Karavina C, Ibaba J D, Gubba A
Acta Virol. 2020;64(1):88-92. doi: 10.4149/av_2020_107.
Tomato spotted wilt virus (TSWV) is an economically important pathogen of many crops worldwide. However, prior to this study, only one complete genome sequence of an African TSWV isolate was available in public databases. This limits genetic diversity and evolutionary studies of the pathogen on the continent. TSWV was detected in symptomatic Zimbabwean chrysanthemum plants using late-ral flow kits. The presence of the pathogen was subsequently confirmed by double antibody sandwich enzyme-linked immunosorbent assay and reverse transcription-polymerase chain reaction (RT-PCR). Total RNAs for RT-PCR and next-generation sequencing (NGS) were extracted using an RNA extraction kit. NGS performed on an Illumina HiSeq platform was used to recover the full TSWV genome and analyzed by different software packages. The tripartite genome of the Zimbabwe TSWV isolate consisted of L, M and S RNAs of 8914, 4824 and 2968 nucleotides, respectively. This isolate shared highest protein and nucleotide sequence identities with the isolate LK-1 from neighboring South Africa. The Zimbabwe TSWV isolate was found to be a non-recombinant and non-resistance-breaking. This study provides the first full genome of TSWV from Zimbabwe. It also adds useful information towards understanding the evolution of the pathogen. Keywords: Africa; tospovirus; phylogenetic analysis; recombination; virus identification.
番茄斑萎病毒（TSWV）是全球许多作物的一种具有经济重要性的病原体。然而，在本研究之前，公共数据库中仅有一个非洲TSWV分离株的完整基因组序列。这限制了该病原体在非洲大陆的遗传多样性和进化研究。使用侧向流动试剂盒在出现症状的津巴布韦菊花植株中检测到了TSWV。随后通过双抗体夹心酶联免疫吸附测定和逆转录 - 聚合酶链反应（RT-PCR）证实了病原体的存在。使用RNA提取试剂盒提取用于RT-PCR和下一代测序（NGS）的总RNA。在Illumina HiSeq平台上进行的NGS用于获得完整的TSWV基因组，并通过不同的软件包进行分析。津巴布韦TSWV分离株的三分体基因组分别由8914、4824和2968个核苷酸的L、M和S RNA组成。该分离株与来自邻国南非的LK-1分离株具有最高的蛋白质和核苷酸序列同一性。发现津巴布韦TSWV分离株是非重组且不打破抗性的。本研究提供了来自津巴布韦的首个TSWV全基因组。它还为理解该病原体的进化增加了有用信息。关键词：非洲；番茄斑萎病毒属；系统发育分析；重组；病毒鉴定。
