Science and Education Publishing American Journal of Infectious Diseases and Microbiology 2328-4064 3 1 2015 02 01 Detection and Molecular Characterization of Respiratory Syncytial Virus (RSV) in Children with Respiratory Signs in Khartoum State, Sudan 2011-2012 6 13 EN Sahar O Khalil Department of Microbiology, University of science and technology, P.O. Box: 30, Omdurman, Sudan Khalid A Enan Ali. Y. H Bashir Salim Isam M Elkhidir AJIDM2015312 10.12691/ajidm-3-1-2 2015 01 07 2015 01 27 2015 02 01 Background: The present study was to investigate the incidence of the respiratory syncytial virus infection in children and to characterize the RSV circulating in Khartoum state during 2011-12 winter seasons. Methodology: Throat swab specimens collected from 224 children less than 5 years old, with respiratory tract infections admitted at Khartoum Hospitals in winter season (2011- 2012), were screened for RSV using direct immunofluorescence assay (DFA) and reverse transcription- polymerase chain reaction (RT-). Isolation in cell culture followed by nucleotide sequencing and bioinformatics analysis based on the G gene, were done for the RT- positive RSV samples. Results: Out of 224 patients, RSV infections were detected in 136 (60.7%) patients, by using DFA technique, and 44 (19.6%) patients using RT-PCR. 22 strains of RSV were isolated in Hep-2 cell line. The clinical symptoms including Bronchiolitis, Pneumonia, Asthma and Allergy showed significantly different rates (p<0.05) in having RSV infection, (P-value = 0.017, 0.002, 0.0001, 0.0001) respectively. Bioinformatics analysis of nucleotide sequences of 7 cell culture isolated RSV strains revealed that all analyzed RSV belonged to the RSV-A genotype. Phylogenetic tree of RSV-A sequences showed that, all Sudanese strains were grouped with strains from Belgium and Saudi Arabia. Conclusions: This is the first report on molecular characterization that describes the circulation of RSV genotype in Sudan. DFA and RT-PCR offers rapid methods for detection of RSV in hospitalized children with Respiratory tract infection (RTI).