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.

Fig. 1

Temporal distribution of HCoVs in Kenya between 2009 to 2012

Fig. 2

Spatial Distribution of HCoVs in Kenya between 2009 and 2012. Mbagathi, Isiolo, Alupe, Kericho, Kisii, Malindi, and Port Reitz District Hospitals are abbreviated as MBG, IDH, ALH, KCH, KSI, MDH and PDH respectively. New Nyanza General provincial hospital is abbreviated as NNY

Fig. 3

Phylogenetic relationships of partial sequences from the HCoV pol gene of the Kenyan isolates with representatives from different species. The Kenyan HCoV sequences are in blue color, the prototype strains are in red and representative strains in black; each sequence is represented by the GenBank accession number. The PEDV in green was used as an out-group. The tree was constructed by Mr. Bayes v3.2, using the general time-reversible nucleotide substitution model. Posterior probability support values are shown as percentages at the nodes