Increased Rotavirus Prevalence in Diarrheal Outbreak Precipitated by Localized Flooding, Solomon Islands, 2014
Forrest K. Jones, Albert I. Ko, Chris Becha, Cynthia Joshua, Jennie Musto, Sarah Thomas, Axelle Ronsse, Carl D. Kirkwood, Alison Sio, Audrey Aumua, and Eric J. Nilles
Author affiliations: Yale School of Public Health, New Haven, Connecticut, USA (F.K. Jones, A.I. Ko); Fundação Oswaldo Cruz, Salvador, Brazil (A.I. Ko); Solomon Islands Ministry of Health and Medical Services, Honiara, Solomon Islands (C. Becha, C. Joshua, A. Sio); World Health Organization, Honiara (C. Joshua, J. Musto, A. Aumua); World Health Organization, Suva, Fiji (J. Musto, A. Ronsse, E.J. Nilles); Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia (S. Thomas, C.D. Kirkwood); La Trobe University, Melbourne, Victoria, Australia. (C.D. Kirkwood)
Figure 2. Nucleotide sequence–based phylogenetic tree of rotavirus viral protein (VP) 7 for isolates obtained in the Solomon Islands during an outbreak of diarrheal illness after flooding in the capital city of Honiara. Four isolates from different provinces had homologous VP7 sequences. We visually analyzed generated electropherograms and constructed contiguous DNA sequence files using the Sequencher Software program version 5.0.1 (Gene Codes Corp Inc., Ann Arbor, MI, USA). We performed nucleotide similarity searches using the BLAST (http://www.ncbi.nlm.nih.gov) and compared the nucleotide and deduced amino acid sequences of the VP7 gene with sequences available in GenBank possessing the entire open reading frame. We constructed multiple nucleotide and amino acid alignments using the MUSCLE algorithm in MEGA 6.0 (http://www.megasoftware.net/). Nucleotide and amino acid distance matrices were calculated by using the p-distance algorithm in MEGA 6.0. We selected the optimal evolutionary model based on the Akaike information criterion (corrected) ranking implemented in jModelTest (GitHub, Heidelberg, Germany) and generated maximum-likelihood phylogenetic trees using the nucleotide substitution model TrN+Gamma 4+I in MEGA 6.0, and assessed the robustness of branches by bootstrap analysis using 1,000 pseudoreplicate runs. Scale bar indicates base substitutions per site.
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