Abstract
Criniviruses accumulate in the phloem tissue and damage crops by reducing chlorophyll which is essential for plant growth and development. Tomato chlorosis crinivirus (ToCV) is vectored by several whitefly species that damage tomato crops throughout the world. In South Africa, ToCV is a poorly studied pathogen of global economic importance. Therefore, a national survey was initiated to investigate the occurrence and distribution of criniviruses infecting tomato crops in South Africa. Whitefly infested tomato crops exhibiting interveinal leaf chlorosis and chlorotic flecking symptoms were assayed for crinivirus infections using a multiplex reverse transcription polymerase reaction (RT-PCR) approach to assess for the presence of crinivirus species that are known to infect solanaceous hosts. Next-generation sequencing (NGS) was used to generate the complete genome of ToCV from South Africa. Results from the survey indicated that ToCV is presently the only crinivirus species infecting tomatoes in South Africa. Blast analysis showed that the RNA-1 segment of ToCV from South Africa (ToCR1-186) matched 99% to Spanish isolates. On the other hand, the RNA-2 (ToCR2-186) segment matched 98% to a South Korean isolate and three Spanish isolates. Although recombination events were not detected, phylogenetic studies showed inconsistencies in the grouping of RNA-1 and RNA-2 segments for some of the ToCV isolates analyzed in this study. Therefore, we suggest the possibility of intraspecific reassortment. This is the first comprehensive study and full genome sequence of ToCV from South Africa. The information generated from this study is intended to raise awareness of ToCV infections on tomato crops in South Africa.
Highlights
Members of the genus Crinivirus belong to the family Closteroviridae and typically comprise a single-stranded bi-partite/tri-partite positive-sense RNA genome, approximately 15.6–17.9 kb in size [1]
Symptoms including interveinal leaf chlorosis, chlorotic flecking, and leaf bronzing that are typically associated with crinivirus infections were observed on tomato crops growing in fields and greenhouses located on commercial, smallholder, or subsistence farms (Fig 2)
Field observations showed that interveinal leaf chlorosis, chlorotic flecking, and leaf bronzing symptoms typically associated with crinivirus infection of tomatoes [10; 21] occurred more frequently amongst growers in South Africa [9] (Fig 2)
Summary
Open field and greenhouse cultivated tomato crops were surveyed during the 2015 and 2016 growing seasons. Tomato cultivation is concentrated in the Limpopo, Mpumalanga (Lowveld and Highveld), Northern KwaZulu Natal, Eastern Cape, and Western Cape provinces, all nine provinces were surveyed which included commercial, smallholder, and subsistence farms (Fig 1 and Table 1). Weed species occurring within proximity to field and greenhouse cultivated tomato crops were collected and analyzed. Each sample was appropriately labeled and assigned the corresponding GPS coordinates. Samples were placed on dry ice and transported to the University of KwaZulu Natal virology lab for further analysis
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