Detection and sequence characterization of the 3'-end of coronavirus genomes harboring the highly conserved RNA motif s2m.
A remarkably conserved 43-nucleotide-long motif present at the 3'-end of the genomes of several members of the polyadenylated RNA virus families Astroviridae, Coronaviridae, and Picornaviridae can be used for the detection and sequence characterization of the viruses harboring it. The procedure makes use of a primer located in the most conserved core of s2m toward a generic anchored oligo(dT) primer in a semispecific PCR. This strategy allows the sequencing of some 50-100 nucleotides from the 3'-end of the virus genome, representing sufficient sequence information for initiation of further genomic characterization in a rapid amplification of cDNA ends (5'-RACE) and primer walking strategy.
Jonassen
Christine Monceyron
CM
Section for Virology and Serology, National Veterinary Institute, Oslo, Norway.
D019200:Astroviridae / Q000235:genetics; D003332:Coronaviridae / Q000235:genetics; D017934:Coronavirus / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D010849:Picornaviridae / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
D012367:RNA, Viral