Pineda, J.A. (Juan A.)

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    Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain
    (European Centre for Disease Control and Prevention (ECDC), 2019) Fernández-Fuertes, E. (Elisa); García-del-Toro, M. (Miguel); Pineda, J.A. (Juan A.); Lemey, P. (Philippe); Chueca, N. (Natalia); Vera, F. (F); Omar, M. (Mohamed); Iglesia, A. (Alberto) de la; Cuypers, L. (Lize); Téllez, F. (Francisco); Aguilera, A. (Antonio); Reina, G. (Gabriel); Garcia, F. (Federico); Pérez, A.B. (Ana Belén); Bernal, E. (Enrique); Arenas, J.I. (Juan Ignacio); Rivero-Juárez, A. (Antonio); Vrancken, B. (Bram); Pascasio, J.M. (Juan Manuel); Wichman, M.A. (Miguel Ángel) von
    Reducing the burden of the hepatitis C virus (HCV) requires large-scale deployment of intervention programmes, which can be informed by the dynamic pattern of HCV spread. In Spain, ongoing transmission of HCV is mostly fuelled by people who inject drugs (PWID) infected with subtype 1a (HCV1a). Aim: Our aim was to map how infections spread within and between populations, which could help formulate more effective intervention programmes to halt the HCV1a epidemic in Spain. Methods: Epidemiological links between HCV1a viruses from a convenience sample of 283 patients in Spain, mostly PWID, collected between 2014 and 2016, and 1,317, 1,291 and 1,009 samples collected abroad between 1989 and 2016 were reconstructed using sequences covering the NS3, NS5A and NS5B genes. To efficiently do so, fast maximum likelihood-based tree estimation was coupled to a flexible Bayesian discrete phylogeographic inference method. Results: The transmission network structure of the Spanish HCV1a epidemic was shaped by continuous seeding of HCV1a into Spain, almost exclusively from North America and European countries. The latter became increasingly relevant and have dominated in recent times. Export from Spain to other countries in Europe was also strongly supported, although Spain was a net sink for European HCV1a lineages. Spatial reconstructions showed that the epidemic in Spain is diffuse, without large, dominant within-country networks. Conclusion: To boost the effectiveness of local intervention efforts, concerted supra-national strategies to control HCV1a transmission are needed, with a strong focus on the most important drivers of ongoing transmission, i.e. PWID and other high-risk populations
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    Optimization of the molecular diagnosis of the acute hepatitis E virus infection
    (2023) Fuentes, A. (Ana); Alados, J.C. (Juan Carlos); Caballero-Gómez, J. (Javier); Pineda, J.A. (Juan A.); Rivero, A. (Antonio); López-López, P. (Pedro); Viciana, I. (Isabel); Reina-González, G. (Gabriel); Aguilera, A. (Antonio); Freyre-Carrillo, C.A. (Carolina A.); Mesquita, J. (Joao); Frias, M. (Mario); Pérez-Jiménez, A.B. (Ana Belén); Rivero-Juárez, A. (Antonio); Ramírez-Arellano, E. (Encarnación)
    To evaluate the diagnostic value of the combination of two broad-range PCR assays targeting two different and conserved regions of the viral genome for the diagnosis of acute Hepatitis E virus (HEV) infection. Patients with acute hepatitis were prospectively recruited. In all, HEV-IgM antibodies were tested together with evaluation of HEV viraemia by two PCR assays (ORF3 and ORF1). The number of individuals exhibiting negative IgM antibody results but carrying viral RNA was calculated by each PCR assay. Four-hundred and seventy individuals were included, of whom 145 (30.8%) were diagnosed as having acute HEV. Of them, 122 (84.1%) exhibited HEV-IgM antibodies, and 81 (55.8%) had detectable viral RNA for at least one PCR. Using the ORF3 molecular assay, 70 (48.3%) individuals were identified with HEV infection. When the ORF1 molecular assay was applied, 49 (33.8%) individuals were identified. The ORF3 assay detected viral RNA in 32 patients not detected by the ORF1 assay. In contrast, the ORF1 assay could amplify viral RNA in 11 patients who were not detected by the ORF3 assay. The parallel use of two broad-range PCR assays significantly increased the performance of the molecular diagnosis of HEV.