Open Access Highly Accessed Research article

Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age

Caroline F Shafik1*, Emad W Mohareb1, Aymen S Yassin2, Madgy A Amin2, Amani El Kholy3, Hanaa El-Karaksy4 and Fouad G Youssef1

Author Affiliations

1 US Naval Medical Research Unit No.3, Cairo 11517, Egypt

2 Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo University, Cairo, Egypt

3 Faculty of Medicine, Department of Clinical Pathology, Cairo University, Giza, Egypt

4 Faculty of Medicine, Department of Pediatrics, Cairo University, Giza, Egypt

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BMC Infectious Diseases 2012, 12:350  doi:10.1186/1471-2334-12-350

Published: 13 December 2012



Lower respiratory tract infections (LRTI) are responsible for a considerable number of deaths among children, particularly in developing countries. In Egypt and the Middle East region, there is a lack of data regarding the viral causes of LRTI. In this study, we aimed to identify the relative prevalence of various respiratory viruses that contribute to LRTIs in young children. Although, nucleic acid-based methods have gained importance as a sensitive tool to determine the viral infections, their use is limited because of their prohibitive cost in low-income countries. Therefore, we applied three different laboratory methods, and presented the different virus prevalence patterns detected by each method.


We collected nasopharyngeal aspirate samples, demographic data and, clinical data from 450 children under five years of age who presented with LRTI at Abou El Reesh hospital in Cairo during a one-year period. To identify the viral causes of the LRTI we used direct fluorescence assay, real-time reverse-transcriptase polymerase chain reaction (rt-RT-PCR), and shell vial culture. We tested for eight major respiratory viruses.


Two hundred sixty-nine patients (59.9%) had a viral infection, among which 10.8% had a co-infection with two or more viruses. By all three methods, respiratory syncytial virus (RSV) was the most predominant, and parainfluenza virus type 2 (HPIV-2), influenza B virus (FLUBV) were the least predominant. Other viral prevalence patterns differed according to the detection method used. The distribution of various viruses among different age groups and seasonal distribution of the viruses were also determined.


RSV and human adenovirus were the most common respiratory viruses detected by rt-RT-PCR. Co-infections were found to be frequent among children and the vast majority of co-infections were detected by nucleic acid-based detection assays.

Egypt; Direct fluorescence assay; Lower respiratory tract infections; Pediatric; Polymerase chain reaction; Respiratory viruses; Shell vial culture