Methods of detecting target polynucleotide sequences may include introducing one or more nucleic acid analytes to a first reaction mixture comprising a single-stranded probe oligonucleotide A0, a pyrophosphorolysing enzyme, and a ligase. The analyte may anneal to the single-stranded probe oligonucleotide A0 to create a first intermediate product which is at least partially double-stranded, where the 3′ end of A0 forms a double-stranded complex with the analyte and where A0 is pyrophosphorylsed in the 3′-5′ direction from the 3′ end to create at least a partially digested strand A1. A1 may undergo ligation to form oligonucleotide A2. The methods may also include detecting a signal derived from the formed oligonucleotides, and inferring therefrom the presence or absence of the target polynucleotide sequence in the analyte.