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Related Concept Videos

Human Virome01:26

Human Virome

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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...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Using Small RNA Deep Sequencing Data to Detect Human Viruses.

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Small RNA sequencing (sRNA-seq) is a powerful tool for unbiased viral detection and identification across various host types.
  • Previous applications of sRNA-seq for viral discovery have focused on plants, invertebrates, and fungi.
  • The utility of sRNA-seq for detecting mammalian and human viruses remains a subject of ongoing investigation and debate.

Purpose of the Study:

  • To evaluate the efficacy of sRNA sequencing for detecting and identifying viruses in human cells and tissues.
  • To analyze a large dataset of sRNA sequencing runs from the NCBI Sequence Read Archive (SRA) for viral discovery.
  • To investigate the potential of sRNA-seq in identifying known and novel viral infections in clinical samples.

Main Methods:

  • Retrieved and analyzed 931 sRNA sequencing datasets from the NCBI SRA database.
  • Applied bioinformatics pipelines to detect and identify viral sequences within human sample data.
  • Cross-referenced identified viruses with existing annotations and clinical information.

Main Results:

  • Successfully detected six distinct viruses: Human Papillomavirus 18 (HPV-18), Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), Human Immunodeficiency Virus 1 (HIV-1), Squirrel Monkey Retrovirus (SMRV), and Epstein-Barr Virus (EBV).
  • Identified viral sequences in 36 of the analyzed sRNA-seq runs.
  • Confirmed four viral detections against previous study annotations.
  • Discovered HIV-1 in clinical samples not previously reported as HIV-positive.
  • Reported the first-time detection of SMRV in Diffuse Large B-Cell Lymphoma cells.

Conclusions:

  • The findings demonstrate that sRNA sequencing is a viable and effective method for detecting viruses in mammalian and human hosts.
  • sRNA-seq offers a valuable approach for viral discovery, even in samples lacking prior diagnostic information.
  • This study supports the broader application of sRNA-seq in clinical diagnostics and infectious disease research for human and animal health.