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.