Structure and dynamics of enterovirus genotype networks

Like all biological populations, viral populations exist as networks of genotypes connected through mutation. Mapping the topology of these networks and quantifying population dynamics across them is crucial to understanding how populations adapt to changes in their selective environment. The influence of mutational networks is especially profound in viral populations which rapidly explore their mutational neighborhoods via high mutation rates. Using a novel single-cell sequencing method, scRNAseq-Enabled Acquisition of mRNA and Consensus Haplotypes Linking Individual Genotypes and Host Transcriptomes (SEARCHLIGHT), we captured and assembled viral haplotypes from hundreds of individual infected cells to reveal the complexity of viral populations. We obtained these genotypes in parallel with host cell transcriptome information, enabling us to link host cell transcriptional phenotypes to the genetic structures underlying virus adaptation. Our examination of these structures reveals the common evolutionary dynamics of enterovirus populations and illustrates how viral populations reach through mutational ‘tunnels’ to span evolutionary landscapes and maintain connection with multiple adaptive genotypes simultaneously.

Methods
These data were collected using 10x single-cell sequencing (10xgenomics.com). After collecting cDNA from the 10x process, the cDNA was processed for long-read sequencing. The resulting short- and long-read sequencing data was then processed through the anchovy script and associated R scripts to generate these outputs as described in the accompanying manuscript.