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Related Concept Videos

Human Virome01:26

Human Virome

The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible only with...

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Automated Annotation and Validation of Human Respiratory Virus Sequences using VADR.

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Accurate viral genome annotation is crucial for research and data sharing.
  • NCBI's Viral Annotation DefineR (VADR) pipeline offers standardized annotation but supports limited viral groups.
  • Expanding VADR's capabilities is essential for comprehensive viral surveillance.

Purpose of the Study:

  • To develop and validate new VADR models for 12 key human respiratory viruses.
  • To improve the accuracy and scalability of viral genome annotation.
  • To support public health initiatives through enhanced viral data analysis.

Main Methods:

  • Constructed reference sequence-based VADR models using intra-species genomic and phylogenetic diversity.
  • Trained models on over 5,000 public viral genomes and tested on hundreds of new genomes.
  • Incorporated analysis of genomic structure, annotation, overlapping ORFs, and potential misassemblies.

Main Results:

  • Achieved high VADR pipeline performance, passing over 96% of tested viral genomes.
  • Successfully identified complex genomic features like overlapping ORFs and transcriptional slippage.
  • Detected novel biological insights, including a human coronavirus NS2 knockout and new coding sequence lengths.

Conclusions:

  • The new VADR models significantly enhance viral genome annotation accuracy and scope.
  • These models are integrated into NCBI's GenBank submission pipeline, improving data quality.
  • Publicly available models facilitate scalable annotation for research and public health.