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. 2015 Dec;21(12):2225–2229. doi: 10.3201/eid2112.150132

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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 trees of strains of Middelburg virus and Sindbis virus identified in horses in South Africa relative to other members of the alphavirus genus. Trees were constructed by using the Tamura-Nei substitution model and midpoint rooted with MEGA5 (http://www.megasoftware.net/). Scale bar indicates 0.1 nt substitutions. Estimates were constructed on the basis of bootstrap resampling performed with 1,000 replicates. Confidence estimates >70 are shown. A) A 200-bp fragment of the nonstructural polyprotein region 4 gene of MDV- and SINV-positive cases. B) A 348-bp fragment of the E1 gene of 7 MIDV cases identified in horses in southern Africa (genome position 10543–10911 corresponding with the MIDV-857 strain in GenBank accession no. EF536323). Reference sequences used in these trees are as previously described (2). Complexes are identified as follows: EEE, Eastern equine encephalitis; MID, Middelburg; SF, Semliki Forest; VEE, Venezuelan equine encephalitis; WEE, Western equine encephalitis. Viruses are identified as follows: AURAV, Aura virus; BEBV, Bebaru virus; BFV, Barmah Forest virus; CABV, Cabassou virus; CHIKV, Chikungunya virus; EEEV, Eastern equine encephalitis virus; EILV, Eilat virus; EVEV, Everglades virus; FMV, Fort Morgan virus; GETV, Getah virus; HJV, Highlands J virus; MAYV, Mayaro virus; MIDV, Middelburg virus; MUCV, Mucambo virus; NDUV, Ndumu virus; ONNV, O’nyong nyong virus; PIXV, Pixuna virus; RNV, Rio Negro virus; RRV, Ross River virus; SAE, South Africa equine virus; SAGV, Sagiyama virus; SESV, Southern elephant seal virus; SFV, Semliki Forest virus; SINV, Sindbis virus; SPDV, Salmon pancreatic disease virus; TONV, Tonate virus; TROV, Trocara virus; UNAV, Una virus; VEEV, Venezuelan equine encephalitis virus; WEEV, Western equine encephalitis virus; WHATV, Whataroanvirus; ZRU, Zoonoses Research Unit virus.