Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples without isolation remains challenging for viruses such as Zika,
where metagenomic sequencing methods may generate insufficient numbers of viral reads.
In contrast, shotgun
metagenomics,
where all DNA from a sample is extracted and
sequenced, provides a culture - independent and explorative alternative to characterize the genetic basis for resistance within microbial communities.