key: cord-306450-sh2mrhoq authors: Appak, Özgür; Duman, Murat; Belet, Nurşen; Sayiner, Ayça Arzu title: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date: 2019-01-03 journal: J Med Virol DOI: 10.1002/jmv.25379 sha: doc_id: 306450 cord_uid: sh2mrhoq Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season. The AusDiagnostics test is based on multiplex tandem PCR A pathogen was detected in 1857 (58.7%) of the study samples. Distribution of PCR positive samples according to age groups was found as follows; 53% (978 of 1857) in less than 2 years age group, 24% (454 of 1857) in 2 to 4 years group, 15% (270 of 1857) in the 5 to 9 years group, and 8% (155 of 1857) in 10 to 17 years group. The positivity rate decreased significantly above 5 years of age (P < 0.05). The mean positivity rate was 44.4% during study period when the AusDignostics assay was used compared with 69.8% of the second part of the study using the Fast Track Diagnostics assay. The difference is statistically significant (P < 0.001; Figure 1A ). RV/EV (17.6%) and RSV (9.2%) were the most commonly detected agents followed by IAV (4.8%; Table 1 ). When the distribution of the agents according to years were examined, RV/EV was the most common agent for each year. RSV and coinfections took the second and third place in the frequency order except 2011 in which they are replaced by PIV-3 and AdV. The study covered only the first 4 months of 2018 where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). When the distribution according to age groups was determined, The first three pathogens were RV/EV, RSV, and coinfections for less than 2 years; RV/EV, coinfections, and influenza A/B for 2 to 4 years; RV/EV, influenza A/B, and coinfections for 5 to 9 and 10 to 17 years (Table 2) . Among the parainfluenza viruses, PIV-3 was the most frequently detected subtype, followed by PIV-1, -2, and -4, respectively (Table 1) . Table 3 . The role and importance of respiratory viruses have become more easily detectable by the use of nucleic acid-based tests in clinical laboratories. Thus it became possible to obtain detailed epidemiological data and to manage the patients better. Our study retrospectively assessed the respiratory tract viruses detected in children with ARTI symptoms of 0 to 18 years between 2011-2018. Two different assays were used during the study period. Ausdiagnostics assay covered a panel of 12 RV as the number one etiologic factor. 6, 12, 13 RSV (9.2%) was the second most common viral agent after RV in this study. It was particularly detected during winter and spring months with a peak between January and March. Consistent with our study, RSV is observed more frequently in winter months in many studies from different regions. 14 RSV and HMPV were usually seen in children under five years of age as the cause of bronchiolitis and pneumonia. In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. 15 IAV and IBV were detected with a frequency of 4.8% and 2.4%, respectively, and peaked between January and March. The presence of RSV and HMPV in circulation during the same period was notable, which necessitates the use of virological methods for the differential There are four subtypes of PIVs (1-4) which may cause croup, pharyngitis, laryngitis, tracheobronchitis, bronchiolitis, and/or pneumonia. 19 PIV-3 was the most commonly detected subtype in our study, followed by PIV-1, -2, and -4. PIV-3 is detected more frequently in April, May, and October. It was not possible to detect the seasonal relation of other PIV subtypes due to a small number of cases. In other studies, PIV-3 was also reported as the most common subtype followed other PIVs similar to our findings. 20, 21 They were frequently detected during spring and early summer months. Bocavirus, after being identified in 2005 has been isolated from 1.5% to 19% of the respiratory tract samples of children who were admitted to the hospital due to respiratory viral disease. 22 Bocavirus causes coinfections up to 90% of the cases with other viruses such as influenza, rhinovirus, parainfluenza, RSV, and metapneumovirus. 23, 24 The prevalence of bocavirus was 2.8% in our study with a coinfection frequency of 48.8%, mainly associated with rhinovirus/enterovirus, RSV, and influenza A/B. Infections were seen throughout the year without a clear seasonal relation although 58% (29 of 50) of cases were between January and March which is parallel to the other reported studies. [25] [26] [27] Coronaviruses were identified nearly 5% of the patients, with OC43 being the most frequent subtype followed by NL63, HKU1, and 229E. Coinfections with rhinovirus or RSV were seen in almost half of the samples. These infections were detected in almost all months except June and August. It was reported that coronavirus infections peaked mainly in winter without any significant difference between the four subtypes in terms of seasonality and origin (community or hospital-acquired) of the infection. 28, 29 Bordetella spp is an agent that can be mistaken as viral infection since can lead to prolonged cough and severe infections in infants, and young children. There were only 28 patients with Bordetella infections in our study which were seen in patients less than 3-months old, except for one. Although can be seen at any age, pertussis is more frequent and cause more severe disease in children younger than 3-months-old because of lack of primary vaccination. 30 High vaccine coverage (at least 95%) is necessary to protect children against vaccine-preventable diseases with the herd immunity. 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