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Phylogenetic Analysis of Chikungunya Virus Strains Circulating in the Western Hemisphere.

ABSTRACT: In December 2013, chikungunya virus (CHIKV) was isolated for the first time in the Western Hemisphere (WH) during an epidemic on the island of St. Martin. Subsequently, the virus has spread to 42 countries or territories in the Caribbean, Central, South, and North America. In this study, we have determined the full genomic sequences of 29 temporally and geographically diverse CHIKV strains from 16 countries of the WH. Phylogenetic analyses revealed minimal evolution among compared emergent CHIKV strains of the New World.

SUBMITTER: Lanciotti RS

PROVIDER: S-EPMC4824221 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Project description:BackgroundCanine distemper (CD) is a highly contagious, systemic, viral disease of dogs seen worldwide. Despite intensive vaccination in developed countries, recent reports suggest both the re-emergence and increased activity of Canine distemper virus (CDV) worldwide, including the United States. CDV is an RNA virus of the genus Morbillivirus within the family Paramyxoviridae. Viral genomic RNA encodes six structural proteins. Of the six structural proteins, the hemagglutinin (H) gene has the greatest genetic variation and is therefore a suitable target for molecular epidemiological studies. The majority of neutralizing epitopes are found on the H protein, making this gene also important for evaluation of changes over time that may result in antigenic differences among strains. The aim of this study was to determine the phylogenetic relationship of CDV strains circulating in the US.MethodsFifty-nine positive canine distemper virus samples collected from dogs from different regions and states from 2014 to 2017 were sequenced with a targeted next-generation sequencing (NGS) method. The sequences of the H, F, and P genes and the matrix-fusion (M-F) intergenic region of the amplified CDVs were analyzed individually.ResultsSequence analysis of the H gene revealed that there are at least 3 different lineages of CDV currently circulating in the US. These lineages include America-3 (Edomex), America-4, and a clade that was previously reported in association with an outbreak in Wyoming, which was linked to a domestic dog-breeding facility in Kansas in 2010. These lineages differ from the historically identified lineages in the US, including America-1, which contains the majority of the vaccine strains. Genetic differences may result in significant changes to the neutralizing epitopes that consequently may lead to vaccine failure. Phylogenetic analyses of the nucleotide sequences obtained in this study of the F and P genes and the M-F intergenic region with sequences from the GenBank database produced similar findings to the H gene analysis.ConclusionsThe CDV lineages currently circulating in the US differ from the historically identified lineages America-1. Continuous surveillance is required for monitoring circulating CDV strains in the US, to prevent potential vaccine breakthrough events.

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Phylogenetic Analysis of Chikungunya Virus Strains Circulating in the Western Hemisphere.

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