Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Abstract

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle.

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses

“…This contrasts even with other highly recombinant pathogens such as HIV-1, which has been shown to give an " # of 0.0423 (Szmaragd & Balloux 2007), indicating that HSV-1 is more recombinogenic than HIV-1. In addition, we found no shared phylogenetic pattern in trees of distant genes ( Supplementary Figure 5), confirming that, as previously described for other herpesviruses like human and murine cytomegaloviruses (Lassalle et al 2016;Smith et al 2013), the evolution of HSV-1 is characterised by pervasive recombination.…”

“…To screen for potential localised genomic recombination, we performed a site-by-site LD analysis within 3000bp sliding windows of the same mapped alignment using the "genome-wide_LD_scan.r" script from the "genomescans" suite (Lassalle et al 2016) (available at https://github.com/flass/genomescans). This scan tests all the association between all pairs of polymorphism patterns within a window using Fisher's exact tests.…”

“…Windows that contained less a minimum number (20) of biallelic sites were excluded; windows containing more than this number of SNPs were subsampled, selecting the most evenly spaced sites. To identify windows with stronger LD than in average genome-wide, it then compares the distribution of pairwise p-values within the window to the distribution obtained combining all possible windows in the genome using a Mann-Whitney-Wilcoxon test, reporting windows with -log10 p-value as a score, the local LD index (LDI, only scores > 5 were considered significant) (Lassalle et al 2016). This was performed on an alignment of genomes from all patient-deduplicated samples in this study, as well as on subalignments of genomes covering the CSF and SWAB samples only, treating them as separate populations.…”

Clinical and biological insights from viral genome sequencing

“…This enables comprehensive antiviral-resistance testing in a single test 12 . In addition, WGS can provide information on antigenic epitopes, virus evolution in a patient over time 12 , and evidence of recombination between HCMV strains 32 . WGS can also detect putative novel drug-resistant variants and predict changes to epitopes, although phenotypic testing of variants is required to confirm clinical resistance 33 and to map epitope changes 34 .…”

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; therapy (23,24). In HTSeq studies of congenital infections by the beta-herpesvirus human cytomegalovirus (HCMV), Renzette et al found evidence for heterogeneous viral populations both within and between hosts (25)(26)(27)(28)(29)(30), which far exceeded the levels of diversity observed in adult HCMV infections (31)(32)(33). Examination of vaccine-associated rashes for varicella zoster virus (VZV; an alpha-herpesvirus) has demonstrated that adult skin vesicles contained a subset of the viral population introduced during vaccination, and found at least 11 VZV genomic loci that were linked to rash formation (34).…”