title: Is there still room for novel viral pathogens in pediatric respiratory tract infections?
abstract: 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.
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Blanca
authors.initials: B
authors.lastname: Taboada
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Marco A
authors.initials: MA
authors.lastname: Espinoza
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Pavel
authors.initials: P
authors.lastname: Isa
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Fernando E
authors.initials: FE
authors.lastname: Aponte
authors.affiliation: Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
authors.forename: María A
authors.initials: MA
authors.lastname: Arias-Ortiz
authors.affiliation: Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
authors.forename: Jesús
authors.initials: J
authors.lastname: Monge-Martínez
authors.affiliation: Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
authors.forename: Rubén
authors.initials: R
authors.lastname: Rodríguez-Vázquez
authors.affiliation: Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
authors.forename: Fidel
authors.initials: F
authors.lastname: Díaz-Hernández
authors.affiliation: Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
authors.forename: Fernando
authors.initials: F
authors.lastname: Zárate-Vidal
authors.affiliation: Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., Mexico.
authors.forename: Rosa María
authors.initials: RM
authors.lastname: Wong-Chew
authors.affiliation: Hospital General de México, México D.F., Mexico.
authors.forename: Verónica
authors.initials: V
authors.lastname: Firo-Reyes
authors.affiliation: Hospital Pediátirco de Coyoacán, México D.F., Mexico.
authors.forename: Carlos N
authors.initials: CN
authors.lastname: del Río-Almendárez
authors.affiliation: Nuevo Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico.
authors.forename: Jesús
authors.initials: J
authors.lastname: Gaitán-Meza
authors.affiliation: Centro de Investigación Biomédica de Occidente, IMSS, Guadalajara, Jalisco, Mexico.
authors.forename: Alberto
authors.initials: A
authors.lastname: Villaseñor-Sierra
authors.affiliation: Unidad de Investigación Biomédica IMSS, Durango, Durango, Mexico.
authors.forename: Gerardo
authors.initials: G
authors.lastname: Martínez-Aguilar
authors.affiliation: Unidad de Investigación Biomédica IMSS, Durango, Durango, Mexico.
authors.forename: Ma del Carmen
authors.initials: Mdel C
authors.lastname: Salas-Mier
authors.affiliation: Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Noyola
authors.affiliation: Hospital Central "Dr. Ignacio Morones Prieto", San Luis Potosí, Mexico.
authors.forename: Luis F
authors.initials: LF
authors.lastname: Pérez-Gónzalez
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Susana
authors.initials: S
authors.lastname: López
authors.affiliation: Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., Mexico.
authors.forename: José I
authors.initials: JI
authors.lastname: Santos-Preciado
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Carlos F
authors.initials: CF
authors.lastname: Arias
mesh_terms: D002648:Child; D002673:Child, Hospitalized; D002675:Child, Preschool; D017934:Coronavirus / Q000235:genetics / Q000502:physiology; D004267:DNA Viruses / Q000145:classification / Q000235:genetics / Q000502:physiology*; D004279:DNA, Viral / Q000032:analysis; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D009305:Nasopharynx / Q000821:virology; D010802:Phylogeny; D011014:Pneumonia / Q000175:diagnosis / Q000821:virology; D012328:RNA Viruses / Q000145:classification / Q000235:genetics / Q000502:physiology*; D012367:RNA, Viral / Q000032:analysis; D012136:Respiratory Syncytial Viruses / Q000235:genetics / Q000502:physiology; D012141:Respiratory Tract Infections / Q000473:pathology / Q000821:virology*; D012229:Rhinovirus / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral