Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. General Disease Description and Standard Laboratory Diagnostic Analyses
2.2. Sampled Pigs and Whole-Genome Sequencing
2.3. Mining Whole-Genome Sequencing Datasets for Virus Sequences
- The development of a comprehensive virus database was based on the NCBI Virus resource (https://www.ncbi.nlm.nih.gov/genome/viruses; accessed on 5 February 2025), which contains DNA sequences of reference viral genomes and their strains. Processing and curating this resource are essential to create a reliable database.
- Host-related reads were removed by aligning sequenced reads to the Sus scrofa genome, which was assembled using Sscrofa11.1. Unmapped reads, which represent non-host DNA, likely originating from microorganisms or viruses, were then extracted.
- Screening for viral sequences involved aligning the extracted unmapped reads to the curated virus database to identify viral sequences. This process included a quick alignment using the BWA v.0.7.17 tool, followed by confirming alignments with a more sensitive approach, like the BLAST+ v.2.7.1 tool. Only viral genomes with a minimum of three aligned read pairs (six reads) were considered representative of the sample.
2.4. Statistical Analyses
3. Results
3.1. Description of the Disease Outbreak at the Farm Level and Standard Laboratory Analyses
3.2. Overview of Virus Sequences in Whole-DNA Sequencing Datasets
3.3. Viral DNA Profiles in the Pigs Studied
3.4. Putative Association of Virus Profiles with a Disease Condition
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ELISA | Enzyme-linked immunosorbent assay |
ENA | European Nucleotide Archive |
Gb | Giga base pairs |
PCV2 | Porcine circovirus 2 |
PCV3 | Porcine circovirus 3 |
PCVAD | Porcine circovirus-associated disease |
PCVM | Porcine cytomegalovirus |
PLHV1 | Porcine lymphotropic herpesvirus 1 |
PLHV2 | Porcine lymphotropic herpesvirus 2 |
PMWS | Post-weaning Multisystemic Wasting Syndrome |
PPV2 | Porcine parvovirus 2 |
PPV3 | Porcine parvovirus 3 |
PPV4 | Porcine parvovirus 4 |
PPV5 | Porcine parvovirus 5 |
PPV6 | Porcine parvovirus 6 |
PRRS | Porcine reproductive and respiratory syndrome |
PRRSV | Porcine reproductive and respiratory syndrome virus |
SIV | Swine influenza virus A |
SuBHV2 | Suid betaherpesvirus 2 |
SuGHV3 | Suid gammaherpesvirus 3 |
SuGHV4 | Suid gammaherpesvirus 4 |
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Pig | Site 1 | Sequenced Reads | Unmapped Reads (%) 2 | Reads of Viral Origin (%) 3 |
---|---|---|---|---|
S1 | #1 | 448,120,122 | 666,430 (0.15%) | 934 (0.140%) |
S2 | #1 | 327,414,198 | 411,866 (0.13%) | 44 (0.011%) |
S3 | #1 | 315,609,910 | 407,978 (0.13%) | 10 (0.002%) |
S4 | #2 | 441,166,336 | 521,010 (0.12%) | 378 (0.073%) |
S5 | #2 | 400,074,484 | 545,276 (0.14%) | 84 (0.015%) |
S6 | #2 | 334,788,158 | 492,688 (0.15%) | 22 (0.004%) |
S7 | #3 | 448,195,724 | 606,724 (0.14%) | 26,720 (4.40%) |
S8 | #3 | 448,168,478 | 572,470 (0.13%) | 14,618 (2.55%) |
S9 | #3 | 416,512,760 | 526,100 (0.13%) | 572 (0.108%) |
Site #1 3 | Site #2 3 | Site #3 3 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Virus Name | Alternative Name 1 | NCBI ID | Depth 2 | S1 | S2 | S3 | S4 | S5 | S6 | S7 | S8 | S9 |
Suid betaherpesvirus 2 | Porcine cytomegalovirus (PCMV) | NC_022233 | 0.119 | - | 40 a | - | 22 b | - | 20 b | 12 b | 8 b | - |
Suid gammaherpesvirus 3 | Porcine lymphotropic herpesvirus 1 (PLHV1) | NC_038264 | 0.172 | - | - | 6 a | - | - | - | - | 6 a | 72 b |
Suid gammaherpesvirus 4 | Porcine lymphotropic herpesvirus 2 (PLHV2) | NC_038265 | 0.593 | - | - | - | 236 | - | - | - | - | - |
Ungulate copiparvovirus 4 | Porcine parvovirus 6 (PPV6) | NC_023860 | 1027 | - | - | - | - | - | - | 26,616 a | 14,596 a | 496 b |
Ungulate tetraparvovirus 3 | Parvovirus YX-2010/CHN CnPPV_JH13; Porcine parvovirus 2 (PPV2) | NC_038883; NC_035180 | 5.400 | 186 a | - | - | 10 b | - | - | - | - | - |
Porcine parvovirus 2 | - | NC_025965 | 11.88 | 394 a | - | - | 36 b | - | - | - | - | - |
Ungulate tetraparvovirus 2 | Porcine hokovirus (p-PARV4) PPV3 | NC_038546 | 2.932 | - | - | - | 34 | 66 | - | - | - | - |
Porcine partetravirus | - | NC_022104 | 0.777 | - | - | 14 | - | 14 | - | - | - | - |
Ungulate copiparvovirus 2 | Porcine parvovirus 4 (PPV4) | NC_014665 | 0.406 | - | - | - | - | - | - | 16 | - | - |
Porcine parvovirus 5 | - | NC_023020 | 1.756 | - | - | - | - | - | - | 68 | - | - |
Porcine circovirus 2 | - | NC_005148 | 6.441 | 76 | - | - | - | - | - | - | - | - |
Rodent protoparvovirus 1 | Minute virus of mice | NC_001510 | 8.503 | 268 a | - | - | 24 b | - | - | - | - | - |
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Bovo, S.; Ribani, A.; Schiavo, G.; Taurisano, V.; Bolner, M.; Bertolini, F.; Fontanesi, L. Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak. Vet. Sci. 2025, 12, 513. https://doi.org/10.3390/vetsci12060513
Bovo S, Ribani A, Schiavo G, Taurisano V, Bolner M, Bertolini F, Fontanesi L. Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak. Veterinary Sciences. 2025; 12(6):513. https://doi.org/10.3390/vetsci12060513
Chicago/Turabian StyleBovo, Samuele, Anisa Ribani, Giuseppina Schiavo, Valeria Taurisano, Matteo Bolner, Francesca Bertolini, and Luca Fontanesi. 2025. "Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak" Veterinary Sciences 12, no. 6: 513. https://doi.org/10.3390/vetsci12060513
APA StyleBovo, S., Ribani, A., Schiavo, G., Taurisano, V., Bolner, M., Bertolini, F., & Fontanesi, L. (2025). Mining Porcine Blood Whole-DNA Sequencing Datasets to Uncover Pig Viromes: An Exploratory Application to Identify Potential Infecting Agents of an Undefined Disease Outbreak. Veterinary Sciences, 12(6), 513. https://doi.org/10.3390/vetsci12060513