TY - JOUR
T1 - Next-Generation Sequencing Coupled With in situ Hybridization
T2 - A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses
AU - Resende, Talita P.
AU - Marshall Lund, Lacey
AU - Rossow, Stephanie
AU - Vannucci, Fabio A.
N1 - 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.
PY - 2019/11/15
Y1 - 2019/11/15
N2 - 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.
AB - 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.
KW - NGS-ISH
KW - PCV3
KW - PPV2
KW - SVA
KW - diagnosis
KW - emerging infectious diseases
KW - pig
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U2 - 10.3389/fvets.2019.00403
DO - 10.3389/fvets.2019.00403
M3 - Review article
C2 - 31803766
AN - SCOPUS:85076044550
SN - 2297-1769
VL - 6
JO - Frontiers in Veterinary Science
JF - Frontiers in Veterinary Science
M1 - 403
ER -