Full-genome amplification and sequencing of Zika viruses using a targeted amplification approach

We have developed methods for full-genome sequencing of Zika viruses (ZIKVs) based on a targeted amplification approach. We used alignments of publicly available complete genome data to design a primer set that selectively amplifies ZIKVs. The approach includes amplification strategies for templates present at both high and low-copy number, and PCR cycling conditions that have been normalized across genome fragments in order to streamline laboratory handling. Abundant templates can be amplified using a strategy that uses 6 overlapping amplicons to cover the complete viral genome, whereas scarce templates can be amplified using a strategy that uses 11 overlapping amplicons of smaller size. The workflow is sequencing platform agnostic, and thus, can be used in low resource settings where access to traditional Sanger sequencing is the only option available. Given the scarcity of tools for ZIKV, this approach should facilitate epidemiological surveillance and other studies that require the generation of complete viral genomic information quickly and cost-effectively.