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Jakab S, Bálint Á, Cseri K, Bali K, Kaszab E, Domán M, Halas M, Szarka K, Bányai K. Genome stability assessment of PRRS vaccine strain with new ARTIC-style sequencing protocol. Front Vet Sci 2024; 10:1327725. [PMID: 38260197 PMCID: PMC10800885 DOI: 10.3389/fvets.2023.1327725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
A tiling amplicon sequencing protocol was developed to analyse the genome sequence stability of the modified live PRRSV vaccine strain, Porcilis MLV. The backbone of the ARTIC-style protocol was formed by 34 individual primer pairs, which were divided into two primer pools. Primer pairs were designed to amplify 532 to 588 bp fragments of the corresponding genomic region. The amplicons are suitable for sequencing on Illumina DNA sequencers with available 600-cycle sequencing kits. The concentration of primer pairs in the pools was optimized to obtain a balanced sequencing depth along the genome. Deep sequencing data of three vaccine batches were also analysed. All three vaccine batches were very similar to each other, although they also showed single nucleotide variations (SNVs) affecting less than 1 % of the genome. In the three vaccine strains, 113 to 122 SNV sites were identified; at these sites, the minority variants represented a frequency range of 1 to 48.7 percent. Additionally, the strains within the batches contained well-known length polymorphisms; the genomes of these minority deletion mutants were 135 to 222 bp shorter than the variant with the complete genome. Our results show the usefulness of ARTIC-style protocols in the evaluation of the genomic stability of PRRS MLV strains.
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Affiliation(s)
- Szilvia Jakab
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Karolina Cseri
- One Health Institute, University of Debrecen, Debrecen, Hungary
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Krisztina Bali
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Eszter Kaszab
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- One Health Institute, University of Debrecen, Debrecen, Hungary
| | - Marianna Domán
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | | | - Krisztina Szarka
- One Health Institute, University of Debrecen, Debrecen, Hungary
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Krisztián Bányai
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
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