A ligase chain reaction targeting two adjacent nucleotides allows the differentiation of cowpox virus from other Orthopoxvirus species

A ligase chain reaction (LCR) assay was developed to distinguish cowpox virus from other Orthopoxvirus species. The LCR targets two adjacent adenosine residues which are only present in the A-type inclusion protein gene (ATI-gene) of cowpox virus. Two primer pairs were designed with a one base pair overlap at the junction site and one primer of each pair was labeled radioactively. Detection of the ligation product was achieved after denaturing polyacrylamide gel electrophoresis and autoradiography. Prior to LCR, the corresponding region of the ATI-gene was amplified by a consensus primer-directed polymerase chain reaction. All 18 cowpox virus isolates investigated could be clearly discriminated from 10 vaccinia virus strains, 5 camelpox virus isolates, as well as from mousepox and monkeypox virus reference strains. The LCR method allows a fast identification of cowpox virus isolates and is a feasible tool for the analysis of small mutations within viral genes.