West Nile virus (WNV) is a mosquito-borne pathogen that poses a significant public and animal health threat in Europe and worldwide. Rapid identification of viral introductions and monitoring of local circulation are essential to support surveillance and control activities. To address these needs, a genomic surveillance system for WNV was implemented within the GenPat platform at the National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis of IZSAM, Teramo, Italy. The system integrates viral genomic sequences with epidemiological, geographical, temporal, and host-related metadata, enabling real-time monitoring of WNV genetic diversity and spread. One of the main features of the platform is the visualization of viral strains through an interactive geographic interface that allows users to explore sequence distribution at multiple spatial scales, from country level down to regional and municipal levels. This approach facilitates detailed analysis of viral circulation patterns and supports rapid identification of clusters and potential introduction events. The surveillance framework routinely incorporates WNV genomic data retrieved from international public databases, including sequences from Europe, Africa, Asia, and the Americas. This enables comparative analyses between Italian strains and globally circulating lineages, supporting the identification of genetically related viruses and the investigation of possible routes of introduction. For each sequence, the platform provides information on collection date, host species, host category, and accumulated genetic mutations, allowing assessment of viral evolution over time. Since WNV circulates in a complex transmission cycle involving mosquitoes, birds, humans, horses, and other hosts, the integration of host metadata is particularly valuable for understanding transmission dynamics. By combining genomic similarity with spatial, temporal, and epidemiological information, the GenPat WNV surveillance system transforms complex genomic data into an intuitive and actionable tool that supports outbreak investigations, enhances surveillance capacity, and improves understanding of WNV evolution and dissemination.
GenPat for WNV: An Integrated Genomic Surveillance System for Monitoring and Characterizing West Nile Virus Strains
Merabi Sepashvili;Alessio Lorusso;
2026-01-01
Abstract
West Nile virus (WNV) is a mosquito-borne pathogen that poses a significant public and animal health threat in Europe and worldwide. Rapid identification of viral introductions and monitoring of local circulation are essential to support surveillance and control activities. To address these needs, a genomic surveillance system for WNV was implemented within the GenPat platform at the National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis of IZSAM, Teramo, Italy. The system integrates viral genomic sequences with epidemiological, geographical, temporal, and host-related metadata, enabling real-time monitoring of WNV genetic diversity and spread. One of the main features of the platform is the visualization of viral strains through an interactive geographic interface that allows users to explore sequence distribution at multiple spatial scales, from country level down to regional and municipal levels. This approach facilitates detailed analysis of viral circulation patterns and supports rapid identification of clusters and potential introduction events. The surveillance framework routinely incorporates WNV genomic data retrieved from international public databases, including sequences from Europe, Africa, Asia, and the Americas. This enables comparative analyses between Italian strains and globally circulating lineages, supporting the identification of genetically related viruses and the investigation of possible routes of introduction. For each sequence, the platform provides information on collection date, host species, host category, and accumulated genetic mutations, allowing assessment of viral evolution over time. Since WNV circulates in a complex transmission cycle involving mosquitoes, birds, humans, horses, and other hosts, the integration of host metadata is particularly valuable for understanding transmission dynamics. By combining genomic similarity with spatial, temporal, and epidemiological information, the GenPat WNV surveillance system transforms complex genomic data into an intuitive and actionable tool that supports outbreak investigations, enhances surveillance capacity, and improves understanding of WNV evolution and dissemination.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
