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

Victorian Infectious Diseases Reference Laboratory, 10 Wreckyn Street, North Melbourne, Victoria 3051, Australia

Correspondence
Doris Chibo
Doris.chibo{at}mh.org.au

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.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are DQ243940 [GenBank] –DQ243962 [GenBank] and DQ243964 [GenBank] –DQ243987 [GenBank] .

A figure showing the phylogenetic analysis using PHYLIP on HCoV-229E isolates and strains identified between 1972 and 2004, and tables showing primers used and their nucleotide position relative to the HCoV-229E complete genome and the summary of amino acid changes in the S and N proteins of HCoV-229E variants studied are available as supplementary material in JGV Online.

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