Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species

Molecular Surveillance, Prevalence, and Distribution of Cacao Infecting Badnavirus Species in Côte d'Ivoire and Ghana

The cacao swollen shoot disease (CSSD) caused by a complex of badnavirus species presents a major challenge for cacao production in West Africa, especially Ghana and Côte d'Ivoire. In this study, CSSD species detection efficiency, diversity, and geographic distribution patterns in cacao plantations in Ghana and Côte d'Ivoire were investigated through field surveillance, PCR detection assays, sequencing of positive amplicons, and phylogeographic clustering. Cumulatively, the detection efficiency of the tested CSSD primer sets that were targeting the movement protein domain of the virus ranged from 0.15% (CSSD-3 primer) to 66.91% (CSSD-1 primer) on all the symptomatic cacao leaf samples assessed. The identified CSSD species differed phylogenetically and overlapped in distribution, with the cacao swollen shoot Togo B virus (CSSTBV) (n = 588 sequences) being the most prevalent and widely distributed compared to the other CSSD species that were encountered in both countries. Geographically, the cacao swollen shoot CE virus (CSSCEV) species (n = 124 sequences) that was identified was largely restricted to the bordering regions of Ghana and Côte d'Ivoire. These results provide updated knowledge of the geographic distribution of the key CSSD species and their diagnostic efficiency and, thus, provide guidance in identifying locations for structured testing of cacao germplasm and optimal diagnostics for the predominant CSSD species in Ghana and Côte d'Ivoire.

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.

Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus

The complete genome sequence of cacao leafroll virus (CaLRV; family Solemoviridae, genus Polerovirus) was determined by high-throughput sequencing of total RNA isolated from symptomatic cacao Theobroma cacao L. plants (n = 4). The CaLRV genome sequences ranged from 5,976 to 5,997 nucleotides (nt) in length and contained seven open reading frames (ORFs). Nucleotide and amino acid (aa) sequence comparisons showed that, among selected well-characterized poleroviruses, the CaLRV genome shared the highest nt sequence identity of 62% with that of potato leafroll virus (PLRV, NC_076505). A comparison of the predicted aa sequence of the CaLRV coat protein indicated that cotton leafroll dwarf virus (CLRDV, NC_014545) and melon aphid-borne yellows virus (MABYV, NC_010809) were the closest relatives, sharing 57% aa sequence identity. Bayesian phylogenetic analysis based on complete genome sequences showed that CaLRV grouped with well-characterized poleroviruses that cause diseases of cereal and vegetable crops. During the course of publishing this work, the nearly complete genome sequence of a member of the same polerovirus species, referred to as "cacao polerovirus" (OR605721), with which CaLRV shares 99% nt sequence identity, was reported.

Epidemiology and Diagnostics of Cacao Swollen Shoot Disease in Ghana: Past Research Achievements and Knowledge Gaps to Guide Future Research

Cacao swollen shoot disease (CSSD) caused by complexes of cacao swollen shoot badnaviruses (family Caulimoviridae, genus Badnavirus) remains highly prevalent and devastating in West Africa. The disease continues to impact substantially on cacao yield loss, cacao tree mortality, and decline in foreign exchange income from cacao bean sales. Currently, the disease is estimated to have a prevalence rate of over 30% in Ghana, as assessed in the ongoing third country-wide surveillance program. Although achievements from past research interventions have greatly elucidated the etiology, biology, epidemiology, diagnostics, and management of the disease, there are some outstanding knowledge gaps. The role of these information gaps and their effect on CSSD epidemiology and prevalence remain unanswered. This paper summarizes existing scientific knowledge from past research achievements that have provided elucidation on CSSD epidemiology, management options, and guided future research. The discussion highlights the need for multidisciplinary research with modern tools and institutional collaborators to holistically bring clarity on knowledge gaps on pathogen biology, virus-host--vector interactions, role of environmental and soil nutrient effects on CSSD severity, evolution pattern, role of alternative hosts on virus species diversity, vector population dynamics, and their overall impact on CSSD prevalence and integrated management in cacao plantations.

Identification of a Novel Polerovirus in Cocoa (Theobroma cacao) Germplasm and Development of Molecular Methods for Use in Diagnostics

The cocoa crop (Theobroma cacao L.) is known to be a host for several badnaviruses, some of which cause severe disease, while others are asymptomatic. Recently, the first preliminary evidence has been published concerning the occurrence of a polerovirus in cacao. We report here the first near-complete genome sequence of cacao polerovirus (CaPV) by combining bioinformatic searches of cacao transcript databases, with cloning from the infected germplasm. The reported novel genome has all the genome features known for poleroviruses from other species. Pairwise identity analyses of RNA-dependent RNA polymerase and coat protein indicates < 60% similarity of CaPV with any reported poleroviruses; hence, we propose that the polerovirus isolate reported in this study is a novel polerovirus. The genome sequence information was also used to develop a multiplex RT-PCR assay, which was applied to screen a selected range of germplasms and to identify several infected clones. Although there is no evidence that this virus causes any severe disease, this new information, together with a robust diagnostic assay, are of strategic importance in developing protocols for the safe international transfer of cacao germplasms.

Cacao Swollen Shoot Viruses in Ghana

Cacao swollen shoot virus causes cacao swollen shoot disease of Theobroma cacao (cacao) plants. At least six cacao-infecting Badnavirus species-Cacao swollen shoot Togo A virus, Cacao swollen shoot Togo B virus (previously known as Cacao swollen shoot virus), Cacao swollen shoot CE virus, Cacao swollen shoot Ghana M virus, Cacao swollen shoot Ghana N virus, and Cacao swollen shoot Ghana Q virus-are responsible for the swollen shoot disease of cacao in Ghana. Each of these species consists of a multiplicity of strains. The New Juaben strain, the most virulent cacao swollen shoot virus strain in Ghana, belongs to the Cacao swollen shoot Togo B virus species, and is a commonly used strain in laboratory transmission assays. Infection of cacao trees with multiple strains of the virus is common and new evidence suggests that these coinfections may have resulted in the emergence of recombinant strains of the virus. The impact of these emerging recombinant strains on disease severity is uncertain. This review focuses largely on the discovery of cacao swollen shoot virus in Ghana, diversity of the virus strains, molecular characterization, propagation of virus infection in cacao plants, emergence of recombinant virus strains, vector-mediated transmission of the virus, and the management of the cacao swollen shoot disease in Ghana. It also contains sections on the botany and origin of the cacao tree, its introduction to Ghana, the role of cacao swollen shoot disease in facilitating Ghana's independence from Britain, and a brief history of chocolate.

Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.

Emerging and Re-Emerging Diseases Caused by Badnaviruses

New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.

Inconsistent PCR detection of Cacao swollen shoot virus (CSSV) is linked to the occurrence of different variants across the cocoa regions of Ghana

Reliable diagnostic tools capable of detecting latent and asymptomatic infections are critically important to support the management of the cocoa swollen shoot virus disease (CSSVD) and also to complement research activities on screening for resistant cocoa varieties. Development of efficient polymerase chain reaction (PCR) assays sensitive for detection of CSSV infections has thus been a major research focus over the years. Advances in the full genome sequence information have resulted in the design of several Cacao swollen shoot virus (CSSV)-specific and degenerate primers. The objective of the present study was to further assess the detection efficiency of ten (10) of the most utilized and novel CSSV primers on isolates of the virus across Ghana. Results from the PCR assays showed a highly variable and poor efficiency of the primers on the 189 samples of CSSV isolates evaluated. The overall detection potential of the primers ranged from 4 % to 23 % with the four best performing primers in terms of PCR positivity being P4 (23 %), CSSD1 (21 %), JOEL (21 %) CSSD2 (19 %) and BADNA (19 %). The generally poor and inconsistent efficiency of the primers are discussed in the context of the genetic variability and also the occurrence of new variants of the virus in Ghana.

Identification of a New Badnavirus in the Chinaberry (Melia azedarach) Tree and Establishment of a LAMP-LFD Assay for Its Rapid and Visual Detection

The Chinaberry tree, a member of the Meliaceae family, is cultivated in China for use in traditional medicines. In 2020, Chinaberry trees with leaf deformation symptoms were found in Hangzhou, Zhejiang province, China. In order to identify possible pathogenic viruses, a symptomatic sample was subjected to deep sequencing of small interfering RNAs. Assembly of the resulting sequences led to the identification of a novel badnavirus, provisionally designated Chinaberry tree badnavirus 1 (ChTBV1). With the recent development of China’s seedling industry and increasing online shopping platforms, the risk of tree virus transmission has increased substantially. Therefore, it is important to detect the occurrence of ChTBV1 to ensure the safety of the Chinaberry tree seedling industry. Here, we describe the development and validation of a sensitive and robust method relying on a loop-mediated isothermal amplification (LAMP) assay, targeting a 197 nt region, to detect ChTBV1 from Chinaberry tree leaves. The LAMP assay was also adapted for rapid visualization of results by a lateral flow dipstick chromatographic detection method.

Mealybug (Hemiptera: Pseudococcidae) Species Associated with Cacao Mild Mosaic Virus and Evidence of Virus Acquisition

Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the most well-known ones belonging to the Badnavirus genus. One of these, cacao mild mosaic virus (CaMMV), is present in the Americas, and is transmitted by several species of Pseudococcidae (mealybugs). To determine which species are associated with virus-affected cacao plants in North America, and to assess their potential as vectors, mealybugs (n = 166) were collected from infected trees in Florida, and identified using COI, ITS2, and 28S markers. The species present were Pseudococcus jackbeardsleyi (38%; n = 63), Maconellicoccus hirsutus (34.3%; n = 57), Pseudococcus comstocki (15.7%; n = 26), and Ferrisia virgata (12%; n = 20). Virus acquisition was assessed by testing mealybug DNA (0.8 ng) using a nested PCR that amplified a 500 bp fragment of the movement protein-coat protein region of CaMMV. Virus sequences were obtained from 34.6 to 43.1% of the insects tested; however, acquisition did not differ among species, X2 (3, N = 166) = 0.56, p < 0.91. This study identified two new mealybug species, P. jackbeardsleyi and M. hirsutus, as potential vectors of CaMMV. This information is essential for understanding the infection cycle of CaMMV and developing effective management strategies.

Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao)

Theobroma cacao is one of the most economically important tropical trees, being the source of chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex, responsible for the cacao swollen shoot virus disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of one specific insert, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities and may also aid novel methods to reduce the impact of such viruses in this crop.

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

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.

A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination

The incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since ~2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in Côte d’Ivoire and Ghana, symptomatic leaves were subjected to high-throughput sequencing. Among the 30 newly determined genomes, three badnaviruses were identified, Cacao swollen shoot Togo B virus (CSSTBV), Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus (CSSCEV). The phylogenetic trees reconstructed for the reverse transcriptase (RT) and ribonuclease H (RNase H) sequences were incongruent with the complete viral genomes, which had the most robust statistical support. Recombination seems to be involved in the CSSD-badnavirus diversification. The genomic diversity varied among different CSSD-badnaviruses, with CSSTBV showing the lowest nucleotide diversity (π = 0.06236), and CSSCEV exhibiting the greatest variability (π = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.

Chocolate Under Threat from Old and New Cacao Diseases

Theobroma cacao, the source of chocolate, is affected by destructive diseases wherever it is grown. Some diseases are endemic; however, as cacao was disseminated from the Amazon rain forest to new cultivation sites it encountered new pathogens. Two well-established diseases cause the greatest losses: black pod rot, caused by several species of Phytophthora, and witches' broom of cacao, caused by Moniliophthora perniciosa. Phytophthora megakarya causes the severest damage in the main cacao producing countries in West Africa, while P. palmivora causes significant losses globally. M. perniciosa is related to a sister basidiomycete species, M. roreri which causes frosty pod rot. These Moniliophthora species only occur in South and Central America, where they have significantly limited production since the beginnings of cacao cultivation. The basidiomycete Ceratobasidium theobromae causing vascular-streak dieback occurs only in South-East Asia and remains poorly understood. Cacao swollen shoot disease caused by Cacao swollen shoot virus is rapidly spreading in West Africa. This review presents contemporary research on the biology, taxonomy and genomics of what are often new-encounter pathogens, as well as the management of the diseases they cause.

The Previously Unidentified, Divergent Badnavirus Species Cacao red vein-banding virus is Associated with Cacao Swollen Shoot Disease in Nigeria

Cacao swollen shoot disease (CSSD) of Theobroma cacao was reported in Nigeria in 1944; however, no badnaviral genome sequences have been found associated with the symptomatic trees. In 2017, leaf samples (n = 18) were collected from cacao trees from Osun and Oyo, Nigeria showing foliar symptoms that included red vein-banding and shoot swelling, and variable secondary mosaic, mottling, and fern-like pattern symptoms. Abutting primers designed around previously determined 500-bp intergenic region sequences were used for polymerase chain reaction (PCR) amplification. Of the 18 samples, 9 yielded an approximately 7,000-bp, apparently genome-size product. The nine genomes were sequenced and found to encode four open reading frames, and to share 86 to 99% nucleotide identity. Pairwise analysis of the Nigerian genomes with 21 previously reported CSSD badnaviruses, at the complete genome and reverse-transcription ribonuclease H (1,230 bp) sequence levels, indicated 71 to 75 and 72 to 76% nucleotide identity, respectively. Phylogenetic analysis of the nine complete genomes indicated that the closest relatives of the divergent Nigerian isolates were previously described West African CSSD badnaviruses. Based on pairwise comparisons and phylogenetic analyses, the Nigerian CSSD isolates constitute a previously unrecognized Badnavirus sp., herein named Cacao red vein-banding virus (CRVBV). Primers designed based on the CRVBV genome sequences amplified a 1,068-bp fragment from 16 of 18 field samples tested by PCR, suggesting the possible existence of additional CRVBV variants.

Identification and characterization of water chestnut Soymovirus-1 (WCSV-1), a novel Soymovirus in water chestnuts (Eleocharis dulcis)

BACKGROUND

A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unknown infectious agent. In this study, we employed this approach to identify viral sequences in water chestnut plants and to explore the molecular interaction of the identified viral pathogen and its natural plant host.

RESULTS

Based on high throughput sequencing of virus-derived small RNAs (vsRNA), we identified the sequence a new-to-science double-strand DNA virus isolated from water chestnut cv. 'Tuanfeng' samples, a widely grown cultivar in Hubei province, China, and analyzed its genomic organization. The complete genomic sequence is 7535 base-pairs in length, and shares 42-52% nucleotide sequence identity with viruses in the Caulimoviridae family. The virus contains nine predicated open reading frames (ORFs) encoding nine hypothetical proteins, with conserved domains characteristic of caulimoviruses. Phylogenetic analyses at the nucleotide and amino acid levels indicated that the virus belongs to the genus Soymovirus. The virus is tentatively named Water chestnut soymovirus-1 (WCSV-1). Phylogenetic analysis of the putative viral polymerase protein suggested that WCSV-1 is distinct to other well established species in the Soymovirus genus. This conclusion was supported by phylogenetic analyses of the amino acid sequences encoded by ORFs I, IV, VI, or VII. The sRNA bioinformatics showed that the majority of the vsRNAs are 22-nt in length with a preference for U at the 5'-terminal nucleotide. The vsRNAs are unevenly distributed over both strands of the entire WCSV-1 circular genome, and are clustered into small defined regions. In addition, we detected WCSV-1 in asymptomatic and symptomatic water chestnut samples collected from different regions of China by using PCR. RNA-seq assays further confirmed the presence of WCSV-1-derived viral RNA in infected plants.

CONCLUSIONS

This is the first discovery of a dsDNA virus in the genus Soymovirus infecting water chestnuts. Data presented also add new information towards a better understanding of the co-evolutionary mechanisms between the virus and its natural plant host.

Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses

The genus Badnavirus is characterized by members that are genetically and serologically heterogeneous which presents challenges for their detection and characterization. The presence of integrated badnavirus-like sequences in some host species further complicates detection using PCR-based protocols. To address these challenges, we have assessed and optimized various RCA protocols including random-primed RCA (RP-RCA), primer-spiked random-primed RCA (primer-spiked RP-RCA), directed RCA (D-RCA) and specific-primed RCA (SP-RCA). Using Dioscorea bacilliform AL virus (DBALV) as an example, we demonstrate that viral DNA amplified using the optimized D-RCA and SP-RCA protocols showed an 85-fold increase in badnavirus NGS reads compared with RP-RCA. The optimized RCA techniques described here were used to detect a range of badnaviruses infecting banana, sugar cane, taro and yam demonstrating the utility of RCA for detection of diverse badnaviruses infecting a variety of host plant species.

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.