Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Abstract

Until fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.

Keywords: bioinformatics; diversity; evolution; genetic recombination; genomics; herpesvirus; minority variant; polymorphism; viral pathogenesis.

FIG 1

Opportunities for change in a given viral population arise both in vivo and in vitro. (A) The viral population in an infected individual (represented by red or red-shaded virion) may change over time due to immune selection or the accumulation of genetic drift. Bottlenecks at transmission to a new host or during introduction to tissue culture may allow a new genotype to become prevalent, akin to a genetic shift. (B) A viral stock grown in culture is also a viral population, which may undergo changes during introduction to an animal model or through plaque purification. See Fig. 2 for an expanded view of the genomes contained in the viral population.

FIG 2

Viral genomes with subtle variations contribute to the overall viral population and enable change over time. A viral population may contain minor variants (A) that remain unnoticed until selective pressures or bottlenecks reveal them (B). Deep sequencing approaches can reveal minor variants in the overall viral population, but most HTS approaches report only the consensus genome population. The consensus genome is a summary of the most common variants (e.g., those indicated by orange and blue stars) found in a majority of the sequenced genomes, but that exact genotype does not necessarily predominate in nature. As shown in the exaggerated example in panel A, the consensus genome (thick gray line) contains variants that are found in the majority of genomes (thin gray lines) but that are found only rarely in the same genome. Minor variants or alleles (e.g., those indicated by green or orange stars) are not included in the consensus genome at all, but a transmission bottleneck or subsequent selective pressure may lead to a minor variant becoming the majority genotype in the future (B). Recombination can also create entirely new genotypes, which can become dominant through bottlenecks or external selective pressures. Gene accordions, as demonstrated in vaccinia virus, result from expansion and subsequent variation of a gene under strong selective pressure.