Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains

Abstract

Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct Human coronavirus 229E (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary Human coronavirus OC43 variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.

Human Coronaviruses 229E and NL63: Close Yet Still So Far

“…Only one study has described the variability of the S and N genes over time, which suggests that genetic drift shapes HCoV-229E evolution. 33 Fortunately, the sequence information allows calculation of the evolution rate of the virus. With this evolutionary rate, the time to the most common recent ancestor of HCoV-NL63 and HCoV-229E could be calculated.…”

Receptor-binding loops in alphacoronavirus adaptation and evolution

“…The alphacoronavirus, HCoV-229E, is particularly valuable as it circulates in the human population and a sequence database of natural variants isolated over the past fifty years is available. Moreover, changes in sequence and serology have suggested that HCoV-229E is changing over time in the human population [36][37][38] .…”

Picornavirus-Like Cytopathic Effects on RD-18S Cell Lines Were Induced by Human Coronavirus 229E Not Picornaviruses

“…We then extracted RNAs from the viral fluid, amplified them with HCoV-specific primers, and performed sequence analysis as reported previously (5). We also used the primers COR229ENUC-R2F and COR229ENUC-R1R for sequence analysis (9). We finally confirmed that all these 5 strains contained HCoV-229E genomes.…”