title: Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009-2012.
abstract: BACKGROUND
  Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya.
  
  
  METHODS
  HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (pol) gene.
  
  
  RESULTS
  The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E.
  
  
  CONCLUSIONS
  There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. This paper reports on the first molecular characterization of human Coronaviruses in Kenya, which play an important role in causing acute respiratory infections among children.
authors.affiliation: College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya. lenata7@gmail.com.
authors.forename: Lenata A
authors.initials: LA
authors.lastname: Sipulwa
authors.affiliation: College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology, (JKUAT), Nairobi, Kenya. julietteongus@jkuat.ac.ke.
authors.forename: Juliette R
authors.initials: JR
authors.lastname: Ongus
authors.affiliation: Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Rodney.Coldren@usamru-k.org.|Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA. Rodney.Coldren@usamru-k.org.
authors.forename: Rodney L
authors.initials: RL
authors.lastname: Coldren
authors.affiliation: Department of Emerging Infectious Diseases, US Army Medical Research Unit-Kenya, P.O. Box 606 00621, Village Market, Nairobi, Kenya. Wallace.bulimo@uonbi.ac.ke.|Special Foreign Activity of the Walter Reed Army Institute of Research, Silver Spring, MD, USA. Wallace.bulimo@uonbi.ac.ke.|Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya. Wallace.bulimo@uonbi.ac.ke.
authors.forename: Wallace D
authors.initials: WD
authors.lastname: Bulimo
mesh_terms: D017934:Coronavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018352:Coronavirus Infections / Q000453:epidemiology* / Q000266:history / Q000821:virology*; D015751:Genes, pol; D049674:History, 21st Century; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D010802:Phylogeny; D011159:Population Surveillance; D015995:Prevalence; D012367:RNA, Viral
chemical_list: D012367:RNA, Viral
references.citation: Nucleic Acids Res. 2004;32(5):1792-7
references.pmid: 15034147
references.citation: Zhonghua Yu Fang Yi Xue Za Zhi. 2004 Mar;38(2):81-3
references.pmid: 15061910
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Virology. 1991 Feb;180(2):567-82
references.pmid: 1846489
references.citation: Adv Exp Med Biol. 1990;276:307-16
references.pmid: 1966417
references.citation: Clin Infect Dis. 2005 Mar 1;40(5):662-9
references.pmid: 15714410
references.citation: Adv Virus Res. 1997;48:1-100
references.pmid: 9233431
references.citation: J Virol. 2005 Jan;79(2):884-95
references.pmid: 15613317
references.citation: Clin Infect Dis. 2005 Jun 15;40(12):1721-9
references.pmid: 15909257
references.citation: Emerg Infect Dis. 2005 Aug;11(8):1225-9
references.pmid: 16102311
references.citation: J Clin Microbiol. 2006 Jun;44(6):2063-71
references.pmid: 16757599
references.citation: J Clin Microbiol. 2006 Jul;44(7):2382-8
references.pmid: 16825353
references.citation: FEMS Microbiol Rev. 2006 Sep;30(5):760-73
references.pmid: 16911043
references.citation: Pediatrics. 2007 Jan;119(1):e70-6
references.pmid: 17130280
references.citation: Exp Biol Med (Maywood). 2009 Oct;234(10):1117-27
references.pmid: 19546349
references.citation: JAMA. 2010 May 26;303(20):2051-7
references.pmid: 20501927
references.citation: J Virol. 2010 Nov;84(21):11255-63
references.pmid: 20719951
references.citation: BMC Infect Dis. 2011;11:65
references.pmid: 21401965
references.citation: J Clin Microbiol. 2011 Jun;49(6):2318-20
references.pmid: 21490188
references.citation: J Clin Virol. 2012 Feb;53(2):135-9
references.pmid: 22188723
references.citation: Syst Biol. 2012 May;61(3):539-42
references.pmid: 22357727
references.citation: PLoS One. 2012;7(6):e38638
references.pmid: 22719912
references.citation: N Engl J Med. 2012 Nov 8;367(19):1814-20
references.pmid: 23075143
references.citation: J Infect Dis. 2012 Dec 15;206 Suppl 1:S46-52
references.pmid: 23169971
references.citation: PLoS One. 2014;9(7):e99782
references.pmid: 25080241
references.citation: Influenza Other Respir Viruses. 2010 May 1;4(3):155-61
references.pmid: 20409212
references.citation: J Infect Dis. 2004 Feb 15;189(4):652-7
references.pmid: 14767819