On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

Abstract

Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovirus, the nucleotide diversity estimates are 10-fold higher for interhost data, while the number of segregating (i.e., polymorphic) sites is 6-fold lower. These results have been interpreted as demonstrating that sampled intrahost variants are strongly deleterious. In reality, however, these observations are fully consistent with standard population genetic expectations. Here, we analyze published intra-and interhost data sets within this framework, utilizing statistical inference tools to quantify the fitness effects of segregating mutations. Further, we utilize population level simulations to clarify expectations under common evolutionary models. Contrary to common claims in the literature, these results suggest that most observed polymorphisms are likely nearly neutral with regard to fitness and that standard population genetic models in fact well predict observed levels of both intra-and interhost variability.IMPORTANCE With the increasing number of evolutionary virology studies examining both intrahost and interhost patterns of genomic variation, a number of seemingly incompatible results have emerged, revolving around the far greater level of observed intrahost than interhost variation. This has led many authors to suggest that the great majority of sampled within-host polymorphisms are strongly deleterious. Here, we demonstrate that there is in fact no incompatibility of these results and, indeed, that the vast majority of sampled within-host variation is likely neutral. These results thus represent a major shift in the current view of observed viral variation.KEYWORDS human cytomegalovirus, interhost diversity, intrahost diversity, population genetics T he majority of evolutionary studies in the virus literature are divided into those examining intrahost data and those examining interhost data. Broadly speaking, intrahost studies deeply sample viral diversity from a limited number of biological samples (e.g., plasma, urine, or saliva), while interhost studies sample viral diversity from a large number of hosts, but with a shallow perspective of variation within each host. These studies are often treated as separate analyses of viral diversity. For example, studies of intrahost human cytomegalovirus (HCMV) populations report per-site nucleotide diversity values of ϳ0.002, with approximately 160,000 segregating (i.e., polymorphic) sites in the ϳ235,000-bp genome, while analyses of interhost data report

Impact of preexisting virus-specific maternal antibodies on cytomegalovirus population genetics in a monkey model of congenital transmission

“…Our identification of shared, minor UCD52 haplotypes between maternal plasma samples, amniotic fluid, placental tissue, and fetal tissues is consistent with previous studies investigating the population genetics of HCMV in newborns [12, 32], which together point towards a loose vertical transmission bottleneck between mother and fetus. While previous studies have estimated transmission bottleneck sizes for HCMV and other viruses, in this study we were unable to quantify transmission bottleneck sizes between mother and fetus due to: 1) low levels of haplotype diversity and 2) haplotype frequencies near the limit of detection.…”

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

“…This inference has primarily been made within a phylogenetic context, relying on the construction of a single consensus sequence per patient. While such a comparison of consensus sequences can be highly mis-leading when making evolutionary inference (see Renzette et al . 2017), these age-estimates also inherently rely on an accurate knowledge of mutation rates in order to invoke the ‘clock-like’ accumulation of neutral mutations as a proxy for time (Menardo et al .…”

“…Finally, we here consider the alleles segregating within a population for inference ( i.e., within a patient), whereas previous studies often call a consensus sequence per patient ( i.e., per population) and make inferences based on a collection of such consensus sequences. Such a summary of population-level variation into a single sequence is difficult to interpret, though what is evident is that a great majority of rare alleles will be neglected, and thus only a small subset of total variation ( i.e., common alleles) will be considered (Renzette et al . 2017).…”

Genotypic and phenotypic diversity within the neonatal HSV-2 population

“…Each isolate was cultured once as part of the diagnostic process with expansion only for the experiments shown here. Although this is a relatively small group of samples due to the constraints discussed previously, it is the largest group of neonatal HSV samples ever compared genotypically or phenotypically, and is similar in size to prior studies of HCMV-infected neonates (25)(26)(27)(28)(29)(30).…”

“…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).…”