Table 6_Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.xlsx

Sweetpotato is a key crop for global food security, particularly in Burkina Faso, where its productivity is increasingly threatened by viral diseases, especially those caused by CRESS-DNA viruses. However, the diversity of these viruses in Burkina Faso remains poorly characterized due to limitations of conventional diagnostic approaches. In this study, nanopore sequencing was used to investigate the diversity of CRESS-DNA viruses infecting sweetpotato in Burkina Faso. Ninety-eight symptomatic dried leaf samples from a previously established biobank were selected and analyzed. Total DNA was extracted, enriched using rolling circle amplification (RCA), and sequenced using the MinION Mk1C platform. In parallel, RNA viruses were also investigated using nanopore sequencing. RCA successfully amplified 53 of the 98 samples, from which 28 complete and 25 partial CRESS-DNA virus genomes were recovered. Sequence analyses revealed high genomic diversity, with sweet potato leaf curl virus (SPLCV) being the most prevalent. Sweet potato symptomless virus 1 (SPSMV-1) was detected for the first time in Burkina Faso in a co-infection with SPLCV. Additionally, 52 deltasatellite genomes (50 complete, 2 partial) were identified in association with SPLCV, displaying approximately 86% nucleotide identity with known sequences, suggesting the presence of genetically distinct putative deltasatellites. RNA virome analysis revealed frequent co-infections involving sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus, with SPFMV commonly co-occurring with SPLCV. Four complete SPFMV genomes were recovered and clustered within phylogroup B, forming a distinct subclade. Overall, this study highlights the remarkable diversity of viruses infecting sweetpotato in Burkina Faso and reports, for the first time, the presence of SPSMV-1 and sweepovirus-associated deltasatellites in the country. These findings underscore the importance of ongoing molecular surveillance to support effective viral disease management strategies and food security.

甘薯是保障全球粮食安全的关键作物，在布基纳法索尤为如此。该国甘薯的生产能力正日益受到病毒病的威胁，尤其是由环状单链DNA（CRESS-DNA）病毒引发的病害。然而，由于传统诊断方法存在局限，布基纳法索境内此类病毒的多样性仍未得到充分解析。本研究采用纳米孔测序技术，对布基纳法索境内感染甘薯的CRESS-DNA病毒多样性展开调查。研究人员从已建成的生物样本库中选取98份表现出症状的干燥叶片样本进行分析。提取总DNA后，采用滚环扩增（rolling circle amplification, RCA）进行富集，随后通过MinION Mk1C测序平台完成测序。与此同时，本研究亦采用纳米孔测序技术对RNA病毒展开调查。RCA成功扩增了98份样本中的53份，从中获得28条完整及25条部分序列的CRESS-DNA病毒基因组。序列分析结果显示病毒基因组多样性极高，其中甘薯曲叶病毒（sweet potato leaf curl virus, SPLCV）最为流行。本研究首次在布基纳法索境内检测到与SPLCV共同侵染的甘薯无症状病毒1号（sweet potato symptomless virus 1, SPSMV-1）。此外，研究人员在与SPLCV相关的样本中鉴定出52个δ卫星（deltasatellite）基因组（其中50个为完整序列，2个为部分序列），其与已知序列的核苷酸同源性约为86%，提示存在遗传特征独特的潜在δ卫星病毒。RNA病毒组（RNA virome）分析结果显示，样本中频繁出现甘薯羽状斑驳病毒（sweet potato feathery mottle virus, SPFMV）与甘薯褪绿矮化病毒（sweet potato chlorotic stunt virus）的复合侵染现象，且SPFMV常与SPLCV共同存在。研究获得4条完整的SPFMV基因组，其聚类于系统发育群B（phylogroup B），形成一个独立的进化亚支（subclade）。总体而言，本研究揭示了布基纳法索境内感染甘薯的病毒具有极高的多样性，并首次报道了该国存在SPSMV-1以及与曲叶病毒属（sweepovirus）相关的δ卫星病毒。本研究结果凸显了持续开展分子监测的重要性，可为制定有效的病毒病防控策略及保障粮食安全提供支撑。