Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

Area of Science:

• Virology
• Pathology
• Genomics

Background:

• Properly stored materials are crucial for novel virus detection.
• Formalin-fixed paraffin-embedded (FFPE) tissues are often the only available samples for retrospective studies of past disease outbreaks.
• The utility of FFPE tissues for novel virus detection remains unclear.

Purpose of the Study:

• To evaluate the effectiveness of sequence-independent amplification combined with next-generation sequencing for detecting viral sequences in FFPE tissues.
• To assess the potential of this technique for identifying novel viruses in retrospective samples.
• To explore the correlation between viral detection in FFPE tissues and histopathological changes.

Main Methods:

• Sequence-independent amplification (SIA) was employed to amplify nucleic acids from FFPE tissues.
• Next-generation sequencing (NGS) was used to sequence the amplified products.
• Bioinformatic analysis was performed to identify viral sequences.

Main Results:

• The SIA-NGS approach successfully detected sequences from both known and unknown viruses in FFPE tissues.
• The sensitivity of detection was relatively low.
• The method allowed for correlation with histopathological findings in the corresponding tissue sections.

Conclusions:

• Sequence-independent amplification and next-generation sequencing offer a viable method for detecting novel viral sequences in FFPE tissues.
• This technique is particularly useful for retrospective studies of diseases with unknown origins when other biological samples are unavailable.
• The approach facilitates the correlation of viral presence with observed histopathological changes, aiding in disease characterization.