Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012

Abstract

BackgroundHuman 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.MethodsHCoV 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.ResultsThe 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.ConclusionsThere 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.

Incidence, significance, and persistence of human coronavirus infection in hematopoietic stem cell transplant recipients

“…The serotype most frequently detected in our population over the duration of the study was OC43, accounting for 40% of all infections, and least common one was 229E (14%). This serotype profile is similar to what has been noted at other institutions in a wide variety of geographical locations [2,3,[6][7][8]. Furthermore, all serotypes demonstrated winter seasonality, consistent with prior reports [3,5].…”

Epidemiologic and Clinical Characteristics of Coronavirus and Bocavirus Respiratory Infections after Allogeneic Stem Cell Transplantation: A Prospective Single-Center Study

“…Regarding the CoV types, and in contrast with Milano et al [11] and others [27], we observed that the most common circulating CoV in our recipients was type OC43 (48%) followed by NL63 (24%), KHU1 (19%), and the 229E subtype (9%). This order agrees with epidemiologic data for infants and adults from several other countries and continents [29,30] and may be valuable for vaccine development purposes. Some authors suggest that this order might be the consequence of the generation of cross-reacting antibodies after CoV-OC43 and CoV-NL63 infections that may protect against HHCoV-HKU1 and HHCoV-229E infections, respectively.…”

Prevalence and genetic diversity analysis of human coronaviruses among cross-border children

“…that the prevalence of NL63 was similar to or even higher than that of OC43 in Brazil, Kenya and Japan [3,[21][22][23]. 229E was detected in low levels throughout years as previous reports and thus the peak activity of 229E could not be determined.…”