Molecular epidemiology of human coronavirus 229E in Hong Kong

Abstract

Human coronaviruses, namely HCoV-229E and HCoV-OC43, have been identified as causal agent of upper respiratory tract infections for decades. The significance of human coronaviruses studies re-emerged after the SARS pandemic. Two novel human coronaviruses, HCoV-NL63 and HCoV-HKU1, were identified after the SARS pandemic. Up till now there are a total of five human coronaviruses being identified. After the discovery of HCoV-HKU1 in 2005, molecular epidemiology and genome studies identified the first natural recombination in human coronaviruses, which has led to the generation of different genotypes. A similar phenomenon was also observed in HCoV-OC43 in a subsequent study, resulting in the emergence of a novel genotype associated with pneumonia. Although HCoV-229E has been discovered for over forty years, information regarding its evolution and epidemiology is little and scattered. In this study, 32 HCoV-229E strains were collected from nasopharyngeal aspirates over a period of 8 years (from April 2004 to January 2012). Three genes, including RdRp (RNA-dependent-RNA polyermase), S (spike) and N (nucleocapsid), were sequenced and analyzed. Phylogenetic studies showed the existence of genetic drift among six chronological groups, including group 1 from 1979 to 1982, group 2 from 1982 to 1984, group 3 from 1990 to 1992, group 4 from 2001 to 2005, group 5 from 2005 to 2008 and group 6 from 2011 to 2012. One particular strain in 2006, HCoV-229E-HK06-24 displayed an incongruent position between the S and N gene, suggesting a possible recombination between group 4 and group 5. Additionally, five strains from 2011 to 2012 showed incongruent positions in RdRp comparing to other strains, which are suspected to be novel group 6. This study revealed the first evidence for a possible natural recombination event in HCoV-229E. The predominate group 6, which is genetically different from previous strains, may have been arisen by genetic drift. Further surveillance is required to monitor the genetic changes in HCoV-229E.