Recombination among human non-polio enteroviruses: implications for epidemiology and evolution

@article{Kyriakopoulou2014RecombinationAH,
  title={Recombination among human non-polio enteroviruses: implications for epidemiology and evolution},
  author={Zaharoula Kyriakopoulou and Vaia Pliaka and Grigoris D. Amoutzias and Panayotis Markoulatos},
  journal={Virus Genes},
  year={2014},
  volume={50},
  pages={177-188}
}
Human enteroviruses (EV) belong to the Picornaviridae family and are among the most common viruses infecting humans. They consist of up to 100 immunologically and genetically distinct types: polioviruses, coxsackieviruses A and B, echoviruses, and the more recently characterized 43 EV types. Frequent recombinations and mutations in enteroviruses have been recognized as the main mechanisms for the observed high rate of evolution, thus enabling them to rapidly respond and adapt to new… 
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References

SHOWING 1-10 OF 247 REFERENCES
Role of recombination in evolution of enteroviruses
TLDR
It can be concluded that the enterovirus species exist as a worldwide reservoir of genetic material comprising a limited quantity of capsid gene sets defining a finite number of serotypes and a range of non‐structural genes that recombine frequently to produce new virus variants.
Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence
TLDR
This review summarizes the current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs.
The Association of Recombination Events in the Founding and Emergence of Subgenogroup Evolutionary Lineages of Human Enterovirus 71
TLDR
Intriguingly, recombination events occurred as a founding event of most subgenogroups immediately preceding their lineage expansion and global emergence, suggesting the possibility that recombination contributed to their subsequent spread through improved fitness requires further biological and immunological characterization.
Frequency and Dynamics of Recombination within Different Species of Human Enteroviruses
TLDR
Together, these findings provide new insights into the dynamics of species A and B enterovirus recombination and evolution and into the contribution of structured sampling to documenting reservoirs, emergence, and spread of novel recombinant forms in human populations.
Natural genetic recombination between co-circulating heterotypic enteroviruses.
TLDR
The results suggest that genetic recombinations between different echovirus serotypes are possible when multiple epidemic strains are circulating simultaneously, and that one of these two E7 and E30 strains has evolved through recombination with the other or that both have acquired the 3D polymerase coding region from a common ancestor.
Evolution of re-emergent virus and its impact on enterovirus 71 epidemics
TLDR
Genetic changes including mutations and recombinations as well as the diversity of antigenic properties among EV71 strains in various outbreaks are described and the impact of genetic changes on viral pathogenesis and vaccine candidate selection are addressed.
Recombination and evolutionary dynamics of human echovirus 6
TLDR
The co‐circulation of different lineages of E6 in the same geographical area associated with its mainly endemic pattern of transmission may have contributed to the extremely short estimated half‐life of E 6 RFs, which contrasts markedly with other species B EVs and EV71 where VP1 lineage expansion and extinction occurred in step with defined recombination events and periodic changes in incidence.
Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes
TLDR
Phylogenetic evidence obtained from analyses of the full genome sequence supports the possible occurrence of inter-typic recombination involving EV-71 and various HEV-A, including CV-A16, the most common causal agent of HFMD.
Genetic Relationship between Cocirculating Human Enteroviruses Species C
TLDR
This first exhaustive genomic analysis of a panel of non-PV HEV-C cocirculating in a small human population highlights the high frequency of inter and intra-typic genetic recombination, constituting a widespread mechanism of genetic plasticity and continually shifting the HEv-C biodiversity.
Recombination strategies and evolutionary dynamics of the Human enterovirus A global gene pool.
TLDR
All coxsackieviruses that differed by more than 7 % of the nucleotide sequence in any genome region were recombinants relative to each other, and Enterovirus 71 (EV71), on the contrary, displayed remarkable genetic stability.
...
...