PDF(Pubmed)
Abstract：
Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapid in situ monitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission. Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the \"lab in a suitcase\" approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities.
摘要：
病毒的爆发是水产养殖的持续威胁,限制生产以改善全球粮食安全。在资源有限的地区缺乏诊断测试和监测，阻碍了迅速应对疾病爆发和防止病毒性病原体在渔业生产水域流行的能力。新兴病毒诊断测试的最新进展，然而,提供了一种快速就地监测病毒爆发的解决方案。此外，基因组流行病学已证明在检测发病机理中涉及的病毒突变并协助解决传播链方面非常有效。这里,我们展示了现场流行病学工具包的应用，以跟踪养殖场水产养殖中的病毒暴发，减少了对诊断实验室的访问，和非破坏性采样。受用于人类病毒病原体基因组监测和COVID19废水监测的“手提箱实验室”方法的启发，我们评估了对鱼类病原体进行实时基因组测序监测的可行性，沃尔塔湖的传染性脾肾坏死病毒（ISKNV）。从装有尼罗罗非鱼（Oreochromisniloticus）的笼子中收集的水样中的病毒级分被浓缩，并被用作全基因组测序的模板，使用以前开发的ISKNV平铺PCR方法。从笼子周围的水中收集的样本中ISKNV的突变与从受感染的笼子里的鱼中收集的样本相匹配，说明水样可用于检测持续爆发中的主要ISKNV变体。这种方法允许ISKNV的检测和变化频率的动态跟踪，因此，可能有助于指导控制措施，以快速隔离和隔离受感染的农场和设施。
