Sweetpotato (Ipomoea batatas L.) is an important staple crop cultivated in over 100 countries, and the storage roots and vines provide food for humans and livestock. Sweetpotato consumption and demand for its value-added products have increased significantly in the last two decades and have led to new cultivar development, expansion in acreage, and increased demand in the United States and its export markets. Despite the known nutritional components and other health benefits, further research is needed to characterize the genetic diversity and chemical composition related to their storage root qualities, essential in developing consumer-preferred cultivars that offer host plant resistance against pests and pathogens. There is a critical need for research on non-pesticidal control approaches that can provide safe, effective, economical, sustainable, and environmentally sound pest and disease management techniques, especially for socially disadvantaged small farmers in the United States. Moreover, climate change can significantly impact future production practices and yield and may directly or indirectly affect crop pests, weeds, and diseases. In this review, we discuss the current status, challenges, and future approaches associated with sweetpotato production practices; health-promoting properties of sweetpotato cultivars; value-added products; genetic diversity and germplasm; pest and disease management; weed and water management; pollination ecology; and other agronomic and cultural practices that may impact sustainable sweetpotato production by small-scale, organic, and large-scale growers. Sweetpotato (Ipomoea batatas L.) is an important staple crop cultivated in over 100 countries. US sweetpotato industry faces many production challenges, including pest and diseases, as well as climate change extremes. A comprehensive review by subject matter experts on the challenges of US sweetpotato industry is not available. This review evaluates the current situation, challenges, and future approaches for improving sweetpotato production. Also, current and future impacts of climate change on global sweetpotato production and demand are discussed.

The prevalence of phytoviruses threatens food security worldwide. A number of factors can contribute to phytoviruses remaining unidentified, including lack of resources and ignorance of their existence. This study aimed to identify and understand the molecular characteristics and phylogeny of shallot latent virus infecting garlic (Allium sativum) in Zimbabwe. Leaf samples, collected from garlic farms in and around Harare Metropolitan Province, Zimbabwe in 2015, 2016 and 2020, were tested for the presence of shallot latent virus (SLV) using DAS ELISA. 89 % of the samples tested positive for SLV. High throughput sequencing (HTS) was subsequently used to recover the genome of the virus isolate. RNA was extracted from SLV-positive samples and used in ribo-depleted RNA-Seq on an Illumina platform. Both de novo and reference assembly were used to generate the full-length genome of the SLV isolate q23-Manresa, accession number MG657357, infecting garlic in Zimbabwe. Its non-recombinant genome consists of 8423 nucleotides excluding the polyA tail. Three relationships were observed from the phylogenetic analyses of the isolate q23-Manresa to homologous non-recombinant SLV isolates identified in different parts of the world depending on the portion of the genome selected. The information generated in this study will contribute towards building a database of garlic-infecting viruses and developing surveillance strategies.

Tobacco (Nicotiana tabacum L.) is an important industrial crop from the Solanaceae family cultivated for its leaves in approximately 100 countries worldwide. In South Africa (SA), tobacco is grown in five of its nine provinces: Limpopo, North West, Western Cape, Eastern Cape, and Mpumalanga. The producer price for unmanufactured tobacco is approximately US$3570/ton annually (FAO, 2021). Emerging and recurrent plant viruses such as tomato spotted wilt orthortospovirus (TSWV) have seriously affected tobacco production yield and quality. Between November 2018 to April 2019 growing season, large thrips (order Thysanoptera) populations were observed in tobacco fields throughout South Africa's major tobacco-growing areas, and plants were showing severe necrosis, yellowing, stunted growth, ringspot, and leaf curling symptoms, which are usually associated with plant virus infections. The disease incidence was estimated at 30%, as per visual observations. Twenty-two symptomatic leaf tissue samples were collected from tobacco farms in Limpopo, Northwest, and Western cape provinces. Samples were initially screened using the double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with LOEWE®Fast Kit (LOEWE®, Germany), which detectsTSWV, groundnut ringspot orthotospovirus (GRSV), and tomato chlorotic spot orthotospovirus (TCSV). Nineteen of these samples tested positive for orthortospoviruses. Subsequently, a reverse transcription-polymerase chain reaction was performed on all ELISA-positive samples using orthotospovirus-specific primers gM410 & gM870c targeting the NSm gene (Chen et al., 2012). All samples were positive for orthotospoviruses, as indicated by the presence of a 500bp amplicon. Nineteen purified PCR products were sequenced in the forward and reverse directions using Sanger sequencing at the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP; South Africa). The sequences were aligned using Muscle in MEGA version X (Kumar et al., 2018) to generate the consensus sequences that were then subjected to the standard nucleotide basic local alignment search tool (blastn) on the NCBI website. Blastn analysis showed that 16 of the 19 samples matched TSWV nucleotide sequences, while three of the sequences; LP14 (accession number OL505552), LP18 (accession number OL505553), and NW4 (accession number OL505554), had a nucleotide sequence identity of 96,38%, 96,97% and 97,29% with the GSRV isolate SA-05 (accession number MH742957; Silva et al., 2019) from South Africa, respectively. This is the first report of GRSV infecting tobacco after TSWV was reported in SA. Previously, GSRV was reported on soybean and groundnut in South Africa by Petersen and Morris in (2002) and Silva et al. in (2019). The results from this study lay a foundation for more detailed studies on GRSV, which will result in the development of effective and sustainable control strategies to manage GRSV diseases on tobacco in SA.

Avocado sunblotch viroid (ASBVd) is found in many avocado-growing regions of the world, where it affects fruit yield and quality. The trees develop two types of infections: symptomatic and symptomless infections. Symptoms are most obvious as yellow streaks on leaves, fruit and green stems of symptomatic trees and symptomless carrier trees do not display any such symptoms. Symptomless carrier trees are considered the primary source of disease transmission in orchards. Hence, this study investigated the impact of ASBVd-infected symptomless carrier trees on tree morphology, fruit maturity, yield and quality of ‘Hass’ avocado from 2019 until 2021. Differences were observed in the orchard between infected and healthy trees; trees with medium and high viroid concentrations excessively produced flowers, lost leaves during flowering and ultimately bore few to no fruit at the end of the season. The dry matter content results showed that ASBVd did not affect the rate of maturity of the fruit, as fruit from infected and healthy trees matured at the same time. Yield counts indicated that medium and highly infected trees produced between 83 and 96% lower yields compared to healthy trees. Postharvest studies showed that medium and highly infected fruit significantly lost firmness and coloured up more rapidly than healthy fruit. Infected, non-stored fruit also developed external rots and shrivels, however, these disorders were reduced in fruit stored at 5 °C for 28 days. Therefore, flower overbearing with the shedding of leaves and lower yields can be used as indicators of ASBVd infection in ‘Hass’ orchards but confirmation with molecular testing is required. These observations can be incorporated into an ASBD management strategy in ‘Hass’ orchards.

Banana bunchy top disease is the most devastating viral disease of bananas worldwide and is caused by banana bunchy top virus (BBTV). The disease is spread by the banana aphid Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and through infected propagation material. In 2016, the virus was detected for the first time in an isolated area in the South Coast region of KwaZulu-Natal Province (KZN), South Africa. The aim of this study was to conduct surveys across all banana-producing regions in South Africa, viz. KwaZulu-Natal, Mpumalanga, and Limpopo provinces. Over 1700 plant and aphid samples were collected from commercial farms and rural households in the three provinces, and more-intense sampling was done in the affected KZN region. A BBTV-specific PCR targeting DNA-R (encoding the master replication initiation protein, M-Rep) was used to detect virus-infected samples, and amplicons of the expected size were sequenced. Comparative phylogenetic analysis showed that the South African BBTV isolates clustered within the Pacific Indian Oceans genomic group, which includes isolates from India and other regions in Africa, with a bootstrap value of 94%. To date, the virus has been identified only in the South Coast region of KwaZulu-Natal Province. Intense management strategies, including scouting, removal of infected plants, and control of aphids, have been implemented in areas where positive samples were identified to minimize the spread of the virus.

Potato virus Y (PVY) infects economically important solanaceous crops in Zimbabwe. However, there is little information on the genome sequences of isolates occurring in this country. In this study, RNASeq of PVY-infected pepper leaves that were sampled from different locations in Zimbabwe was performed. The PVY genome sequences recovered by de novo assembly of the generated reads were checked for recombination patterns before phylogenetic analyses. Three PVY isolates: d7-Bindura, prime-e5, and q19-Harare were all found to have arisen from a single recombination event involving PVYO and PVYC strains. Phylogenetic analyses provided further evidence of recombination. The isolates in this study were grouped with a pepper-infecting PVY isolate previously found in South Africa. More studies of this kind need to be conducted in Africa to determine the outspread of this particular recombinant virus.

Objectives: Plant-infecting viruses remain a serious challenge towards achieving food security worldwide. Cucurbit virus surveys were conducted in Zimbabwe during the 2014 and 2015 growing seasons. Leaf samples displaying virus-like symptoms were collected and stored until analysis. Three baby marrow samples were subjected to next-generation sequencing and the data generated were analysed using genomics technologies. Zucchini shoestring virus (ZSSV), a cucurbit-infecting potyvirus previously described in South Africa was one of the viruses identified. The genomes of the three ZSSV isolates are described analysed in this note. Results: The three ZSSV isolates had the same genome size of 10297 bp excluding the polyA tail with a 43% GC content. The large open reading frame was found at positions 69 to 10106 on the genome and encodes a 3345 amino acids long polyprotein which had the same cleavage site sequences as those described on the South African isolate except for the P1-pro site. Genome sequence comparisons of all the ZSSV isolates showed that the isolates F7-Art and S6-Prime had identical sequence across the entire genome while sharing 99.06% and 99.34% polyprotein nucleotide and amino acid sequence identities respectively with the isolate S7-Prime.

Emerging pests and diseases are a major threat to food production worldwide. In a recent survey, Tomato torrado virus (ToTV) was identified on tomato crops in the Limpopo province of South Africa and a first report of the disease was published. In this follow-up study, the full genome sequence of a tomato-infecting isolate of ToTV from South Africa was elucidated. High-throughput sequencing was used to generate the full genome of ToTV infecting tomato crops in South Africa. The longest contig obtained for the RNA-1 and RNA-2 genome of ToTV was comprised of 7420 and 5381 nucleotides (nt), respectively. Blast analysis of the RNA-1 sequence of ToTV from South Africa (ToT-186) matched 99% to a Spanish and Polish isolate; the RNA-2 segment of ToTV from South Africa (ToT-186) matched 99% to ToTV isolates from Italy and Poland, respectively. The information presented in this study will go a long way towards better understanding the emergence and spread of ToTV and devising sustainable management of ToTV diseases.

High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

Tomato spotted wilt virus (TSWV) is an economically important pathogen of many crops worldwide. However, prior to this study, only one complete genome sequence of an African TSWV isolate was available in public databases. This limits genetic diversity and evolutionary studies of the pathogen on the continent. TSWV was detected in symptomatic Zimbabwean chrysanthemum plants using late-ral flow kits. The presence of the pathogen was subsequently confirmed by double antibody sandwich enzyme-linked immunosorbent assay and reverse transcription-polymerase chain reaction (RT-PCR). Total RNAs for RT-PCR and next-generation sequencing (NGS) were extracted using an RNA extraction kit. NGS performed on an Illumina HiSeq platform was used to recover the full TSWV genome and analyzed by different software packages. The tripartite genome of the Zimbabwe TSWV isolate consisted of L, M and S RNAs of 8914, 4824 and 2968 nucleotides, respectively. This isolate shared highest protein and nucleotide sequence identities with the isolate LK-1 from neighboring South Africa. The Zimbabwe TSWV isolate was found to be a non-recombinant and non-resistance-breaking. This study provides the first full genome of TSWV from Zimbabwe. It also adds useful information towards understanding the evolution of the pathogen. Keywords: Africa; tospovirus; phylogenetic analysis; recombination; virus identification.

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.

Whitefly-transmitted viruses are a growing threat to modern day agriculture. Their impact on South Africa's vegetable industry results in unprecedented economic losses. Tomatoes are important vegetable crops that are highly susceptible to whiteflies and an almost indispensable part of meal preparation in many South African homes. Against this background, tomato crops and nearby weed species in South Africa were surveyed for whitefly-transmitted viruses. In addition, some pepper crops in adjacent tomato fields were also included in this study. Field and greenhouse crops were inspected for the development of virus-like symptoms in the presence of whitefly infestations. Leaf samples exhibiting virus-like symptoms were collected and analyzed for whitefly-transmitted crini-, torrado-, begomo-, ipomo- and carla viruses using molecular assays. The identity of each virus positive sample was confirmed by Sanger sequencing and used in subsequent phylogenetic studies. Tomato chlorosis crinivirus (ToCV), Tomato torrado virus (ToTV) and Tomato curly stunt begomovirus (ToCSV) were three major viruses identified in the study. ToCV was the most abundant whitefly-transmitted virus in South Africa with an overall prevalence of 47.1% (tomatoes) and 21% (weeds). ToCV isolates from South Africa matched ≥97% to isolates from Spain and Sudan. ToTV outbreaks emerged on tomato crops in the northern parts of South Africa in the presence of abnormally high whitefly populations. ToTV infections of tomatoes were restricted to the Limpopo province, however, a second isolate was identified on an unknown arable weed that did not infect nearby tomato crops. ToTV isolates from South Africa matched 99% and 92.8% to Polish and Italian isolates and had an overall incidence of 7.5% (tomatoes) and 11% (weeds). ToCSV isolates from South Africa matched 100% with Mozambican isolates. Phylogenetic analysis showed that current ToCSV isolates in South Africa were distantly related to a previously identified South African ToCSV isolate. The disease was identified on tomatoes in three provinces and had an overall incidence of 9.4%. On the contrary, whitefly-transmitted viruses were not identified on pepper crops exhibiting virus-like symptoms. In this study, whitefly-transmitted viruses infecting tomatoes, and some weed species in South Africa were elucidated. These findings are intended to raise awareness on the impact of whitefly-transmitted viruses in South Africa's tomato industry.

Agriculture faces the huge challenge of meeting increasing food demands while simultaneously reducing its environmental footprint and meeting sustainability goals. Climate change is a major risk to sub-Saharan Africa and the southern Africa region. Pests are, and will continue to be responsible for crop losses which may amount to more than 40% worldwide. Climate change and weather patterns directly affect the distribution, development and population dynamics of insect pests and it may facilitate the spread of indigenous and exotic species. The aim of the study was to identify and evaluate major pests of vegetables in South Africa and Zimbabwe in relation to climate variability. Quantitative and qualitative research methods were used to solicit data from respondents. This was done across all nine provinces of South Africa and five agro-ecological zones in Zimbabwe. Key informants and focus groups were used to triangulate the data. Whiteflies and aphids collected from field and greenhouse sampling sites were phenotyped to determine the possible species present. In Zimbabwe, farmers perceived an increase in the abundance of insect pests such as aphids, whiteflies, stem borers, ball worms, red spider mite, termites and diamondback moths and the emergence of new pests. The increase in pest populations was perceived to be caused by short winters, higher temperatures and lengthy dry spells. In South Africa, the major pest outbreaks were aphids, whiteflies, red spider mites and thrips. Moreover, some of these pests are vectors of destructive viral pathogens. Emerging whitefly-transmitted torrado, crini, and begomoviruses were identified in major vegetable growing regions throughout South Africa. From this study, Tomato torrado virus (ToTV) was reported for the first time from continental Africa continent. In addition, several weed species significantly contributed to the epidemiology of vector-borne disease in commercial and smallholder farming communities. Preliminary risk maps for possible pest and disease outbreaks were produced for the two countries. The major policy directions require governments in Africa to start documenting new and emerging pests and diseases of major crops. Furthermore, surveillance systems should be initiated to monitor pest populations and extension programs that create awareness to farmers on new and existing pests and how to manage them. A collaborative effort is paramount for the development of appropriate integrated pest management systems to reduce the losses incurred by the agricultural pests in Africa and abroad.

Iris yellow spot virus (IYSV) is an important pathogen of Allium species worldwide. It has a tripartite genome consisting of the large (L), medium (M) and small (S) RNA segments. Despite its worldwide distribution, very few complete gene and genome sequences are available in public databases. The aim of this study was to obtain full gene sequences of a garlic-infecting IYSV isolate by next-generation sequencing (NGS) for understanding its evolution. Total RNA was extracted from an IYSV-positive garlic leaf and sequenced on the Illumina HiSeq platform using paired-end chemistry 125 × 125 bp reads. The quality of raw reads was assessed using FastQC software before trimming with Trimmomatic version 0.36. The resultant paired-end sequences were used for both de novo and reference-based genome assembly. The resultant consensus gene sequences were analyzed using SIAS (for sequence identity and composition), ExPASy (for protein molecular weight) and ORF Finder (for open reading frame identification). Three full gene sequences, that is, nucleocapsid (N), nonstructural protein (NSs) and movement protein (NSm) were recovered. The N gene did not display any distinct clustering patterns based on geographical locations and was most identical to an onion-infecting isolate from Serbia (Accession KT272878). The NSs and NSm genes clustered closely with homologous sequences of IYSV isolates that were retrieved from GenBank and EMBL. This study lays the foundation for complete genome studies of IYSV in Zimbabwe. Key words: Allium species, emerging pathogen, reverse transcription polymerase chain reaction (RT-PCR), serology, tospovirus.

The monoculture vegetable production systems practiced by Zimbabwean farmers has resulted in major disease outbreaks, causing major production constraints. There is need to determine the intensity of pesticides usage and methods of alternative disease management strategies. This study was carried out using 250 randomly selected vegetable farmers by administering questionnaires. The study objectives were to determine farmers’ perceptions on vegetable disease incidence and severity in relation to prevailing weather conditions, and determine common control methods practiced to manage fungal and bacterial disease outbreaks. The results indicated significant increases in fungal and bacterial disease incidence of 84.6% (within community cropping fields) and severity of 73.1% (within individual farmer fields) over the past 5-10 years (P £ 0.05). It also revealed disease incidence being highest [30.8%] during winter (May – July) and rainy months [23.1%] (November – February). Results further indicated 96.2% of the respondents relied on chemical methods, 53.8% used cultural control, and 11.5% used natural control methods. However, none of the farmers used bio-pesticide/biological control methods. In conclusion: farmers are aware of the disease shifts in response to different climate variability but seem unaware of the negative effects of extensive chemical use, nor existence of alternative bio-pesticide/biological disease management strategies.

A tomato-infecting tomato mosaic virus (ToMV) isolate was detected in Zimbabwe using lateral flow kits and double-antibody sandwich enzyme-linked immunosorbent assay. Next-generation sequencing and de novo assembly were subsequently performed to determine its genome sequence. The ToMV genome of the Zimbabwe isolate is the second to be reported in Africa.

Several alleles at the pvr2 locus are known to control recessive resistance to Potato virus Y (PVY) in pepper. In this study, PVY resistant F2 pepper lines were developed from local germplasm carrying recessive genes (pvr21 and pvr22) using marker-assisted selection (MAS). The F1 and F2 generations were assessed for the presence of resistant/susceptible alleles (pvr2+/pvr21/pvr22) at the pvr2-elF4E locus using the tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) procedure. Our results show that ARMS-PCR can be used to successfully screen pepper genotypes for alleles that confer PVY resistance thereby contributing to the improvement of pepper production.

Viruses, as they replicate in the plant host, can disrupt cellular processes and host physiology to cause disease. The range in disease reactions, from yellowing to dwarfing and reduction in host fecundity, culminates in sizable losses along with decreases in the aesthetic value in commercial cultivations, landscape plants, or home gardens. Typically, these reactions occur in plants that have not developed specific defensive responses against virulence factors produced by the virus. However, there can be instances where plants, in both natural and cultivated populations, carry inherent disease resistance but are not protected against virus infections. Successful disease management strategies are therefore aimed at the prevention or the reduction of virus infections and require an understanding of how viruses survive and spread between crops and across seasons. Since different diseases have distinct ecological and epidemiological characteristics, there is no "one-size-fits-all" approach to management. Diseases caused by plant viruses affecting cassava, sweet potato, banana, corn, rice, wheat, and various vegetable crops are examined in this chapter.