Skip directly to search Skip directly to A to Z list Skip directly to page options Skip directly to site content

Volume 21, Number 8—August 2015

Dispatch

Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014

Charles Y. Chiu, Vanessa Bres, Guixia Yu, David Krysztof, Samia N. Naccache, Deanna Lee, Jacob Pfeil, Jeffrey M. Linnen, and Susan L. StramerComments to Author 
Author affiliations: University of California San Francisco, San Francisco, California, USA (C.Y. Chiu, G. Yu, S.N. Naccache, D. Lee, J. Pfeil); University of California San Francisco–Abbott Viral Diagnostics and Discovery Center, San Francisco (C.Y. Chiu, G. Yu, S.N. Naccache, D. Lee, J. Pfeil); Hologic, Inc., San Diego, California, USA (V. Bres, J.M. Linnen); American Red Cross, Gaithersburg, Maryland, USA (D. Krysztof, S.L. Stramer)

Main Article

Figure 2

Phylogeny of chikungunya virus (CHIKV). (Upper panel) All 188 nearly-full or full genome CHIKV sequences available in the National Center for Biotechnology Information nucleotide database as of March 2015, including the 3 new genomes from Puerto Rico recovered in this study (red boldface) were aligned by using the multiple alignment fast Fourier transform (MAFFT) algorithm, and phylogenetic trees were constructed by using the MrBayes algorithm in the Geneious software package (12). Branch length

Figure 2. Phylogeny of chikungunya virus (CHIKV). (Upper panel) All 188 nearly-full or full genome CHIKV sequences available in the National Center for Biotechnology Information nucleotide database as of March 2015, including the 3 new genomes from Puerto Rico recovered in this study (red boldface) were aligned by using the multiple alignment fast Fourier transform (MAFFT) algorithm, and phylogenetic trees were constructed by using the MrBayes algorithm in the Geneious software package (12). Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node. (Lower panel) Molecular clock analysis of the Southeast Asian/Pacific branch containing the Caribbean sublineage (pink) was performed by using BEAST software (13). Branch lengths are drawn proportionally to the number of years before January 1, 2015, and the number of years is shown for each node. The 3 major lineages and Caribbean-associated sublineage are shown in different colors, and the nodes corresponding to the Caribbean (orange) and Puerto Rico (red) offshoots are highlighted.

Main Article

TOP