Identification of Coronaviral Conserved Sequences and Application to Viral Genome Amplification
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Our work with the porcine epidemic diarrhoea virus (PEDV) has led us to look more closely at sequences and sequence motifs which are conserved between different coronaviral genomes. This is possible, since sequence information from at least part of the genomes of twelve coronaviruses is now available. Many of these motifs are specific to coronaviruses while others are shared with other positive strand RNA viruses, for example with the torovirus Berne virus and the flavivirus equine arteritis virus1. Functions can be assigned to some of these conserved regions, for example the spike (S) and membrane (M) protein transmembrane regions and the S leucine-zipper motif2. Other well conserved domains, including regions within the M and nucleocapsid (N) protein genes, have as yet no defined role. The identification of such conserved sequences is important for the recognition of functional domains of the viral RNA and proteins and also of regions useful in the cloning of novel coronaviruses using techniques based on the polymerase chain reaction (per). They can also be used to assess the evolutionary relationships of different virus groups. We plan to discuss the nature and possible functions of the conserved sequence motifs in more detail elsewhere, and to concentrate on the application of these sequences to viral genome amplification in this article.
KeywordsPorcine Epidemic Diarrhoea Virus Infectious Bronchitis Virus Conserve Sequence Motif Fold Degenerate Rare Amino Acid
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