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Leveraging wastewater sequencing to strengthen global public health surveillance.

作者信息

Gordeev Victor, Hölzer Martin, Desirò Daniel, Goraichuk Iryna V, Knyazev Sergey, Solo-Gabriele Helena, Skums Pavel, Karthikeyan Smruthi, Evans Alexandria, Agrawal Shelesh, Lucaci Alexander G, Mason Christopher E, Su Justin M, Gibas Cynthia, Nagarajan Niranjan, Peres da Silva Rafael, Drabcinski Nicolae, Munteanu Viorel, Zhan Lingyu, Rubin Julia, Wu Nicholas C, Trister Andrew, Ciorba Dumitru, Bostan Viorel, Lobiuc Andrei, Covasa Mihai, Ophoff Roel A, Zelikovsky Alex, Dimian Mihai, Mangul Serghei

机构信息

Department of Electrical Engineering and Computer Science, Ștefan cel Mare University of Suceava, Suceava, 720229, Romania.

Department of Computers, Informatics, and Microelectronics, Technical University of Moldova, Chisinau, 2045, Republic of Moldova.

出版信息

BMC Glob Public Health. 2025 Mar 21;3(1):23. doi: 10.1186/s44263-025-00138-w.

DOI:10.1186/s44263-025-00138-w
PMID:40119458
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11927347/
Abstract
摘要

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Sequence modeling and design from molecular to genome scale with Evo.基于 Evo 在从分子到基因组尺度上进行序列建模和设计。
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SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.SWAMPy：模拟 SARS-CoV-2 废水扩增子宏基因组。
Bioinformatics. 2024 Sep 2;40(9). doi: 10.1093/bioinformatics/btae532.
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Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data.参考设计对从废水测序数据估计新冠病毒谱系丰度的影响。
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae051.
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Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater.通过对废水进行深度核酸测序来研究病原体动态和发现新型病毒和酶。
Environ Int. 2024 Aug;190:108875. doi: 10.1016/j.envint.2024.108875. Epub 2024 Jul 8.
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Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.追踪废水中的 SARS-CoV-2 关切变异株：使用模拟基因组数据评估九种计算工具。
Microb Genom. 2024 May;10(5). doi: 10.1099/mgen.0.001249.
6
Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond.基于污水的监测作为公共卫生行动的工具：SARS-CoV-2 及其他。
Clin Microbiol Rev. 2024 Mar 14;37(1):e0010322. doi: 10.1128/cmr.00103-22. Epub 2023 Dec 14.
7
Wastewater sequencing reveals community and variant dynamics of the collective human virome.污水宏基因组测序揭示了人类病毒组的群落和变体动态。
Nat Commun. 2023 Oct 28;14(1):6878. doi: 10.1038/s41467-023-42064-1.
8
Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater.比较宏基因组和靶向方法从废水中测序人类致病病毒。
mBio. 2023 Dec 19;14(6):e0146823. doi: 10.1128/mbio.01468-23. Epub 2023 Oct 25.
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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.污水测序揭示了早期隐匿性 SARS-CoV-2 变异株的传播。
Nature. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6. Epub 2022 Jul 7.
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Critical Assessment of Metagenome Interpretation: the second round of challenges.宏基因组解读的关键评估：第二轮挑战。
Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8.