Federal Institution of Brasília, Brasília, Federal District, Brazil.
Department of Plant Pathology, University of California, Davis, CA, USA.
J Gen Virol. 2024 Oct;105(10). doi: 10.1099/jgv.0.002033.
We present the complete sequence of the genomic RNA of an isolate of squash vein yellowing virus () from California (SqVYV-CA) and show it is a recombinant virus with a highly divergent 5' UTR and proximal P1a gene. The evolution of SqVYV-CA involved an intrageneric event between unknown potyviruses, related to isolates of papaya ringspot virus () from the Old World, and an intergeneric event between this recombinant potyvirus (minor parent) and an isolate of SqVYV from Israel (SqVYV-IL) (major parent). These events occurred in mixed infections and in the potyvirus P1 and ipomovirus P1a recombination hotspots and resulted in SqVYV-CA having a potyvirus 5' UTR and chimeric P1-P1a gene/protein and the remainder of the genome from SqVYV-IL. The SqVYV-CA chimeric P1-P1a gene is under positive selection, and the protein is intrinsically disordered and may localize to the nucleus via nuclear localization signals in the P1 part. The C-terminal SqVYV-IL P1a part also diverged but retained the conserved serine protease motif. Furthermore, substantial divergence in SqVYV isolates from the Middle East was associated with genetic drift and a long evolutionary history in this region. The finding that the host range and symptomatology in cucurbits of SqVYV-CA is similar to those of SqVYV from Florida and SqVYV-IL, indicated that the recombinant part of the genome had no obvious effect on the virus-host interaction. A divergent part of the P1 sequence of the SqVYV-CA P1-P1a gene was used to develop a primer pair and RT-PCR test for specific detection of SqVYV-CA. This test was used to detect spread of SqVYV-CA to a new production area of California in 2021 and 2022. Together, these results demonstrate (i) a high level of genetic diversity exists among isolates of SqVYV and involved intra- and intergeneric recombination and genetic drift (mutation), (ii) evidence that SqVYV originated in the Middle East and that there were independent introductions into the New World and (iii) the remarkable genetic flexibility of the 5' proximal genes of these viruses.
我们展示了来自加利福尼亚州的西葫芦叶脉黄化病毒（SqVYV-CA）基因组 RNA 的完整序列，并表明它是一种重组病毒，具有高度分化的 5'UTR 和近端 P1a 基因。SqVYV-CA 的进化涉及到未知马铃薯 Y 病毒之间的种内事件，与旧世界的木瓜环斑病毒（PRSV）分离株有关，以及这个重组马铃薯 Y 病毒（小亲本）与来自以色列的 SqVYV 分离株（大亲本）之间的属间事件。这些事件发生在混合感染中，在马铃薯 Y 病毒 P1 和番茄斑萎病毒 P1a 重组热点中，导致 SqVYV-CA 具有马铃薯 Y 病毒 5'UTR 和嵌合 P1-P1a 基因/蛋白，而其余基因组来自 SqVYV-IL。SqVYV-CA 的嵌合 P1-P1a 基因受到正选择，蛋白质是内在无序的，可能通过 P1 部分的核定位信号定位于核内。C 末端 SqVYV-IL P1a 部分也发生了分化，但保留了保守的丝氨酸蛋白酶基序。此外，中东地区 SqVYV 分离株的大量分化与遗传漂变和该地区的长期进化历史有关。SqVYV-CA 在葫芦科植物中的宿主范围和症状与佛罗里达州的 SqVYV 和 SqVYV-IL 相似，这表明基因组的重组部分对病毒-宿主相互作用没有明显影响。SqVYV-CA 的 P1-P1a 基因 P1 序列的一个分化部分被用来开发一对引物和 RT-PCR 测试，用于特异性检测 SqVYV-CA。该测试用于检测 2021 年和 2022 年 SqVYV-CA 传播到加利福尼亚州的一个新生产区。总之，这些结果表明：（i）SqVYV 分离株之间存在高水平的遗传多样性，涉及种内和种间重组和遗传漂变（突变）；（ii）有证据表明 SqVYV 起源于中东，并且有独立的引入到新世界；（iii）这些病毒的 5'近端基因具有显著的遗传灵活性。
