Natarajan Aravind, Fremin Brayon J, Schmidtke Danica T, Wolfe Marlene K, Zlitni Soumaya, Graham Katherine E, Brooks Erin F, Severyn Christopher J, Sakamoto Kathleen M, Lacayo Norman J, Kuersten Scott, Koble Jeff, Caves Glorianna, Kaplan Inna, Singh Upinder, Jagannathan Prasanna, Rezvani Andrew R, Bhatt Ami S, Boehm Alexandria B
Department of Genetics, Stanford University, Stanford, CA, USA.
Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
bioRxiv. 2023 Jan 10:2023.01.09.523366. doi: 10.1101/2023.01.09.523366.
Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers’ sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker.
Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of fecal host-associated MST markers. Here we design and test novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool, and highly abundant in human stool and wastewater samples.
微生物源追踪（MST）利用与粪便宿主相关的标记物来识别环境中粪便污染的来源。虽然有许多细菌MST标记物，但病毒标记物却很少。在此，我们基于番茄褐色皱纹果病毒（ToBRFV）基因组设计并测试了新型病毒MST标记物。我们从美国旧金山湾区的废水和粪便样本中组装了8个近乎完整的ToBRFV基因组。接下来，我们基于ToBRFV基因组的保守区域开发了两种新型基于探针的RT-PCR检测方法，并使用人类和非人类动物粪便以及废水测试了这些标记物的敏感性和特异性。ToBRFV标记物灵敏且特异；在人类粪便和废水中，它们比目前使用的标记物——辣椒轻斑驳病毒（PMMoV）衣壳蛋白（CP）基因更为普遍和丰富。我们应用这些检测方法来检测城市雨水样本中的粪便污染，发现ToBRFV标记物在样本中的流行率与已确立的病毒MST标记物交叉组装噬菌体（crAssphage）相当。综上所述，ToBRFV是一种很有前景的与人类相关的病毒MST标记物。
人类接触环境中的粪便污染可导致传染病传播。微生物源追踪（MST）能够识别粪便污染的来源，从而可以对污染进行治理并减少人类接触。MST需要使用与粪便宿主相关的MST标记物。在此，我们从番茄褐色皱纹果病毒（ToBRFV）基因组设计并测试了新型MST标记物。这些标记物对人类粪便灵敏且特异，并且在人类粪便和废水样本中含量很高。
