Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements

PLoS Neglected Tropical Diseases
Kenneth A StaplefordMarco Vignuzzi

Abstract

Chikungunya virus (CHIKV), an alphavirus and member of the Togaviridae family, is capable of causing severe febrile disease in humans. In December of 2013 the Asian Lineage of CHIKV spread from the Old World to the Americas, spreading rapidly throughout the New World. Given this new emergence in naïve populations we studied the viral genetic diversity present in infected individuals to understand how CHIKV may have evolved during this continuing outbreak. We used deep-sequencing technologies coupled with well-established bioinformatics pipelines to characterize the minority variants and diversity present in CHIKV infected individuals from Guadeloupe and Martinique, two islands in the center of the epidemic. We observed changes in the consensus sequence as well as a diverse range of minority variants present at various levels in the population. Furthermore, we found that overall diversity was dramatically reduced after single passages in cell lines. Finally, we constructed an infectious clone from this outbreak and identified a novel 3' untranslated region (UTR) structure, not previously found in nature, that led to increased replication in insect cells. Here we preformed an intrahost quasispecies analysis of the new CHIKV outbr...Continue Reading

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Citations

Feb 9, 2019·Human Vaccines & Immunotherapeutics·Arturo Reyes-Sandoval
May 17, 2019·Microorganisms·Laura I Levi, Marco Vignuzzi
Jun 28, 2019·Journal of Medical Virology·Massimo CiccozziSilvia Angeletti
Jul 5, 2019·MSphere·Carlo FischerJan Felix Drexler
Sep 1, 2019·Viruses·Adriano de Bernardi SchneiderMichael T Wolfinger
Nov 12, 2019·PLoS Pathogens·James Weger-LucarelliMarco Vignuzzi
May 23, 2018·Current Clinical Microbiology Reports·Víctor Hugo Peña-GarcíaRebecca C Christofferson
May 21, 2020·Viruses·Edward I PattersonNaomi L Forrester
Sep 5, 2020·PLoS Pathogens·Laura Sandra LelloAndres Merits
Feb 14, 2019·Memórias do Instituto Oswaldo Cruz·Allan Henrique Depieri CataneoJuliano Bordignon
Aug 8, 2019·Viruses·Kame A Galan-HuertaAna M Rivas-Estilla
Oct 9, 2019·Annual Review of Entomology·Scott C WeaverMawlouth Diallo
Mar 20, 2018·Scientific Reports·Martha ZakrzewskiAndreas Suhrbier
Jul 28, 2019·Nucleic Acids Research·Catherine KendallAndrew Tuplin
Jul 17, 2020·Frontiers in Microbiology·Marcela S CunhaLuciana J da Costa
Sep 21, 2017·Emerging Infectious Diseases·Marcela S CunhaClarissa R Damaso
Dec 29, 2017·PloS One·Somphavanh SomlorMarc Grandadam
Sep 11, 2019·EBioMedicine·Alicia Martinez-LopezFelipe Diaz-Griffero
Jul 16, 2020·Seminars in Cell & Developmental Biology·Claudia V FilomatoriDiego E Alvarez
Jan 28, 2021·Nature Communications·Jianying LiuScott C Weaver
Jan 13, 2021·Nature Reviews. Microbiology·Scott C WeaverNikos Vasilakis
Feb 17, 2021·The Journal of General Virology·Christian K FungIrina Maljkovic Berry

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Methods Mentioned

BETA
PCR

Software Mentioned

PhyML
mcf
fastq
mem
CLUSTAL W
bwa
ViVAn
Model Generator

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