A proofreading-impaired herpesvirus generates populations with quasispecies-like structure

An Author Correction to this article was published on 01 October 2019

Abstract

RNA virus populations are composed of highly diverse individuals that form a cloud of related sequences commonly referred to as a ‘quasispecies’1,2,3. This diversity arises as a consequence of low-fidelity genome replication4,5. By contrast, DNA virus populations contain more uniform individuals with similar fitness6. Genome diversity is often correlated with increased fitness in RNA viruses, while DNA viruses are thought to require more faithful genome replication. During DNA replication, erroneously incorporated bases are removed by a 3′-5′ exonuclease, a highly conserved enzymatic function of replicative DNA but not RNA polymerases. This proofreading process enhances replication fidelity and ensures the genome integrity of DNA organisms, including large DNA viruses7. Here, we show that a herpesvirus can tolerate impaired exonucleolytic proofreading, resulting in DNA virus populations, which, as in RNA viruses8, are composed of highly diverse genotypes of variable individual fitness. This indicates that herpesvirus mutant diversity may compensate for individual fitness loss. Notably, in vivo infection with diverse virus populations results in a marked increase in virulence compared to genetically homogenous parental virus. While we cannot exclude that the increase in virulence is caused by selection of and/or interactions between individual genotypes, our findings are consistent with quasispecies dynamics. Our results contrast with traditional views of DNA virus replication and evolution, and indicate that a substantial increase in population diversity can lead to higher virulence.

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Fig. 1: Design and properties of MDV DNA polymerase mutants.
Fig. 2: Genetic diversity of quasispecies-like populations in cell culture.
Fig. 3: Genetic diversity of viruses determines disease outcome.
Fig. 4: Genetic diversity of viruses in vivo.

Data availability

The SNPs analysed in this study are supplied as Supplementary Tables. Illumina short reads (FASTQ) have been uploaded to the Short Read Archive and can be accessed under Bioproject no. PRJNA553690.

Code availability

The custom code used to analyse the sequencing data is available at the public repository github (https://github.com/NG-viro/Shannon_Entropy).

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Acknowledgments

We thank the animal caretakers of the Robert-von-Ostertag-Haus for their expert assistance. J.T. was supported by a stipend from the Studienstiftung des Deutschen Volkes.

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J.T. performed and analysed the virological, genetic, biochemical, sequencing and animal experiments. N.G. performed the sequence analyses. S.H. and D.P.M. performed the phylogenetic analyses. K.E. and N.O. determined some of the virus growth properties. D.P.M., D.K. and N.O. supervised the study. J.T., D.P.M. and N.O. wrote the paper.

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Correspondence to Nikolaus Osterrieder.

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Trimpert, J., Groenke, N., Kunec, D. et al. A proofreading-impaired herpesvirus generates populations with quasispecies-like structure. Nat Microbiol 4, 2175–2183 (2019). https://doi.org/10.1038/s41564-019-0547-x

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