ena-STUDY-Instituto de Biotecnologia-UNAM-26-09-2014-17:40:02:959-640
Metagenomic approach to examine respiratory samples from children with upper respiratory tract infections
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. This observation has led investigators to wonder if novel respiratory viruses are still to be discovered. In this work, we used a metagenomic approach to examine respiratory samples from children with upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasopharyngeal swabs from 46 outpatient children (out of 526) from five different cities of the state of Veracruz, Mexico were studied. All the samples were pooled into 25 DNA libraries for sequencing. DNA reads for at least one virus commonly associated to respiratory infections was found in 22 of the 25 sequenced libraries, while in all other, but one, pathogenic bacteria were detected. Reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found as saffold, anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses. No novel viruses were identified.
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. This observation has led investigators to wonder if novel respiratory viruses are still to be discovered. In this work, we used a metagenomic approach to examine respiratory samples from children with upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasopharyngeal swabs from 46 outpatient children (out of 526) from five different cities of the state of Veracruz, Mexico were studied. All the samples were pooled into 25 DNA libraries for sequencing. DNA reads for at least one virus commonly associated to respiratory infections was found in 22 of the 25 sequenced libraries, while in all other, but one, pathogenic bacteria were detected. Reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found as saffold, anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses. No novel viruses were identified.