Badnaviruses are plant pararetroviruses that infect economically important crops worldwide, and several badnaviral species have been reported causing significant economic losses in cacao plantations in West Africa. Based on the available full-length genome sequences of cacao swollen shoot disease (CSSD)-associated badnaviruses (n = 66), four primer pairs (CSSD1-CSSD4) were designed to amplify a fragment of the 5′ region of open reading frame (ORF) 3, which comprises the movement protein, by polymerase chain reaction (PCR). Primers were evaluated for their ability to amplify a badnaviral fragment(s) from symptomatic and asymptomatic cacao leaf samples collected in Côte d’Ivoire during 2017–2019. The PCR products obtained by amplification with the CSSD1 primers showed high sequence variability and were phylogenetically related to one of three different badnaviral species, Cacao swollen shoot Togo B virus, Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus, while the CSSD2 and CSSD4 amplicon sequences grouped exclusively with either cacao swollen shoot Togo B virus (CSSTBV) and Cacao swollen shoot Ghana M virus isolates, respectively. The majority of the isolates obtained here were most closely phylogenetically related to CSSTBV, with which they shared 81.0–98.0% nucleotide identity, making the CSSTBV-like isolates the predominant species associated with badnavirus-infected cacao trees tested in Côte d’Ivoire.

巴达那病毒是一种感染植物的逆转录病毒，在世界范围内都具有重要的经济意义，据报导有几种巴达那病毒物种在西非的可可种植园中造成了重大的经济损失。基于与可可肿芽病（CSSD）相关的巴达纳病毒的可用全长基因组序列（n = 66），设计了四个引物对（CSSD1-CSSD4），以通过聚合酶链反应（PCR）扩增包含运动蛋白的开放阅读框（ORF）3的5'区片段。评估了引物在2017-2019年间从科特迪瓦收集的有症状和无症状可可叶样本中扩增病毒病毒片段的能力。通过CSSD1引物扩增获得的PCR产物具有较高的序列变异性，并与三种不同的毒株一起进化，其中三种病毒分别为可可肿大的Togo B病毒，可可肿大的CD病毒和可可肿大的CE病毒。，而CSSD2和CSSD4扩增子序列分别与可可肿大的芽多哥B病毒（CSSTBV）和可可肿大的芽加纳M病毒分离株分别分组。在这里获得的大多数分离株与CSSTBV的亲缘关系最密切，它们具有81.0–98.0％的核苷酸同一性，这使得CSSTBV样分离株成为在科特迪瓦测试的与感染杆状病毒的可可树相关的主要物种。