Search results for "Viral Evolution"
showing 10 items of 72 documents
The population genetics and evolutionary epidemiology of RNA viruses.
2004
Key Points The authors discuss the main mechanisms of RNA virus evolution — mutation, recombination, natural selection, genetic drift and migration, and how these interact to shape the genetic structure of populations.The quasispecies model of RNA virus evolution is explained and the question of whether this model provides an accurate description of RNA virus evolution is discussed.Experiments that can be carried out to test the basic principles of evolutionary theory are briefly described. The authors review what such experiments have told us about virus evolution and, more widely, what these experiments have revealed in terms of general evolutionary principles.RNA viruses evolve quickly, …
HIV plays (and wins) a game of T cell Brinkmanship.
2013
HIV, unlike other viruses, may benefit from immune recognition by preserving the sequence of its T cell epitopes, thereby enhancing transmission between cells.
Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus.
2009
Although viral variability studies have focused traditionally on consensus sequences, the relevance of molecular clone sequences for studying viral evolution at the intra-host level is being increasingly recognized. However, for this approach to be reliable, RT-PCR artifacts do not have to contribute excessively to the observed variability. Molecular clone sequences were obtained from an in vitro transcript to estimate the maximum error rate associated to RT-PCR for the Hepatitis C virus (HCV) E1-E2 region. On average, the frequency of RT-PCR errors was one order of magnitude lower than the level of intra-host genetic variability observed in samples from an HCV outbreak. However, RT-PCR err…
Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection.
2016
The treatment of HCV infection has seen significant progress, particularly since the approval of new direct-acting antiviral drugs. However these clinical achievements have been made despite an incomplete understanding of HCV replication and within-host evolution, especially compared with HIV-1. Here, we undertake a comprehensive analysis of HCV within-host evolution during chronic infection by investigating over 4000 viral sequences sampled longitudinally from 15 HCV-infected patients. We compare our HCV results to those from a well-studied HIV-1 cohort, revealing key differences in the evolutionary behaviour of these two chronic-infecting pathogens. Notably, we find an exceptional level o…
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
2018
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…
Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage
2021
The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy—termed the "R-clamp”—that favors the formation …
Quasispecies dynamics and fixation of a synonymous mutation in hantavirus transmission.
2008
RNA-dependent RNA polymerases, the key enzymes in replication of RNA viruses, have a low fidelity; thus, these viruses replicate as a swarm of mutants termed viral quasispecies. Constant generation of new mutations allows RNA viruses to adapt swiftly to a novel environment through selection of both pre-existing and de novo-generated genetic variants. Here, quasispecies dynamics were studied in vivo in controlled hantavirus transmission from experimentally infected to naïve rodents through infested cage bedding. An elementary step of virus microevolution was apparent, as one synonymous mutation (A759G) repeatedly became fixed in the viral RNA quasispecies populations in the recipient animals.
Is the Quasispecies Concept Relevant to RNA Viruses?
2002
The study of RNA virus evolution has blossomed over the last 20 years. Despite the emergence of this new discipline, there has been little active debate over perhaps the most fundamental question of all. Do RNA viruses evolve in a manner that is qualitatively different from other life forms? For
Molecular evolution of tomato black ring virus and de novo generation of a new type of defective RNAs during long‐term passaging in different hosts
2020
Tomato black ring virus (TBRV) is a worldwide-distributed RNA virus infecting a wide range of different host plants, including crop species, trees, shrubs, and weeds. Here, we investigated the molecular evolution of TBRV and its adaptability to different plant species. The TBRV-Pi isolate was used to generate five independent evolution lineages serially passaged in either quinoa, tobacco, or tomato plants. After 15 passages, the genetic variability present in all the lineages was characterized for the movement (MP) and coat (CP) coding cistrons. We addressed two main questions: to what extent does the amount of genetic variability in the TBRV genome depend on the host species, and are there…
The Social Life of Viruses
2021
Despite their simplicity, viruses exhibit certain types of social interactions. Situations in which a given virus achieves higher fitness in combination with other members of the viral population have been described at the level of transmission, replication, suppression of host immune responses, and host killing, enabling the evolution of viral cooperation. Although cellular coinfection with multiple viral particles is the typical playground for these interactions, cooperation between viruses infecting different cells is also established through cellular and viral-encoded communication systems. In general, the stability of cooperation is compromised by cheater genotypes, as best exemplified…