bodnev, Tatyana Vladimirovna Tregubchak, Alexander Nikolayevich Shvalov, Denis Victorovich Antonets, Paola Cristina Resende, Stephanie Goya, Amandine Perrin, Raphael Tc Lee, Shilpa Yadahalli, Alvin X Han, Colin A Russell, Stefan Schmutz, Maryam Zaheri, Verena Kufner, Michael Huber, Alexandra Trkola, Markus Antwerpen, Mathias C Walter, Sylvie van der Werf, Fabiana Gambaro, Sylvie Behillil, Vincent Enouf, Flora Donati, Monta Ustinova, Vita Rovite, Janis Klovins, Oksana Savicka, Anke K Wienecke-Baldacchino, Catherine Ragimbeau, Guillaume Fournier, Joël Mossong, Stephan W Aberle, Mattias Haukland, Theresa Enkirch, Abdolreza Advani, Maria Lind Karlberg, Oskar Karlsson Lindsjö, Sandra Broddesson, Monika Sláviková, Martina Ličková, Boris Klempa, Edita Staroňová, Elena Tichá, Tomáš Szemes, Diana Rusňáková, Tanja Stadler, Josep Quer, Andres Anton, Cristina Andres, Maria Piñana, Damir Garcia-Cehic, Tomas Pumarola, Jacques Izopet, Georgia Gioula, Maria Exindari, Anna Papa, Dimitrios Chatzidimitriou, Symeon Metallidis, Stella Pappa, Milan Macek Jr, Jan Geryk, Petr Brož, Aleš Briksí, Petr Hubáček, Pavel Dřevínek, Miroslav Zajac, Petr Kvapil, Michal Holub, Kateřina Kvapilová, Adam Novotný, Martin Kašný, Petr Klempt, Olli Vapalahti, Teemu Smura, Tarja Sironen, Philippe Selhorst, Colin Anthony, Kevin Ariën, Etienne Simon-Loriere, Lukasz Rabalski, Krystyna Bienkowska-Szewczyk, Vítor Borges, Joana Isidro, João Paulo Gomes, Raquel Guiomar, Pedro Pechirra, Inês Costa, Sílvia Duarte, Luís Vieira, Krzysztof Pyrc, Neta S Zuckerman, Shahlo Turdikulova, Alisher Abdullaev, Dilbar Dalimova, Abror Abdurakhimov, Adriano Tagliabracci, Federica Alessandrini, Filomena Melchionda, Valerio Onofri, Chiara Turchi, Patrizia Bagnarelli, Stefano Menzo, Sara Caucci, Laura Di Sante, Alexandra Popa, Jakob-Wendelin Genger, Benedikt Agerer, Alexander Lercher, Lukas Endler, Mark Smyth, Thomas Penz, Michael Schuster, Martin Senekowitsch, Jan Laine, Christoph Bock, Andreas Bergthaler, Alexandr Shevtsov, Ruslan Kalendar, Yerlan Ramanculov, Alexander Graf, Maximilian Muenchhoff, Oliver T Keppler, Stefan Krebs, Helmut Blum, Alessandro Marcello, Danilo Licastro, Pierlanfranco D'Agaro, Florian Laubscher, Dejan Vidanovic, Bojana Tesovic, Jeremy Volkening, Nicola Clementi, Nicasio Mancini, Maja Rupnik, Aleksander Mahnic, Andreas Walker, Torsten Houwaart, Tobias Wienemann, Malte Kohns Vasconcelos, Daniel Strelow, Björn-Erik Ole Jensen, Tina Senff, Lisanna Hülse, Ortwin Adams, Marcel Andree, Sandra Hauka, Torsten Feldt, Verena Keitel, Detlef Kindgen-Milles, Jörg Timm, Klaus Pfeffer, Alexander T Dilthey, Catherine Moore, Aykut Ozdarendeli, Shaikh Terkis Islam Pavel, Hazel Yetiskin, Gunsu Aydin, Can Holyavkin, Muhammet Ali Uygut, Ceren Cevik, Alexey Shchetinin, Vladimir Gushchin, Gizem Dinler-Doganay, Levent Doganay, Tugba Kizilboga-Akgun, Ilker Karacan, Katarzyna Pancer, Piet Maes, Joan Martí-Carreras, Tony Wawina-Bokalanga, Bert Vanmechelen, Andrea Thürmer, Marianne Wedde, Ralf Dürrwald, Max Von Kleist, Oliver Drechsel, Thorsten Wolff, Stephan Fuchs, Rene Kmiecinski, Janine Michel, 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H., Taylor, S., European Centre for Disease Prevention and Control (ECDC), Public Health Wales Microbiology Cardiff, Faculty of Agriculture and Forestry, Department of Agricultural Sciences, and Institute of Biotechnology
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Infecções Respiratórias ,0301 basic medicine ,MESH: Coronavirus Infections ,Epidemiology ,[SDV]Life Sciences [q-bio] ,Distribution (economics) ,Wastewater ,MESH: Base Sequence ,Severe Acute Respiratory Syndrome ,MESH: World Health Organization ,Pandemic ,MESH: Coronavirus ,MESH: COVID-19 ,Sequencing ,Viral ,Clade ,Nomenclature ,Genome ,biology ,COVID-19 ,Europe ,NGS ,SARS-CoV-2 ,WGS ,nomenclature ,sequencing ,Base Sequence ,Betacoronavirus ,Coronavirus ,Coronavirus Infections ,Genome, Viral ,Humans ,Phylogeography ,Pneumonia, Viral ,RNA, Viral ,RNA-Dependent RNA Polymerase ,Spatio-Temporal Analysis ,World Health Organization ,Pandemics ,C500 ,European region ,3. Good health ,Geography ,MESH: Phylogeography ,MESH: RNA-Dependent RNA Polymerase ,MESH: RNA, Viral ,MESH: Betacoronavirus ,Spatio-Temporal Analysi ,MESH: Genome, Viral ,Cartography ,Human ,Bioquímica ,MESH: Pandemics ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Coronaviru ,030106 microbiology ,03 medical and health sciences ,MESH: Spatio-Temporal Analysis ,MESH: Severe Acute Respiratory Syndrome ,Virology ,MESH: SARS-CoV-2 ,Whole genome sequencing ,MESH: Humans ,Whole Genome Sequencing ,Betacoronaviru ,Coronavirus Infection ,business.industry ,Public Health, Environmental and Occupational Health ,Pneumonia ,biology.organism_classification ,B900 ,030104 developmental biology ,MESH: Pneumonia, Viral ,RNA ,SARS_CoV-2 ,3111 Biomedicine ,MESH: Europe ,Human medicine ,business - Abstract
8 páginas, 3 figuras, We 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., We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCoV Database used in the phylogenetic analysis. We gratefully acknowledge all the staff working with sample collection, sample preparation, sequencing, data analysis and data sharing in all laboratories in the WHO European Region for making this work possible.
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41. Early experience on universal prophylaxis in infants against RSV: Facts and expectations.
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Soriano Arandes A, Creus-Costa A, Perramon-Malavez A, Andrés C, Vila J, Gatell A, Piñana M, Serrano P, González-Sánchez A, Capdevila R, Prats C, Soler-Palacin P, and Antón A
- Abstract
During the 2023-2024 season, nirsevimab significantly reduced the risk of bronchiolitis and confirmed RSV infections in primary care, hospital, and pediatric intensive care unit admissions among infants aged 0 to 11 months, even in a season with a high community RSV burden, particularly for older infants. These findings are very useful for public health authorities to continue to implement immunization campaigns against RSV in the coming seasons. Moreover, universal immunization against RSV represents a transformative step towards reducing the burden of RSV in infants. With promising evidence from recent published studies, the expectations for a reduction of RSV-associated hospitalizations, alongside the improvement of public health outcomes and an equitable access to these measures, are high. However, achieving these goals will require addressing challenges related to vaccine uptake, funding, and RSV surveillance to prompt detect resistances due to mutations of the virus. These interventions need to be integrated into public health strategies because they hold the potential to make a significant impact on infant's health worldwide., Competing Interests: A. S-A. has received honorarium for attending scientific meetings from Sanofi and Pfizer. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (Thieme. All rights reserved.)
- Published
- 2025
- Full Text
- View/download PDF
42. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients.
- Author
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Andrés C, Garcia-Cehic D, Gregori J, Piñana M, Rodriguez-Frias F, Guerrero-Murillo M, Esperalba J, Rando A, Goterris L, Codina MG, Quer S, Martín MC, Campins M, Ferrer R, Almirante B, Esteban JI, Pumarola T, Antón A, and Quer J
- Subjects
- Adult, Aged, COVID-19, Computational Biology, Female, Gene Deletion, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Pandemics, RNA Cleavage, SARS-CoV-2, Sequence Analysis, RNA, Betacoronavirus genetics, Coronavirus Infections virology, Genome, Viral genetics, Pneumonia, Viral virology, Quasispecies genetics, Respiratory Tract Infections virology, Spike Glycoprotein, Coronavirus genetics
- Abstract
The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.
- Published
- 2020
- Full Text
- View/download PDF
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