Next-Generation Sequencing Coupled With in situ Hybridization: A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses

Talita P. Resende, Lacey Marshall Lund, Stephanie Rossow, Fabio A. Vannucci

Research output: Contribution to journalReview articlepeer-review

1 Scopus citations

Abstract

Next generation sequencing (NGS) can be applied to identify and characterize the entire set of microbes within a sample. However, this platform does not provide a morphological context or specific association between the viral or bacterial sequences detected and the histological lesions. This limitation has generated uncertainty whether the sequences identified by NGS are actually contributing or not for the clinical outcome. Although in situ hybridization (ISH) and immunohistochemistry (IHC) can be used to detect pathogens in tissue samples, only ISH has the advantage of being rapidly developed in a context of an emerging disease, especially because it does not require development of specific primary antibodies against the target pathogen. Based on the sequence information provided by NGS, ISH is able to check the presence of a certain pathogen within histological lesions, by targeting its specific messenger RNA, helping to build the relationship between the pathogen and the clinical outcome. In this mini review we have compiled results of the application of NGS-ISH to the investigation of challenging diagnostic cases or emerging pathogens in pigs, that resulted in the detection of porcine circovirus type 3, porcine parvovirus type 2, Senecavirus A, and Mycoplasma hyorhinis.

Original languageEnglish (US)
Article number403
JournalFrontiers in Veterinary Science
Volume6
DOIs
StatePublished - Nov 15 2019

Bibliographical note

Funding Information:
TR was supported by CAPES-Brazil. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© Copyright © 2019 Resende, Marshall Lund, Rossow and Vannucci.

Keywords

  • NGS-ISH
  • PCV3
  • PPV2
  • SVA
  • diagnosis
  • emerging infectious diseases
  • pig

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