Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts

Abstract

The presence of bottlenecks in the transmission cycle of many RNA viruses leads to a severe reduction of number of virus particles and this occurs multiple times throughout the viral transmission cycle. Viral replication is then necessary for regeneration of a diverse mutant swarm. It is now understood that any perturbation of the mutation frequency either by increasing or decreasing the accumulation of mutations in an RNA virus results in attenuation of the virus. To determine if altering the rate at which a virus accumulates mutations decreases the probability of a successful virus infection due to issues traversing host bottlenecks, a series of mutations in the RNA-dependent RNA polymerase of Venezuelan equine encephalitis virus (VEEV), strain 68U201, were tested for mutation rate changes. All RdRp mutants were attenuated in both the mosquito and vertebrate hosts, while showing no attenuation during in vitro infections. The rescued viruses containing these mutations showed some evidence of change in fidelity, but the phenotype was not sustained following passaging. However, these mutants did exhibit changes in the frequency of specific types of mutations. Using a model of mutation production, these changes were shown to decrease the number of stop codons generated during virus replication. This suggests that the observed mutant attenuation in vivo may be due to an increase in the number of unfit genomes, which may be normally selected against by the accumulation of stop codons. Lastly, the ability of these attenuated viruses to transition through a bottleneck in vivo was measured using marked virus clones. The attenuated viruses showed an overall reduction in the number of marked clones for both the mosquito and vertebrate hosts, as well as a reduced ability to overcome the known bottlenecks in the mosquito. This study demonstrates that any perturbation of the optimal mutation frequency whether through changes in fidelity or by alterations in the mutation frequency of specific nucleotides, has significant deleterious effects on the virus, especially in the presence of host bottlenecks.

Publication DOI: https://doi.org/10.1371/journal.ppat.1007610
Additional Information: © 2019 Warmbrod et al. This is an openaccess 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. Funding Information: This work was funded by grants to NLF from the National Institutes of Health, R01-AI095753-01A1 and R01 AI125902. https://www. nih.gov The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publication ISSN: 1553-7374
Last Modified: 15 May 2024 07:22
Date Deposited: 07 Sep 2022 14:23
Full Text Link:
Related URLs: https://journal ... al.ppat.1007610 (Publisher URL)
PURE Output Type: Article
Published Date: 2019-04-04
Accepted Date: 2019-01-31
Authors: Warmbrod, K. Lane
Patterson, Edward I.
Kautz, Tiffany F.
Stanton, Adam
Rockx-Brouwer, Dedeke
Kalveram, Birte K.
Khanipov, Kamil
Thangamani, Saravanan
Fofanov, Yuriy
Forrester, Naomi L.

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