add news sars-cov-2 ww paper

content/news/2023-10-25-paper-sars-cov-2-ww-surveillance/index.md

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+---
+title: "Galaxy and workflows: advancing SARS-CoV-2 genomic surveillance in wastewater"
+date: "2023-10-25"
+authors: Polina Polunina
+tease: "Galaxy empowered research in SARS-CoV-2 surveillance in wastewater"
+hide_tease: true
+subsites: [all-eu,global]
+---
+
+## Galaxy and workflows: advancing SARS-CoV-2 genomic surveillance in wastewater
+
+A study in *Nature* titled ["SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses"](https://www.nature.com/articles/s41467-023-41369-5) by Mukhlid Yousif et. al. has unveiled the potential of Galaxy and its workflows in epidemiological research. The research delved into identifying SARS-CoV-2 variants in wastewater samples from South African urban centers, shedding light on virus transmission dynamics.
+
+### Wastewater surveillance's vital role
+
+With a decline in global SARS-CoV-2 infections, alternative surveillance methods were needed. Wastewater surveillance emerged as a key tool, offering a cost-effective way to gain insights into the virus's spread across communities. Over 70 countries now use this approach to monitor wastewater SARS-CoV-2 levels, complementing clinical surveillance.
+
+### Galaxy empowers genomic surveillance
+
+The research's standout feature was its use of Galaxy ([usegalaxy.eu](https://usegalaxy.eu/)), an open-source, user-friendly tool for biomedical research. Researchers employed Galaxy to analyze the extensive genomic data from wastewater samples, utilizing its workflows for sequence analysis up to variant calling, which was followed by the usage of the Freyja tool. Galaxy has greatly assisted in managing the vast amount of raw sequence data.
+
+### Freyja: lineage analysis
+
+Significant to the research was [Freyja](https://github.com/andersen-lab/Freyja), an open-source tool that is also available on Galaxy ([GitHub repo](https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja)). Freyja estimated the relative abundance of SARS-CoV-2 lineages in wastewater samples, employing a unique barcode library to define known lineages. This analysis provided insights consistent with Variants of Concern (VOCs) in clinical specimens, highlighting the limitations of clinical surveillance's sampling biases.
+
+### Uncovering uncommon mutations
+
+The research also identified numerous amino acid mutations in the SARS-CoV-2 spike protein. Some of these mutations were rare in clinical samples but prevalent in wastewater, suggesting the emergence of cryptic lineages or unique evolutionary events.
+
+### Looking ahead
+
+This research not only enhanced our understanding of SARS-CoV-2 transmission in wastewater but also demonstrated Galaxy's prowess in handling complex genomic data. Galaxy's user-friendly interface and versatile tools remain at the forefront of cutting-edge research, offering a means to decode intricate biological data.
+
+In our ongoing battle against emerging pathogens, the synergy of advanced technology and scientific research, as exemplified by Galaxy, promises more breakthroughs in infectious disease understanding, surveillance, and control strategies.