Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. The proposed methods treat the molecules in a quasispecies as individuals of competing species in an ecosystem, where the haplotypes are the competing species, and the ecosystem is the quasispecies in a host, and the evolution of the system is quantified by monitoring changes in haplotype frequencies. The correlation between the proposed indices is also discussed, and the R code used to generate the simulations, the data and the plots is provided. The virtues of the proposed indices are finally shown on a clinical case.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9867078 | PMC |
| http://dx.doi.org/10.3390/ijms24021301 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Mathematical model of replication-mutation dynamics in coronaviruses.
Math Biosci
August 2025
Department of Mathematics, University of Sussex, Brighton BN1 9QH, UK.
RNA viruses are known for their fascinating evolutionary dynamics, characterised by high mutation rates, fast replication, and ability to form quasispecies - clouds of genetically related mutants. Fast replication in RNA viruses is achieved by a very fast but error-prone RNA-dependent RNA polymerase (RdRP). High mutation rates are a double-edged sword: they provide RNA viruses with a mechanism of fast adaptation to a changing environment or host immune system, but at the same time they pose risk to virus survivability in terms of either virus population being dominated by mutants (error catastrophe), or extinction of all viral sequences due to accumulation of mutations (lethal mutagenesis).
View Article and Find Full Text PDFExperimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2.
Virus Evol
July 2025
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, MN, 55108, United States.
Despite extensive use of vaccination, porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) continues to evolve, likely driven by escape from natural or vaccine-derived immunity. However, direct evidence of vaccine-induced evolutionary pressure remains limited. Here, we tracked the evolution of PRRSV-2 sublineage 1A strain IA/2014 (variant 1A-unclassified) genome from infection chains of sequentially infected pigs under different immune conditions.
View Article and Find Full Text PDFAlgorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.
Methods Mol Biol
July 2025
Harvard Medical School, Boston, MA, USA.
RNA viruses, such as HIV, HCV, and SARS-CoV-2, show high levels of intrahost genetic diversity. Many different haplotypes can be present in a single infection, which can be studied using next-generation sequencing. However, full-length haplotype reconstruction from short reads is computationally challenging due to the presence of low-frequency mutants, as well as sequencing errors.
View Article and Find Full Text PDFOccult Hepatitis C Virus Infection: A Narrative Review.
J Viral Hepat
August 2025
Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
Hepatitis C virus (HCV) infections occur worldwide. Approximately 75% of these acute infections lead to chronic hepatitis C with few symptoms, at least during the initial phase of infection. Occult hepatitis C develops in some infected patients.
View Article and Find Full Text PDFNear extinction of the HBV quasispecies driven by the hard selective sweep in chronic hepatitis B.
mBio
August 2025
Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou, China.
The viral quasispecies play an important role in pathogenesis. However, little is known about the nature of hepatitis B virus (HBV) quasispecies and its impact on the outcomes of chronic hepatitis B. Here, we characterized the bona fide quasispecies viral populations from 16 chronically infected patients by analyzing the near full-length viral genomes obtained by single genome sequencing.
View Article and Find Full Text PDF