Genotyping Rotavirus RNA from Archived Rotavirus-Positive Rapid Test Strips
Lester M. Shulman , Ilana Silberstein, Jacqueline Alfandari, and Ella Mendelson
Author affiliations: Author affiliations: Central Virology Laboratory, Tel Hashomer, Israel (L.M. Shulman, I. Silberstein, J. Alfandari, E. Mendelson); Tel Aviv University, Ramat Aviv, Israel (L.M. Shulman, E. Mendelson)
Figure. Neighbor-joining phylogenetic trees for viral protein (VP) 7 G1, G2, G3, and G9 genotypes of hospitalized children in Israel, including sequences recovered from archived rotavirus dipsticks. Representative isolates for lineages and sublineages of VP7 genotypes G1 (A), G2 (B), G3 (C), and G9 (D) were chosen from Phan et al. (15) Page and Steele (16), Wang et al. (17), and Martinez-Laso et al. (18), respectively, and the sequences were downloaded from the European Molecular Biology Laboratory/GenBank/DNA Data Bank of Japan. These sequences were aligned with Israeli sequences by using the Sequencher program (Genecodes, Ann Arbor, MI, USA) and truncated to the longest segment common to all sequences in the alignment; 515 nt for G1, 547 nt for G2, 274 nt for G3, and 207 nt for G9. Each of the 4 phylogenetic trees was prepared by using ClustalX (13) for data bootstrapped 1,000× and was analyzed with NJplot (14). Whole numbers indicate bootstrap values for branches; fractional numbers indicate genetic distances. The genotype, lineage, and, where relevant, sublineage of each isolate appears in brackets after the name of the isolate: for example, KY3303[G2.2a] is VP7 genotype G 2, lineage 2, sublineage a for isolate KY3303. A letter at the end of the name of the Israeli sequences indicates the source of the RNA (D for dipstick or S for fecal suspension). D&S appears when the sequences were identical. The GenBank accession numbers for all sequences in this figure appear in the online Appendix Table (Table A). Scale bars indicate percent of nucleotide substitutions per site.
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