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The recent emergence of West Nile virus (WNV) and Usutu virus (USUV) in some European countries has triggered an increase in animal and human cases across Europe. Wild birds, serving as key reservoirs for WNV and USUV, often act as crucial indicators for the introduction and spread of these viruses. Currently, there is no durable large-scale monitoring for WNV in Belgium, and specific monitoring for USUV is lacking. In Flanders, passive WNV monitoring in birds has been in place for many years, while initial efforts to initiate active monitoring started in 2022. Here, we present the results of a limited study conducted during the vector seasons of 2022 and 2023 in Flemish bird populations to actively and passively monitor the prevalence of WNV and additionally assess the presence of USUV. Several real-time reverse transcription-PCR tests were employed for virus detection, revealing the absence of WNV-RNA during both vector seasons. Conversely, USUV-RNA was identified in 2022 through active surveillance, affecting two (5.5%) out of 36 birds (Corvus corone), and in passive surveillance, impacting eight (72.7%) out of 11 birds (Turdus merula [6] and Rhea pennata [2]). In 2023, active surveillance was more extensive and identified 16 (7.2%) USUV-RNA positive birds (Buteo buteo [1], T. merula [14] and Athene noctua [1]) out of 222 examined birds, while passive surveillance detected two (7.1%) positive birds (T. merula [1], and Larus marinus [1]) out of 28. Viral sequence information was obtained from seven USUV-positive birds using whole genome sequencing or Sanger sequencing. Phylogenetic analysis placed all identified strains within the Africa 3 lineage. This restricted WVN monitoring effort in Flanders did not reveal WNV presence, but found indications of an endemic USUV circulation in Belgium. It is crucial to intensify monitoring efforts for WNV in the coming years, considering its endemic status in several European countries and its expanding geographical range in northern Europe.
Pubmed ID: 40303116
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Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsNIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsOpen, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
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