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1.
J Clin Microbiol ; 60(1): e0160921, 2022 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-34669457

RESUMEN

Determining SARS-CoV-2 viral infectivity is crucial for patient clinical assessment and isolation decisions. We assessed subgenomic RNA (sgRNA) as a surrogate marker of SARS-CoV-2 infectivity in SARS-CoV-2-positive reverse transcription PCR (RT-PCR) respiratory samples (n = 105) in comparison with viral culture as the reference standard for virus replication. sgRNA and viral isolation results were concordant in 99/105 cases (94%), indicating highly significant agreement between the two techniques (Cohen's kappa coefficient 0.88, 95% confidence interval [CI] 0.78 to 0.97, P < 0.001). sgRNA RT-PCR showed a sensitivity of 97% and a positive predictive value of 94% to detect replication-competent virus, further supporting sgRNA as a surrogate marker of SARS-CoV-2 infectivity. sgRNA RT-PCR is an accurate, rapid, and affordable technique that can overcome culture and cycle threshold (CT) value limitations and be routinely implemented in hospital laboratories to detect viral infectivity, which is essential for optimizing patient monitoring, the efficacy of treatments/vaccines, and work reincorporation policies, as well as for safely shortening isolation precautions.


Asunto(s)
COVID-19 , SARS-CoV-2 , Biomarcadores , Humanos , ARN , ARN Viral/genética , Transcripción Reversa
2.
J Med Virol ; 93(8): 4840-4845, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-33543795

RESUMEN

Conjunctivitis is a frequent ocular disorder caused by human adenoviruses (HAdVs). Only a few of the 45 HAdV-D species are associated with epidemic keratoconjunctivitis, including HAdV-D8. Nosocomial outbreaks due to HAdV-D8 have been rarely described, because keratoconjunctivitis cases are clinically diagnosed and treated without having to characterize the causative agent. Moreover, molecular typing is tedious when using classical techniques. In this study, a hospital outbreak of conjunctivitis caused by HAdV-D8 was characterized using the recently developed whole-genome sequencing (WGS) method. Of the 363 patients attending the Ophthalmology Department between July 13 and August 13, 2018, 36 may have acquired intrahospital conjunctivitis. Also, 11 of 22 samples sent to the Virology section were selected for WGS analysis. The WGS results revealed that 10 out of 11 HAdV-D8 strains were closely related. The remaining strain (Case 28) was more similar to a strain from an outbreak in Germany obtained from a public sequence database. WGS results showed that outbreak HAdV-D8 strains had a minimum percentage of identity of 94.3%. WGS is useful in a clinical setting, because it avoids carrying out viral culture or specific polymerase chain reaction sequencing. The public availability of sequence reads makes it easier to compare clusters in circulation. In conclusion, WGS can play an important role in standard routines to describe viral outbreaks.


Asunto(s)
Infecciones por Adenovirus Humanos/epidemiología , Adenovirus Humanos/genética , Infección Hospitalaria/epidemiología , Brotes de Enfermedades , Genoma Viral/genética , Queratoconjuntivitis/epidemiología , Infecciones por Adenovirus Humanos/virología , Adenovirus Humanos/aislamiento & purificación , Adulto , Anciano , Anciano de 80 o más Años , Infección Hospitalaria/virología , ADN Viral/genética , Femenino , Humanos , Queratoconjuntivitis/virología , Masculino , Persona de Mediana Edad , Filogenia , España/epidemiología , Centros de Atención Terciaria , Secuenciación Completa del Genoma
3.
Biol Blood Marrow Transplant ; 25(5): 1022-1030, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-30639821

RESUMEN

The current study evaluates the clinical effect of sirolimus exposure on the occurrence of cytomegalovirus (CMV) DNAemia necessitating preemptive antiviral therapy. A total of 167 consecutive recipients of reduced-intensity conditioning (RIC) allogeneic hematopoietic stem cell transplantation (allo-HSCT) who received sirolimus- and tacrolimus-based graft-versus-host disease (GVHD) prophylaxis and whose CMV serostatus was positive for donors and/or recipients were included in this multicenter retrospective study. A parametric model with consecutive sirolimus blood levels describing the time to CMV DNAemia-RAT was developed using NONMEM version 7.4. Overall, 122 of 167 patients (73%) were allografted from an unrelated donor, and the donor CMV-serostatus was negative in 51 cases (31%). Fifty-six recipients (34%) developed CMV DNAemia necessitating preemptive therapy, with a cumulative incidence of 36% at a median follow-up of 25 months. Time to CMV DNAemia necessitating preemptive therapy was best described using a Gompertz function. CMV DNAemia necessitating preemptive therapy-predicting factors were antithymocyte globulin-based conditioning regimen (hazard ratio [HR], 2.2; 95% confidence interval [CI], 1.1 to 4.1; P < .01) and sirolimus concentration (HR, .94; 95% CI, .87 to .99; P < .01). The risk of CMV DNAemia-RAT decreased by 6% for each 1 ng/mL increase in sirolimus trough concentration. In conclusion, we provide evidence on the association between sirolimus blood concentration and incidence of CMV DNAemia necessitating preemptive therapy in allo-HSCT recipients. Moreover, this study presents the first predictive model describing the time to CMV DNAemia necessitating preemptive antiviral therapy as a function of sirolimus drug concentration.


Asunto(s)
Antivirales/uso terapéutico , Infecciones por Citomegalovirus/prevención & control , Trasplante de Células Madre Hematopoyéticas/efectos adversos , Premedicación/métodos , Sirolimus/efectos adversos , Adulto , Infecciones por Citomegalovirus/etiología , Relación Dosis-Respuesta a Droga , Femenino , Humanos , Inmunosupresores/efectos adversos , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Sirolimus/sangre , Trasplante Homólogo
4.
Euro Surveill ; 24(7)2019 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-30782267

RESUMEN

IntroductionEnterovirus A71 (EV-A71) is an emerging pathogen that causes a wide range of disorders including severe neurological manifestations. In the past 20 years, this virus has been associated with large outbreaks of hand, foot and mouth disease with neurological complications in the Asia-Pacific region, while in Europe mainly sporadic cases have been reported. In spring 2016, however, an EV-A71 outbreak associated with severe neurological cases was reported in Catalonia and spread further to other Spanish regions.AimOur objective was to investigate the epidemiology and clinical characteristics of the outbreak.MethodsWe carried out a retrospective study which included 233 EV-A71-positive samples collected during 2016 from hospitalised patients. We analysed the clinical manifestations associated with EV-A71 infections and performed phylogenetic analyses of the 3'-VP1 and 3Dpol regions from all Spanish strains and a set of EV-A71 from other countries.ResultsMost EV-A71 infections were reported in children (mean age: 2.6 years) and the highest incidence was between May and July 2016 (83%). Most isolates (218/233) were classified as subgenogroup C1 and 217 of them were grouped in one cluster phylogenetically related to a new recombinant variant strain associated with severe neurological diseases in Germany and France in 2015 and 2016. Moreover, we found a clear association of EV-A71-C1 infection with severe neurological disorders, brainstem encephalitis being the most commonly reported.ConclusionAn emerging recombinant variant of EV-A71-C1 was responsible for the large outbreak in 2016 in Spain that was associated with many severe neurological cases.


Asunto(s)
Brotes de Enfermedades/estadística & datos numéricos , Enterovirus Humano A/genética , Enterovirus Humano A/aislamiento & purificación , Infecciones por Enterovirus/epidemiología , Enfermedades del Sistema Nervioso/diagnóstico , Enfermedades del Sistema Nervioso/virología , ARN Viral/genética , Infecciones del Sistema Respiratorio/virología , Antígenos Virales , Preescolar , Enterovirus Humano A/clasificación , Infecciones por Enterovirus/diagnóstico , Infecciones por Enterovirus/virología , Hospitalización , Humanos , Lactante , Epidemiología Molecular , Enfermedades del Sistema Nervioso/líquido cefalorraquídeo , Enfermedades del Sistema Nervioso/epidemiología , Filogenia , Filogeografía , ARN Viral/aislamiento & purificación , Infecciones del Sistema Respiratorio/epidemiología , Estudios Retrospectivos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Análisis de Secuencia de ARN , España/epidemiología
5.
Euro Surveill ; 23(47)2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-30482263

RESUMEN

Acute flaccid paralysis (AFP) surveillance is key for global polio eradication. It allows detecting poliovirus (PV) reintroductions from endemic countries. This study describes AFP surveillance in Spain from 1998 to 2015. During this time, 678 AFP cases were reported to the Spanish National Surveillance Network. The mean notification rate was 0.58 AFP cases/100,000 population under 15 years old (range: 0.45/100,000-0.78/100,000). Two periods (P) are described: P1 (1998-2006) with the AFP notification rate ranging from 0.66/100,000 to 0.78/100,000, peaking in 2001 (0.84/100,000); and P2 (2007-2015) when the AFP rate ranged from 0.43/100,000 to 0.57/100,000, with the lowest rate in 2009 (0.31/100,000). No poliomyelitis cases were caused by wild PV infections, although two Sabin-like PVs and one imported vaccine-derived PV-2 were detected. Overall, 23 (3.4%) cases met the hot case definition. Most cases were clinically diagnosed with Guillain-Barré syndrome (76.9%; 504/655). The adequate stool collection rate ranged from 33.3% (7/21) to 72.5% (29/40). The annual proportion of AFP cases with non-polio enterovirus findings varied widely across the study period. AFP surveillance with laboratory testing for non-polio enteroviruses must be maintained and enhanced both to monitor polio eradication and to establish sensitive surveillance for prompt detection of other enteroviruses causing serious symptoms.


Asunto(s)
Brotes de Enfermedades/prevención & control , Parálisis/epidemiología , Poliomielitis/prevención & control , Vacuna Antipolio Oral/administración & dosificación , Vacunas contra Poliovirus/administración & dosificación , Poliovirus/aislamiento & purificación , Vigilancia de la Población/métodos , Adolescente , Niño , Preescolar , Erradicación de la Enfermedad , Notificación de Enfermedades , Femenino , Humanos , Lactante , Masculino , Poliomielitis/epidemiología , Poliomielitis/virología , España/epidemiología
6.
J Med Virol ; 89(3): 435-442, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-27505281

RESUMEN

The epidemiology and clinical association of enterovirus (EV) and parechovirus (HPeV) infections, as well as the type-distribution-according-to-age, were determined during a 4-year study period in Spain. During 2010-2013, a total of 21,832 clinical samples were screened for EV and the detection frequency was 6.5% (1,430). Of the total EV-negative samples, only 1,873 samples from 2011 to 2013 were available for HPeV testing. HPeV was detected in 42 (2%) of them. Positive samples were genotyped using PCR and sequencing. EV infections occurred in all age groups of patients: neonates (17%), children 28 days to 2 years (29%), children 2-14 years (40%), and adults (14%). Thirty-four different EV types were identified. HPeV infections were detected exclusively in infants <8 m (70% neonates, P < 0.05). All but one HPeV were HPeV-3. Differences in type frequency detection were found according to age and clinical manifestation. Coxsackievirus (CV)-B4 (61%), CV-B5 (83%), and HPeV-3 (64%) were more frequent in neonates than in older patients (P < 0.05). Echovirus (E)-3 (60%), E-18 (47%), E-25 (62%), CV-A6 (61%), CV-A16 (72%), and EV-71 (75%) were mainly detected in children 28 days to 2 years (P < 0.05), whereas, E-6 (79%), E-20 (88%), and E-30 (85%) were predominant in children >2 years and adults (P < 0.05). Clinically, meningitis was associated with EV (P < 0.01) whereas, encephalitis was more frequent in HPeV-infected patients. CV-B types were associated with myocarditis (90%; P < 0.05) and EV species A with hand-foot-mouth-disease/atypical exanthema (88%; P < 0.05). J. Med. Virol. 89:435-442, 2017. © 2016 Wiley Periodicals, Inc.


Asunto(s)
Infecciones por Enterovirus/epidemiología , Enterovirus/clasificación , Enterovirus/genética , Genotipo , Parechovirus/clasificación , Parechovirus/genética , Infecciones por Picornaviridae/epidemiología , Adolescente , Adulto , Factores de Edad , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Enterovirus/aislamiento & purificación , Infecciones por Enterovirus/patología , Infecciones por Enterovirus/virología , Femenino , Técnicas de Genotipaje , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Parechovirus/aislamiento & purificación , Infecciones por Picornaviridae/patología , Infecciones por Picornaviridae/virología , Reacción en Cadena de la Polimerasa , Prevalencia , Análisis de Secuencia de ADN , España/epidemiología , Adulto Joven
7.
J Med Virol ; 88(1): 45-50, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26100363

RESUMEN

Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.


Asunto(s)
Técnicas de Diagnóstico Molecular/métodos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones del Sistema Respiratorio/diagnóstico , Virus/clasificación , Virus/aislamiento & purificación , Preescolar , Femenino , Humanos , Lactante , Masculino , Nasofaringe/virología , Infecciones del Sistema Respiratorio/virología , Sensibilidad y Especificidad , Virus/genética
8.
Arch Virol ; 161(5): 1365-70, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26898312

RESUMEN

Epidemiological and clinical characteristics of coxsackievirus B3 infections in Spain were investigated. This enterovirus (EV) type was detected mainly in young children (<6 months) and was associated with neurological (78 %) and respiratory diseases (10 %) but also with myo/pericarditis (10 %). Two myocarditis cases were fatal. Phylogenetic analysis of the VP1 region showed that genotype III circulated in the country between 2004 and 2008 and was replaced by genotype V in 2010. Furthermore, phylogenetic analysis of the 3D region indicated that recombination events have occurred and contributed to the genetic evolution of this EV type.


Asunto(s)
Infecciones por Coxsackievirus/epidemiología , Enterovirus Humano B/genética , Infecciones por Coxsackievirus/patología , Infecciones por Coxsackievirus/virología , Humanos , Lactante , Recién Nacido , Epidemiología Molecular , Filogenia , España/epidemiología
9.
Eur J Pediatr ; 174(11): 1511-6, 2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-25982340

RESUMEN

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.


Asunto(s)
Encefalitis Viral/epidemiología , Infecciones por Enterovirus/epidemiología , Enterovirus/aislamiento & purificación , Parechovirus/aislamiento & purificación , Infecciones por Picornaviridae/epidemiología , Viremia/epidemiología , Encefalitis Viral/diagnóstico , Encefalitis Viral/virología , Enterovirus/genética , Infecciones por Enterovirus/diagnóstico , Infecciones por Enterovirus/virología , Femenino , Genotipo , Humanos , Recién Nacido , Masculino , Parechovirus/genética , Infecciones por Picornaviridae/diagnóstico , Infecciones por Picornaviridae/virología , Prevalencia , Estudios Prospectivos , Reacción en Cadena en Tiempo Real de la Polimerasa , España/epidemiología , Viremia/diagnóstico , Viremia/virología
10.
Sci Rep ; 14(1): 12725, 2024 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-38830902

RESUMEN

Humoral immunity in COVID-19 includes antibodies (Abs) targeting spike (S) and nucleocapsid (N) SARS-CoV-2 proteins. Antibody levels are known to correlate with disease severity, but titers are poorly reported in mild or asymptomatic cases. Here, we analyzed the titers of IgA and IgG against SARS-CoV-2 proteins in samples from 200 unvaccinated Hospital Workers (HWs) with mild COVID-19 at two time points after infection. We analyzed the relationship between Ab titers and patient characteristics, clinical features, and evolution over time. Significant differences in IgG and IgA titers against N, S1 and S2 proteins were found when samples were segregated according to time T1 after infection, seroprevalence at T1, sex and age of HWs and symptoms at infection. We found that IgM + samples had higher titers of IgG against N antigen and IgA against S1 and S2 antigens than IgM - samples. There were significant correlations between anti-S1 and S2 Abs. Interestingly, IgM + patients with dyspnea had lower titers of IgG and IgA against N, S1 and S2 than those without dyspnea. Comparing T1 and T2, we found that IgA against N, S1 and S2 but only IgG against certain Ag decreased significantly. In conclusion, an association was established between Ab titers and the development of infection symptoms.


Asunto(s)
Anticuerpos Antivirales , COVID-19 , Inmunoglobulina A , Inmunoglobulina G , SARS-CoV-2 , Humanos , COVID-19/inmunología , COVID-19/virología , COVID-19/sangre , Inmunoglobulina A/sangre , Inmunoglobulina A/inmunología , Inmunoglobulina G/sangre , Inmunoglobulina G/inmunología , Masculino , SARS-CoV-2/inmunología , Femenino , Anticuerpos Antivirales/inmunología , Anticuerpos Antivirales/sangre , Adulto , Persona de Mediana Edad , Glicoproteína de la Espiga del Coronavirus/inmunología , Proteínas de la Nucleocápside de Coronavirus/inmunología , Inmunoglobulina M/sangre , Inmunoglobulina M/inmunología , Inmunidad Humoral , Fosfoproteínas/inmunología
11.
J Med Virol ; 85(1): 116-20, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23124895

RESUMEN

Cell culture is still the gold standard for the diagnosis of human enteroviruses (HEVs) although molecular techniques are required for detection of some serotypes. Due to the diversity of HEVs, a single cell line is not susceptible to all serotypes, and several lines are required to optimize the isolation of HEVs. In this study, the results of HEV isolation during the last 25 years are reported. A total of 1,192 HEVs were isolated and isolation rates varied depending on the cell line used. MRC5 cells yielded the best results (70.7%), followed by A549 cells (52.6%), RD cells (37.5%), and HEp-2 cells (29.7%). A total of 521 HEVs were characterized, and HEV-B was the most frequent species (81%). Polioviruses (PV) and HEV-A were isolated less frequently (17% and 1%, respectively). None of the cell lines detected all the enteroviruses. MRC5 cells were the most susceptible for isolation of echoviruses (85.7%) and PVs (85.4%), whereas HEp2 was the most susceptible for Coxsackieviruses B (82.6%). Some serotypes were isolated in one cell line only. 40.5% of echoviruses were isolated in MRC5 cells whereas 42.3% and 23.9% of Coxsackieviruses B were isolated in RD cells and HEp2 cells, respectively. Although A549 cells did not achieve the best performance for any enterovirus serotypes, they isolated 52.6% of the total HEVs. In view of these results, MRC5 cells, A549 cells, and RD cells should be combined to optimize isolation of HEVs.


Asunto(s)
Técnicas de Laboratorio Clínico/métodos , Infecciones por Enterovirus/diagnóstico , Infecciones por Enterovirus/virología , Enterovirus/crecimiento & desarrollo , Enterovirus/aislamiento & purificación , Virología/métodos , Animales , Técnicas de Cultivo de Célula/métodos , Línea Celular , Humanos
12.
Artículo en Inglés | MEDLINE | ID: mdl-37230840

RESUMEN

INTRODUCTION: Enteroviruses are a type of RNA-strained virus with more than 100 different genotypes. Infection can be asymptomatic, and, if any, symptoms can range from mild to severe. Some patients can develop neurological involvement, such as aseptic meningitis, encephalitis, or even cardiorespiratory failure. However, in children, the risk factors for developing severe neurological involvement are not well understood. The aim of this retrospective study was to analyze some characteristics associated with severe neurological involvement in children hospitalized for neurological disease after enterovirus infection. METHODS: retrospective observational study analyzing clinical, microbiological and radiological data of 174 children hospitalized from 2009 to 2019 in our hospital. Patients were classified according to the World Health Organization case definition for neurological complications in hand, foot and mouth disease. RESULTS: Our findings showed that, in children between 6 months old and 2 years of age, the appearance of neurological symptoms within the first 12h from infection onset-especially if associated with skin rash-was a significant risk factor for severe neurological involvement. Detection of enterovirus in cerebrospinal fluid was more likely in patients with aseptic meningitis. By contrast, other biological samples (e.g., feces or nasopharyngeal fluids) were necessary to detect enterovirus in patients with encephalitis. The genotype most commonly associated with the most severe neurological conditions was EV-A71. E-30 was mostly associated with aseptic meningitis. CONCLUSIONS: Awareness of the risk factors associated with worse neurological outcomes could help clinicians to better manage these patients to avoid unnecessary admissions and/or ancillary tests.

13.
Virus Res ; 330: 199089, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-37011863

RESUMEN

BACKGROUND: Influenza B viruses (FLUBV) have segmented genomes which enables the virus to evolve by segment reassortment. Since the divergence of both FLUBV lineages, B/Victoria/2/87 (FLUBV/VIC) and B/Yamagata/16/88 (FLUBV/YAM), PB2, PB1 and HA have kept the same ancestor, while some reassortment events in the other segments have been reported worldwide. The aim of the present study was to find out reassortment episodes in FLUBV strains detected in cases attended at Hospital Universitari Vall d'Hebron and Hospital de la Santa Creu i Sant Pau (Barcelona, Spain) from 2004 to 2015 seasons. METHODS: From October 2004 to May 2015, respiratory specimens were received from patients with respiratory tract infection suspicion. Influenza detection was carried out by either cell culture isolation, immunofluorescence or PCR-based assays. A RT-PCR was performed to distinguish both lineages by agarose gel electrophoresis. Whole genome amplification was performed using the universal primer set by Zhou et al. in 2012, and subsequently sequenced using Roche 454 GS Junior platform. Bioinformatic analysis was performed to characterise the sequences with B/Malaysia/2506/2007 and B/Florida/4/2006 corresponding sequences as reference of (B/VIC) and (B/YAM), respectively. RESULTS: A total of 118 FLUBV (75 FLUBV/VIC and 43 FLUBV/YAM), from 2004 to 2006, 2008-2011 and 2012-2015 seasons, were studied. The whole genome of 58 FLUBV/VIC and 42 FLUBV/YAM viruses was successfully amplified. Based on HA sequences, most FLUBV/VIC viruses (37; 64%) belonged to clade 1A (B/Brisbane/60/2008) except to 11 (19%), which fell within clade 1B (B/HongKong/514/2009) and 10 (17%) to B/Malaysia/2506/2004. Nine (20%) FLUBV/YAM viruses belonged to clade 2 (B/Massachusetts/02/2012), 18 (42%) to clade 3 (B/Phuket/3073/2013) and 15 (38%) fell within Florida/4/2006. Numerous intra-lineage reassortments in PB2, PB1, NA and NS were found in 2 2010-2011 viruses. An important inter-lineage reassortment event from 2008 to 2009 (11), 2010-2011 (26) and 2012-2013 (3) FLUBV/VIC (clade 1) strains to FLUBV/YAM (clade 3) was found, in addition to 1 reassortant NS in 2010-2011 B/VIC virus. CONCLUSIONS: Intra- and inter-lineage reassortment episodes were revealed by WGS. While PB2-PB1-HA remained in complex, NP and NS reassortant viruses were found in both lineages. Despite reassorment events are not often, the characterisation only by HA and NA sequences might be underestimating their detection.


Asunto(s)
Gripe Humana , Humanos , España/epidemiología , Estaciones del Año , Virus de la Influenza B/genética , Virus Reordenados/genética , Secuenciación Completa del Genoma , Filogenia
14.
Arch Virol ; 157(3): 551-4, 2012 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-22193975

RESUMEN

Enterovirus 99 is a recently described genotype of virus belonging to the species Human enterovirus C. So far, only a few sequences of this enterovirus type have been available. In 2010, during Spanish enterovirus surveillance, an enterovirus 99 strain was found in an acute flaccid paralysis patient. The virus was detected and typed in the clinical samples using molecular methods. Phylogenetic analysis in the 3Dpol region revealed recombination events with other species-C enteroviruses. This is the first finding of this unusual type in Spain.


Asunto(s)
Enterovirus Humano C/clasificación , Enterovirus Humano C/aislamiento & purificación , Infecciones por Enterovirus/virología , Preescolar , Análisis por Conglomerados , Enterovirus Humano C/genética , Infecciones por Enterovirus/complicaciones , Femenino , Genotipo , Humanos , Datos de Secuencia Molecular , Parálisis/virología , Filogenia , ARN Viral/genética , Recombinación Genética , Análisis de Secuencia de ADN , España , Proteínas Virales/genética
15.
J Clin Virol ; 152: 105167, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35523105

RESUMEN

BACKGROUND: Knowing how long SARS-CoV-2-positive individuals can remain infective is crucial for the design of infection prevention and control strategies. Viral culture is the gold standard for detecting an active-replicative virus and evaluating its infectious potential. OBJECTIVE: To assess the correlation of SARS-CoV-2 infectivity with the number of days from symptom onset and the Ct value, using culture as a reference method. Also, to describe a detailed protocol for SARS-CoV-2 culture and immunofluorescence confirmation based on our experience with other respiratory viruses. STUDY DESIGN: 100 consecutive respiratory samples positive for SARS-CoV-2 by RT-PCR from different subjects were inoculated into VERO E6 cells. RESULTS: Viral isolation was successful in 58% of samples. The median number of days from symptom onset for culture-positive samples was 2, and 15 for culture-negative samples. Six positive cultures were obtained in patients ≥14 days after symptom onset, all of whom were immunocompromised or with severe COVID-19. The mean Ct value was 12.64 units higher in culture-negative than in culture-positive samples. The probability of successfully isolating SARS-CoV-2 in samples with a Ct value <22 was 100%, decreasing to 3.1% when >27. CONCLUSIONS: Our findings show a significant positive correlation between the probability of isolating SARS-CoV-2 in culture, fewer days of symptoms and a lower RT-PCR Ct value. SARS-CoV-2 infectivity lasts no more than 14 days from symptom onset in immunocompetent individuals. In contrast, in immunocompromised patients or those with severe COVID-19 infectivity may remain after 14 days. Ct value <22 always indicates infectivity.


Asunto(s)
COVID-19 , COVID-19/diagnóstico , Prueba de COVID-19 , Técnica del Anticuerpo Fluorescente , Humanos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , SARS-CoV-2
16.
Microorganisms ; 10(3)2022 Mar 09.
Artículo en Inglés | MEDLINE | ID: mdl-35336167

RESUMEN

There is a growing interest in echovirus 30 (E30), an enterovirus responsible for neurological disease and hospitalization. There are multiple studies of outbreaks, but few that study the epidemiology over long periods of time. Our study aims to describe the clinical, epidemiological and microbiological characteristics of a series of E30 infections detected over 26 years. Data were retrospectively collected from a database of all enterovirus infections identified in our laboratory. They were detected by viral isolation or nucleic acid detection in patients presenting with respiratory or neurological infections, rash, sepsis-like syndrome, or gastroenteritis. Enterovirus genotyping was performed by amplification of the VP1 gene using RT-nested PCR, followed by sequencing and BLAST analysis. Of the 2402 enterovirus infections detected, 1619 were linked to at least one genotype and 173 were caused by E30. Clinical information was available for 158 (91.3%) patients. E30 was associated with neurological infection in 107 (67.8%) cases and it was detected almost every year. Phylogenetic analysis was performed with 67 sequences. We observed that E30 strains circulating in Catalonia from 1996 to 2016 belong to two lineages (E and F), although the majority cluster was in F. In 2018, lineage I emerged as the dominant lineage.

17.
Influenza Other Respir Viruses ; 16(4): 756-766, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35170253

RESUMEN

BACKGROUND: Few long-term reports have been published on the epidemiology of respiratory viruses despite their frequent involvement in extremely common infections. The aim here was to determine the frequency and distribution of respiratory viruses in a temperate climate area (Barcelona, Spain) throughout a 24-year period. METHODS: We collected data on all respiratory viruses detected from 1997 to 2020 in our institution. Clinical specimens were analyzed mainly by conventional techniques, and molecular techniques were also used. RESULTS: Of the 59,579 specimens analyzed, 21,382 (35.9%) were positive for at least one virus. The number of positive samples during cold months was significantly higher than in warm months. Respiratory virus infections were detected in patients of all ages, above all in children under 3 years of age, who were most frequently infected with the respiratory syncytial virus, whereas Influenza A virus predominated in the other groups, especially in adults. A clear demographic and seasonal pattern was established for some viruses. Circulation of other respiratory viruses during the FLUAV H1N1pdm09 and SARS-CoV-2 pandemics was observed. CONCLUSIONS: This long-term study provides new knowledge about the prevalence of respiratory viruses in a Mediterranean region. Throughout the study period, the frequency of some viruses remained constant, whereas others varied with the year. A clear demographic and seasonal pattern was established for some viruses. Patients suffering from severe respiratory infections should be examined for a range of respiratory viruses regardless of gender, age, or season.


Asunto(s)
COVID-19 , Virus de la Influenza A , Virus Sincitial Respiratorio Humano , Infecciones del Sistema Respiratorio , Virosis , Adulto , Niño , Preescolar , Humanos , Lactante , Prevalencia , Infecciones del Sistema Respiratorio/epidemiología , SARS-CoV-2 , Estaciones del Año , Virosis/epidemiología
19.
An Pediatr (Engl Ed) ; 88(2): 82-88, 2018 Feb.
Artículo en Español | MEDLINE | ID: mdl-28365283

RESUMEN

INTRODUCTION: Human parechovirus (HPeV) is one of the recently described picornaviridae viruses that have been associated with fever of unknown origin (FUO), clinical sepsis, gastroenteritis, meningitis, or encephalitis in very young infants. The aim of this study is to describe the epidemiology and clinical features of these viruses. PATIENTS AND METHODS: A prospective multicentre 3-year study was conducted in 12 hospitals in Spain. Out of 850 specimens examined, 47 were positive (5.52%), with HPeV-3 being the most frequent (29 cases). Infections occurred throughout the year, but mainly in May and July, and a biennial distribution was observed. More than half (57%) were neonates, and only 2 children were older than 3 months. Fever was present in all children, with irritability in 45%, rash in 18.6%, and diarrhoea in 14%. The results of biochemical tests were all in normal range. The most common final diagnosis was FUO (61%), followed by clinical sepsis (29%). Up to 29% of infants were admitted to the intensive care unit, but only one patient had sequelae. RESULTS: Out of 850 specimens examined, 47 were positive (5.52%) for HPeV, with HPeV-3 being the most frequent (29 cases). Infections occurred throughout the year, but mainly in May and July, and a biennial distribution was observed. More than half (57%) were neonates, and only 2 children were older than 3 months. Fever was present in all children, with irritability in 45%, rash in 18.6%, and diarrhoea in 14%. The results of biochemical tests were all in normal range. The most common final diagnosis was FUO (61%), followed by clinical sepsis (29%). Up to 29% of infants were admitted to the intensive care unit, but only one patient had sequelae CONCLUSIONS: HPeV circulates in our country, mainly during spring and summer, and affects young infants with a FUO and clinical sepsis. Molecular diagnostic techniques in all hospitals could help in improving the management of patients with these infections.


Asunto(s)
Parechovirus , Infecciones por Picornaviridae/diagnóstico , Infecciones por Picornaviridae/epidemiología , Femenino , Hospitalización , Humanos , Lactante , Recién Nacido , Masculino , Infecciones por Picornaviridae/terapia , Estudios Prospectivos , España
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