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Case Reports
. 2016 Sep;54(9):2348-53.
doi: 10.1128/JCM.00877-16. Epub 2016 Jul 13.

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

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Case Reports

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

Silvia I Sardi et al. J Clin Microbiol. 2016 Sep.

Abstract

Metagenomic next-generation sequencing (mNGS) of samples from 15 patients with documented Zika virus (ZIKV) infection in Bahia, Brazil, from April 2015 to January 2016 identified coinfections with chikungunya virus (CHIKV) in 2 of 15 ZIKV-positive cases by PCR (13.3%). While generally nonspecific, the clinical presentation corresponding to these two CHIKV/ZIKV coinfections reflected infection by the virus present at a higher titer. Aside from CHIKV and ZIKV, coinfections of other viral pathogens were not detected. The mNGS approach is promising for differential diagnosis of acute febrile illness and identification of coinfections, although targeted arbovirus screening may be sufficient in the current ZIKV outbreak setting.

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Figures

FIG 1
FIG 1
Log-log plot of detected ZIKV reads against viral titer. The number of mNGS reads is normalized to reads per million (RPM) of raw reads sequenced. A power trendline is fitted to the data, showing an R2 correlation of 0.73255.
FIG 2
FIG 2
Whole-genome phylogeny of CHIKV and ZIKV. (A, upper portion) Phylogeny of all 314 CHIKV genomes available in NCBI GenBank as of March 2016 and 2 new complete or partial genomes from the current study. The three major lineages of CHIKV are shown in different colors. (A, lower portion) Phylogeny of 14 genomes corresponding to a local cluster within the ECSA (East/Central/South African) clade outlined with a dashed box in the upper portion. An ECSA CHIKV isolate located outside the cluster, HM045809, is included as an outgroup. (B) Phylogeny of all 44 ZIKV genomes available in NCBI GenBank as of March 2016 and 3 new complete or partial genomes from the current study. Genomes corresponding to the 2015-2016 ZIKV outbreak in Latin America are highlighted with a light orange background. The asterisks denote genomes corresponding to ZIKV cases in returning travelers. New CHIKV and ZIKV genomes sequenced in the current study are highlighted in boldface red, with the percent genome recovery provided in parentheses. Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node.

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