Title
Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection
UMMS Affiliation
Department of Microbiology and Physiological Systems; Department of Medicine, Division of Infectious Diseases and Immunology; Department of Pediatrics
Publication Date
2013-09-26
Document Type
Article
Disciplines
Genetics | Immunology and Infectious Disease | Population Biology | Virology
Abstract
Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and plasma of 5 infants with symptomatic congenital HCMV infection were analyzed. Temporal and compartmental variability of viral populations were quantified using high throughput sequencing and population genetics approaches. HCMV populations were generally stable over time, with ~88% of SNPs displaying similar frequencies. However, samples collected from plasma and urine of the same patient at the same time were highly differentiated with approximately 1700 consensus sequence SNPs (1.2% of the genome) identified between compartments. This inter-compartment differentiation was comparable to the differentiation observed in unrelated hosts. Models of demography (i.e., changes in population size and structure) and positive selection were evaluated to explain the observed patterns of variation. Evidence for strong bottlenecks (>90% reduction in viral population size) was consistent among all patients. From the timing of the bottlenecks, we conclude that fetal infection occurred between 13-18 weeks gestational age in patients analyzed, while colonization of the urine compartment followed roughly 2 months later. The timing of these bottlenecks is consistent with the clinical histories of congenital HCMV infections. We next inferred that positive selection plays a small but measurable role in viral evolution within a single compartment. However, positive selection appears to be a strong and pervasive driver of evolution associated with compartmentalization, affecting >/= 34 of the 167 open reading frames (~20%) of the genome. This work offers the most detailed map of HCMV in vivo evolution to date and provides evidence that viral populations can be stable or rapidly differentiate, depending on host environment. The application of population genetic methods to these data provides clinically useful information, such as the timing of infection and compartment colonization.
Keywords
UMCCTS funding
Rights and Permissions
Copyright 2013 Renzette et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI of Published Version
10.1371/journal.pgen.1003735
Source
Renzette N, Gibson L, Bhattacharjee B, Fisher D, Schleiss MR, et al. (2013) Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection. PLoS Genet 9(9): e1003735. doi:10.1371/journal.pgen.1003735 Link to article on publisher's site
Journal/Book/Conference Title
PLoS genetics
Related Resources
PubMed ID
24086142
Repository Citation
Renzette N, Gibson LL, Bhattacharjee B, Fisher D, Schleiss MR, Jensen JD, Kowalik TF. (2013). Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. Open Access Articles. https://doi.org/10.1371/journal.pgen.1003735. Retrieved from https://escholarship.umassmed.edu/oapubs/2410
Included in
Genetics Commons, Immunology and Infectious Disease Commons, Population Biology Commons, Virology Commons