Prevalence of influenza and viral co-pathogens with severe acute respiratory infection visiting at tertiary care hospital in Nepal

Abstract

Background: Respiratory infections are one of the major public health problems in Nepal. Data on prevalence and seasonality of respiratory viruses are poorly characterized and hence empirical antimicrobial agents are used in Nepal. The objective of this study was to describe the prevalence and seasonality of influenza and viral co-pathogen in elderly patients with severe acute respiratory infection. Methods and materials: A descriptive cross sectional study was conducted at Central Diagnostic Laboratory and Research Center, Nepal during the year 2017/018. A total of 882 throat & nasopharyngeal swab were collected from patient with severe acute respiratory infection (SARI) according to WHO case definition. Total nucleic acid was extracted using Pure Link viral RNA/DNA mini kit (Invitrogen) and multiplex RT-PCR assays were performed. Results: Of the total 882 specimens; respiratory viruses were found in 556 (63.0%) specimens. Human metapneumovirus 130 (14.7%) was most frequently detected in SARI cases followed by rhinovirus 121 (13.7%), respiratory syncytial virus 37 (4.2%) and enterovirus 36 (4.0%) respectively. The rate of human metapneumovirus 60 (15.7%) co-infection was high than rhinovirus 51 (13.4%), respiratory syncytial virus 13 (3.4%) and enterovirus 12 (3.1%) infection in elderly patients. Co-infection of human metapneumovirus, respiratory syncytial virus, and enterovirus were detected with influenza. Respiratory viruses were detected year-round in Nepal. Incidence of human metapneumovirus virus infection was most commonly detected in summer (July–Aug) and winter (Jan–Feb) season. Conclusion: Respiratory viruses are significantly higher in elderly patient with severe acute respiratory infection. Our findings highlight the importance of real time diagnostic facility for clinical management and minimize the use of antimicrobial agents for respiratory infections in Nepal.