Chimeric sequences form during PCR amplification. Although chimeras can be formed by a number of mechanisms, the majority of chimeras are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence ([Smith et al. 2010], [Thompson et al., 2002], [Meyerhans et al., 1990], [Judo et al., 1998], [Odelberg, 1995]).

A chimeric template is created during one round, then amplified by subsequent rounds to produce chimeric amplicons that are difficult to distinguish from amplicons derived from a single biological sequence.