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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)

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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.

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References
  1. Leparc-Goffart  I, Nougairede  A, Cassadou  S, Prat  C, de Lamballerie  X. Chikungunya in the Americas. Lancet. 2014;383:514. DOIPubMedGoogle Scholar
  2. Halstead  SB. Reappearance of chikungunya, formerly called dengue, in the Americas. Emerg Infect Dis. 2015;21:557–61.PubMedGoogle Scholar
  3. Appassakij  H, Khuntikij  P, Kemapunmanus  M, Wutthanarungsan  R, Silpapojakul  K. Viremic profiles in asymptomatic and symptomatic chikungunya fever: a blood transfusion threat? Transfusion. 2013;53:2567–74. DOIPubMedGoogle Scholar
  4. Hoad  VC, Speers  DJ, Keller  AJ, Dowse  GK, Seed  CR, Lindsay  MD, First reported case of transfusion-transmitted Ross River virus infection. Med J Aust. 2015;202:267–9. DOIPubMedGoogle Scholar
  5. Greninger  AL, Chen  EC, Sittler  T, Scheinerman  A, Roubinian  N, Yu  G, A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS ONE. 2010;5:e13381.PubMedGoogle Scholar
  6. Chiu  CY, Rouskin  S, Koshy  A, Urisman  A, Fischer  K, Yagi  S, Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin Infect Dis. 2006;43:e71–6. DOIPubMedGoogle Scholar
  7. Pfeffer  M, Linssen  B, Parke  MD, Kinney  RM. Specific detection of chikungunya virus using a RT-PCR/nested PCR combination. J Vet Med B Infect Dis Vet Public Health. 2002;49:49–54. DOIPubMedGoogle Scholar
  8. Stramer  SL, Linnen  JM, Carrick  JM, Foster  GA, Krysztof  DE, Zou  S, Dengue viremia in blood donors identified by RNA and detection of dengue transfusion transmission during the 2007 dengue outbreak in Puerto Rico. Transfusion. 2012;52:1657–66. DOIPubMedGoogle Scholar
  9. Stramer  SL, Dodd  RY, Chiu  CY. Advances in testing technology to ensure transfusion safety–NAT and beyond. [ISBT Science Series]. Vox Sang. 2015;10(Suppl 1):55–64. DOIGoogle Scholar
  10. Naccache  SN, Federman  S, Veeraraghavan  N, Zaharia  M, Lee  D, Samayoa  E, A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014;24:1180–92. DOIPubMedGoogle Scholar
  11. Lanciotti  RS, Valadere  AM. Transcontinental movement of Asian genotype chikungunya virus. Emerg Infect Dis. 2014;20:1400–2. DOIPubMedGoogle Scholar
  12. Kearse  M, Moir  R, Wilson  A, Stones-Havas  S, Cheung  M, Sturrock  S, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647–9. DOIPubMedGoogle Scholar
  13. Drummond  AJ, Suchard  MA, Xie  D, Rambaut  A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. DOIPubMedGoogle Scholar
  14. Gallian  P, de Lamballerie  X, Salez  N, Piorkowski  G, Richard  P, Paturel  L, Prospective detection of chikungunya virus in blood donors, Caribbean 2014. Blood. 2014;123:3679–81. DOIPubMedGoogle Scholar
  15. Farrugia  A, Kreil  TR. Reflections on the emergence of chikungunya virus in the United States: time to revisit a successful paradigm for the safety of blood-derived therapies. Transfusion. 2015;55:224–6. DOIPubMedGoogle Scholar

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Page updated: July 15, 2015
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