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. Overall design: The template-switch oligonucleotide (TSO) conjugated to the Gel Beads in the 10X Genomics 5' scRNA sequencing protocol (Fig. 1B) captures and barcodes transcripts generated during cDNA synthesis, addressing each read to an individual source cell and transcript, by a 'cell barcode' and 'unique molecular identifier' (UMI), respectively. We add virus-specific primers tiled at regular 2kb intervals across the viral RNA genome alongside poly-dT primers during in-droplet reverse transcription. Taking advantage of the TSO, reverse transcription generates barcoded cDNA transcripts (of ~2kb) that cover the entire viral genome and can be amplified for long-read sequencing. Short-read and long-read library preparation from the same barcoded scRNAseq cDNA pools allows us to reconstruct the consensus genotype from each cell and map them directly onto the transcriptome and viral RNA count information from matched infected cells.