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.

Genotypic and phenotypic diversity within the neonatal HSV-2 population

“…http://dx.doi.org/10.1101/262055 doi: bioRxiv preprint first posted online Feb. 8, 2018; MV than others (Figure 6). This could be indicative of mixed viral populations or changes in polymerase fidelity (24,22). As in congenital HCMV infections (25,28,30), these data suggested that patients experiencing neonatal infection with HSV-2 may harbor mixed or diverse viral populations that are distinct from those observed in adult infections.…”

“…There is growing evidence that most herpesviruses contain significant genetic variation, including HSV-1 and HSV-2 (19,22,50,51,64,65). The potential contributions of viral genetic variation to clinical disease in neonates therefore warrants…”

“…An early analysis by Rosenthal and colleagues provided proof of principle that a heterogeneous HSV population can exist in an invasive neonatal infection (20,21). Recent advances in high-throughput sequencing (HTSeq) have now enabled similar studies to analyze herpesvirus genome-wide variation, and to detect the presence of minority variants within a single viral isolate or patient (22). These minor alleles can manifest as the new dominant allele or genotype after bottlenecks or selective pressure such as antiviral peer-reviewed) is the author/funder.…”

“…Additionally, the HSV genome is challenging to sequence and assemble with high confidence, due to its large size (~152 kb), high G+C content (~70%), and repeat-rich genome (22). Many earlier studies of HSV diversity (35)(36)(37)(38)(39) or the effect of HSV genetic variation on disease (40)(41)(42) have relied on low-resolution restriction fragment length polymorphism (RFLP) or single-gene PCR analyses.…”

Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes

“…These include sequencing only mRNAs loaded onto ribosomes (11,12) or the use of specific adaptors to generate sequencing libraries limited to full-length polyadenylated RNAs (13). Lastly, it is important to keep in mind that technical and analytical requirements for transcriptome studies are different from those of genomic studies that might characterize new viruses, detect low frequency variants, or trace the origins and consequences of sequence diversity within populations (14).…”