Papers by Carlos Del Río-almendárez
a<p>RSV, respiratory syncytial virus; RV-A, rhinovirus species A; RV-B; rhinovirus species ... more a<p>RSV, respiratory syncytial virus; RV-A, rhinovirus species A; RV-B; rhinovirus species B; RV-C; rhinovirus species C; HBoV, human bocavirus, HCoV, human coronavirus OC43; TTV, torque teno virus; TTMV, torque teno mini virus; TTMDV, torque teno midi virus; BKV, bovine kobuvirus; BVDV, bovine viral diarrhea virus; BatPV, bat picornavirus; HPV, human papillomavirus; PVY, potato virus Y, ToMV, tomato mosaic virus; CMV, cucumber mosaic virus; HHV, human herpes virus; HVE-A, human enterovirus A; SAFV, Saffold virus; WSSV, white spot syndrome virus; HASTV, human astrovirus.</p><p>Genome coverage for viruses present in URTI samples.</p
a<p>When more than one sample were pooled for sequencing, the code for the various samples ... more a<p>When more than one sample were pooled for sequencing, the code for the various samples is mentioned.</p>b<p>Number of valids DNA reads in the sample por the corresponding pathogen.</p><p>Pathogens identified by NGS in children with upper respiratory tract infections.</p
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, Jan 30, 2017
Acute respiratory infections are the leading cause of mortality in children worldwide, especially... more Acute respiratory infections are the leading cause of mortality in children worldwide, especially in developing countries. Pneumonia accounts for 16% of all deaths of children under 5 years old, killing 935,000 children in 2015. Despite its frequency and severity the information about its etiology is limited. The aim of the study was to identify respiratory viruses associated with community acquired pneumonia (CAP) in children younger than 5 years old. 1,404 children younger than 5 years old with clinical and/or radiological diagnosis of CAP from 11 hospitals in Mexico were included. Nasal washes were collected, placed in viral medium and frozen at -70°C until processing. The first 832 samples were processed by the multiplex Bioplex/Luminex system and the remaining 572 samples by the Anyplex multiplex RT-PCR. Clinical data regarding diagnosis, clinical signs and symptoms, radiographic pattern and risk factors were obtained and recorded. 81.6% of the samples were positive for viruses...
Virology Journal, 2015
Background: Most of the studies characterizing the incidence of rhinovirus (RV) have been carried... more Background: Most of the studies characterizing the incidence of rhinovirus (RV) have been carried out in hospitalized children and in developed countries. In those studies, RV-C has been associated with more severe respiratory tract infections than RV species A and B. In this study we determined the frequency and diversity of RV strains associated with upper and lower respiratory tract infections (URTI, LRTI) in Mexico, and describe the clinical characteristics of the illness associated with different RV species. Methods: A prospective surveillance of 526 and 250 children with URTI and LRTI was carried out. Respiratory samples were analyzed by RT-PCR for viruses. The 5′ untranslated region of the RV genome was amplified and sequenced. Results: In the case of URTI, 17.5% were positive for RV, while this virus was found in 24.8% of LRTI. The RV species was determined in 73 children with URTI: 61.6% were RV-A, 37% RV-C and, 1.4% RV-B; and in 43 children with LRTI: 51.2% were RV-A, 41.8% RV-C, and 7% RV-B. No significant differences in clinical characteristics were found in patients with RV-A or RV-C infections. A high genetic diversity of RV strains was found in both URTI and LRTI. Conclusions: Both RV-A and RV-C species were frequently found in hospitalized as well as in outpatient children. This study underlines the high prevalence and genetic diversity of RV strains in Mexico and the potential severity of disease associated with RV-A and RV-C infections.
<p>Valid DNA reads obtained by NGS of LRTI and URTI clinical samples were split into human,... more <p>Valid DNA reads obtained by NGS of LRTI and URTI clinical samples were split into human, bacterial, fungal, and viral origin. Those reads not present in the four previous categories were classified as "undefined". Average values for all LRTI and URTI samples are shown.</p
RESUMEN Presentamos el caso de una niña de diez años previamente sana. Fue traída de urgencia por... more RESUMEN Presentamos el caso de una niña de diez años previamente sana. Fue traída de urgencia por presentar vómitos de contenido gastroali-mentario de 20 días de evolución, acompañados de cefalea diaria, sin relación con actividad física. A su ingreso presenta marcha atáxica, debilidad muscular y lateralización derecha. Una tomografía computada (TAC) de cráneo mostró una masa que ocupaba el cuarto ven-trículo. Se hizo estudio de resonancia magnética cerebral para precisar las características de la masa así como su extensión antes del tratamiento quirúrgico. La paciente fue operada; se resecó el 90% del tumor. El estudio histopatológico reveló un linfoma difuso de células grandes B. Actualmente la paciente recibe primer protocolo de quimioterapia. Palabras clave: Linfoma, Linfoma primario del sistema nervioso central, cuarto ventrículo. ABSTRACT We report a 10-year old previously healthy girl, who was brought to the Emergency Room because of gastric-content vomit, accompanied by dail...
Acta Pediatrica De Mexico, Jul 9, 2014
La varicela es una enfermedad viral exantemática frecuente en la infancia, con una tasa elevada d... more La varicela es una enfermedad viral exantemática frecuente en la infancia, con una tasa elevada de complicaciones, que pueden ser fatales principalmente en pacientes inmunodeprimidos. Las sobreinfecciones bacterianas son las más frecuentes. Desde la década de los años ochenta del siglo XX, han resurgido las infecciones severas por estreptococo beta hemolítico del grupo A (SBHGA), que afectan a la mitad de los pacientes con varicela menores de cinco años. Se hizo una revisión sobre infecciones invasivas severas producidas por SBGHA, a fin de señalar que la forma óptima de mejorar su pronóstico es el conocimiento de las mismas y su diagnóstico precoz y tratamiento temprano.
Virology Journal, 2015
Most of the studies characterizing the incidence of rhinovirus (RV) have been carried out in hosp... more Most of the studies characterizing the incidence of rhinovirus (RV) have been carried out in hospitalized children and in developed countries. In those studies, RV-C has been associated with more severe respiratory tract infections than RV species A and B. In this study we determined the frequency and diversity of RV strains associated with upper and lower respiratory tract infections (URTI, LRTI) in Mexico, and describe the clinical characteristics of the illness associated with different RV species. A prospective surveillance of 526 and 250 children with URTI and LRTI was carried out. Respiratory samples were analyzed by RT-PCR for viruses. The 5&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; untranslated region of the RV genome was amplified and sequenced. In the case of URTI, 17.5% were positive for RV, while this virus was found in 24.8% of LRTI. The RV species was determined in 73 children with URTI: 61.6% were RV-A, 37% RV-C and, 1.4% RV-B; and in 43 children with LRTI: 51.2% were RV-A, 41.8% RV-C, and 7% RV-B. No significant differences in clinical characteristics were found in patients with RV-A or RV-C infections. A high genetic diversity of RV strains was found in both URTI and LRTI. Both RV-A and RV-C species were frequently found in hospitalized as well as in outpatient children. This study underlines the high prevalence and genetic diversity of RV strains in Mexico and the potential severity of disease associated with RV-A and RV-C infections.
PLoS ONE, 2014
Viruses are the most frequent cause of respiratory disease in children. However, despite the adva... more Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.
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Papers by Carlos Del Río-almendárez