Amman Fabian, Markt Rudolf, Endler Lukas, Hupfauf Sebastian, Agerer Benedikt, Schedl Anna, Richter Lukas, Zechmeister Melanie, Bicher Martin, Heiler Georg, Triska Petr, Thornton Matthew, Penz Thomas, Senekowitsch Martin, Laine Jan, Keszei Zsofia, Klimek Peter, Nägele Fabiana, Mayr Markus, Daleiden Beatrice, Steinlechner Martin, Niederstätter Harald, Heidinger Petra, Rauch Wolfgang, Scheffknecht Christoph, Vogl Gunther, Weichlinger Günther, Wagner Andreas Otto, Slipko Katarzyna, Masseron Amandine, Radu Elena, Allerberger Franz, Popper Niki, Bock Christoph, Schmid Daniela, Oberacher Herbert, Kreuzinger Norbert, Insam Heribert, Bergthaler Andreas
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
Nat Biotechnol. 2022 Dec;40(12):1814-1822. doi: 10.1038/s41587-022-01387-y. Epub 2022 Jul 18.
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.
基于污水的流行病学对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的监测有望为对个体病例进行测序提供一种补充方法。然而，对现有策略而言，对变异株进行可靠定量以及从头检测新出现的变异株仍然具有挑战性。从2020年12月到2022年2月，我们对代表94个城市集水区的3413份污水样本进行了深度测序，覆盖了奥地利超过59%的人口。我们为提高稳健性而设计的污水管道变异株定量系统（称为VaQuERo）使我们能够从复杂的污水样本中推断出预定义变异株的时空丰度。这些结果通过对超过31.1万个个体病例的流行病学记录进行了验证。此外，我们描述了德尔塔变异株流行期间病毒遗传多样性的增加，提供了一个预测新出现变异株的框架，并通过从污水中计算变异株特异性繁殖数来衡量关注变异株的繁殖优势。总之，这项研究证明了全国范围内基于污水的流行病学在支持公共卫生方面的作用，并为没有广泛个体监测的国家带来了特别的价值。
