Emerging geminivirus problems: A serious threat to crop production

Geminiviruses form the second largest family of plant viruses, the Geminiviridae, represented by four genera: Mastrevirus, Curtovirus, Topocuvirus and Begomovirus. During the last two decades these viruses have emerged as devastating pathogens, particularly in the tropics and subtropics, causing huge economic losses and threatening crop production. Epidemics caused by re‐emerging and newly emerging geminiviruses are becoming frequent even in regions that were earlier free from these viruses. Compared to mastreviruses and curtoviruses, begomoviruses have emerged as more serious problems in a variety of crops, for example, cassava, cotton, grain legumes and vegetables. Major contributory factors for the emergence and spread of new geminivirus diseases are the evolution of variants of the viruses, the appearance of the whitefly ‘B’ biotype and the increase in the vector population. Variability in geminiviruses has arisen through mutations, recombination and pseudorecombination. Genomic recombination in geminiviruses, not only between the variants of the same virus but also between species and even between genera, has resulted in rapid diversification. From the disease point of view, most virulent variants have developed through recombination of viral genomes such as those associated with cassava mosaic, cotton leaf curl, and tomato leaf curl diseases. Heterologous recombinants containing parts of the host genome and/or sequences from satellite‐like molecules associated with monopartite begomoviruses provide unlimited evolutionary opportunities. Human activity has also played an important role in the emergence of serious geminivirus diseases across the globe, like the changes in cropping systems, the introduction of new crops, the movement of infected planting materials and the introduction of host susceptibility genes through the exchange of germplasm.     

Small RNA deep sequencing‐based detection and further evidence of DNA viruses infecting sweetpotato plants in Tanzania

Small interfering RNA deep sequencing (SRDS) was used to detect viruses in 23 sweetpotato plants, collected from various locations in Tanzania. Alignment of small RNA reads using a MAQ program recovered genomes of viruses from five families, namely Geminiviridae (2), Closteroviridae (1), Betaflexiviridae (1), Caulimoviridae (1) and Potyviridae (1). This was in agreement with the variation of symptoms observed on sweetpotato plants in fields and screen house, which included leaf curl, vein yellowing, chlorosis, stunted growth and brown blotches. PCR was also used to confirm the occurrence of viruses associated with leaf curl and symptomless infections. A complete genome (2768 nucleotides) was obtained for a sweepovirus that was 89.9% identical to the strain of Sweet potato leaf curl Sao Paulo virus (SPLCSPV; Begomovirus) reported in South Africa. Sweepoviruses are known to undergo frequent recombinations and evidence for this was found in the SPLCSPV sequence studied. The SRDS‐based results indicated occurrence of the poorly studied Sweet potato badnavirus B (SPBV‐B) and Sweet potato badnavirus A (collectively known as Sweet potato pakakuy virus; SPPV; Caulimoviridae) in sweetpotato plants in Tanzania. A 5′‐end partial sequence (3065 nucleotides), encoding hypothetical, movement and coat proteins, was obtained and found to be 86.3% and 73.1% identical to SPBV‐B and SPBV‐A, respectively. A survey for the distribution of SPPV and Sweet potato symptomless mastrevirus 1 (SPSMV‐1) showed that these viruses were wide spread and co‐infecting sweetpotato plants in Tanzania. The importance of East Africa as a hot spot for the diversity and evolution of sweet potato viruses is discussed.