1
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Sanbonmatsu-Gámez S, Pedrosa-Corral I, Navarro-Marí JM, Pérez-Ruiz M. Update in Diagnostics of Toscana Virus Infection in a Hyperendemic Region (Southern Spain). Viruses 2021; 13:v13081438. [PMID: 34452304 PMCID: PMC8402649 DOI: 10.3390/v13081438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
The sandfly fever Toscana virus (TOSV, genus Phlebovirus, family Phenuiviridae) is endemic in Mediterranean countries. In Spain, phylogenetic studies of TOSV strains demonstrated that a genotype, different from the Italian, was circulating. This update reports 107 cases of TOSV neurological infection detected in Andalusia from 1988 to 2020, by viral culture, serology and/or RT-PCR. Most cases were located in Granada province, a hyperendemic region. TOSV neurological infection may be underdiagnosed since few laboratories include this virus in their portfolio. This work presents a reliable automated method, validated for the detection of the main viruses involved in acute meningitis and encephalitis, including the arboviruses TOSV and West Nile virus. This assay solves the need for multiple molecular platforms for different viruses and thus, improves the time to results for these syndromes, which require a rapid and efficient diagnostic approach.
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Affiliation(s)
- Sara Sanbonmatsu-Gámez
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (S.S.-G.); (I.P.-C.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), 28029 Madrid, Spain
| | - Irene Pedrosa-Corral
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (S.S.-G.); (I.P.-C.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
| | - José María Navarro-Marí
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (S.S.-G.); (I.P.-C.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), 28029 Madrid, Spain
| | - Mercedes Pérez-Ruiz
- Instituto de Investigación Biosanitaria ibs.Granada, 18012 Granada, Spain
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), 28029 Madrid, Spain
- Servicio de Microbiología, Hospital Regional Universitario de Málaga, 29010 Málaga, Spain
- Correspondence:
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2
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López MG, Chiner-Oms Á, García de Viedma D, Ruiz-Rodriguez P, Bracho MA, Cancino-Muñoz I, D’Auria G, de Marco G, García-González N, Goig GA, Gómez-Navarro I, Jiménez-Serrano S, Martinez-Priego L, Ruiz-Hueso P, Ruiz-Roldán L, Torres-Puente M, Alberola J, Albert E, Aranzamendi Zaldumbide M, Bea-Escudero MP, Boga JA, Bordoy AE, Canut-Blasco A, Carvajal A, Cilla Eguiluz G, Cordón Rodríguez ML, Costa-Alcalde JJ, de Toro M, de Toro Peinado I, del Pozo JL, Duchêne S, Fernández-Pinero J, Fuster Escrivá B, Gimeno Cardona C, González Galán V, Gonzalo Jiménez N, Hernáez Crespo S, Herranz M, Lepe JA, López-Causapé C, López-Hontangas JL, Martín V, Martró E, Milagro Beamonte A, Montes Ros M, Moreno-Muñoz R, Navarro D, Navarro-Marí JM, Not A, Oliver A, Palop-Borrás B, Parra Grande M, Pedrosa-Corral I, Pérez González MC, Pérez-Lago L, Pérez-Ruiz M, Piñeiro Vázquez L, Rabella N, Rezusta A, Robles Fonseca L, Rodríguez-Villodres Á, Sanbonmatsu-Gámez S, Sicilia J, Soriano A, Tirado Balaguer MD, Torres I, Tristancho A, Marimón JM, Coscolla M, González-Candelas F, Comas I. The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant. Nat Genet 2021; 53:1405-1414. [PMID: 34594042 PMCID: PMC8481935 DOI: 10.1038/s41588-021-00936-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.
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Affiliation(s)
- Mariana G. López
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Álvaro Chiner-Oms
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Darío García de Viedma
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain ,grid.413448.e0000 0000 9314 1427CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
| | - Paula Ruiz-Rodriguez
- grid.5338.d0000 0001 2173 938XInstituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-Universitat de València), Valencia, Spain
| | - Maria Alma Bracho
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Irving Cancino-Muñoz
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Giuseppe D’Auria
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.428862.2FISABIO, Servicio de Secuenciación, València, Spain
| | | | - Neris García-González
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain
| | - Galo Adrian Goig
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Inmaculada Gómez-Navarro
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Santiago Jiménez-Serrano
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | | | - Paula Ruiz-Hueso
- grid.428862.2FISABIO, Servicio de Secuenciación, València, Spain
| | - Lidia Ruiz-Roldán
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain
| | - Manuela Torres-Puente
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Juan Alberola
- grid.411289.70000 0004 1770 9825Servicio de Microbiología. Hospital Dr Peset, Valencia, Spain ,grid.424970.c0000 0001 2353 2112Conselleria de Sanitat i Consum, Generalitat Valenciana, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain
| | - Eliseo Albert
- grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Maitane Aranzamendi Zaldumbide
- grid.411232.70000 0004 1767 5135Servicio de Microbiología, Hospital Universitario Cruces, Bilbao, Spain ,Grupo de Microbiología y Control de Infección, Instituto de Investigación Sanitaria Biocruces Bizkaia, Barakaldo, Spain
| | - María Pilar Bea-Escudero
- grid.460738.ePlataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Jose Antonio Boga
- grid.411052.30000 0001 2176 9028Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain ,grid.511562.4Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Antoni E. Bordoy
- grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Andrés Canut-Blasco
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - Ana Carvajal
- grid.4807.b0000 0001 2187 3167Animal Health Department, Universidad de León, León, Spain
| | - Gustavo Cilla Eguiluz
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | - Maria Luz Cordón Rodríguez
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - José J. Costa-Alcalde
- grid.411048.80000 0000 8816 6945Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María de Toro
- grid.460738.ePlataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | | | - Jose Luis del Pozo
- grid.411730.00000 0001 2191 685XServicio de Enfermedades Infecciosas y Microbiología clínica, Clínica Universidad de Navarra, Pamplona, Spain
| | - Sebastián Duchêne
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Jovita Fernández-Pinero
- grid.419190.40000 0001 2300 669XInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria, O.A., M.P. – INIA, Madrid, Spain
| | - Begoña Fuster Escrivá
- grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain ,grid.106023.60000 0004 1770 977XServicio de Microbiología, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Concepción Gimeno Cardona
- grid.106023.60000 0004 1770 977XServicio de Microbiología, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Verónica González Galán
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Nieves Gonzalo Jiménez
- grid.411093.e0000 0004 0399 7977Servicio Microbiología, Departamento de Salud de Elche-Hospital General, Elche, Alicante, Spain
| | - Silvia Hernáez Crespo
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - Marta Herranz
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain ,grid.413448.e0000 0000 9314 1427CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
| | - José Antonio Lepe
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Carla López-Causapé
- grid.411164.70000 0004 1796 5984Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - José Luis López-Hontangas
- grid.84393.350000 0001 0360 9602Hospital Universitario y Politécnico La Fe, Servicio de Microbiología, Valencia, Spain
| | - Vicente Martín
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.4807.b0000 0001 2187 3167Research Group on Gene-Environment Interactions and Health. Institute of Biomedicine (IBIOMED), Universidad de León, León, Spain
| | - Elisa Martró
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Ana Milagro Beamonte
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Milagrosa Montes Ros
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | | | - David Navarro
- grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain ,grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - José María Navarro-Marí
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Anna Not
- grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Antonio Oliver
- grid.411164.70000 0004 1796 5984Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain ,Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Begoña Palop-Borrás
- grid.411457.2Servicio de Microbiologia, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Mónica Parra Grande
- grid.507938.0Laboratorio de Microbiología, Hospital Marina Baixa, Villajoyosa, Spain
| | - Irene Pedrosa-Corral
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Maria Carmen Pérez González
- grid.411250.30000 0004 0399 7109Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Laura Pérez-Lago
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mercedes Pérez-Ruiz
- grid.411457.2Servicio de Microbiologia, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Luis Piñeiro Vázquez
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | - Nuria Rabella
- grid.413396.a0000 0004 1768 8905Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain ,CREPIMC, Institut d’Investigació Biomèdica Sant Pau, Barcelona, Spain ,grid.7080.fDepartament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola, Spain
| | - Antonio Rezusta
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain ,grid.488737.70000000463436020Instituto de Investigación Sanitaria de Aragón, Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain ,grid.11205.370000 0001 2152 8769Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Lorena Robles Fonseca
- grid.411094.90000 0004 0506 8127Hospital General Universitario de Albacete, Albacete, Spain
| | - Ángel Rodríguez-Villodres
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Sara Sanbonmatsu-Gámez
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Jon Sicilia
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alex Soriano
- grid.410458.c0000 0000 9635 9413Servicio de Enfermedades Infecciosas, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Ignacio Torres
- grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Alexander Tristancho
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain ,grid.488737.70000000463436020Instituto de Investigación Sanitaria de Aragón, Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain
| | - José María Marimón
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | | | - Mireia Coscolla
- grid.5338.d0000 0001 2173 938XInstituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-Universitat de València), Valencia, Spain
| | - Fernando González-Candelas
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Iñaki Comas
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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3
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Venturi G, Aberle SW, Avšič-Županc T, Barzon L, Batejat C, Burdino E, Carletti F, Charrel R, Christova I, Connell J, Corman VM, Emmanouil M, Jääskeläinen AJ, Kurolt I, Lustig Y, Martinez MJ, Koopmans M, Nagy O, Nguyen T, Papa A, Pérez-Ruiz M, Pfeffer M, Protic J, Reimerink J, Rossini G, Sánchez-Seco Fariñas MP, Schmidt-Chanasit J, Söderholm S, Sudre B, Van Esbroeck M, Reusken CB. Specialist laboratory networks as preparedness and response tool - the Emerging Viral Diseases-Expert Laboratory Network and the Chikungunya outbreak, Thailand, 2019. ACTA ACUST UNITED AC 2020; 25. [PMID: 32265004 PMCID: PMC7140599 DOI: 10.2807/1560-7917.es.2020.25.13.1900438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We illustrate the potential for specialist laboratory networks to be used as preparedness and response tool through rapid collection and sharing of data. Here, the Emerging Viral Diseases-Expert Laboratory Network (EVD-LabNet) and a laboratory assessment of chikungunya virus (CHIKV) in returning European travellers related to an ongoing outbreak in Thailand was used for this purpose. EVD-LabNet rapidly collected data on laboratory requests, diagnosed CHIKV imported cases and sequences generated, and shared among its members and with the European Centre for Disease Prevention and Control. Data across the network showed an increase in CHIKV imported cases during 1 October 2018–30 April 2019 vs the same period in 2018 (172 vs 50), particularly an increase in cases known to be related to travel to Thailand (72 vs 1). Moreover, EVD-LabNet showed that strains were imported from Thailand that cluster with strains of the ECSA-IOL E1 A226 variant emerging in Pakistan in 2016 and involved in the 2017 outbreaks in Italy. CHIKV diagnostic requests increased by 23.6% between the two periods. The impact of using EVD-LabNet or similar networks as preparedness and response tool could be improved by standardisation of the collection, quality and mining of data in routine laboratory management systems.
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Affiliation(s)
- Giulietta Venturi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, Ljubljana, Slovenia
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Christoph Batejat
- Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur, Paris, France
| | - Elisa Burdino
- Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, Turin, Italy
| | - Fabrizio Carletti
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - Rémi Charrel
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IRBA, IHU Méditerranée Infection), Marseille, France
| | - Iva Christova
- National Reference Vector-borne pathogens Laboratory, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Jeff Connell
- National Virus Reference Laboratory, University College Dublin, Ireland
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany.,Department of Virology, Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Mary Emmanouil
- Diagnostic Services Laboratory, Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
| | - Anne J Jääskeläinen
- Virology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ivan Kurolt
- Research unit, University Hospital for Infectious Diseases 'Dr. Fran Mihaljević', Zagreb, Croatia
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Miguel J Martinez
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Orsolya Nagy
- Department of Virology, National Public Health Center, Budapest, Hungary
| | - Trung Nguyen
- Département de Microbiologie, Laboratoire national de santé, Luxemburg
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria, Granada, Spain
| | - Martin Pfeffer
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig, Germany
| | - Jelena Protic
- National Reference Laboratory for ARBO viruses and haemorrhagic fever, Belgrade, Serbia
| | - Johan Reimerink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Giada Rossini
- Regional Reference Centre for Microbiological Emergencies (CRREM), Unit of Clinical Microbiology, St Orsola Malpighi Hospital, Bologna, Italy
| | | | - Jonas Schmidt-Chanasit
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sandra Söderholm
- Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Bertrand Sudre
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chantal B Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.,Department of Viroscience, Erasmus Medical Centre, Rotterdam, the Netherlands
| | -
- The members of the CHIKV-Working Group are listed at the end of the article
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4
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de Salazar A, Aguilera A, Trastoy R, Fuentes A, Alados JC, Causse M, Galán JC, Moreno A, Trigo M, Pérez-Ruiz M, Roldán C, Pena MJ, Bernal S, Serrano-Conde E, Barbeito G, Torres E, Riazzo C, Cortes-Cuevas JL, Chueca N, Coira A, Sanchez-Calvo JM, Marfil E, Becerra F, Gude MJ, Pallarés Á, Pérez Del Molino ML, García F. Sample pooling for SARS-CoV-2 RT-PCR screening. Clin Microbiol Infect 2020; 26:1687.e1-1687.e5. [PMID: 32919074 PMCID: PMC7481316 DOI: 10.1016/j.cmi.2020.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/21/2022]
Abstract
Objective To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of coronavirus disease 2019 (COVID-19) by using different commercial platforms for nucleic acid extraction and amplification. Methods A total of 3519 nasopharyngeal samples received at nine Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of ten samples and 11 pools of nine samples) according to the existing methodology in place at each centre. Results We found that 253 pools (2519 samples) were negative and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples), we found discordant results when compared to their correspondent individual samples, as follows: in 22 of 29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity and positive and negative predictive values for pooling were 97.10% (95% confidence interval (CI), 94.11–98.82), 100%, 100% and 99.79% (95% CI, 99.56–99.90) respectively; accuracy was 99.80% (95% CI, 99.59–99.92), and the kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted in a median loss of 2.87 (95% CI, 2.46–3.28) cycle threshold (Ct) for E gene, 3.36 (95% CI, 2.89–3.85) Ct for the RdRP gene and 2.99 (95% CI, 2.56–3.43) Ct for the N gene. Conclusions We found a high efficiency of pooling strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA testing across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity and positive and negative predictive values.
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Affiliation(s)
- Adolfo de Salazar
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Antonio Aguilera
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Rocio Trastoy
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Ana Fuentes
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Juan Carlos Alados
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Manuel Causse
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan Carlos Galán
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Antonio Moreno
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Matilde Trigo
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Mercedes Pérez-Ruiz
- Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain; Clinical Microbiology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Carolina Roldán
- Clinical Microbiology Unit, Hospital Universitario de Jae, Jaen, Spain
| | - Maria José Pena
- Clinical Microbiology Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de GC, Gran Canaria, Spain
| | - Samuel Bernal
- Unit of Infectious Disease and Clinical Microbiology, Hospital Universitario de Valme, Seville, Spain
| | - Esther Serrano-Conde
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Gema Barbeito
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Eva Torres
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Cristina Riazzo
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | | | - Natalia Chueca
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Amparo Coira
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | | | - Eduardo Marfil
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Federico Becerra
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María José Gude
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Ángeles Pallarés
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - María Luisa Pérez Del Molino
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Federico García
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain.
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5
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Romo-Ibáñez Á, Calatrava-Hernández E, Gutiérrez-Soto B, Pérez-Ruiz M, Navarro-Marí JM, Gutiérrez-Fernández J. High clinical impact of rapid susceptibility testing on CHROMID ESBL ® medium directly from swabs. Ann Transl Med 2020; 8:604. [PMID: 32566630 PMCID: PMC7290529 DOI: 10.21037/atm.2020.02.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Antibiotic resistance is a serious public health challenge exacerbated by the widespread use of β-lactam and glycopeptide antibiotics. The identification of resistances is crucial, and CHROMID ESBL medium has been developed to detect enterobacteria with extended-spectrum β-lactamases (ESBL). The objective of this study was to evaluate the potential of this medium to detect other types of resistant bacteria. Methods Vancomycin, cefoxitin, imipenem, and cefepime disks were used to measure growth on CHROMID ESBL medium of β-lactam-resistant Gram-negative (83 with ESBL, 57 with carbapenemases, 35 with AmpC and 3 Stenotrophomonas maltophilia) and Gram-positive [37 vancomycin-susceptible (vancoS) microorganisms and 21 vancomycin-resistant (vancoR) Enterococcus faecium] clinical isolates (retrospective study) and colonization by the aforementioned bacteria (prospective study), using 649 rectal swabs, 314 pharyngeal swabs, and 44 swabs from other localizations. Results Retrospective study: species grown on the medium exhibited different colors. Growth on the medium was observed for: all ESBL enterobacteria, which were susceptible to imipenem and cefoxitin; 95% of isolates with carbapenemases, mostly resistant to imipenem; 80% of those with AmpC; 86% of vancoR E. faecium isolates; and 42% of vancoS E. faecalis isolates, with large growth inhibition halos around the vancomycin disk. Prospective study: vancoR E. faecium, ESBL Klebsiella, Pseudomonas with carbapenemases, A. baumannii (mostly from rectal swabs), S. maltophilia, Achromobacter xylosoxidans, and Burkholderia cenocepacia (mostly from pharyngeal swabs) were isolated from the 246 positive samples. Conclusions CHROMID ESBL medium permitted the differential growth of Gram-negative bacteria, many with ESBL and carbapenemases. ESBL enterobacteria were susceptible to imipenem, carbapenemase-producing microorganisms grew around the imipenem disk, and vancoR E. faecium was isolated on the medium. Results of the prospective study demonstrate the potential clinical relevance of this medium. S. maltophilia was more frequently detected with pharyngeal swabs and ESBL Klebsiella, A. baumannii, and Pseudomonas with rectal swabs.
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Affiliation(s)
- Álvaro Romo-Ibáñez
- Department of Microbiology, School of Medicine, University of Granada-Instituto de Investigación Biosanitaria, Granada, Spain
| | - Elisabeth Calatrava-Hernández
- Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria, Granada, Spain
| | | | - Mercedes Pérez-Ruiz
- Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria, Granada, Spain
| | - José Gutiérrez-Fernández
- Department of Microbiology, School of Medicine, University of Granada-Instituto de Investigación Biosanitaria, Granada, Spain.,Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria, Granada, Spain
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6
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López-Ruiz N, Montaño-Remacha MDC, Durán-Pla E, Pérez-Ruiz M, Navarro-Marí JM, Salamanca-Rivera C, Miranda B, Oyonarte-Gómez S, Ruiz-Fernández J. West Nile virus outbreak in humans and epidemiological surveillance, west Andalusia, Spain, 2016. ACTA ACUST UNITED AC 2019; 23. [PMID: 29637890 PMCID: PMC5894251 DOI: 10.2807/1560-7917.es.2018.23.14.17-00261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In Andalusia, Spain, West Nile virus (WNV) surveillance takes place from April to November, during the active vector period. Within this area seroconversion to this virus was evidenced in wild birds in 2004, affecting horses and two humans for the first time in 2010. Since 2010, the virus has been isolated every year in horses, and national and regional surveillance plans have been updated with the epidemiological changes found. WNV is spreading rapidly throughout southern Europe and has caused outbreaks in humans. Here we describe the second WNV outbreak in humans in Andalusia, with three confirmed cases, which occurred between August and September 2016, and the measures carried out to control it. Surveillance during the transmission season is essential to monitor and ensure prompt identification of any outbreaks.
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Affiliation(s)
- Nuria López-Ruiz
- Department of Preventive Medicine and Public Health, University Hospital Puerta del Mar, Cadiz, Spain.,Surveillance Department, Andalusian Regional Ministry of Health, Seville, Spain
| | | | - Enric Durán-Pla
- Surveillance Department, Andalusian Regional Ministry of Health, Seville, Spain
| | - Mercedes Pérez-Ruiz
- Network Cooperative Research in Tropical Diseases (RICET), Carlos III Institute of Health (ISCIII), Madrid, Spain.,Institute of Biosanitary Research, Granada, Spain.,Department of Microbiology, University Hospital Virgen de las Nieves, Granada, Spain
| | - Jose María Navarro-Marí
- Network Cooperative Research in Tropical Diseases (RICET), Carlos III Institute of Health (ISCIII), Madrid, Spain.,Institute of Biosanitary Research, Granada, Spain.,Department of Microbiology, University Hospital Virgen de las Nieves, Granada, Spain
| | - Celia Salamanca-Rivera
- Department of Preventive Medicine and Public Health, University Hospital Virgen del Rocío, Seville, Spain
| | | | | | - Josefa Ruiz-Fernández
- General Secretary for Public Health and Consumption, Regional Ministry of Health, Andalusia, Spain
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7
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Pérez-Ruiz M, Pedrosa-Corral I, Sanbonmatsu-Gámez S, Gómez-Camarasa C, Navarro-Marí JM. Analytical validation of viral CNS Flow Chip kit for detection of acute meningitis and encephalitis. J Virol Methods 2018; 259:54-59. [PMID: 29902492 DOI: 10.1016/j.jviromet.2018.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/17/2018] [Accepted: 06/10/2018] [Indexed: 01/14/2023]
Abstract
A new molecular assay (Viral CNS Flow Chip kit, Master Diagnóstica, Spain) has been developed for the detection of eight viruses causing acute meningitis and encephalitis, i.e. herpes simplex viruses 1-2, varicella zoster virus, human enterovirus, human parechovirus, Toscana virus, human cytomegalovirus and Epstein Barr virus. The new assay is a multiplex one-step RT-PCR followed by automatic flow-through hybridization, colorimetric detection and image analysis. The limit of detection was 50 copies/reaction, and 10 copies/reaction for human enterovirus and the other seven viruses, respectively. The analytical validation was performed with nucleic acids extracted from 268 cerebrospinal fluid samples and the results were compared with routine molecular assays. An excellent coefficient of agreement was observed between V-CNS and routine assays [kappa index: 0.948 (95%CI: 0.928-0.968)]. The overall sensitivity and specificity was 95.9% (95%CI: 91.2-98.3%) and 99.9% (95%CI: 99.6-100%), respectively. Viral CNS Flow Chip kit is an efficient multiplex platform for the detection of the main viruses involved in acute meningitis and encephalitis. The inclusion of a TOSV genome target may improve the laboratory diagnosis of viral neurological infections in endemic areas.
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Affiliation(s)
- Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain.
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - Cristina Gómez-Camarasa
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - José María Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
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8
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Fonollá J, Gracián C, Maldonado-Lobón JA, Romero C, Bédmar A, Carrillo JC, Martín-Castro C, Cabrera AL, García-Curiel JM, Rodríguez C, Sanbonmatsu S, Pérez-Ruiz M, Navarro JM, Olivares M. Effects of Lactobacillus coryniformis K8 CECT5711 on the immune response to influenza vaccination and the assessment of common respiratory symptoms in elderly subjects: a randomized controlled trial. Eur J Nutr 2017; 58:83-90. [PMID: 29124387 PMCID: PMC6424921 DOI: 10.1007/s00394-017-1573-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/27/2017] [Indexed: 11/28/2022]
Abstract
Purpose Elderly people are particularly vulnerable to seasonal influenza. Therefore, vaccination is strongly recommended. However, the vaccine efficacy is lower in the elderly, owing to immunosenescence. The objective of the present study was to evaluate the ability of the probiotic strain Lactobacillus coryniformis K8 CECT5711 to enhance the immune response to the influenza vaccine in the elderly and to assess the effects on symptoms related to respiratory infections. Methods A randomized, double-blind, placebo-controlled trial was conducted between November 2015 and April 2016. A total of 98 nursing home residents, more than 65 years of age were randomly assigned to receive L. coryniformis K8 CECT5711 (3 × 109 CFU/day) or a placebo for 2 weeks before influenza vaccination. The primary outcome was the percentage of seroconversion. The secondary outcomes were the incidence of influenza-like illness (ILI) and respiratory symptoms associated with respiratory infections during the 5-month follow-up period. The serum cytokine and immunoglobulin levels were also evaluated. Results The percentage of responders to vaccination was higher in the probiotic group than in the control group (p = 0.036). L. coryniformis ingestion was associated with a significantly lower incidence of respiratory symptoms commonly associated with respiratory infections (p = 0.007) and lower consumption of analgesics (p = 0.008). Conclusion The administration of L. coryniformis K8 CECT5711 to an elderly population increased the immune response against the influenza vaccine and decreased symptoms associated with respiratory infections. Probiotic administration may be a natural and safe strategy to improve the efficacy of vaccines and to protect against common respiratory infections in susceptible populations.
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Affiliation(s)
| | - Carlos Gracián
- Nursing home "Residencia de Mayores Claret", Granada, Spain.,Nursing home "Residencia Entreálamos", Granada, Spain.,Nursing home "Residencia de Mayores San Juan de Dios", Granada, Spain
| | | | - Carlos Romero
- Nursing home "Residencia Hermanitas de los Pobres", Granada, Spain
| | - Alicia Bédmar
- Nursing home "Residencia Fray Leopoldo", Granada, Spain
| | | | | | | | | | | | - Sara Sanbonmatsu
- Microbiology Service of Hospital "Virgen de las Nieves", Institute of Biosanitary Research of Granada, Granada, Spain
| | - Mercedes Pérez-Ruiz
- Microbiology Service of Hospital "Virgen de las Nieves", Institute of Biosanitary Research of Granada, Granada, Spain
| | - Jose M Navarro
- Microbiology Service of Hospital "Virgen de las Nieves", Institute of Biosanitary Research of Granada, Granada, Spain
| | - Mónica Olivares
- Biosearch Life, Camino de Purchil 66, 18004, Granada, Spain.
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9
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Carrillo-Ávila JA, Sorlózano-Puerto A, Pérez-Ruiz M, Gutiérrez-Fernández J. Multilocus Sequence Typing analysis of human Campylobacter coli in Granada (Spain). Rev Esp Quimioter 2016; 29:332-335. [PMID: 27701619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE Different subtypes of Campylobacter spp. have been associated with diarrhoea and a Multilocus Sequence Typing (MLST) method has been performed for subtyping. In the present work, MLST was used to analyse the genetic diversity of eight strains of Campylobacter coli. METHODS Nineteen genetic markers were amplified for MLST analysis: AnsB, DmsA, ggt, Cj1585c, CJJ81176-1367/1371, Tlp7, cj1321-cj1326, fucP, cj0178, cj0755/cfrA, ceuE, pldA, cstII, cstIII. After comparing the obtained sequences with the Campylobacter MLST database, the allele numbers, sequence types (STs) and clonal complexes (CCs) were assigned. RESULTS The 8 C. coli isolates yielded 4 different STs belonging to 2 CCs. Seven isolates belong to ST-828 clonal complex and only one isolate belong to ST-21. Two samples came from the same patient, but were isolated in two different periods of time. CONCLUSIONS MLST can be useful for taxonomic characterization of C. coli isolates.
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Affiliation(s)
| | | | | | - J Gutiérrez-Fernández
- José Gutiérrez-Fernández, Departamento de Microbiología. Facultad de Medicina. Avenida de la Investigación 11. E-18016 Granada, Spain.
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10
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Riazzo C, Pérez-Ruiz M, Sanbonmatsu-Gámez S, Pedrosa-Corral I, Gutiérrez-Fernández J, Navarro-Marí JM. Analytical performance of the Alere™ i Influenza A&B assay for the rapid detection of influenza viruses. Enferm Infecc Microbiol Clin 2015; 35:438-440. [PMID: 26620605 PMCID: PMC7103361 DOI: 10.1016/j.eimc.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
The analytical performance of the new Alere™ i Influenza A&B kit (AL-Flu) assay, based on isothermal nucleic acids amplification, was evaluated and compared with an antigen detection method, SD Bioline Influenza Virus Antigen Test (SDB), and an automated real-time RT-PCR, Simplexa™ Flu A/B & VRS Direct assay (SPX), for detection of influenza viruses. An “in-house” RT-PCR was used as the reference method. Sensitivity of AL-Flu, SDB, and SPX was 71.7%, 34.8%, and 100%, respectively. Specificity was 100% for all techniques. The turnaround time was 13 min for AL-Flu, 15 min for SDB, and 75 min for SPX. The Alere™ i Influenza A&B assay is an optimal point-of-care assay for influenza diagnosis in clinical emergency settings, and is more sensitive and specific than antigen detection methods.
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Affiliation(s)
- Cristina Riazzo
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain.
| | - Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - José Gutiérrez-Fernández
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - José-María Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
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11
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Sanbonmatsu-Gámez S, Pérez-Ruiz M, Lara-Oya A, Pedrosa-Corral I, Riazzo-Damas C, Navarro-Marí JM. Analytical performance of the automated multianalyte point-of-care mariPOC® for the detection of respiratory viruses. Diagn Microbiol Infect Dis 2015; 83:252-6. [PMID: 26283523 PMCID: PMC7132759 DOI: 10.1016/j.diagmicrobio.2015.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/23/2015] [Accepted: 07/16/2015] [Indexed: 12/18/2022]
Abstract
The analytical performance of mariPOC® respi test (ArcDia® Laboratories, Turku, Finland) was evaluated using nucleic acid amplification techniques (NAATs) as the gold standard. The mariPOC assay allows automated detection of antigens from 8 respiratory viruses: influenza A and B viruses, respiratory syncytial virus, adenovirus, human metapneumovirus, and parainfluenza viruses 1-3. Positive results from samples with high viral load are available in 20min. Nasopharyngeal aspirates (n=192) from patients with acute respiratory infection and from previously positive samples were analyzed by mariPOC and NAATs (Simplexa(TM) FluA/FluB & RSV kit [n=118] and Luminex® Respiratory virus panel xTAG® RVP FAST [n=74]). Sensitivity, specificity, positive predictive value, and negative predictive value of mariPOC were 85.4%, 99.2%, 95.9%, and 97%, respectively, and 84.6% of positive results were reported in 20min. The good analytical performance and extended portfolio of mariPOC show this rapid assay as a good alternative for the etiological diagnosis of acute respiratory infection in laboratories that are not equipped with molecular assays.
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Affiliation(s)
- Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain; Instituto de Investigación Biosanitaria de Granada, Calle Dr Azpitarte 4, 18012 Granada, Spain.
| | - Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain; Instituto de Investigación Biosanitaria de Granada, Calle Dr Azpitarte 4, 18012 Granada, Spain
| | - Ana Lara-Oya
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain; Instituto de Investigación Biosanitaria de Granada, Calle Dr Azpitarte 4, 18012 Granada, Spain
| | - Cristina Riazzo-Damas
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain
| | - José María Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida de las Fuerzas Armadas 2, 18012 Granada, Spain; Instituto de Investigación Biosanitaria de Granada, Calle Dr Azpitarte 4, 18012 Granada, Spain
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12
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Cabrerizo M, Trallero G, Pena MJ, Cilla A, Megias G, Muñoz-Almagro C, Del Amo E, Roda D, Mensalvas AI, Moreno-Docón A, García-Costa J, Rabella N, Omeñaca M, Romero MP, Sanbonmatsu-Gámez S, Pérez-Ruiz M, Santos-Muñoz MJ, Calvo C. Comparison of epidemiology and clinical characteristics of infections by human parechovirus vs. those by enterovirus during the first month of life. Eur J Pediatr 2015; 174:1511-6. [PMID: 25982340 PMCID: PMC4623089 DOI: 10.1007/s00431-015-2566-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 11/13/2022]
Abstract
UNLABELLED Human parechoviruses (HPeV) have been recently recognized as important viral agents in paediatric infections. The aims of this study were to investigate the HPeV infection prevalence in infants <1 month in Spain and, secondly, to analyse the clinical and epidemiological characteristics of the infected patients compared with those infected by enterovirus (EV). Infants <1 month with neurological or systemic symptoms were included in a multicentre prospective study. EV and HPeV detection by RT-PCR and genotyping were performed in cerebrospinal fluids (CSF), sera or throat swabs. Out of the total of 84 infants studied during 2013, 32 were EV positive (38 %) and 9 HPeV positive (11 %). HPeV-3 was identified in eight cases and HPeV-5 in one. Mean age of HPeV-positive patients was 18 days. Diagnoses were fever without source (FWS) (67 %), clinical sepsis (22 %) and encephalitis (11 %). Leukocytes in blood and CSF were normal. Pleocytosis (p = 0.03) and meningitis (p = 0.001) were significantly more frequent in patients with EV infections than with HPeV. CONCLUSIONS Although HPeV-3 infections were detected less frequently than EV, they still account for approximately 10 % of the cases analysed in infants younger than 1 month. HPeV-3 was mainly associated with FWS and without leukocytosis and pleocytosis in CSF. In these cases, HPeV screening is desirable to identify the aetiologic agent and prevent unnecessary treatment and prolonged hospitalization.
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Affiliation(s)
- María Cabrerizo
- Enterovirus Unit, National Centre for Microbiology, Health Institute "Carlos III", Madrid, Spain.
| | - Gloria Trallero
- Enterovirus Unit, National Centre for Microbiology, Health Institute "Carlos III", Madrid, Spain.
| | | | | | | | | | | | - Diana Roda
- Hospital San Joan de Deu, Barcelona, Spain.
| | | | | | | | | | | | | | | | | | - María José Santos-Muñoz
- Pediatrics Department, Hospital Severo Ochoa, Avda. Orellana, s.n., Leganés, 28911, Madrid, Spain.
| | - Cristina Calvo
- Pediatrics Department, Hospital Severo Ochoa, Avda. Orellana, s.n., Leganés, 28911, Madrid, Spain.
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13
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Cabrerizo M, Calvo C, Rabella N, Muñoz-Almagro C, del Amo E, Pérez-Ruiz M, Sanbonmatsu-Gámez S, Moreno-Docón A, Otero A, Trallero G. Design and validation of a real-time RT-PCR for the simultaneous detection of enteroviruses and parechoviruses in clinical samples. J Virol Methods 2014; 208:125-8. [PMID: 25152526 DOI: 10.1016/j.jviromet.2014.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 11/30/2022]
Abstract
Human enteroviruses (EVs) and parechoviruses (HPeVs) are important etiological agents causing infections such as meningitis, encephalitis and sepsis-like disease in neonates and young children. We have developed a real-time RT-PCR for simultaneous detection of EV and HPeV in clinical samples. Primers and probe sets were designed from the conserved 5'-noncoding region of the genomes. The sensitivity, specificity and reproducibility of the technique were measured using a set of 25 EV and 6 HPeV types. All EVs but no HPeVs were detected with the EV primers-probe set. The HPeV primers-probe set detected only the 6 HPeV types. The lower detection limit was found to be 4 and 40CCID50/ml for HPeV and EV respectively, demonstrating high sensitivity of the technique for both viruses. The threshold cycle values were highly reproducible on repeat testing of positive controls among assay runs. The assay was evaluated in 53 clinical samples of suspected meningitis, sepsis or febrile syndromes from children under 3 years. In 11 of these (21%) EVs were detected, while 4, i.e. 7.5%, were HPeV positive. Molecular typing was carried out for 73% of the viruses. In summary, the RT-PCR method developed demonstrated effectively both EV and HPeV detection, which can cause similar clinical symptoms in infants.
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Affiliation(s)
- María Cabrerizo
- Enterovirus Unit, National Centre for Microbiology, Health Institute "Carlos III", Madrid, Spain.
| | | | | | | | | | | | | | | | - Almudena Otero
- Enterovirus Unit, National Centre for Microbiology, Health Institute "Carlos III", Madrid, Spain
| | - Gloria Trallero
- Enterovirus Unit, National Centre for Microbiology, Health Institute "Carlos III", Madrid, Spain
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14
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Navarro-Marí JM, Pérez-Ruiz M, Galán Montemayor JC, Marcos Maeso MÁ, Reina J, de Oña Navarro M, Cilla Eguiluz CG. Circulation of other respiratory viruses and viral co-infection during the 2009 pandemic influenza. Enferm Infecc Microbiol Clin 2013; 30 Suppl 4:25-31. [PMID: 23116789 PMCID: PMC7130202 DOI: 10.1016/s0213-005x(12)70101-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Coinciding with the pandemic wave of the influenza A(H1N1)pdm09 virus, other respiratory viruses have co-circulated in our area and were responsible for many acute respiratory infections and influenza-like illness (ILI). Apart from the pandemic virus that was responsible for most ILI cases, incidence rates of other viruses have varied among geographical areas. In general, human rhinovirus was the most frequent among individuals from the community, and respiratory syncytial virus among hospitalized patients. Detection rates of other respiratory viruses such as human metapneumovirus, adenovirus or parainfluenza viruses have been much lower. On the basis of an interference mechanism, human rhinovirus may contribute to modulate the pandemic wave, although available data are not conclusive to support this hypothesis. In contrast, the epidemic wave of respiratory syncytial virus during 2009–2010 was similar to previous seasons. Overall, incidence rates of respiratory viruses other than influenza did not change significantly during the pandemic season compared to other seasons. No association has been found between coinfection of pandemic influenza and other respiratory viruses with the prognosis of patients with influenza. The involvement of clinical virology laboratories in the etiological diagnosis of ILI cases has improved and has optimized diagnostic procedures.
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15
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Cabrerizo M, Trallero G, Echevarría JE, Moreno-Docón A, Pena MJ, Pérez-Ruiz M, Avellón A, de Ory F. Molecular characterization of enteroviruses associated with neurological infections in Spain, 2008. J Med Virol 2013; 85:1975-7. [PMID: 23893817 DOI: 10.1002/jmv.23693] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2013] [Indexed: 11/06/2022]
Abstract
In order to investigate the etiology of viral neurological infections in Spain, a national study was performed in 2008. The results obtained have been published. Enteroviruses were the most frequent cause of the aseptic meningitis and infant febrile syndromes. The present report supplements the previous study with the genotyping of the detected enteroviruses. Typing was by amplification of partial VP1 region and sequencing in 70 (53%) of the 132 available cerebrospinal fluid samples positive for enteroviruses. Twelve different genotypes within the B species were identified. Echovirus 4 was predominant (24%), followed by echovirus 30 (19%), echovirus 9 (17%), and echovirus 6 (14%). In summary, a co-circulation of several enterovirus types associated with meningitis in children under 15 years old was observed. Although infrequently detected, echovirus 4 was the predominant genotype identified due to an aseptic meningitis outbreak which occurred in the Canary Islands in 2008.
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Affiliation(s)
- M Cabrerizo
- National Center for Microbiology, Health Institute "Carlos III", Madrid, Spain.
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16
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Navarro-Marí JM, Gómez-Camarasa C, Pérez-Ruiz M, Sanbonmatsu-Gámez S, Pedrosa-Corral I, Jiménez-Valera M. Clinic-epidemiologic study of human infection by Granada virus, a new phlebovirus within the sandfly fever Naples serocomplex. Am J Trop Med Hyg 2013; 88:1003-6. [PMID: 23419365 DOI: 10.4269/ajtmh.12-0732] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Granada virus (GRV), a new phlebovirus within the Naples serocomplex, has been recently described in phlebotomine sandflies from Spain. The presence of anti-GRV immunoglobulin G (IgG) antibodies was investigated by indirect fluorescence assay (IFA) and neutralization test (NT) in 920 serum samples from the Granada population. By IFA, an overall GRV seroprevalence of 15.8% (N = 145) was observed, significantly increasing up to 65 years. NT was positive in 18% of anti-GRV IFA-positive samples. IgG antibodies against Toscana virus (TOSV), a hyperendemic phlebovirus within Granada province, were detected in 40% of anti-GRV-positive cases. Anti-GRV IgM antibodies were detected in 36 (6.6%) of 547 acute-phase serum samples from individuals with febrile illness, exanthema, and/or acute respiratory infection. All positives were anti-TOSV IgM-negative. GRV may infect humans, with most cases being asymptomatic. The codetection of anti-GRV and anti-TOSV IgG antibodies could be attributable to cross-reactivity or exposure to the same transmission vector.
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Pérez-Ruiz M, Navarro-Marí JM, Sánchez-Seco MP, Gegúndez MI, Palacios G, Savji N, Lipkin WI, Fedele G, de Ory-Manchón F. Lymphocytic choriomeningitis virus-associated meningitis, southern Spain. Emerg Infect Dis 2013; 18:855-8. [PMID: 22515986 PMCID: PMC3358079 DOI: 10.3201/eid1805.111646] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lymphocytic choriomeningitis virus (LCMV) was detected in 2 patients with acute meningitis in southern Spain within a 3-year period. Although the prevalence of LCMV infection was low (2 [1.3%] of 159 meningitis patients), it represents 2.9% of all pathogens detected. LCMV is a noteworthy agent of neurologic illness in immunocompetent persons.
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18
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de Ory F, Avellón A, Echevarría JE, Sánchez-Seco MP, Trallero G, Cabrerizo M, Casas I, Pozo F, Fedele G, Vicente D, Pena MJ, Moreno A, Niubo J, Rabella N, Rubio G, Pérez-Ruiz M, Rodríguez-Iglesias M, Gimeno C, Eiros JM, Melón S, Blasco M, López-Miragaya I, Varela E, Martinez-Sapiña A, Rodríguez G, Marcos MÁ, Gegúndez MI, Cilla G, Gabilondo I, Navarro JM, Torres J, Aznar C, Castellanos A, Guisasola ME, Negredo AI, Tenorio A, Vázquez-Morón S. Viral infections of the central nervous system in Spain: a prospective study. J Med Virol 2012; 85:554-62. [PMID: 23239485 DOI: 10.1002/jmv.23470] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2012] [Indexed: 11/10/2022]
Abstract
The aim of the study was to determine the incidence of viruses causing aseptic meningitis, meningoencephalitis, and encephalitis in Spain. This was a prospective study, in collaboration with 17 Spanish hospitals, including 581 cases (CSF from all and sera from 280): meningitis (340), meningoencephalitis (91), encephalitis (76), febrile syndrome (7), other neurological disorders (32), and 35 cases without clinical information. CSF were assayed by PCR for enterovirus (EV), herpesvirus (herpes simplex [HSV], varicella-zoster [VZV], cytomegalovirus [CMV], Epstein-Barr [EBV], and human herpes virus-6 [HHV-6]), mumps (MV), Toscana virus (TOSV), adenovirus (HAdV), lymphocytic choriomeningitis virus (LCMV), West Nile virus (WNV), and rabies. Serology was undertaken when methodology was available. Amongst meningitis cases, 57.1% were characterized; EV was the most frequent (76.8%), followed by VZV (10.3%) and HSV (3.1%; HSV-1: 1.6%; HSV-2: 1.0%, HSV non-typed: 0.5%). Cases due to CMV, EBV, HHV-6, MV, TOSV, HAdV, and LCMV were also detected. For meningoencephalitis, 40.7% of cases were diagnosed, HSV-1 (43.2%) and VZV (27.0%) being the most frequent agents, while cases associated with HSV-2, EV, CMV, MV, and LCMV were also detected. For encephalitis, 27.6% of cases were caused by HSV-1 (71.4%), VZV (19.1%), or EV (9.5%). Other positive neurological syndromes included cerebellitis (EV and HAdV), seizures (HSV), demyelinating disease (HSV-1 and HHV-6), myelopathy (VZV), and polyradiculoneuritis (HSV). No rabies or WNV cases were identified. EVs are the most frequent cause of meningitis, as is HSV for meningoencephalitis and encephalitis. A significant number of cases (42.9% meningitis, 59.3% meningoencephalitis, 72.4% encephalitis) still have no etiological diagnosis.
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Affiliation(s)
- F de Ory
- National Centre for Microbiology, Majadahonda, Spain.
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Pérez-Ruiz M, Pedrosa-Corral I, Sanbonmatsu-Gámez S, Navarro-Marí M. Laboratory detection of respiratory viruses by automated techniques. Open Virol J 2012; 6:151-9. [PMID: 23248735 PMCID: PMC3522051 DOI: 10.2174/1874357901206010151] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/11/2012] [Accepted: 09/20/2012] [Indexed: 12/26/2022] Open
Abstract
Advances in clinical virology for detecting respiratory viruses have been focused on nucleic acids amplification techniques, which have converted in the reference method for the diagnosis of acute respiratory infections of viral aetiology. Improvements of current commercial molecular assays to reduce hands-on-time rely on two strategies, a stepwise automation (semi-automation) and the complete automation of the whole procedure. Contributions to the former strategy have been the use of automated nucleic acids extractors, multiplex PCR, real-time PCR and/or DNA arrays for detection of amplicons. Commercial fully-automated molecular systems are now available for the detection of respiratory viruses. Some of them could convert in point-of-care methods substituting antigen tests for detection of respiratory syncytial virus and influenza A and B viruses. This article describes laboratory methods for detection of respiratory viruses. A cost-effective and rational diagnostic algorithm is proposed, considering technical aspects of the available assays, infrastructure possibilities of each laboratory and clinic-epidemiologic factors of the infection.
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Affiliation(s)
- Mercedes Pérez-Ruiz
- Laboratorio de Referencia de Salud Pública para Enfermedades con Sospecha de Etiología Vírica en Andalucía (Consejería de Salud), Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda, Fuerzas Armadas, 2, 18014 Granada, Spain
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20
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Torres-Martos E, Pérez-Ruiz M, Pedrosa-Corral I, Peña-Caballero M, Jiménez-Valera MM, Pérez-Ramírez MD, Navarro-Marí JM. [Evaluation of the LightCycler® SeptiFast test in newborns and infants with clinical suspicion of sepsis]. Enferm Infecc Microbiol Clin 2012; 31:375-9. [PMID: 23137657 DOI: 10.1016/j.eimc.2012.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Neonatal sepsis is a significant cause of morbidity and mortality. Early diagnosis and prompt antimicrobial therapy are crucial for a favorable outcome of the newborn child. Blood culture, the current "gold standard" method for diagnosing bloodstream infections, has a low sensitivity in newborns. We evaluated the multiplex real-time PCR LightCycler(®) SeptiFast (LC-SF) for detection of bloodstream infections in newborns, compared with conventional blood culture. METHODS A total of 42 blood samples were obtained from 35 subjects presenting with a febrile episode and hospitalized in neonatal intensive care unit at Hospital Universitario Virgen de las Nieves. Two samples were collected during each febrile episode in order to carry out LC-SF assay and blood culture, respectively. RESULTS Sensitivity and specificity of 79% and 87%, respectively, compared with clinical diagnosis, were obtained for LC-SF. Contamination rate of blood cultures was 16.7%, mainly due to coagulase-negative staphylococci (CoNS) and viridans groups of streptococci. Contamination rate of LC-SF by CoNS was 2.4%. Concordance between LC-SF and blood culture was moderate (kappa index: 0.369). LC-SF demonstrated a higher concordance (kappa index: 0.729) with the final clinical diagnosis than blood culture (kappa index: 0.238). CONCLUSION LC-SF assay could be a useful diagnostic tool, along with a conventional blood culture, in newborn, for confirming or ruling out those cases that blood culture could not determine, shortening the time to result to 7 hours.
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Affiliation(s)
- Eva Torres-Martos
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, España.
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Bautista-Marín MF, Rojo-Martín MD, Pérez-Ruiz M, Miranda-Casas C, Martínez-Muñoz P, Navarro-Marí JM. Implementation and monitoring of a quality management system based on the standard UNE-EN-ISO 15189 in a urine culture unit. Clin Biochem 2012; 45:374-7. [DOI: 10.1016/j.clinbiochem.2011.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/16/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
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Pedrosa-Corral I, Pérez-Ruiz M, Navarro-Marí JM, Ruiz-Bravo A. Association of Human bocavirus with Respiratory Infections in Outpatients and in Patients Attended at a Reference Hospital. Indian J Virol 2011; 22:84-9. [PMID: 23637508 PMCID: PMC3550741 DOI: 10.1007/s13337-011-0042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 06/28/2011] [Indexed: 10/25/2022]
Abstract
The role of Human bocavirus (HBoV) in human infectious disease is unclear due to the frequent detection of this virus in association with other respiratory viruses with a recognized pathogenic role in acute respiratory infection. We have analyzed the impact of HBoV in outpatients and in patients requiring hospitalisation or emergency attention for acute respiratory infections. Respiratory viruses were investigated by real-time PCR, direct antigen detection and/or viral culture by shell-vial assay. Nasopharyngeal aspirates, BAL and/or sputum samples from patients attended at a reference hospital, and nasal/throat swabs from outpatients were used. Respiratory viruses were detected in 660 samples (47%). HBoV detection rate was 12.6%, only preceded by respiratory syncytial virus (25%). Co-detections were observed in 12.9% of samples, and HBoV was present in 81% of them. Similar detection rates of HBoV were obtained in individuals with positive and negative results for other respiratory viruses (12.5% and 12.7%, respectively). The crossing point value was taken as a measure of HBoV viral load. Higher HBoV loads were observed in children, and in patients from the hospital. HBoV viral load was not associated with symptoms of upper respiratory tract infection or lower respiratory tract disease. Although HBoV is frequently detected in respiratory specimens, there is a poor association between HBoV-positive specimens and clinical parameters. A clinical impact of HBoV in respiratory infection probably occurs in few cases.
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Affiliation(s)
- Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
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Collao X, Palacios G, de Ory F, Sanbonmatsu S, Pérez-Ruiz M, Navarro JM, Molina R, Hutchison SK, Lipkin WI, Tenorio A, Sánchez-Seco MP. Granada virus: a natural phlebovirus reassortant of the sandfly fever Naples serocomplex with low seroprevalence in humans. Am J Trop Med Hyg 2010. [PMID: 20889862 DOI: 10.4269/ajtmh.2010.09-069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A new member of the phlebovirus genus, tentatively named Granada virus, was detected in sandflies collected in Spain. By showing the presence of specific neutralizing antibodies in human serum collected in Granada, we show that Granada virus infects humans. The analysis of the complete genome of Granada virus revealed that this agent is likely to be a natural reassortant of the recently described Massilia virus (donor of the long and short segments) with a yet unidentified phlebovirus (donor of the medium segment).
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Affiliation(s)
- Ximena Collao
- Department of Virology, National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain.
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Collao X, Palacios G, de Ory F, Sanbonmatsu S, Pérez-Ruiz M, Navarro JM, Molina R, Hutchison SK, Lipkin WI, Tenorio A, Sánchez-Seco MP. Granada virus: a natural phlebovirus reassortant of the sandfly fever Naples serocomplex with low seroprevalence in humans. Am J Trop Med Hyg 2010; 83:760-5. [PMID: 20889862 DOI: 10.4269/ajtmh.2010.09-0697] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A new member of the phlebovirus genus, tentatively named Granada virus, was detected in sandflies collected in Spain. By showing the presence of specific neutralizing antibodies in human serum collected in Granada, we show that Granada virus infects humans. The analysis of the complete genome of Granada virus revealed that this agent is likely to be a natural reassortant of the recently described Massilia virus (donor of the long and short segments) with a yet unidentified phlebovirus (donor of the medium segment).
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Affiliation(s)
- Ximena Collao
- Department of Virology, National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain.
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Navarro-Marí JM, Palop-Borrás B, Pérez-Ruiz M, Sanbonmatsu-Gámez S. Serosurvey study of Toscana virus in domestic animals, Granada, Spain. Vector Borne Zoonotic Dis 2010; 11:583-7. [PMID: 20925529 DOI: 10.1089/vbz.2010.0065] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Toscana virus (TOSV) is transmitted by infected sandflies. In Mediterranean countries, TOSV is one of the major viral pathogens involved in aseptic meningitis and meningoencephalitis in humans. It remains unclear if there are animal reservoirs able to maintain the virus through the cold months of the year, when the vector is not circulating. From May to October of 2006 and 2007, we conducted a serosurvey study on domestic animals from Granada province (southern Spain). TOSV was investigated in 1186 serum samples from horses, goats, pigs, cats, dogs, sheep, and cows by serology (indirect fluorescence assay), viral culture, and RT-polymerase chain reaction. Specific anti-TOSV antibodies were detected in 429 (36.2%) serum samples. The highest seropositivity rates were observed in cats (59.6%) and dogs (48.3%). These results suggest that an important percentage of the domestic animals have been infected by TOSV. Significantly different seroprevalence rates were detected in goats among distinct geographical areas. All viral cultures were negative. TOSV was detected by RT-polymerase chain reaction in only one serum sample from a goat. Thus, the studied animals do not seem to act as reservoirs for TOSV; otherwise, they could be amplifying hosts for the virus.
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Collao X, Palacios G, Sanbonmatsu-Gámez S, Pérez-Ruiz M, Negredo AI, Navarro-Marí JM, Grandadam M, Aransay AM, Lipkin WI, Tenorio A, Sánchez-Seco MP. Genetic diversity of Toscana virus. Emerg Infect Dis 2009; 15:574-7. [PMID: 19331735 PMCID: PMC2671431 DOI: 10.3201/eid1504.081111] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Distribution of Toscana virus (TOSV) is evolving with climate change, and pathogenicity may be higher in nonexposed populations outside areas of current prevalence (Mediterranean Basin). To characterize genetic diversity of TOSV, we determined the coding sequences of isolates from Spain and France. TOSV is more diverse than other well-studied phleboviruses (e.g.,Rift Valley fever virus).
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Reina-González G, Pérez-Ruiz M, Avellón A, Trallero G, Otero A, de la Rosa-Fraile M, Jiménez-Valera M, Navarro-Marí JM. Enterovirus 75, un nuevo virus patógeno en nuestro medio. Enferm Infecc Microbiol Clin 2007; 25:566-9. [DOI: 10.1157/13111182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Acute respiratory infections (ARI) of viral origin are one of the main causes of morbidity and mortality worldwide. In addition to traditional viruses, such as the influenza virus, respiratory syncytial virus, rhinovirus, parainfluenza viruses 1 to 4, and adenovirus, other viruses such as metapneumovirus, new coronaviruses (human coronavirus NL63 and HKU1 and severe acute respiratory syndrome [SARS]-coronavirus), and recently bocaviruses, have been identified as causal agents of ARI. Although most of these viral infections follow a benign and selflimiting course in healthy adults, the consequences for the health care systems increase when they involve children, the elderly, immunosuppressed individuals, or those with chronic underlying diseases. These viral infections are an important cause of hospitalization and death, mainly during the cold months of the year, and, from a social-health perspective, ARI are a drain on economic resources and a frequent cause of work absenteeism. Occasionally, some of these viruses may cause emergent world health problems, as has occurred with the influenza virus pandemic strain and SARScoronavirus. While classical diagnostic methods based on culture and antigen detection remain useful for traditional respiratory viruses, recently described viruses are diagnosed mainly by molecular amplification techniques.
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Pérez-Ruiz M, Yeste R, Ruiz-Pérez MJ, Ruiz-Bravo A, de la Rosa-Fraile M, Navarro-Marí JM. Testing of diagnostic methods for detection of influenza virus for optimal performance in the context of an influenza surveillance network. J Clin Microbiol 2007; 45:3109-10. [PMID: 17652478 PMCID: PMC2045238 DOI: 10.1128/jcm.00697-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza surveillance networks must detect early the viruses that will cause the forthcoming annual epidemics and isolate the strains for further characterization. We obtained the highest sensitivity (95.4%) with a diagnostic tool that combined a shell-vial assay and reverse transcription-PCR on cell culture supernatants at 48 h, and indeed, recovered the strain.
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Affiliation(s)
- Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain.
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Pérez-Ruiz M, Collao X, Navarro-Marí JM, Tenorio A. Reverse transcription, real-time PCR assay for detection of Toscana virus. J Clin Virol 2007; 39:276-81. [PMID: 17584525 DOI: 10.1016/j.jcv.2007.05.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 04/28/2007] [Accepted: 05/09/2007] [Indexed: 02/07/2023]
Abstract
BACKGROUND The arthropod-borne Toscana virus is a common cause of acute neurological infection in the Mediterranean basin. Recently, a new lineage, highly divergent from the Italian prototype, has been reported in Spain. OBJECTIVE We describe a reverse transcription, real-time PCR assay for detection of both Toscana virus genotypes. The real-time PCR uses a TaqMan probe and an internal control to identify false negative results. STUDY DESIGN A conserved region of the two known lineages of Toscana virus, located at the 3' end of the small segment of their genomes, was chosen to design both the primers and the probe. RESULTS The sensitivity of the assay was 0.0158 TICD(50) per reaction of Toscana virus, equivalent to seven copies of cDNA. No other phleboviruses or RNA viruses were amplified by this specific real-time PCR. CONCLUSIONS The assay seems to be sensitive, reliable and easy to be applied in the diagnosis of autochthonous and/or imported suspected cases of Toscana virus infection.
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Affiliation(s)
- Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain.
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Sanbonmatsu-Gámez S, Pérez-Ruiz M, Collao X, Sánchez-Seco MP, Morillas-Márquez F, de la Rosa-Fraile M, Navarro-Mari JM, Tenorio A. Toscana virus in Spain. Emerg Infect Dis 2006; 11:1701-7. [PMID: 16318721 PMCID: PMC3367369 DOI: 10.3201/eid1111.050851] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Toscana virus (TOSV, Phlebovirus, family Bunyaviridae) infection is one of the most prevalent arboviruses in Spain. Within the objectives of a multidisciplinary network, a study on the epidemiology of TOSV was conducted in Granada, in southern Spain. The overall seroprevalence rate was 24.9%, significantly increasing with age. TOSV was detected in 3 of 103 sandfly pools by viral culture or reverse transcription-polymerase chain reaction from a region of the L gene. Nucleotide sequence homology was 99%-100% in TOSV from vectors and patients and 80%-81% compared to the Italian strain ISS Phl.3. Sequencing of the N gene of TOSV isolates from patients and vectors indicated 87%-88% and 100% homology at the nucleotide and amino acid levels, respectively, compared to the Italian strain. These findings demonstrate the circulation of at least 2 different lineages of TOSV in the Mediterranean basin, the Italian lineage and the Spanish lineage.
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Affiliation(s)
- Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda. Fuerzas Armadas, s/n 18014-Granada, Spain
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Navarro-Marí JM, Pérez-Ruiz M, Cantudo-Muñoz P, Petit-Gancedo C, Jiménez-Valera M, Rosa-Fraile M. Influenza-like illness criteria were poorly related to laboratory-confirmed influenza in a sentinel surveillance study. J Clin Epidemiol 2005; 58:275-9. [PMID: 15768487 DOI: 10.1016/j.jclinepi.2004.08.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To analyze the most related clinical data for influenza and the utility of influenza-like illness criteria as the clinical threshold for sampling in an influenza sentinel surveillance over a 3-year period. METHODS Sentinel physicians collected throat specimens and data from outpatients with acute respiratory infection (< or = 72 hours duration). Laboratory-confirmed influenza infection was compared with independent symptoms and the influenza-like illness criteria, as defined by the Classification Committee of the World Organization of Family Doctors. RESULTS From 1934 patients, 359 (18.56%) yielded positive results for influenza viruses. Only 199 (55.4%) of laboratory-confirmed cases fulfilled clinical criteria of influenza-like illness: positive and negative predictive value (PPV and NPV) of 0.36 and 0.88, respectively. Fever, cough, and rhinorrhea individually correlated with influenza infections (PPV: 0.30, 0.20, and 0.20, respectively; NPV: 0.92, 0.87, and 0.85, respectively). Multivariate analysis demonstrated that the correlation of influenza infection with the presence of fever and cough was similar to the correlation between influenza infection and influenza-like illness criteria (odds ratio 2.24 vs. 2.71, respectively). CONCLUSION Influenza-like illness criteria are poorly related to laboratory-confirmed influenza. For early detection of influenza viruses in surveillance systems, a less restrictive clinical criterion (specifically, acute respiratory infection) perhaps should be followed.
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Navarro JM, Fernández-Roldán C, Pérez-Ruiz M, Sanbonmatsu S, de la Rosa M, Sánchez-Seco MP. [Meningitis by Toscana virus in Spain: description of 17 cases]. Med Clin (Barc) 2004; 122:420-2. [PMID: 15066251 DOI: 10.1016/s0025-7753(04)74259-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND OBJECTIVE We aimed to analyze the clinical and epidemiological data from the first series of patients with meningitis by Toscana virus in Spain. PATIENTS AND METHOD We analyzed a total of 724 cerebrospinal fluid (CSF) samples from patients with suspicion of aseptic meningitis for virus isolation in cell culture. The clinical records of patients in whom Toscana virus was isolated were analyzed. RESULTS Toscana virus was isolated in CSF in 17 patients (7% of all viral isolates). The first case was diagnosed in June 1988 and the last one in August 2002. The mean age was 27 years (range: 10-64 years). Most patients were based in rural area (n = 11, 64.7%). Most common symptoms were headache (holocranial or focal) present in all patients and moderate fever observed in 76.5% of them with a mean duration of 48 h (range: 18 h-5 days). Nuchal rigidity was present in 9 patients (53%). All cases were seen between June and October, and predominantly in August (53%). The outcome was favorable in all cases, and the mean time of duration of the disease was 7 days (range: 3-10 days). CONCLUSIONS Toscana virus must be taken into account among those agents responsible of lymphocytic meningitis in Spain.
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Affiliation(s)
- José María Navarro
- Servicio de Microbiología. Hospital Universitario Virgen de las Nieves. Granada. España.
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Navarro JM, Fernández-Roldán C, Pérez-Ruiz M, Sanbonmatsu S, de la Rosa M, Sánchez-Seco MP. [Meningitis by Toscana virus in Spain: description of 17 cases]. Med Clin (Barc) 2004. [PMID: 15066251 DOI: 10.1157/13059539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND OBJECTIVE We aimed to analyze the clinical and epidemiological data from the first series of patients with meningitis by Toscana virus in Spain. PATIENTS AND METHOD We analyzed a total of 724 cerebrospinal fluid (CSF) samples from patients with suspicion of aseptic meningitis for virus isolation in cell culture. The clinical records of patients in whom Toscana virus was isolated were analyzed. RESULTS Toscana virus was isolated in CSF in 17 patients (7% of all viral isolates). The first case was diagnosed in June 1988 and the last one in August 2002. The mean age was 27 years (range: 10-64 years). Most patients were based in rural area (n = 11, 64.7%). Most common symptoms were headache (holocranial or focal) present in all patients and moderate fever observed in 76.5% of them with a mean duration of 48 h (range: 18 h-5 days). Nuchal rigidity was present in 9 patients (53%). All cases were seen between June and October, and predominantly in August (53%). The outcome was favorable in all cases, and the mean time of duration of the disease was 7 days (range: 3-10 days). CONCLUSIONS Toscana virus must be taken into account among those agents responsible of lymphocytic meningitis in Spain.
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Affiliation(s)
- José María Navarro
- Servicio de Microbiología. Hospital Universitario Virgen de las Nieves. Granada. España.
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Pérez-Ruiz M, Rodríguez-Granger JM, Bautista-Marín MF, Romero-Noguera J, Rosa-Fraile M. Genetic diversity of Streptococcus agalactiae strains colonizing the same pregnant woman. Epidemiol Infect 2004; 132:375-8. [PMID: 15061514 PMCID: PMC2870115 DOI: 10.1017/s0950268803001845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pulsed-field gel electrophoresis (PFGE) of SmaI-DNA digests and serotyping was performed on 15 colonies of Streptococcus agalactiae (GBS) from each of 30 vaginal rectal colonized women. Five distinct GBS serotypes were observed among the 30 specimens (Ia, Ib, II, III and V). In 29 of the 30 samples, the same serotype was observed among all 15 colonies; in the remaining specimen, the 15 colonies yielded two serotypes (II and V). The PFGE profiles of all colonies in 27 of the 30 subjects were indistinguishable within each subject. In the remaining women, different DNA profiles were identified among the colonies in each specimen, one of whom carried two different serotypes. Furthermore, strains of the same serotype belonging to different women were genetically heterogeneous.
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Affiliation(s)
- M Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avenida Fuerzas Armadas, s/n 18014, Granada, Spain
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Pérez-Ruiz M, Navarro-Marí JM, Palacios Del Valle E, Rosa-Fraile M. Human rhabdomyosarcoma cells for rapid detection of enteroviruses by shell-vial assay. J Med Microbiol 2003; 52:789-791. [PMID: 12909656 DOI: 10.1099/jmm.0.05237-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The ability of the RD (rhabdomyosarcoma) and MRC-5 cell-lines to detect enteroviruses in 33 clinical samples (cerebrospinal fluid, stools and throat swabs) was evaluated. The samples had previously tested enterovirus-positive by traditional tube-culture and had been frozen after their initial processing. By traditional tube-culture, 100 and 85 % of samples were positive for enterovirus in RD and MRC-5 cells, respectively. By rapid shell-vial assay, 94 and 45.5 % were positive after 48 h incubation in RD and MRC-5 cells, respectively. RD cells supported growth of all enterovirus serotypes, whereas MRC-5 cells were not able to detect any of the three coxsackieviruses that were found (one coxsackievirus A9 and two coxsackievirus B5). The shell-vial assay with RD cell-lines may be a useful tool for rapid diagnosis of enteroviral infection.
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Affiliation(s)
- M Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda Fuerzas Armadas s/n, 18014 Granada, Spain
| | - J M Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda Fuerzas Armadas s/n, 18014 Granada, Spain
| | - E Palacios Del Valle
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda Fuerzas Armadas s/n, 18014 Granada, Spain
| | - M Rosa-Fraile
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda Fuerzas Armadas s/n, 18014 Granada, Spain
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Navarro-Marí JM, Palacios Del Valle E, Pérez-Ruiz M, De La Rosa M. The impact of influenza viruses on hospitalizations in infants younger than two years old during epidemics of respiratory syncytial virus infection. Clin Microbiol Infect 2003; 9:959-63. [PMID: 14616686 DOI: 10.1046/j.1469-0691.2003.00672.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to evaluate the association of influenza viruses with hospitalizations for acute respiratory infection in infants younger than two years old during epidemics of respiratory syncytial virus infection, we studied 512 nasal washes from this population. The samples were obtained from 1997 to 2000. A total of 337 viruses were isolated: 264 respiratory syncytial viruses, 62 influenza viruses, eight parainfluenza viruses, two adenovirus and one rhinovirus. Hospitalizations for acute respiratory infection were owing to influenza and respiratory syncytial viruses in 18.3% vs. 78.3% of all cases, and 32.5% vs. 65.8%, respectively, in the group of infants between 6 months and 2 years old.
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Affiliation(s)
- J M Navarro-Marí
- The Microbiology Service, Hospital Universitario Virgen de las Nieves, Granada, Spain.
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Pérez-Ruiz M, Fernández-Roldán C, Navarro-Martí JM, de la Rosa-Fraile M. Evaluación preliminar de nuevos métodos de detección de antígeno para el diagnóstico rápido de virus respiratorio sincitial. Enferm Infecc Microbiol Clin 2003; 21:602-3. [PMID: 14642264 DOI: 10.1016/s0213-005x(03)73019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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de la Rosa M, Rodríguez-Granger J, Pérez-Ruiz M, Sampedro A. [Use of the Granada media and quality control of culture media]. Enferm Infecc Microbiol Clin 2000; 18:427. [PMID: 11153215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Pérez-Ruiz M, Barroso-DelJesus A, Berzal-Herranz A. Specificity of the hairpin ribozyme. Sequence requirements surrounding the cleavage site. J Biol Chem 1999; 274:29376-80. [PMID: 10506198 DOI: 10.1074/jbc.274.41.29376] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Substrate sequence requirements of the hairpin ribozyme have been partially defined by both mutational and in vitro selection experiments. It was considered that the best targets were those that included the N downward arrowGUC sequence surrounding the cleavage site. In contrast to previous studies that failed to evaluate all possible combinations of these nucleotides, we have performed an exhaustive analysis of the cleavage of 64 substrate variants. They represent all possible sequence combinations of the J2/1 nucleotides except the well established G(+1). No cleavage was observed with 24 sequences. C(+2) variants showed little or no cleavage, whereas U(+2) substrates were all cleavable. The maximal cleavage rate was obtained with the AGUC substrate. Cleavage rates of sequences HGUC (H = A, C, or U), GGUN, GGGR (R = A or G), AGUU, and UGUA were up to 5 times lower than the AGUC one. This shows that other sequences besides NGUC could also be considered as good targets. A second group of sequences WGGG (W = A or U), UGUK (K = G or U), MGAG (M = A or C), AGUA, and UGGA were cleaved between 6 and 10 times less efficiently. Furthermore, the UGCU sequence of a noncleavable viral target was mutated to AGUC resulting in a proficiently cleavable substrate by its cognate hairpin ribozyme. This indicates that our conclusions may be extrapolated to other hairpin ribozymes with different specificity.
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Affiliation(s)
- M Pérez-Ruiz
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, Ventanilla 11, 18001 Granada, Spain
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Navarro-Marí JM, Sanbonmatsu-Gámez S, Pérez-Ruiz M, De La Rosa-Fraile M. Rapid detection of respiratory viruses by shell vial assay using simultaneous culture of HEp-2, LLC-MK2, and MDCK cells in a single vial. J Clin Microbiol 1999; 37:2346-7. [PMID: 10364611 PMCID: PMC85156 DOI: 10.1128/jcm.37.7.2346-2347.1999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A shell vial assay with simultaneous culture of HEp-2, LLC-MK2, and MDCK cell lines in a single tube (CoHLM SV assay) was compared with traditional tube culture (TC) for the detection of the main respiratory viruses in 358 nasal wash specimens. A total of 170 strains were isolated from 168 virus-positive samples. A total of 94. 1% of the strains (160 strains; 128 respiratory syncytial viruses and 32 other viruses) were detected by the CoHLM SV assay in 48 h, whereas 98.2% of the strains (167 strains; 132 respiratory syncytial viruses and 35 other viruses) were detected by TC in a mean time of 6 days. The CoHLM SV assay may be useful for the rapid detection of respiratory viruses.
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Affiliation(s)
- J M Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
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Pérez-Ruiz M, Ros J, Morales-Ruiz M, Navasa M, Colmenero J, Ruiz-del-Arbol L, Cejudo P, Clária J, Rivera F, Arroyo V, Rodés J, Jiménez W. Vascular endothelial growth factor production in peritoneal macrophages of cirrhotic patients: regulation by cytokines and bacterial lipopolysaccharide. Hepatology 1999; 29:1057-63. [PMID: 10094946 DOI: 10.1002/hep.510290416] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vascular endothelial growth factor (VEGF) is an angiogenic peptide with vascular permeability and relaxing properties. This study assessed whether peritoneal macrophages of cirrhotic patients can be up-regulated to produce VEGF under proper stimulatory conditions. Macrophages were isolated from ascites. VEGF protein secretion and mRNA expression were measured in basal conditions and after stimulation with lipopolysaccharide (LPS), tumor necrosis factor alpha (TNF-alpha), and interleukin-1 (IL-1). These substances induced a time- and dose-dependent increase in both VEGF production and transcript expression. Assays with actinomycin D showed that VEGF mRNA induction is secondary to both higher VEGF gene transcription and mRNA stability. Ascites and plasma concentration of VEGF was also measured in cirrhotic patients with (n = 15) and without (n = 10) spontaneous bacterial peritonitis (SBP). Plasma values did not differ between both groups of patients. However, ascites VEGF levels were higher in SBP patients than in noninfected cirrhotic patients (710 +/- 183 vs. 94 +/- 15 pg/mL; P <.025). These results indicate that cytokines and LPS markedly increase VEGF protein secretion and mRNA expression in macrophages of cirrhotic patients, and suggest that this substance could be an important mediator of the pronounced arterial vasodilation frequently occurring in SBP patients.
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Affiliation(s)
- M Pérez-Ruiz
- Hormonal Laboratory, Hospital Clínic Universitari and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) and Instituto Reina Sofia de Investigaciones Nefrológicas (IRSIN), University of Barcelona, Barcelona, Spain
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Pérez-Ruiz M, Sievers D, García-López PA, Berzal-Herranz A. The antisense sequence of the HIV-1 TAR stem-loop structure covalently linked to the hairpin ribozyme enhances its catalytic activity against two artificial substrates. Antisense Nucleic Acid Drug Dev 1999; 9:33-42. [PMID: 10192287 DOI: 10.1089/oli.1.1999.9.33] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This work is an in vitro study of the efficiency of catalytic antisense RNAs whose catalytic domain is the wild-type sequence of the hairpin ribozyme, derived from the minus strand of the tobacco ringspot virus satellite RNA. The sequence in the target RNA recognized by the antisense molecule was the stem-loop structure of the human immunodeficiency virus-1 (HIV-1) TAR region. This region was able to form a complex with its antisense RNA with a binding rate of 2 x 10(4) M(-1)s(-1). Any deletion of the antisense RNA comprising nucleotides of the stem-loop resulted in a decrease in binding rate. Sequences 3' of the stem in the sense RNA also contributed to binding. This stem-loop TAR-antisense segment, covalently linked to a hairpin ribozyme, enhanced its catalytic activity. The highest cleavage rate was obtained when the stem-loop structure was present in both ribozyme and substrate RNAs and they were complementary. Similarly, an extension at the 5'-end of the hairpin ribozyme increased the cleavage rate when its complementary sequence was present in the substrate. Inclusion of the stem-loop at the 3'-end and the extension at the 5'-end of the hairpin ribozyme abolished the positive effect of both antisense units independently. These results may help in the design of hairpin ribozymes for gene silencing.
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Affiliation(s)
- M Pérez-Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra CSIC, Granada, Spain
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Pérez-Ruiz M, Torres C, García-López PA, Ruiz-Extremera A, Salmerón J, Berzal-Herranz A. Determination of HCV RNA concentration by direct quantitation of the products from a single RT-PCR. J Virol Methods 1997; 69:113-24. [PMID: 9504757 DOI: 10.1016/s0166-0934(97)00155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel method for the estimation of HCV RNA levels in vivo was developed, based on competitive RT-PCR. The use of the Tth DNA polymerase and 5' 32P-labeled antisense primer respectively reduced cross-contamination and permitted the direct quantification of viral loads by the analysis of the radioactivity of PCR products derived from a clinical sample and a competitive deleted template, separated previously on a polyacrilamide gel. A HCV fragment (H) and a competitive (deltaH) RNA templates were synthesized for optimizing the method. The minimal starting RNA detectable by RT-PCR was 40 copies. RT-PCR performed with ratios deltaH/H ranging from 1/1 to 1/20 revealed different relative percentages of both H and deltaH products, changing from 90% of deltaH product when the ratio was 1/1 to 5%, when it was 1/20. Regression analysis was adjusted to a linear model and served to further estimate HCV RNA loads from clinical samples. HCV RNA quantitation was carried out in 19 patients. Higher viral loads were related to type 1b infection and persistence of HCV RNA after interferon therapy. This method is simple, reproducible and useful for rapid estimation of HCV RNA load in vivo.
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Affiliation(s)
- M Pérez-Ruiz
- Instituto de Parasitología y Biomedicina López Neyra CSIC, Hospital Clínico Universitario, Granada, Spain
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Salmerón FJ, Palacios A, Pérez-Ruiz M, Torres C, Oyonarte S, Fernández-Montoya A, Ruiz-Extremera A. Epidemiology, serological markers, and hepatic disease of anti-HCV ELISA-2-positive blood donors. Dig Dis Sci 1996; 41:1933-8. [PMID: 8888703 DOI: 10.1007/bf02093592] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The epidemiology associated with hepatitis C virus (HCV) infection, serologic reactivity, and hepatic disease related to anti-HCV-positive donors of Granada were researched. From 1990 through 1993, medical and epidemiological information and anti-HCV and HCV RNA testing were evaluated in 46,741 blood donors. Serum samples were obtained for anti-HCV ELISA and RIBA and HCV RNA determination. A liver biopsy was conducted in all anti-HCV positives by confirmatory second-generation RIBA to analyze the hepatic lesion and the presence of HCV RNA. The anti-HCV prevalence was 1.12%. A total of 228 anti-HCV second-generation ELISA positive blood donors were analyzed. Intrafamiliar transmission rate was 1.7%. Transfusion and intravenous drug abuse (IVDA) antecedents were associated with a higher risk of seroconversion. A RIBA-positive result was related to high second- and third-generation ELISA ratios (90%), HCV RNA positivity (89%), and elevated alanine aminotransferase (ALT) levels (88%). Approximately 50% of donors with normal ALT levels had high ELISA ratios and second-generation RIBA and HCV RNA positive results. Of the second-generation RIBA indeterminate results, 42% and 82% of the c22 and 33% and 100% of the c100 reactivities were third-generation RIBA and HCV RNA positive, respectively. Liver biopsy was conducted in 85 donors, 74% of whom had a chronic hepatitis and 83% had detectable HCV RNA levels. Chronic hepatitis was diagnosed in 88% vs 43% of donors with elevated and normal alanine aminotransferase levels, respectively. ELISA and confirmatory HCV RNA determinations should be routinely employed in donor screening. A liver biopsy should be conducted in patients with elevated ALT levels and normal ALT levels when viremic.
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