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. 2011 Aug;17(8):1534–1536. doi: 10.3201/eid1708.101794

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This is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.

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Maximum-likelihood comparison of a partial section of the E-protein gene (A) and NS5 gene (B) of West Nile virus (WNV) lineage 2 strains isolated in South Africa (SA) in 2010 from a mare with fatal neurologic disease and representative sequences of other WNV lineages from various regions of the world. The lineage 1 strain, SAE75/10, identified in South Africa is indicated by a triangle and arrow. Sequences were aligned with MAFFT version 6 (http://align.bmr.kyushu-u.ac.jp/mafft/software) and edited with BioEdit version 7.0.9.0 (www.mbio.ncsu.edu/bioedit). Maximum-likelihood midpoint rooted trees were drawn by using PHYML (www.atgc-montpellier.fr/phyml) under 100 bootstrap repetitions and the HKY codon position substitution model and drawn to scale with the bars indicating 0.07 nt substitutions. Only bootstrap values >70 are shown. Reference strains used from GenBank that were most closely related to SA L1: PAH001, Tunisia (AY268133); Ast04-2-824A, Russia (DQ374652); Ast02-2-25, Russia (DQ374653); Ast02-2-692, Russia (DQ411031); Ast01-187, Russia (DQ411035); Ge1b/B, Spain (FJ766331); GE-2o/V, Spain (FJ766332); WNV Italy-1998-equine, Italy (AF404757); WNV15803, Italy (FJ483549); and Ita09, Italy (GU011992).