Nappo Alessandra, Petricciuolo Maya, Berno Giulia, Carnevali Agnese, Gruber Cesare Ernesto Maria, Bicchieraro Giulia, Spaccapelo Roberta, Rueca Martina, Carletti Fabrizio, Spezia Pietro Giorgio, Veneri Carolina, La Rosa Giuseppina, Suffredini Elisabetta, Focosi Daniele, Chillemi Giovanni, Federici Ermanno, Maggi Fabrizio
Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, 00149 Rome, Italy.
Bioinformatics Research Unit in Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, 00149 Rome, Italy.
Life (Basel). 2025 May 24;15(6):850. doi: 10.3390/life15060850.
Wastewater surveillance has proven to be a cost-effective, non-invasive method for monitoring the spread and evolution of SARS-CoV-2, yet its value during today's low-incidence phase is still being defined. Between August 2023 and July 2024, 42 composite wastewater samples were collected in Perugia, Italy and analyzed using RT-qPCR and whole-genome sequencing to identify circulating SARS-CoV-2 lineages. In parallel, clinical samples (respiratory tract samples) were collected and analyzed, allowing for direct comparisons to confirm the robustness of the wastewater findings. The sewage viral loads ranged from 8.9 × 10 to 4.9 × 10 genome copies inhabitant day, outlining two modest community waves (September-December 2023 and May-July 2024). Sequencing resolved 403 Omicron lineages and revealed three successive subvariant phases: (i) XBB.* dominance (August-October 2023), when late-Omicron XBB subvariants (mainly EG.5.* and XBB.1.5) accounted for almost all genomes; (ii) a BA.2.86/JN surge (November 2023-March 2024), during which the BA.2.86 subvariant, driven mainly by its JN descendants (especially JN.1), rapidly displaced XBB.* and peaked at 89% in February 2024; and (iii) KP.* takeover (April-July 2024), with JN.1-derived KP subvariants rising steadily and KP.3 reaching 81% by July 2024, thereby becoming the dominant lineage. Comparisons of data from wastewater and clinical surveillance demonstrated how the former presented a much higher diversity of circulating viral lineages. Importantly, some subvariants (including BA.2.86*) were detected in wastewater weeks to months prior to clinical identification, and for longer periods. Taken together, the obtained data validated wastewater surveillance as an effective early warning system, especially during periods of low infection prevalence and/or limited molecular testing efforts. This methodology can thus complement clinical surveillance by offering valuable insights into viral dynamics at the community level and enhancing pandemic preparedness.
废水监测已被证明是一种经济高效、非侵入性的监测新冠病毒传播和演变的方法，但其在当前低发病率阶段的价值仍有待明确。2023年8月至2024年7月期间，在意大利佩鲁贾采集了42份混合废水样本，并使用逆转录定量聚合酶链反应（RT-qPCR）和全基因组测序进行分析，以识别流行的新冠病毒谱系。同时，收集并分析了临床样本（呼吸道样本），以便进行直接比较，以确认废水监测结果的可靠性。污水病毒载量范围为每居民日8.9×10至4.9×10个基因组拷贝，勾勒出两个适度的社区传播高峰（2023年9月至12月和2024年5月至7月）。测序解析了403个奥密克戎谱系，并揭示了三个连续的亚变体阶段：（i）XBB.*占主导地位（2023年8月至10月），当时晚期奥密克戎XBB亚变体（主要是EG.5.和XBB.1.5）几乎占所有基因组；（ii）BA.2.86/JN激增（2023年11月至2024年3月），在此期间，主要由其JN后代（特别是JN.1）驱动的BA.2.86亚变体迅速取代了XBB.，并在2024年2月达到89%的峰值；以及（iii）KP.*占据主导（2024年4月至7月），源自JN.
