A method is disclosed for determining a target nucleic acid sequence, where the target nucleic acid sequence is comprised in a preparation comprising a non-target nucleic acid sequence, the target nucleic acid sequence and the non-target nucleic acid sequence each having a first region of common sequence upstream of a first region of dissimilar sequence upstream of a second region of dissimilar sequence, and includes the steps of contacting the preparation with an oligonucleotide primer complementary to at least a portion of the first region of common sequence, under conditions to hybridise the primer thereto; contacting the preparation with a first labelled nucleotide bearing a first label, wherein the first labelled nucleotide is complementary to a first template nucleotide comprised in the first region of dissimilar sequence of either the target nucleic acid sequence or the non-target nucleic acid sequence, under conditions to incorporate the first labelled nucleotide either into the primer hybridised to the target nucleic acid sequence or into the primer hybridised to the non-target nucleic acid sequence but not into both; and subjecting the preparation to a sequencing reaction, thereby extending the primer to form one or more first-labelled sequencing products comprising the first labelled nucleotide and one or more non-first-labelled sequencing products comprising no first labelled nucleotide; and determining at least a portion of the sequence of the first-labelled sequencing products and/or the non-first-labelled sequencing products, thereby determining at least the second region of dissimilar sequence of the target nucleic acid sequence.