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Viruses
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Economically Important Viruses in African Crops
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Economically Important Viruses in African Crops

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (31 October 2025) | Viewed by 6241

Special Issue Editors

Dr. James Peter Legg

E-Mail Website
Guest Editor
International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
Interests: plant-virus; cassava
Dr. Stephen Winter

E-Mail Website
Guest Editor
Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
Interests: plant virus; cassava; virus resistance
Dr. Rudolph Rufini Shirima

E-Mail Website
Guest Editor
International Institute of Tropical Agriculture (IITA-Tanzania), Dar es Salaam P.O. BOX 34441, Tanzania
Interests: plant viruses; cassava
Dr. Samar Sheat

E-Mail Website
Guest Editor
Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
Interests: cassava resistance; cassava viruses; virus localization

Special Issue Information

Dear Colleagues,

Viruses continue to adversely impact crops in sub-Saharan Africa causing diseases that devastate crop production and leave millions of people at risk of food insecurity. Viral diseases in sub-Saharan Africa affect root and tuber crops including cassava, banana and plantains, sweet potato, potato, and yams. The damaging effects of viral diseases also reduce the productivity of key legumes such as beans and cowpeas and horticultural crops like tomatoes and peppers. In maize, lethal necrosis continues to cause widespread damage to Africa’s most important cereal crop while there still is no resistance to protect rice from the damaging rice yellow mottle virus. There is a considerable production in several African countries of fruits, including passionfruit and tamarillo, vegetables, including chili and okra, and ornamental plants (cut flowers, vegetative propagules and entire plants) for export and those are affected by plant viruses as well carrying the risk of transboundary virus spread. Fruit trees, including cacao are prone to severe virus attacks and for cacao, cause critical shortages of raw product for the chocolate industry.  

This Special Issue published in the Viruses Journal and aims to provide a one-stop platform for the latest breakthroughs and innovations that address the rapidly evolving challenges of crop viruses in Africa. There is no particular restriction to the themes allowed for individual papers, and submissions will be welcome on all aspects of major crop viruses in Africa, including molecular biology, epidemiology, host and vector interactions, crop loss and impact, as well as host plant resistance, management tactics and strategies. We would be delighted to receive your manuscript on your current research (interest) related to our subject by the end of October 2025 or, a notification of intent.  A rolling publication approach is anticipated, so articles submitted early will be published as soon as they have successfully passed the review process. All papers will be independently peer reviewed.

Please feel free to share this invitation with colleagues or anyone you believe would be interested in contributing to this Special Issue.

We look forward to working together with you on this endeavour

Dr. James Peter Legg
Dr. Stephen Winter
Dr. Rudolph Rufini Shirima
Dr. Samar Sheat
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • economically important viruses
  • african crops
  • cassava
  • banana
  • potato
  • yams
  • beans
  • cowpeas
  • maize
  • cacao
  • tomatoes
  • peppers
  • rice yellow mottle virus
  • chili
  • okra

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Published Papers (6 papers)

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Research

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21 pages, 4949 KB  
Article
Epidemiological Surveys of Yam Fields in Côte d’Ivoire Revealed the First Detection of YMMV and Evidence of Episomal Badnavirus
by Maïmouna M. Koné, Justin S. Pita, Cyrielle Ndougonna, Daniel H. Otron, Mariam Combala, Guy R. Eboulem, William J.-L. Amoakon, Bekanvié S. M. Kouakou, Angela O. Eni, Fatogoma Sorho and Fidèle Tiendrébéogo
Viruses 2025, 17(12), 1586; https://doi.org/10.3390/v17121586 - 5 Dec 2025
Viewed by 660
Abstract
Yam (Dioscorea spp.) is a major staple food, contributing significantly to food security and income generation for millions of people worldwide. In 2019, surveys were conducted across the seven agro-ecological zones (AEZs) of Côte d’Ivoire, the third highest producer of yam globally, [...] Read more.
Yam (Dioscorea spp.) is a major staple food, contributing significantly to food security and income generation for millions of people worldwide. In 2019, surveys were conducted across the seven agro-ecological zones (AEZs) of Côte d’Ivoire, the third highest producer of yam globally, to ascertain the current status of viral diseases. In the 324 fields surveyed, a total of 1242 yam leaf samples were collected and tested for the presence of Potyvirus yamtesselati (yam mosaic virus, YMV), Potyvirus yamplacidum (yam mild mosaic virus, YMMV), Cucumovirus CMV (cucumber mosaic virus, CMV), and the badnaviruses using PCR, RT-PCR, and RCA followed by Sanger or MinION sequencing. The incidence of yam viral disease varied across the AEZs, with the lowest mean incidence observed in yam farms within the AEZ VII (71.95%) and the highest in AEZ V (88.15%). Viral disease symptom severity was moderate across the country, with more severe symptoms identified in AEZs II and VI. The virus screening revealed a potyvirus detection rate of 35.83% in all the AEZs. YMMV infection (25.12%) is the most prevalent in the samples, followed by YMV infection (15.61%). RCA-MinION sequencing revealed the presence of badnaviruses belonging to the T15 episomal groups K8, K9, and K5. Also, the use of this technique enabled the amplification and sequencing of four full-length episomal badnaviruses, namely Dioscorea bacilliform AL virus in group K8 and Dioscorea bacilliform RT virus in group K5. CMV was not detected in all the samples. It is noteworthy that 22.13% of mixed infections were detected in asymptomatic samples. This study revealed the first occurrence of YMMV in all the AEZs of Côte d’Ivoire. Of the yam species, Dioscorea alata was more widespread (78.03%) than Dioscorea cayenensis-rotundata (21.92%) in the visited fields. Also, D. alata had a highest incidence of YMMV (23.67%) infection than Dioscorea cayenensis-rotundata, while D. cayenensis-rotundata registered the highest incidence of YMV (15.84%) infection compared to D. alata. Phylogenetic analysis of representative of the various viruses detected in the country revealed that the sequences have high diversity for each virus species. This study revealed that viruses infecting yam are widespread and occur in mixed infection, which poses a real threat to yam production in Côte d’Ivoire. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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18 pages, 2246 KB  
Article
Molecular Identification of the Viruses Associated with Sweetpotato Diseases in Côte d’Ivoire
by El Hadj Hussein Tapily, Justin S. Pita, William J.-L. Amoakon, Angela Eni, Kan Modeste Kouassi, Nazaire K. Kouassi and Fidèle Tiendrébéogo
Viruses 2025, 17(11), 1494; https://doi.org/10.3390/v17111494 - 12 Nov 2025
Viewed by 907
Abstract
Sweetpotato (Ipomoea batatas) is a staple crop of strategic importance in West Africa, particularly in Côte d’Ivoire. However, its productivity is increasingly under threat due to viral diseases. Given the lack of updated epidemiological data over the past three decades, a [...] Read more.
Sweetpotato (Ipomoea batatas) is a staple crop of strategic importance in West Africa, particularly in Côte d’Ivoire. However, its productivity is increasingly under threat due to viral diseases. Given the lack of updated epidemiological data over the past three decades, a nationwide survey was conducted in September 2023 across 94 fields in 83 locations covering seven agroecological zones of the country. A total of 221 symptomatic and asymptomatic leaf samples were analyzed using PCR for DNA viruses and RT-PCR for RNA viruses. The overall viral incidence rate calculated was 65.61%, with significant regional variations (35–97.18%, p < 0.001) and notable differences in the severity of symptoms (p = 0.0095). Agroecological zone I was the most affected, while agroecological zones IV and V were the least impacted. Four viruses were identified: cucumber mosaic virus (CMV), sweet potato leaf curl virus (SPLCV), sweet potato feathery mottle virus (SPFMV), and sweet potato chlorotic stunt virus (SPCSV). No badnaviruses were found. CMV was the most common virus found in single infections (43.44%), followed by SPLCV (5.43%). SPFMV and SPCSV were only observed in mixed infections, particularly CMV/SPLCV (14.03%) and CMV/SPFMV (1.81%). Two triple infections were also detected: SPFMV/SPCSV/CMV and SPFMV/SPLCV/CMV. In total, 34 partial coat protein sequences were obtained (28 SPLCV, 4 SPFMV, 1 CMV, 1 SPCSV). Phylogenetic analysis revealed a high similarity between SPLCV isolates characterized in Côte d’Ivoire and those from Burkina Faso, Europe (Spain, Italy), and the Americas (USA, Puerto Rico) with nucleotide identity values ranging from 98% to 100%. The Côte d’Ivoire SPCSV sequence showed 97.92% nucleotide identity with European isolates, whereas SPFMV sequences exhibited greater diversity (77–89% identity) but clustered within the West African lineage. Sweetpotato viral diseases were detected mostly in mixed-cropping fields (66.85%). This work provides the first epidemiological update on sweetpotato viral diseases since 1987 and the first molecular evidence of the nationwide presence of SPLCV and SPCSV in Côte d’Ivoire. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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21 pages, 3657 KB  
Article
Reinfection Dynamics of Disease-Free Cassava Plants in Three Agroecological Regions of Côte d’Ivoire
by John Steven S. Seka, Justin S. Pita, Modeste K. Kouassi, William J. -L. Amoakon, Bekanvié S. M. Kouakou, Mariam Combala, Daniel H. Otron, Brice Sidoine Essis, Konan Evrard B. Dibi, Angela O. Eni, Nazaire K. Kouassi and Fidèle Tiendrébéogo
Viruses 2025, 17(10), 1393; https://doi.org/10.3390/v17101393 - 20 Oct 2025
Viewed by 717
Abstract
Cassava mosaic disease (CMD) is caused by begomoviruses and can result in yield losses of up to 90% in susceptible varieties. Using disease-free planting material from in vitro cultures is one of the most effective ways of controlling this disease. A CMD epidemiological [...] Read more.
Cassava mosaic disease (CMD) is caused by begomoviruses and can result in yield losses of up to 90% in susceptible varieties. Using disease-free planting material from in vitro cultures is one of the most effective ways of controlling this disease. A CMD epidemiological assessment was conducted in fields established with disease-free plantlets in Bouaké, Dabou, and Man, selected for their contrasting agroecological and CMD prevalence conditions. Virus and whitefly species characterisation was performed using PCR and sequencing. CMD incidence and severity were lowest at the Man site and highest at the Dabou site. Although whitefly abundance was relatively low at the Man and Bouaké sites compared to the Dabou site, they were a significant factor in the spread of the disease. While all resistant varieties remained asymptomatic, susceptible and tolerant varieties became infected, and some tolerant varieties were able to recover from the disease. Molecular analyses revealed the presence of two viral species: Begomovirus manihotis (ACMV) and Begomovirus manihotiscameroonense (EACMCMV). No viral infection was detected 4 weeks after planting (WAP). Cases of single infection and double infection were observed at 12 and 20 WAP. Also, no double infections were found at the Man site, in contrast to the Bouaké site (12 WAP: 2.36%) and Dabou site (12 WAP: 2.59%; 20 WAP: 5.76%). EACMCMV was found in a single infection in Bouaké (12 WAP: 1.39%) and Man (20 WAP: 0.66%). The whitefly species Bemisia tabaci and Bemisia afer were most commonly found feeding on all cassava varieties. A high diversity of whitefly species was observed in Bouaké and Dabou compared to Man. Furthermore, the Bemisia tabaci species identified in this study was found to be able to transmit ACMV and EACMCMV viruses. These highlights would contribute to improving CMD management and control strategies. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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18 pages, 5578 KB  
Article
Insights into Novel Viral Threats in Sweetpotato from Burkina Faso: Characterisation of Unexplored Pathogens
by Pakyendou E. Name, Ezechiel B. Tibiri, Fidèle Tiendrébéogo, Seydou Sawadogo, Florencia Djigma, Lassina Traoré, Angela O. Eni and Justin S. Pita
Viruses 2025, 17(9), 1222; https://doi.org/10.3390/v17091222 - 7 Sep 2025
Cited by 1 | Viewed by 1693
Abstract
Sweetpotato is a key staple crop in tropical and subtropical regions. Its vegetative propagation makes it a persistent reservoir, facilitating the emergence and spread of complex infections. Understanding its virome is crucial for disease management and food security. We investigated the sweetpotato virome [...] Read more.
Sweetpotato is a key staple crop in tropical and subtropical regions. Its vegetative propagation makes it a persistent reservoir, facilitating the emergence and spread of complex infections. Understanding its virome is crucial for disease management and food security. We investigated the sweetpotato virome in Burkina Faso using rolling circle amplification and Oxford Nanopore sequencing. Eight symptomatic leaf samples, previously undiagnosed using conventional methods, were analysed. Bioinformatic pipelines were employed followed by phylogenetic comparisons. Two viruses known to infect sweetpotato, namely sweet potato leaf curl virus (SPLCV) and sweet potato leaf curl deltasatellite 3 (SPLCD3), were consistently detected in all samples. Additionally, pepper yellow vein Mali virus (PepYVMV), cotton leaf curl Gezira alphasatellite (CLCuGeA) and cotton leaf curl Gezira betasatellite (CLCuGeB) were identified for the first time in this crop. Phylogenetic analysis confirmed their genetic proximity to isolates from tomato, okra and pepper. Their co-occurrence with SPLCV and SPLCD3 indicates a complex viral landscape that could influence disease severity. This study highlights the underestimated role of sweetpotato as a viral reservoir, influencing virus evolution and transmission. Further studies should assess their pathogenicity, co-infection dynamics and vector-mediated transmission to improve crop productivity. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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Review

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14 pages, 5558 KB  
Review
Virus Diseases of Economic Importance on Food Legumes in Africa and Their Control
by Adane Abraham
Viruses 2025, 17(12), 1555; https://doi.org/10.3390/v17121555 - 28 Nov 2025
Viewed by 497
Abstract
Virus diseases are among the major constraints in the production of food legumes in Africa, causing substantial crop losses. Common bean mosaic and black root, cowpea mosaic, chickpea stunt, faba bean necrotic yellows and stunt, groundnut rosette, and soybean mosaic are the six [...] Read more.
Virus diseases are among the major constraints in the production of food legumes in Africa, causing substantial crop losses. Common bean mosaic and black root, cowpea mosaic, chickpea stunt, faba bean necrotic yellows and stunt, groundnut rosette, and soybean mosaic are the six diseases considered economically significant in Africa. Past research enabled the description of the main characteristics of the causal viruses, including particle and genome properties, modes of transmission, host range, and virus–vector relationships. Such information in many cases assisted in developing effective diagnostics and disease management methods such as host resistance, chemical vector control, and cultural practices. Integrating two or more of these approaches is usually more effective. The major challenge, however, remains ensuring the adoption of such recommendations at a sufficiently large scale by many farmers to have an impact over wider geographical areas. Future work should focus on scaling up the adoption of available control technologies and generating new information, including epidemiological data, to support future management decisions. Furthermore, since the occurrence and significance of viruses on food legumes in many African countries are still not studied, large-scale surveys to identify viruses, establish their distribution and impact, and working out suitable control measures are required. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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Other

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8 pages, 1274 KB  
Brief Report
Identification and Full-Genome Characterisation of Genomoviruses in Cassava Leaves Infected with Cassava Mosaic Disease
by Olabode Onile-ere, Oluwagboadurami John, Oreoluwa Sonowo, Pakyendou Estel Name, Ezechiel Bionimian Tibiri, Fidèle Tiendrébéogo, Justin Pita, Solomon Oranusi and Angela O. Eni
Viruses 2025, 17(11), 1418; https://doi.org/10.3390/v17111418 - 25 Oct 2025
Viewed by 674
Abstract
This study identified and characterised three Genomoviruses during a circular DNA-enriched sequencing project aimed at assessing the evolution of Cassava mosaic begomoviruses in Nigeria. Using a combination of rolling circle amplification, Oxford Nanopore Sequencing and targeted amplicon sequencing, three full-length Genomovirus genomes were [...] Read more.
This study identified and characterised three Genomoviruses during a circular DNA-enriched sequencing project aimed at assessing the evolution of Cassava mosaic begomoviruses in Nigeria. Using a combination of rolling circle amplification, Oxford Nanopore Sequencing and targeted amplicon sequencing, three full-length Genomovirus genomes were recovered. The recovered genomes ranged from 2090 to 2188 nucleotides in length, contained two open reading frames (Rep and CP) in an ambisense orientation and shared between 84.81 and 95.37% nucleotide similarity with isolates in the NCBI GenBank repository. Motif analyses confirmed the presence of conserved rolling circle replication (RCR) and helicase motifs in all three isolates; however, one isolate lacked the RCR II motif. Phylogenetic inference using Rep and CP nucleotide sequences suggested that the isolates belonged to a divergent lineage within the Genomovirus family. These findings expand current knowledge of Genomovirus diversity and highlight the potential of cassava as a source for identifying novel CRESS-DNA viruses. Full article
(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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