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Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance

Authors :
Szilvia Jakab
Krisztina Bali
Csongor Freytag
Anna Pataki
Enikő Fehér
Máté Halas
Ákos Jerzsele
István Szabó
Krisztina Szarka
Ádám Bálint
Krisztián Bányai
Source :
Animals, Vol 13, Iss 20, p 3223 (2023)
Publication Year :
2023
Publisher :
MDPI AG, 2023.

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019–2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.

Details

Language :
English
ISSN :
13203223 and 20762615
Volume :
13
Issue :
20
Database :
Directory of Open Access Journals
Journal :
Animals
Publication Type :
Academic Journal
Accession number :
edsdoj.fea079448f774e888a1ba5108faf9acf
Document Type :
article
Full Text :
https://doi.org/10.3390/ani13203223