Principle and design of molecular barcodes tagged on the viral
genome
The molecular barcoding strategy has been successfully employed in
“omics” techniques for virus studies (summarized in Table 1). The
principle of molecular barcoding is to tag the viral genome with a
string of random nucleotides in order to distinguish one virus from
another. Molecular barcodes can be introduced into a template by using
different approaches. First, molecular barcodes can be embedded into
sequencing adaptors while constructing sequencing libraries (Figure 1A).
A classical example was given by Schmitt et al.
(2012)[19].
They constructed sequencing libraries with two independent molecular
barcodes associated at both ends of each library to correct sequencing
errors present on every sequencing read. It is noteworthy to point out
the difference between “molecular barcodes” and “sample barcodes
(sample indexes)” here. Although both are common to be used in the same
sequencing reads, molecular barcodes aim to correct sequencing errors
and increase sequencing accuracy or define true mutations; whereas
sample barcodes enable multiple samples to be sequenced together, so
called multiplexed into the same lane of flow cells (Figure 1B). The
second approach is to employ molecular inversion probes (MIP) carrying
molecular barcodes. A good example of this approach is the single
molecule Molecular Inversion Probes
method[23](Figure 1C), which combines the MIP strategy for targeted
capture[32–34]at a single-molecule
level[12,13,16,17,21–22].
Third, molecular barcodes can also be introduced on a template by PCR
amplification with target-specific primers (Figure 1D).