Positive Selection of Synonymous Mutations in Vesicular Stomatitis Virus

The amount and nature of preexisting variation in a population of RNA viruses is an important determinant of the virus's ability to adapt rapidly to a changed environment. However, direct quantification of this preexisting variation may be cumbersome, because potentially beneficial alleles are typically rare, and isolation of a large number of subclones is required. Here, we propose a simpler method. We infer the initial population structure of vesicular stomatitis virus (VSV) by fitting a mathematical model of asexual evolution to an extensive set of measurements of VSV fitness dynamics under various conditions, including new and previously published data. The inferred variation of fitness in the initial population agrees very well with the results of direct experiments with subclone fitness quantification. From the same procedure, we also estimate the mean fitness effect of beneficial mutations (selection coefficient s), the percentage of sites in the genome that are under moderate positive or negative selection, and the percentage of sites where beneficial mutations may potentially occur. For VSV strain MARM U evolving in BHK-21 cells, the three parameters have values of 0.39, 9%, and 0.06%, respectively. The method can be generalized and applied easily to other rapidly evolving microbes, including both asexual microorganisms and those with recombination.

Section: Discussionsupporting

confidence: 85%

Rapid Adaptive Amplification of Preexisting Variation in an RNA Virus

Dutta

Rouzine

Smith

et al. 2008

“…Consistent with this interpretation are the results obtained from the strains undergoing regimens of acute replication in mammalian and/or insect cells (31). These viruses show increased fitness in both cell types, and the determination of their genomic sequences reveals three mutations found in the strains from persistently infected cells (32). The C3U transition at nt 2257 (corresponding to a Ser33Thr change in the M protein) and the G3U transversion at nt 4122 (Val-3493Phe in the G protein) have been identified in viruses with a history of replication exclusively in BHK-21 cells.…”

Section: Discussionsupporting

confidence: 61%

Vesicular Stomatitis Virus Evolution during Alternation between Persistent Infection in Insect Cells and Acute Infection in Mammalian Cells Is Dominated by the Persistence Phase

Zárate

Novella

2004

Vesicular stomatitis virus has the potential for very rapid evolution in the laboratory, but like many other arboviruses, it evolves at a relatively slow rate in the natural environment. Previous work showed that alternating replication in different cell types does not promote stasis. In order to determine whether other factors promote stasis, we compared the fitness trajectories of populations evolving during acute infections in mammalian cells, populations evolving during persistent infections in insect cells, and populations evolving during alternating acute and persistent infection cycles. Populations evolving under constant conditions increased in fitness in the environment in which they replicated. An asymmetric trade-off was observed such that acute infection had no cost for persistence but persistent replication had a dramatic cost for acute infection in mammalian cells. After an initial period of increase, fitness remained approximately constant in all the populations that included persistent replication, but fitness continuously increased in populations evolving during acute infections. Determination of the consensus sequence of the genes encoding the N, P, M, and G proteins showed that the pattern of mutation accumulation was coherent with fitness changes during persistence so that once fitness reached a maximum, the rate of mutation accumulation dropped. Persistent replication dominated both the genetic and the phenotypic evolution of the populations that alternated between acute infection of mammalian cells and persistence in insect cells, and fitness loss was observed in the mammalian environment despite periodic replication in mammalian cells. These results show that stasis can be achieved without good levels of adaptation to both the mammalian and the insect environments.The high mutation rates exhibited by RNA viruses during replication contribute to their ability to evolve rapidly and adapt to the changes in their environments (14, 15). The mutation rate has been estimated to be between 10 Ϫ3 and 10 Ϫ5substitutions per nucleotide (nt) per round of replication (16). Considering the lengths of most RNA viral genomes, this translates into one mutation per genome copied, which gives the viral populations great diversity and plasticity. As do other RNA viruses, vesicular stomatitis virus (VSV) exhibits high adaptability and the capacity to increase fitness very rapidly in laboratory experiments, making it an ad hoc model for studying viral evolution (28). VSV is an arbovirus and a member of the Vesiculovirus genus in the Rhabdoviridae family. A single molecule of negative-sense, single-stranded RNA composes its genome (41). The life cycle of VSV involves horizontal transmission from insects to mammals (9, 24, 25) and vertical transmission from infected female insects to their offspring (37). Despite the high evolvability of VSV, virus isolates from the same ecological zones have the same genotypes regardless of the year of isolation and viruses from different ecological zones have different genotype...

“…6C) confirmed that the synonymous mutations in the target seed region were indeed responsible for the lack of sensitivity of those viruses to hsa-miR-296-5p. It has been reported that synonymous mutations may be a strategy by which RNA viruses can evade the suppression of host miRNAs as well as siRNAs (43,50). Synonymous mutations in the viral genome can affect the replicative properties of many viruses.…”

Section: Discussionmentioning

confidence: 99%

“…To confirm the effects of the mutations on inhibition of EV71 replication by miRNA-296, RD cells transfected with hsa-miR-296-5p mimics were infected with each of the mutant viruses (2115mt, 2896mt, and double mut) or WT virus (BrCr) at an MOI of 5. At 12 hpi, virus titers were determined and expressed as TCID 50 . The titer of the WT virus (BrCr) was significantly decreased by hsa-miR-296-5p, while all of the mutant viruses were insensitive to treatment by the hsa-miR-296-5p mimic (Fig.…”

Section: Hsa-mir-296-5p Suppresses Enterovirus 71 Replicationmentioning

confidence: 99%

Human MicroRNA hsa-miR-296-5p Suppresses Enterovirus 71 Replication by Targeting the Viral Genome

Zheng

Wang

et al. 2013

167

155

Enterovirus 71 (EV71) has emerged as a major cause of neurological disease following the near eradication of poliovirus. Accumulating evidence suggests that mammalian microRNAs (miRNAs), a class of noncoding RNAs of 18 to 23 nucleotides (nt) with important regulatory roles in many cellular processes, participate in host antiviral defenses. However, the roles of miRNAs in EV71 infection and pathogenesis are still unclear. Here, hsa-miR-296-5p expression was significantly increased in EV71-infected human cells. As determined by virus titration, quantitative real-time PCR (qRT-PCR), and Western blotting, overexpression of hsa-miR-296-5p inhibited, while inhibition of endogenous hsa-miR-296-5p facilitated, EV71 infection. Additionally, two potential hsa-miR-296-5p targets (nt 2115 to 2135 and nt 2896 to 2920) located in the EV71 genome (strain BrCr) were bioinformatically predicted and validated by luciferase reporter assays and Western blotting. Genomic alignment of various EV71 strains revealed synonymous mutations in hsa-miR-296-5p target sequences. Furthermore, the introduction of synonymous mutations into the EV71 BrCr genome by site-directed mutagenesis impaired the viral inhibitory effects of hsa-miR-296-5p and facilitated mutant virus infection. Meanwhile, compensatory mutations in corresponding hsa-miR-296-5p target sequences of the EV71 HeN strain (GenBank accession number JN256064) restored the inhibitory effects of the miRNA. These results indicate that hsa-miR-296-5p inhibits EV71 replication by targeting the viral genome. Our findings support the notion that cellular miRNAs can inhibit virus infection and that the virus mutates to escape suppression by cellular miRNAs.