Survey of causative agents for acute respiratory infections among patients in Khartoum- State, Sudan, 2010–2011
Tóm tắt
This study was carried out to determine causative agents of acute respiratory illness of patients in Khartoum State, Sudan. 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. 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). 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.
Tài liệu tham khảo
Greenberg SB: Respiratory viral infections in adults. Curr Opin Pulm Med 2002, 8: 201-208. 10.1097/00063198-200205000-00009
Hall CB: Respiratory syncytial virus and parainfluenza virus. N Engl J Med 2001, 344: 1917-1928. 10.1056/NEJM200106213442507
Feikin DR, Ope MO, Aura B, Fuller JA, Gikunju S, Vulule J, Ng’ang’a Z, Njenga MK, Breiman RF, Katz M: The population-based burden of influenza-associated hospitalization in rural western Kenya, 2007–2009. Bull World Health Organ 2012, 90: 256-263A.
Steffen C, Debellut F, Gessner BD, Kasolo FC, Yahaya AA, Ayebazibwe N, Bassong O, Cardoso Y, Kebede S, Manoncourt S, Vandemaele KA, Mounts AW: Improving influenza surveillance in sub-Saharan Africa. Bull World Health Organ 2012, 90: 301-305.
Salim AR: Hong Kong influenza in the Sudan. Bull World Health Organ 1971,44(5):713-716.
Steffen C, Diop OM, Gessner BD, Hacen MM, Hassar M, Katz MA, Miller MA, Paget WJ, Schoub BD, Vernet G, Ndumbe PM: Afriflu – international conference on influenza disease burden in Africa, 1–2 June 2010, Marrakech, Morocco. Vaccine 2011, 29: 363-369. 10.1016/j.vaccine.2010.11.029
WHO: Recommended composition of influenza virus vaccines for use in the 2013–14 northern hemisphere influenza season. [http://www.who.int/influenza/vaccines/virus/recommendations/201302_recommendation.pdf] []
WHO: Recommended composition of influenza virus vaccines for use in the 2013 southern hemisphere influenza season. [http://www.who.int/influenza/vaccines/virus/recommendations/201209_recommendation.pdf] []
Expanded immunization program in Sudan (Arabic) [http://www.episudan.info] []
Viboud C, Alonso WJ, Simonsen L: Influenza in tropical regions. PLoS Med 2006, 3: e89. 10.1371/journal.pmed.0030089
Akinloye OM, Rönkkö E, Savolainen-Kopra C, Ziegler T, Iwalokun BA, Deji-Agboola MA, Oluwadun A, Roivanen M, Adu FD, Hovi T: Specific viruses detected in Nigerian children in association with acute respiratory disease. J Trop Med 2011, 2011: 690286.
Salih MA, Herrmann B, Grandien M, El Hag MM, Yousif BE, Abdelbagi M, Mårdh PA, Ahmed H: Viral pathogens and clinical manifestations associated with acute lower respiratory tract infections in children of the Sudan. Clin Diagn Virol 1994,2(3):201-209. 10.1016/0928-0197(94)90023-X
Kim C, Ahmed JA, Eidex RB, Nyoka R, Waiboci LW, Erdman D, Tepo A, Mahamud AS, Kabura W, Nguhi M, Muthoka P, Burton W, Breiman RF, Njenga MK, Katz MA: Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays. PLoS One 2011,6(6):e21610. 10.1371/journal.pone.0021610
5th Sudan population and housing census—2008, priority results submitted to the Presidency by Population Census Council (2009) [http://southsudaninfo.net/wp-content/uploads/reference_library/reports/5th_sudan_census26_april_2009.pdf] []
CDC Protocol of real time RT-PCR for influenza A(H1N1) [http://www.who.int/csr/resources/publications/swineflu/realtimeptpcr/en/index.html] []
Lieberman D, Lieberman D, Shimoni A, Keren-Naus A, Steinberg R, Shemer-Avni Y: Identification of respiratory viruses in adults: nasopharyngeal versus oropharyngeal sampling. J Clin Microbiol 2009, 47: 3439-3443. 10.1128/JCM.00886-09
Mackay IM, Jacob KC, Woolhouse D, Waller K, Syrmis MW, Whiley DM, Siebert DJ, Nissen M, Sloots TP: Molecular assays for detection of human metapneumovirus. J Clin Microbiol 2003, 41: 100-105. 10.1128/JCM.41.1.100-105.2003
Gunson RN, Collins TC, Carman WF: Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions. J Clin Virol 2005, 33: 341-344. 10.1016/j.jcv.2004.11.025
Schweiger B, Zadow I, Heckler R, Timm H, Pauli G: Application of a fluorogenic PCR assay for typing and subtyping of influenza viruses in respiratory samples. J Clin Microbiol 2000, 38: 1552-1558.
National Institute of Infectious Diseases (NIID) Japan: Influenza Diagnostic Manual (Japanese). 2nd edition. Japan: Infectious Diseases Surveillance Center; 2012.
Annual Report: 2011/2012 (covering the period from September 16, 2011 to September 15, 2012 of the project “Developing Sustainable Influenza Surveillance Network”). Mongolia: National Influenza Center, National Center of Communicable Diseases, Ministry of Health; p.138. [http://www.flu.mn/eng/images/stories/lavlamj/REPORT_2011-2012_English.pdf] []
Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30: 3059-3066. 10.1093/nar/gkf436
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D: The influenza virus resource at the national center for biotechnology information. J Virol 2008, 82: 596-601. 10.1128/JVI.02005-07
Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4: 406-425.
Felsenstein J: PHYLIP - Phylogeny inference package (Version 3.2). Cladistics 1989, 5: 164-166.
Rambaut A: Molecular evolution, phylogenetics and epidemiology. 2009.http://tree.bio.ed.ac.uk/software/figtree/ []