Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Collection of Oral Fluids from Polish Herds
2.2. Assessment of swIAV Detection Using RT-qPCR Pre- and Post-Storage
2.3. Evaluation of Two IAV Sequencing Protocols for Oral Fluids
2.4. Genome Assembly and Epidemiological Analysis of Polish swIAV Segment Sequences
2.5. Statistical Analysis
3. Results
3.1. Impact of Storage Temperature, Time, and Oral Fluid Sample Quality on swIAV Detection
3.2. Impact of IAV Sequencing Protocol on Sequencing Success of the Eight IAV Gene Segments
3.3. Genetic Diversity of swIAV Strains in Polish Farms between 2017 and 2020
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Surface Genes | Internal Genes | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Farm | Year | Subtype | Genotype | S4 HA | S6 NA | S1 PB2 | S2 PB1 | S3 PA | S5 NP | S7 M | S8 NS | ||
A/swine/Poland/BY_171030_OF5/2017 | BY | 2017 | HxNx | Und. | * | ||||||||
A/swine/Poland/GNI_170321_OF9B/2017 | GNI | HxN1 | Und. | ||||||||||
A/swine/Poland/PBK_170322_OF5A/2017 | PBK | H1N1 | A | ||||||||||
A/swine/Poland/AGR_170718_OF5_2017 | AGR | H1N2 | T | ||||||||||
A/swine/Poland/AGR_170718_OF7/2017 | H1N2 | T | |||||||||||
A/swine/Poland/ZA_171031_OF5/2017 | ZA | H1N1 | U | ||||||||||
A/swine/Poland/HRU_190405_OF7/2019 | HRU | 2019 | H1N1 | U | |||||||||
A/swine/Poland/HRU_200616_OF7/2020 | 2020 | H1N1 | U | ||||||||||
A/swine/Poland/KRY_190723_OF5/2019 | KRY | 2019 | H1N2 | T | |||||||||
A/swine/Poland/KRY_200821_OF5/2020 | 2020 | H1N1 | P | * | * | ||||||||
A/swine/Poland/KRY_200821_OF7/2020 | H1N1 | P | |||||||||||
A/swine/Poland/KUJ_190717_OF9/2019 | KUJ | 2019 | H1N2 | T | |||||||||
A/swine/Poland/LEK_190725_OF5_2019 | LEK | H1N2 | T | ||||||||||
A/swine/Poland/LEK_190128_OF11/2019 | H1N1 | P | |||||||||||
A/swine/Poland/LEK_200304_OF9/2020 | 2020 | H1N2 | T | ||||||||||
A/swine/Poland/ZAG1_191104_OF7/2019 | ZAG1 | 2019 | H1N1 | U | |||||||||
A/swine/Poland/ZAG1_191104_OF11/2019 | H1Nx | Und. | |||||||||||
A/swine/Poland/ZYW_191104_OF6b/2019 | ZYW | H1Nx | Und. | ||||||||||
A/swine/Poland/PLA_190902_OF5/2019 | PLA | H1N2 | T | ||||||||||
A/swine/Poland/PLA_190902_OF17/2019 | H1N2 | T | |||||||||||
A/swine/Poland/PLA_190128_OF7/2019 | H1N2 | T | * | ||||||||||
A/swine/Poland/CHO_200819_OF5/2020 | CHO | 2020 | H1N2 | T | |||||||||
A/swine/Poland/KCZ_200617_OF7/2020 | KCZ | H1N2 | T | ||||||||||
European avian-like H1N1 | |||||||||||||
2009 pandemic H1N1 | |||||||||||||
Human-like H3N2 | |||||||||||||
Genetic information not available |
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Vereecke, N.; Woźniak, A.; Pauwels, M.; Coppens, S.; Nauwynck, H.; Cybulski, P.; Theuns, S.; Stadejek, T. Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds. Viruses 2023, 15, 435. https://doi.org/10.3390/v15020435
Vereecke N, Woźniak A, Pauwels M, Coppens S, Nauwynck H, Cybulski P, Theuns S, Stadejek T. Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds. Viruses. 2023; 15(2):435. https://doi.org/10.3390/v15020435
Chicago/Turabian StyleVereecke, Nick, Aleksandra Woźniak, Marthe Pauwels, Sieglinde Coppens, Hans Nauwynck, Piotr Cybulski, Sebastiaan Theuns, and Tomasz Stadejek. 2023. "Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds" Viruses 15, no. 2: 435. https://doi.org/10.3390/v15020435