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.
Highlights
Acute respiratory infections (ARIs) are the most common illnesses in humans and are associated with significant morbidity and mortality in young children in developing countries and elderly people in developed countries
With the improvement of diagnostic methods, rhinovirus (RV), which had been thought to be mostly associated with mild-to-moderate upper respiratory tract infections (URTI) was found to be associated with severe respiratory infections [7,8] and, in the last decade, several new respiratory viruses have been identified, such as human metapneumovirus, HCoV-NL63 and -HKU1, human bocavirus (HBoV), parechovirus (HPeV), polyomavirus KI and WU, and enterovirus 104 and 109 [9,10,11,12,13,14,15]
We reported the presence of a respiratory virus in about 71% of nasal samples obtained from children with lower tract respiratory infections (LRTI) and URTI (Aponte et al, manuscript in preparation; see the Pathogen Detection section above), using a PCR method able to detect 15 different respiratory viruses
Summary
Acute respiratory infections (ARIs) are the most common illnesses in humans and are associated with significant morbidity and mortality in young children in developing countries and elderly people in developed countries. With the improvement of diagnostic methods, rhinovirus (RV), which had been thought to be mostly associated with mild-to-moderate upper respiratory tract infections (URTI) was found to be associated with severe respiratory infections [7,8] and, in the last decade, several new respiratory viruses have been identified, such as human metapneumovirus (hMPV), HCoV-NL63 and -HKU1, human bocavirus (HBoV), parechovirus (HPeV), polyomavirus KI and WU, and enterovirus 104 and 109 [9,10,11,12,13,14,15] In this regard, the fact that even with state-of-the-art diagnostic tools in most studies a virus is detected in only 50% to 80% of upper and lower ARIs [4,5,6,16,17,18,19] a wonder is if there are more respiratory viruses associated to ARIs than those currently known [20]. This study contributes to the description of the viral and bacterial populations present in nasopharyngeal samples from children with lower and upper ARIs using a metagenomic approach, which so far has been employed in limited studies [21,22,23], and suggests that the current diagnostic methods likely miss known respiratory pathogens, which might explain the relatively high proportion of undiagnosed cases
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
