Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.

Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited underst...

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Published in:PLOS Neglected Tropical Diseases
Main Authors: Yi Tan, Brett E Pickett, Susmita Shrivastava, Lionel Gresh, Angel Balmaseda, Paolo Amedeo, Lihui Hu, Vinita Puri, Nadia B Fedorova, Rebecca A Halpin, Matthew P LaPointe, Marshall R Cone, Lea Heberlein-Larson, Laura D Kramer, Alexander T Ciota, Aubree Gordon, Reed S Shabman, Suman R Das, Eva Harris
Format: Article in Journal/Newspaper
Language:English
Published: Public Library of Science (PLoS) 2018
Subjects:
Online Access:https://doi.org/10.1371/journal.pntd.0006670
https://doaj.org/article/e239973cf73946e08afd2ac79925a578
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spelling ftdoajarticles:oai:doaj.org/article:e239973cf73946e08afd2ac79925a578 2023-05-15T15:11:29+02:00 Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic. Yi Tan Brett E Pickett Susmita Shrivastava Lionel Gresh Angel Balmaseda Paolo Amedeo Lihui Hu Vinita Puri Nadia B Fedorova Rebecca A Halpin Matthew P LaPointe Marshall R Cone Lea Heberlein-Larson Laura D Kramer Alexander T Ciota Aubree Gordon Reed S Shabman Suman R Das Eva Harris 2018-07-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0006670 https://doaj.org/article/e239973cf73946e08afd2ac79925a578 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC6085065?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0006670 https://doaj.org/article/e239973cf73946e08afd2ac79925a578 PLoS Neglected Tropical Diseases, Vol 12, Iss 7, p e0006670 (2018) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2018 ftdoajarticles https://doi.org/10.1371/journal.pntd.0006670 2022-12-30T20:54:30Z Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited understanding of the molecular evolution of CHIKV in the Americas during this epidemic. We sequenced 185 complete CHIKV genomes collected mainly from Nicaragua in Central America and Florida in the United States during the 2014-2015 Caribbean/Americas epidemic. Our comprehensive phylogenetic analyses estimated the epidemic history of the Asian genotype and the recent Caribbean outbreak (CO) clade, revealed considerable genetic diversity within the CO clade, and described different epidemiological dynamics of CHIKV in the Americas. Specifically, we identified multiple introductions in both Nicaragua and Florida, with rapid local spread of viruses in Nicaragua but limited autochthonous transmission in Florida in the US. Our phylogenetic analysis also showed phylogeographic clustering of the CO clade. In addition, we identified the significant amino acid substitutions that were observed across the entire Asian genotype during its evolution and examined amino acid changes that were specific to the CO clade. Deep sequencing analysis identified specific minor variants present in clinical specimens below-consensus levels. Finally, we investigated the association between viral phylogeny and geographic/clinical metadata in Nicaragua. To date, this study represents the largest single collection of CHIKV complete genomes during the Caribbean/Americas epidemic and significantly expands our understanding of the emergence and evolution of CHIKV CO clade in the Americas. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 12 7 e0006670
institution Open Polar
collection Directory of Open Access Journals: DOAJ Articles
op_collection_id ftdoajarticles
language English
topic Arctic medicine. Tropical medicine
RC955-962
Public aspects of medicine
RA1-1270
spellingShingle Arctic medicine. Tropical medicine
RC955-962
Public aspects of medicine
RA1-1270
Yi Tan
Brett E Pickett
Susmita Shrivastava
Lionel Gresh
Angel Balmaseda
Paolo Amedeo
Lihui Hu
Vinita Puri
Nadia B Fedorova
Rebecca A Halpin
Matthew P LaPointe
Marshall R Cone
Lea Heberlein-Larson
Laura D Kramer
Alexander T Ciota
Aubree Gordon
Reed S Shabman
Suman R Das
Eva Harris
Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
topic_facet Arctic medicine. Tropical medicine
RC955-962
Public aspects of medicine
RA1-1270
description Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited understanding of the molecular evolution of CHIKV in the Americas during this epidemic. We sequenced 185 complete CHIKV genomes collected mainly from Nicaragua in Central America and Florida in the United States during the 2014-2015 Caribbean/Americas epidemic. Our comprehensive phylogenetic analyses estimated the epidemic history of the Asian genotype and the recent Caribbean outbreak (CO) clade, revealed considerable genetic diversity within the CO clade, and described different epidemiological dynamics of CHIKV in the Americas. Specifically, we identified multiple introductions in both Nicaragua and Florida, with rapid local spread of viruses in Nicaragua but limited autochthonous transmission in Florida in the US. Our phylogenetic analysis also showed phylogeographic clustering of the CO clade. In addition, we identified the significant amino acid substitutions that were observed across the entire Asian genotype during its evolution and examined amino acid changes that were specific to the CO clade. Deep sequencing analysis identified specific minor variants present in clinical specimens below-consensus levels. Finally, we investigated the association between viral phylogeny and geographic/clinical metadata in Nicaragua. To date, this study represents the largest single collection of CHIKV complete genomes during the Caribbean/Americas epidemic and significantly expands our understanding of the emergence and evolution of CHIKV CO clade in the Americas.
format Article in Journal/Newspaper
author Yi Tan
Brett E Pickett
Susmita Shrivastava
Lionel Gresh
Angel Balmaseda
Paolo Amedeo
Lihui Hu
Vinita Puri
Nadia B Fedorova
Rebecca A Halpin
Matthew P LaPointe
Marshall R Cone
Lea Heberlein-Larson
Laura D Kramer
Alexander T Ciota
Aubree Gordon
Reed S Shabman
Suman R Das
Eva Harris
author_facet Yi Tan
Brett E Pickett
Susmita Shrivastava
Lionel Gresh
Angel Balmaseda
Paolo Amedeo
Lihui Hu
Vinita Puri
Nadia B Fedorova
Rebecca A Halpin
Matthew P LaPointe
Marshall R Cone
Lea Heberlein-Larson
Laura D Kramer
Alexander T Ciota
Aubree Gordon
Reed S Shabman
Suman R Das
Eva Harris
author_sort Yi Tan
title Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
title_short Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
title_full Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
title_fullStr Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
title_full_unstemmed Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.
title_sort differing epidemiological dynamics of chikungunya virus in the americas during the 2014-2015 epidemic.
publisher Public Library of Science (PLoS)
publishDate 2018
url https://doi.org/10.1371/journal.pntd.0006670
https://doaj.org/article/e239973cf73946e08afd2ac79925a578
geographic Arctic
geographic_facet Arctic
genre Arctic
genre_facet Arctic
op_source PLoS Neglected Tropical Diseases, Vol 12, Iss 7, p e0006670 (2018)
op_relation http://europepmc.org/articles/PMC6085065?pdf=render
https://doaj.org/toc/1935-2727
https://doaj.org/toc/1935-2735
1935-2727
1935-2735
doi:10.1371/journal.pntd.0006670
https://doaj.org/article/e239973cf73946e08afd2ac79925a578
op_doi https://doi.org/10.1371/journal.pntd.0006670
container_title PLOS Neglected Tropical Diseases
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