Ecological Niche Modeling, Yield Impact Assessment and Improved Detection of SPFMV, SPCSV, and SPLCV in Sweetpotato in Kenya

Abstract

Viral diseases in Kenya and sub-Saharan Africa cause significant crop losses. Over 30 viruses have been reported to infect sweetpotato. Sweet potato cholorotic stunt virus and Sweet potato feathery mottle virus are considered the most wide-spread and devastating. Sweetpotato begomoviruses (sweepoviruses) have increasingly been recognized as common in recent years. They cause no or show mild symptoms but result in 40 to 80% yield losses. This study aimed: i) To develop an ecological niche model for predicting the potential geographic distribution and risk areas of sweepoviruses in Kenya; ii) To assess the yield impact of begomoviruses and their interaction with sweetpotato feathery mottle virus and sweetpotato chlorotic stunt virus; iii) To validate a loop-mediated isothermal amplification assays for on-site detection of the main sweetpotato infecting viruses and iv) To evaluate tube array for the multiplex detection of sweetpotato viruses. The study developed an ecological niche model to predict the geographic distribution and risk areas of sweepoviruses in Kenya. Field surveys were conducted during 2017 and 2018 cropping seasons, targeting the main sweetpotato growing regions. Ecological niche models were constructed using MaxEnt software, incorporating bioclimatic variables and International Soil Reference and Information Centre (ISRIC) factors. MaxEnt consistently surpasses other methods in terms of predicting accuracy, and is highly user-friendly. Results showed high, medium, and low probability for sweepovirus persistence and spatial distribution in regions like Western, Nyanza, and South Rift. Central and Eastern regions showed medium suitability, while the coastal region was predicted to be medium to high risk. The model provided valuable insights for developing effective disease risk management strategies. The impact of Sweet potato leaf curl virus (SPLCV) infection on root yield in Kenyan sweetpotato varieties 'Kakamega' and 'Ejumula' was investigated. Results showed significant differences in yield loss from SPLCV infection, with 'Ejumula' suffering no significant loss, while 'Kakamega', more resistant to Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV), suffered an average of 47% loss. The results highlight the variability in sensitivity to SPLCV between sweetpotato cultivars and the lack of correlation between SPLCV-related symptoms and susceptibility to the virus. The study also highlighted the lack of correlation between resistance to RNA viruses SPCSV and SPFMV and DNA virus SPLCV. A simple and rapid loop‐mediated isothermal amplification (LAMP) assay for the detection of SPFMV, SPCSV and begomoviruses related to SPLCV (sweepoviruses) was developed. Laboratory validation recorded 100% diagnostic sensitivity for all three viruses. The LAMP assays were customized for field testing using a lyophilized thermostable isothermal master mix in a ready-to-use form that required no cold chain. The average time to positivity (TTP) was: SPFMV 5-30 mins, SPCSV 15-43 mins and begomoviruses 28-45 mins. LAMP on-site testing results were comparable to PCR and RT-PCR confirmatory laboratory tests. The LAMP assay is a powerful tool for rapid sweetpotato virus detection at a reasonable cost and thus could serve as quality control systems for planting materials. The operational performance of STAR (Sweet potato virus Tube-Array) for simultaneous detection of sweetpotato viruses was evaluated. STAR assay was compared with the conventional method Nitrocellulose Membrane Enzyme-Linked Immunosorbent Assay (NCM-ELISA), with 25 samples tested in parallel in Lima and Nairobi. Cohen's kappa index revealed a disagreement between the two assays, with STAR being more sensitive and detecting more viruses not detected by NCM-ELISA. Concordance analysis accessed by Bland-Altman plot and regression analysis results from the two labs agreed closely. STAR was found to be more sensitive and detected more viruses than NCM-ELISA. STAR's sensitivity, specificity, accuracy, and short turnaround time make it suitable for routine diagnosis, epidemiological studies, quarantine, and certification of the sweetpotato seed system.