What is a Primer ID?

A Primer ID is a degenerate string of nucleotides introduced into a primer during the oligonucleotide synthesis reaction. As primers are synthesized de novo, a population of primers will contain unique combinations at that degenerate block. For example, a Primer ID containing a block of 8 degenerate bases will have 65,536 (48) unique combinations.

Why use a Primer ID?

Next generation high-throughput sequencing protocols require a large amount of starting genomic material. PCR is typically a necessary first step in sequencing viral populations, as templates are limiting. During PCR, the polymerase will introduce errors into the viral population. These errors will be reported by the high resolution of next generation sequencing platforms. A Primer ID allows for tracking of individual viral genomes through the PCR and sequencing protocol and direct error correction. Without a Primer ID, artifactual errors have to be removed from biological diversity through statistical means.