Abstract
Acute respiratory infections (ARIs) are one of the major public health problems in developing countries like Nepal. Besides the influenza, several other pathogens are responsible for acute respiratory infection in children. Etiology of infections is poorly characterized at the course of clinical management, and hence empirical antimicrobial agents are used. The objective of this study was to characterize the influenza and other respiratory pathogens by real-time PCR assay. A total of 175 throat swab specimens of influenza-positive cases collected at National Influenza Center, Nepal, during the 2015/16 winter season were selected for detecting other respiratory copathogens. Total nucleic acid was extracted using Pure Link viral RNA/DNA mini kit (Invitrogen), and multiplex RT-PCR assays were performed. Influenza A and B viruses were found in 120 (68.6%) and 55 (31.4%) specimens, respectively, among which coinfections were found in 106 (60.6%) specimens. Among the influenza A-positive cases, 25 (20.8%) were A/H1N1 pdm09 and 95 (79.2%) were A/H3 subtypes. Viruses coinfected frequently with influenza virus in children were rhinovirus (26; 14.8%), respiratory syncytial virus A/B (19; 10.8%), adenovirus (14; 8.0%), coronavirus (CoV)-HKU1 (14; 8.0%), CoV-OC43 (5; 2.9%), CoV-229E (2; 1.1%), metapneumovirus A/B (5; 2.9%), bocavirus (6; 3.4%), enterovirus (5; 2.9%), parainfluenza virus-1 (3; 1.7%), and parainfluenza virus-3 (2; 1.1%). Coinfection of Mycoplasma pneumoniae with influenza virus was found in children (5; 2.8%). Most of the viral infection occurred in young children below 5 years of age. In addition to influenza virus, nine different respiratory pathogens were detected, of which coinfections of rhinovirus and respiratory syncytial virus A/B were predominantly found in children. This study gives us better information on the respiratory pathogen profile and coinfection combinations which are important for diagnosis and treatment of ARIs.
Highlights
Acute respiratory infections (ARIs) are one of the major causes of mortality and morbidity in children especially in developing countries [1]. e World Health Organization (WHO) estimated that 1.9 million children die every year due to respiratory tract infections (RTIs), mainly pneumonia in African and Southeast Asian countries [2]. e incidence of influenza-like illness (ILI) is almost similar between developed and developing countries like Nepal; the mortality rates are higher in developing countries. e frequency of mixed infections of noninfluenza ARI viruses with influenza virus varies from 10 to 30%, and studies have suggested an association between mixed viral infections could increase the disease progression or clinical severity [3]
A laboratory-based ILI surveillance system is well established in Nepal and has greatly contributed to outbreak investigation, surveillance, and timely response since the emergence of pandemic influenza in 2009. e influenza viruses circulating in Nepal have many similarities with our neighboring countries and the regions
A total of 394 throat swab specimens were collected from children aged two months to 12 years with symptoms of influenza-like illness (ILI) during the winter season visiting at National Influenza Center (NIC), National Public Health Laboratory, Kathmandu, Nepal
Summary
ARIs are one of the major causes of mortality and morbidity in children especially in developing countries [1]. e World Health Organization (WHO) estimated that 1.9 million children die every year due to respiratory tract infections (RTIs), mainly pneumonia in African and Southeast Asian countries [2]. e incidence of influenza-like illness (ILI) is almost similar between developed and developing countries like Nepal; the mortality rates are higher in developing countries. e frequency of mixed infections of noninfluenza ARI viruses with influenza virus varies from 10 to 30%, and studies have suggested an association between mixed viral infections could increase the disease progression or clinical severity [3].e most common etiology of ARI worldwide includes influenza virus (InfV), respiratory syncytial virus (RSV), rhinovirus (RV), metapneumovirus (MPV), bocavirus (BV), adenovirus (AV), enterovirus (EV), Mycoplasma pneumoniae, parainfluenza virus (PIV), coronavirus (CoV) OC43, NL63, 229E, and HKU1 [4]. ARIs are one of the major causes of mortality and morbidity in children especially in developing countries [1]. E incidence of influenza-like illness (ILI) is almost similar between developed and developing countries like Nepal; the mortality rates are higher in developing countries. Annual epidemics of influenza virus alone can cause 5–15% ARI globally. In tropical and subtropical countries in the South East Asia such as ailand, Singapore, Malaysia, and China, the etiologic agents associated with ILI have been well characterized. A laboratory-based ILI surveillance system is well established in Nepal and has greatly contributed to outbreak investigation, surveillance, and timely response since the emergence of pandemic influenza in 2009. We attempt to characterize the influenza and other ARI pathogens by the multiplex PCR assay in children with influenza-like illness cases
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