Virus Sequencing From Single Plaques

Researchers from the Craig Venter Center have recently published a way to sequence the viral genome from a single virus plaque.

They are amplifying the viral genomes with an optimized SISPA (Sequence Independent Single Primer Amplification) protocol. While the whole genome amplification using the ɸ 29 phage polymerase requires at least 1 ng of template (equivalent to about 2 000 000 particles), the SISPA protocol can amplify the genome from a single plaque only (about 10 pg of template). The sequencing reads of the study were produced with both, Roche 454 and Illumina HiSeq platforms.

The feasibility of the approach was shown for the Influenza A virus (segmented RNA virus), but the SISPA approach can also be used for de novo whole genome sequencing of any other virus species.

In my opinion, the study is an important breakthrough for all applications that require a rapid determination of viruses like during an outbreak, or when propagation of viruses is very difficult and time-consuming.

Nevertheless I think that one needs to be careful when interpreting the SNPs and INDELs of such generated sequences and validate the identified variances. The high level of amplification can result in detection of false-positive SNPs that actually derive from amplification errors.

The full publication can be read here.

Regina Dick

About Regina Dick

Regina is a driving supporter of next generation sequencing activities.

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