Journal of Computer Science & Systems Biology

Single-Cell Genome Sequencing for Viral-Host Interactions

Abstract

Vikram Dhillon and Xiaoman Li

Viruses are the most abundant biological entities and infectious agents present in almost every ecosystem on the planet. Yet our understanding of how viral-mediated gene transfer and metabolic reprogramming influence the evolutionary history of their hosts and microbial communities remains poor at best. At the same time, identifying and modeling the community dynamics of viruses from the environment through conventional plaque assays is complicated because less than one percent of microbial hosts have been cultivated in vitro. Computational methods in metagenomics and phage isolation techniques have limitations in identifying the uncultured hosts of most viruses. Moreover, the model system-based measurements derived from such techniques rarely reflect the network properties of natural microbial communities. To address these problems, development of high-throughput, massively parallel sequencing approaches that do not rely on cultivation to identify specific virus-host relations such as single-cell genomic sequencing (SCGS) has become critical. SCGS has advanced our capacity to understand the genomic and transcriptomic diversity that occurs during viral-host interactions in an individual uncultured host. Here, we review the major technological and biological challenges and the breakthroughs achieved, describe the remaining challenges, and provide a glimpse into the recent advancements.