Molecular epidemiology of human coronavirus NL63 in Hong Kong

Abstract

Human coronaviruses were first discovered in 1960s and believed to be the causative agents of only mild respiratory tract infections. In 2003, the worldwide outbreak of Severe Acute Respiratory Syndrome caused by SARS-CoV had greatly boosted the research interest on coronaviruses. Two more human coronaviruses – HCoV-NL63 and HCoV-HKU1 were then discovered in 2004 and 2005 respectively. Events of recombination between different genotypes had also been detected in HCoV-OC43 and HCoV-HKU1 in natural circulating strains that are causing infections. Creation of novel genotypes is resulted, which may possibly associate with more severe disease. In this study, twenty seven HCoV-NL63 strains in Hong Kong from 2004 to 2012 were included in the investigation. RNA-Dependent RNA Polymerase gene, Spike gene and the Nucleocapsid gene of these strains were sequenced, followed by phylogenetic analysis and bootscan analysis. Antigenic drift from genotype A (in 2004-2006) to B (in 2003-2010) and C (in 2009-2012) were observed. Two local strains clustered with an American strain in all three genes, which the American strain had been formed by recombination between genotype A and C. Five recent strains from 2009 to 2012, along with two Beijing strains, may belong to a potential novel genotype. Two more strains were discovered with atypical genomic profile. Complete genome sequencing would be the further work for clear investigation on their sites of recombination. No clear association between the genotypes and clinical features had been observed.