Loop-Mediated Isothermal Amplification assays for on-site detection of the main sweetpotato infecting viruses

Wanjala, Bramwel W.; Ateka, Elijah; Miano, Douglas Watuku; Fuentes, Segundo; Pérez, Antonio Martín; Low, Jan; Kreuze, Jan

doi:10.1016/j.jviromet.2021.114301

Cited by 13 publications

(14 citation statements)

References 43 publications

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“…LAMP is an alternative nucleic acid amplification method that is nearly as sensitive as qPCR, but more straightforward to use because the enzyme is tolerant to inhibitors and crude sample preparations can be used avoiding the need of nucleic acid extractions. LAMP assays have been developed and validated for the three sweetpotato viruses used in this study ( Wanjala et al., 2021 ). To evaluate if LAMP could be used as a cheaper, routine substitute for qPCR for the quantitative determination of virus load in genotypes to support virus resistance screening, we analyzed the same sample in the same equipment by both methods using a simple measure corresponding to the inverse C(t) to estimate relative virus loads in the sample.…”

Section: Discussionmentioning

confidence: 99%

“…For the first determination, miRNA kits (OMEGA bio-tek, USA) were used to purify nucleic acid for LAMP and qPCR assays. The second sampling used APEG buffer (2 mL for each bulked sample) as a quick nucleic acid extraction method ( Wanjala et al., 2021 ) for LAMP, and miRNA kits for purifying nucleic acid for qPCR assays. A separate experiment was performed to compare LAMP performance after alkaline polyethylene glycol and kit extraction from an identical sample.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato

Kreuze,

Ramírez,

Fuentes

et al. 2024

Virus Research

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato

Kreuze,

Ramírez,

Fuentes

et al. 2024

Virus Research

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“…LAMP assay from the laboratory to the field for detection of common sweetpotato viruses Wanjala et al (2021) developed a field-deployable LAMP assay for major sweetpotato viruses (SPFMV, SPCSV, and begomoviruses). Figure 4 illustrates the workflow of the LAMP assay in the field.…”

Section: 5mentioning

confidence: 99%

“…Wanjala et al (2021) developed a sensitive, cost-effective, and robust LAMP assay for detecting SPFMV, SPCSV, and SPLCV on-site.Crop health monitoring and early diagnosis of emerging infections are crucial for reducing disease transmission and facilitating successful field management practices. The SweetGAINS project trained East African NPPOs in using LAMP technology for sweetpotato virus diagnostics, enabling sample testing in the field, unlike other lab-based infrastructure-based methods.…”

mentioning

confidence: 99%

Loop‐mediated isothermal amplification assay: A novel disease diagnostics tool in sweetpotato seed quality assurance

Wanjala,

Kreuze,

McEwan

et al. 2024

Crop Science

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Sweetpotato is an important food crop in global production. However, sweetoptato viruses pose a threat to sustainable agriculture and cause significant economic loss. More than 30 viruses have been reported to date, with sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV) occurring frequently and in combination, causing sweetpotato virus disease. The detection of viruses directly from sweetpotato is still a challenge, and efforts are being made toward this front. Therefore, rapid detection of viruses is critical for effective control. Current diagnostic tests are not sufficiently sensitive to reliably detect viruses directly from sweetpotato and require expensive laboratory equipment and a high level of skilled experience. Loop‐mediated isothermal amplification (LAMP) is sensitive and specific for both DNA/RNA amplification; it is affordable and its characteristics make it potentially suitable for on‐site testing. LAMP assays have been developed for several sweetpotato viruses: SPCSV, SPFMV, and sweet potato leaf curl virus (and related sweepoviruses). Laboratory validation showed a 100% diagnostic sensitivity for all three viruses. The LAMP on‐site testing results were comparable to those of polymerase chain reaction and reverse transcriptase polymerase chain reaction confirmatory laboratory tests. Interlab validation and packaging into affordable kits will ensure high adoption in sub‐Saharan Africa. The LAMP assay can be used for field surveys and monitoring the phytosanitary status of pre‐basic seed production in quarantine or certification program. This guarantees pathogen‐free planting material enters the seed system. We discuss opportunities for LAMP as a diagnostic assay for the rapid detection of sweetpotato viruses and its adoption as a quality control system for planting materials.

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“…This poses a risk of leaving a high reservoir of symptomless viruses in the seed multiplication plots, which can later cause SPVD . The Loop-mediated Isothermal Amplification (LAMP) is among the technologies that can be deployed easily for field-based detection of SPCSV, SPFMV and SPLCV whose assays have already been developed (Wanjala et al, 2021).…”

mentioning

confidence: 99%

Degeneration of sweetpotato seed in Tanzania: can cleaned-up, virus-tested seed help?

Ogero

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Low yields caused by poor phytosanitary quality of seed vines are a major challenge to sweetpotato farming in Tanzania. Poor seed quality is largely caused by viruses, especially the co-infection of sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). These two viruses are the most devastating ones in East Africa and when combined cause the sweetpotato virus disease (SPVD), often leading to 56 − 100% yield losses. Being vegetatively propagated, sweetpotato accumulates viruses across generations. The use of virus-infected material obtained from the previous crop is the most common source of viruses. The accumulation of viruses in the propagating material leads to progressive yield loss and is called seed degeneration. Use of clean seed disseminated through a formal system is one of the options to address this. However, clean seed can get infected once in the field and it is not known how it will perform following several seasons of on-farm propagation. Moreover, successful use of clean seed requires an understanding of the current practices that farmers use when sourcing sweetpotato seed. This research started by assessing the performance of clean seed and farmer-sourced seed of varieties that are susceptible or relatively resistant to viruses grown in environments with high or low virus pressure. The results showed that starting propagation with clean seed slows down degeneration especially in susceptible varieties grown in high-viruspressure environments. The findings also showed yield stability for farmer-sourced material of virus resistant varieties. The yield stability for farmer-sourced material of the relatively virus-resistant variety illustrates why farmers recycle planting material. The findings also showed that regular replacement by clean seed is especially economic in areas with high virus pressure and for susceptible varieties. In addition, it is important to consider cultivar resistance and agroecology when promoting adoption of clean seed.To understand farmers' experiences with degeneration a 'Small-N' survey was conducted with 37 respondents. We found that female farmers reported degeneration more frequent than male farmers. The main action to address degeneration was to acquire a new variety, mostly from close sources in the farmers' social networks (friends, neighbors and relatives). Planting material was mostly acquired and shared as gifts. Farm seed recycling still dominates. These networks will continue to play an important role in sweetpotato seed flows and therefore it is important to devise innovative ways of linking them with the formal seed system for access to clean seed and improved varieties.Clean seed is not immune to viruses and can get infected once planted in the open fields. We investigated the efficiency of insect-proof net tunnels in reducing degeneration of clean seed at seed producer level. Results from a 21-month experiment showed that insect-proof net tunnels can prevent infection in an area with high virus pressure for up to 20 months....

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Loop-Mediated Isothermal Amplification assays for on-site detection of the main sweetpotato infecting viruses

Abstract: Graphical abstract LAMP on-site sweetpotato virus detection workflow.

Cited by 13 publications

References 43 publications

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato

Loop‐mediated isothermal amplification assay: A novel disease diagnostics tool in sweetpotato seed quality assurance

Degeneration of sweetpotato seed in Tanzania: can cleaned-up, virus-tested seed help?

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