Journal
INFECTION GENETICS AND EVOLUTION
Volume 63, Issue -, Pages 295-306Publisher
ELSEVIER
DOI: 10.1016/j.meegid.2017.09.029
Keywords
Pathogen evolution; Recombination; Mutation; Evolutionary analysis; HBV evolution; HIV-1 evolution
Categories
Funding
- fellowship Ramon y Cajal from the Spanish Government [RYC-2015-18241]
- Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) [444071/2014-8]
- NORTE2020 (Portugal) [NORTE-01-0145-FEDER-000029]
- FCT
- CONICYT-FONDECYT de iniciacion en la investigacion [11160905]
- DC D-CFAR pilot award
- University Facilitating Fund Award from George Washington University, USA from the NIH National Center for Advancing Translational Sciences [NIH CCNS214443F, NIH UL1TR000075]
- District of Columbia Center for AIDS Research, an NIH [P30AI117970]
- NIH
- NIAID
- NCI
- NICHD
- NHLBI
- NIDA
- NIMH
- NIA
- FIC
- NIGMS
- NIDDK
- OAR
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Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-theart analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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