Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages
Abstract
:1. Introduction
2. Material and Methods
2.1. Overview of SAV Nanopore Sequencing Approach
2.2. Samples, Reverse Transcription and PCR
2.3. ONT Library Preparation, MinION Sequencing, Basecalling, and Trimming
2.4. Mapping, Consensus Sequence Generation, and Filtering
2.5. Phylogenetic and Phylogeographic Reconstructions
2.6. Sanger Sequencing of Additional SAV2 Genomes
3. Results
3.1. Nanopore Sequencing of SAV from Norwegian Field Samples
3.2. SAV2 Genetic Diversity in Recent Norwegian Aquaculture
3.3. Phylogeographical Reconstructions of SAV2
3.3.1. Phylogeographical Reconstructions of SAV2a
3.3.2. Phylogeographical Reconstructions of SAV2b
3.4. Novel SAV3 Strains Detected in Fish Co-Infected with SAV2 and SAV3
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Amplicon | Forward Primer (5’–3’) | Reverse Primer (5’–3’) | Product Length 1 | Genomic Location 1 |
---|---|---|---|---|
1 | AGACTGCGTTTCCAGGGTTC | CCCGTAGATGCCAATCGTGT | 2162 bp | 89–2251 bp |
2 | GAATACGTTTACGAATTGTCCTCC | ACCGAGACGGACTTGAAATACC | 1967 bp | 2083–4049 bp |
3 | GACCTGGTGTTTTGTGACGC | TCCCGTGTTAGCCCTCTAGG | 1895 bp | 3838–5732 bp |
4 | GCAGCGTCCACRGCCATAGT | CATCAGGCGTTTTACAGGGTC | 2015 bp | 5531–7545 bp |
5 | ATGTTTCCCATGCAATTCACCAAC | GGTGCGGCTTGCCCTGGGTGAT | 1816 bp | 7818–9633 bp |
6 | AGAGAACGCAGCAAGGGC | GGCACTTCTTCACCACGCA | 2431 bp | 9318–11,748 bp |
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Macqueen, D.J.; Eve, O.; Gundappa, M.K.; Daniels, R.R.; Gallagher, M.D.; Alexandersen, S.; Karlsen, M. Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses 2021, 13, 2549. https://doi.org/10.3390/v13122549
Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S, Karlsen M. Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses. 2021; 13(12):2549. https://doi.org/10.3390/v13122549
Chicago/Turabian StyleMacqueen, Daniel J., Oliver Eve, Manu Kumar Gundappa, Rose Ruiz Daniels, Michael D. Gallagher, Svein Alexandersen, and Marius Karlsen. 2021. "Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages" Viruses 13, no. 12: 2549. https://doi.org/10.3390/v13122549