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Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and sw...

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Autores principales: Goldstein, Stephen A., Brown, Joe, Pedersen, Brent S., Quinlan, Aaron R., Elde, Nels C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872347/
https://www.ncbi.nlm.nih.gov/pubmed/33564759
http://dx.doi.org/10.1101/2021.02.03.429646
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author Goldstein, Stephen A.
Brown, Joe
Pedersen, Brent S.
Quinlan, Aaron R.
Elde, Nels C.
author_facet Goldstein, Stephen A.
Brown, Joe
Pedersen, Brent S.
Quinlan, Aaron R.
Elde, Nels C.
author_sort Goldstein, Stephen A.
collection PubMed
description The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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spelling pubmed-78723472021-02-10 Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens Goldstein, Stephen A. Brown, Joe Pedersen, Brent S. Quinlan, Aaron R. Elde, Nels C. bioRxiv Article The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health. Cold Spring Harbor Laboratory 2021-06-28 /pmc/articles/PMC7872347/ /pubmed/33564759 http://dx.doi.org/10.1101/2021.02.03.429646 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Goldstein, Stephen A.
Brown, Joe
Pedersen, Brent S.
Quinlan, Aaron R.
Elde, Nels C.
Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title_full Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title_fullStr Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title_full_unstemmed Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title_short Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
title_sort extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872347/
https://www.ncbi.nlm.nih.gov/pubmed/33564759
http://dx.doi.org/10.1101/2021.02.03.429646
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