Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units
Summary Genetic diversity enables a virus to colonize novel hosts, evade immunity, and evolve drug resistance. However, viral diversity is typically assessed at the population level. Given the existence of cell-to-cell variation, it is critical to understand viral genetic structure at the single-cell level. By combining single-cell isolation with ultra-deep sequencing, we characterized the genetic structure and diversity of a RNA virus shortly after single-cell bottlenecks. Full-length sequences from 881 viral plaques derived from 90 individual cells reveal that sequence variants pre-existing in different viral genomes can be co-transmitted within the same infectious unit to individual cell…
Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qβ.
Abstract Genome sizes and mutation rates covary across all domains of life. In unicellular organisms and DNA viruses, they show an inverse relationship known as Drake’s rule. However, it is still unclear whether a similar relationship exists between genome sizes and mutation rates in RNA genomes. Coronaviruses, the RNA viruses with the largest genomes (∼30 kb), encode a proofreading 3′ exonuclease that allows them to increase replication fidelity. However, it is unknown whether, conversely, the RNA viruses with the smallest genomes tend to show particularly high mutation rates. To test this, we measured the mutation rate of bacteriophage Qβ, a 4.2-kb levivirus. Amber reversion-based Luria–D…
Human norovirus hyper-mutation revealed by ultra-deep sequencing
Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To mor…
Bacteriophage richness reduces bacterial niche overlap in experimental microcosms
Antagonistic interactions such as competition and predation shape the structure and dynamics of ecological communities. Their combined effects can affect the species richness within a particular trophic level. Despite theory linking the complementarity of interactions across trophic levels and ecosystem functioning, there is a shortage of empirical tests of such predictions. We present an experimental investigation of these combined effects within a bacteria-phage interaction network. We measured the biomass yield of combinations of bacterial strains under increasing levels of bacteriophage richness. Our results show an increasing impact of phage on bacteria with increasing phage diversity.…
Variation in RNA virus mutation rates across host cells.
It is well established that RNA viruses exhibit higher rates of spontaneous mutation than DNA viruses and microorganisms. However, their mutation rates vary amply, from 10−6 to 10−4 substitutions per nucleotide per round of copying (s/n/r) and the causes of this variability remain poorly understood. In addition to differences in intrinsic fidelity or error correction capability, viral mutation rates may be dependent on host factors. Here, we assessed the effect of the cellular environment on the rate of spontaneous mutation of the vesicular stomatitis virus (VSV), which has a broad host range and cell tropism. Luria-Delbrück fluctuation tests and sequencing showed that VSV mutated similarly…
Variability and host-dependency of RNA virus mutation rates
Los virus de ARN pueden infectar todo tipo de organismos, desde los procariotas a los eucariotas superiores, y estos agentes infecciosos parecen particularmente propensos a causar enfermedades emergentes tanto en humanos, animales, como en plantas. Su habilidad para escapar del sistema inmunitario, evadir estrategias antivirales o infectar a nuevas especies son aspecto más de su rápida evolución. Por lo tanto, comprender los procesos básicos del la evolución de los virus de ARN podría ayudar en el diseño de nuevas estrategias antivirales. Una de las principales características de los virus de ARN es su tasa de mutación extremadamente alta. De hecho, la alta diversidad genética de las poblac…
Variability in the mutation rates of RNA viruses
ABSTRACT: It is well established that RNA viruses show extremely high mutation rates, but less attention has been paid to the fact that their mutation rates also vary strongly, from 10-6 to 10-4 substitutions per nucleotide per cell infection. The causes explaining this variability are still poorly understood, but candidate factors are the viral genome size and polarity, host-specific gene expression patterns, or the intracellular environment. Differences between animal and plant viruses, or between arthropod-borne and directly transmitted viruses have also been postulated. Finally, RNA viruses may be able to regulate the rate at which new mutations spread in the population by modifying f…