Identifying the native hosts of giant viruses in the natural environment using single-cell transcriptomics

The discovery of giant viruses, with their immense size and complex metabolic pathways, has revolutionized our perspective on the viral world and on cell biology in general. We now know that viruses are far more complex than we had thought and that they play a significant role in the global ecology. Giant viruses routinely infect marine phytoplankton–unicellular photosynthetic organisms that are responsible for 50% of annual primary production. As phytoplankton form the basis of the marine food web, their consequent death by giant virus infection has profound importance to the marine ecosystem. Many studies in recent years have focused on the life cycle of giant viruses within marine phytoplankton and revealed their abundance in the ocean through metagenomic analysis. However, we still know very little about their ecological role and their native hosts.

To shed light on host-virus interactions in the marine environment, we developed a novel approach to detect active viral infection on a single cell resolution from a natural sample. We performed 10x Genomics Chromium Single-cell RNA-Seq of natural plankton communities and detected transcriptomic signatures of actively infected cells of diverse species. We identified the infected cells, assembled single-cell transcripts from each cell, and identified the target hosts and their specific viruses. Using this novel approach, we revealed new hosts and viruses interacting on a single cell level that were never described before. We foresee that this approach can be used in samples obtained from the natural environment to disentangle the host-virus interactions within diverse ecosystems around the globe.