title: Survey of causative agents for acute respiratory infections among patients in Khartoum-State, Sudan, 2010-2011.
abstract: BACKGROUND
  This study was carried out to determine causative agents of acute respiratory illness of patients in Khartoum State, Sudan.
  
  
  METHODS
  Four hundred patients experiencing respiratory infections within January-March 2010 and January-March 2011 were admitted at Khartoum Hospital and had their throat swab samples subjected to multiplex real-time RT-PCR to detect influenza viruses (including subtypes) and other viral agents. Isolation, nucleotide sequence and phylogenetic analysis on some influenza viruses based on the HA gene were done.
  
  
  RESULTS
  Out of 400 patients, 66 were found to have influenza viruses (35, 27, 2, and 2 with types A, B, C, and A and B co-infections, respectively). Influenza viruses were detected in 28, 33 and 5 patients in the age groups <1, 1-10, and 11-30 years old, respectively but none in the 31-50 years old group. Out of 334 patients negative for influenza viruses, 27, 14, and 2 were positive for human respiratory syncytial virus, rhinovirus and adenovirus, respectively. Phylogenetic tree on influenza A (H1N1) pdm09 subtype shows that Sudan strains belong to the same clade and are related to those strains from several countries such as USA, Japan, Italy, United Kingdom, Germany, Russia, Greece, Denmark, Taiwan, Turkey and Kenya. Seasonal A H3 subtypes have close similarity to strains from Singapore, Brazil, Canada, Denmark, USA and Nicaragua. For influenza B, Sudan strains belong to two different clades, and just like influenza A (H1N1) pdm09 and A H3 subtypes, seem to be part of worldwide endemic population (Kenya, USA, Brazil, Russia, Taiwan and Singapore).
  
  
  CONCLUSIONS
  In Sudan, the existence of respiratory viruses in patients with acute respiratory infection was confirmed and characterized for the first time by using molecular techniques.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Enan
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nabeshima
authors.forename: Toru
authors.initials: T
authors.lastname: Kubo
authors.forename: Corazon C
authors.initials: CC
authors.lastname: Buerano
authors.forename: Abdel Rahim M
authors.initials: AR
authors.lastname: El Hussein
authors.forename: Isam M
authors.initials: IM
authors.lastname: Elkhidir
authors.forename: Eltahir A G
authors.initials: EA
authors.lastname: Khalil
authors.affiliation: Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan. moritak@nagasaki-u.ac.jp.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Morita
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D004267:DNA Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008875:Middle Aged; D060885:Multiplex Polymerase Chain Reaction; D010614:Pharynx / Q000821:virology; D015995:Prevalence; D012328:RNA Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000821:virology*; D013397:Sudan / Q000453:epidemiology; D014777:Virus Diseases / Q000453:epidemiology* / Q000821:virology*; D055815:Young Adult