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We describe a statistical framework for reconstructing the sequence of transmission events between observed cases of an endemic infectious disease using genetic, temporal and spatial information. Previous approaches to reconstructing transmission trees have assumed all infections in the study area originated from a single introduction and that a large fraction of cases were observed. There are as yet no approaches appropriate for endemic situations in which a disease is already well established in a host population and in which there may be multiple origins of infection, or that can enumerate unobserved infections missing from the sample. Our proposed framework addresses these shortcomings, enabling reconstruction of partially observed transmission trees and estimating the number of cases missing from the sample. Analyses of simulated datasets show the method to be accurate in identifying direct transmissions, while introductions and transmissions via one or more unsampled intermediate cases could be identified at high to moderate levels of case detection. When applied to partial genome sequences of rabies virus sampled from an endemic region of South Africa, our method reveals several distinct transmission cycles with little contact between them, and direct transmission over long distances suggesting significant anthropogenic influence in the movement of infected dogs.

The efficacy of fungicides in managing soybean rust was evaluated in 12 environments in South America and southern Africa over three growing seasons from 2002 to 2005. There were differences in final soybean rust severity, defoliation, and yield among the treatments at most locations. In locations where soybean rust was not severe, all the fungicides evaluated reduced severity. In locations where soybean rust was severe, applications of triazole and triazole + strobilurin fungicides resulted in lower severity and higher yields compared with other fungicides. The strobilurin fungicides provided the highest yields in many locations; however, severity tended to be higher than that of the triazole fungicides. There also were differences in yield and severity between the trials with two and three applications of several fungicides, with three applications resulting in less severe soybean rust and higher yields. However, the third application of tebuconazole, tetraconazole, and the mixtures containing azoxystrobin and pyraclostrobin was not needed to maintain yield. These fungicides were among the most effective for managing soybean rust and maintaining yield over most locations.

During April 2004, a 150-m 2 dry bean (Phaseolus vulgaris) plot growing adjacent to rust-infected soybean (Glycine max) at Cedara Agricultural Research Farm (29°32'S 30°16'E) was observed to be infected with two distinct rust types. Common bean rust (caused by Uromyces appendiculatus) with reddish brown uredinia and black telia was readily identified. A second rust with smaller sporulating uredinia (1.0 to 1.5 mm 2 ), which were gray in appearance, was also found. Visual rust severity on the dry bean plants, which were in mid pod-fill, was high (approximately 30 to 40% disease incidence). Twenty plants were examined and observed to be infected with both rusts. With microscopic examination of no fewer than 20 leaves per plant, the urediniospores from the smaller lesions were determined to be morphologically similar to Phakopsora pachyrhizi (3). Real-time fluorescent polymerase chain reaction assays on six leaves and sequence analysis of the nuclear ribosomal internal transcribed spacer region 2 (1) verified the identity of the urediniospores as P. pachyrhizi. Although P. vulgaris is a known host of P. pachyrhizi, to our knowledge this is the first time since the arrival of soybean rust in 2001 that P. pachyrhizi has been observed on an alternate host plant in South Africa (2). Since dry beans are grown all year in frost-free areas, the implications are that dry beans may serve as an important overwintering host and source of inoculum for seasonal soybean rust outbreaks. References: (1) R. D. Frederick et al. Phytopathology 92:217, 2002. (2) Z. A. Pretorius et al. Plant Dis. 85:1288, 2001. (3) J. B. Sinclair and G. L. Hartman. Soybean Rust. Pages 25-26 in: Compendium of Soybean Diseases, 4th ed. G. L. Hartman et al. eds. The American Phytopathological Society, St. Paul, MN, 1999.