Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Collection of Samples
- (a)
- Oyster (Crassostrea gigas) sampling within the “European baseline survey of norovirus in oysters” [28,29] (November 2016–October 2018). Samples were taken every two months from four production areas (one class A and three class B, according to the EU Commission Implementing Regulation 2019/627) located in the northern and southern Adriatic and Thyrrenian sea, respectively (Venetian Lagoon, Apulia, Gulf of La Spezia and Sardinia). A total of 48 oyster samples were collected.
- (b)
- Bivalve shellfish (Mytilus galloprovincialis, Crassostrea gigas, Ostrea edulis) sampling in the Gulf of La Spezia (December 2020–December 2021). Samples were taken monthly from nine production areas (two class A and seven class B). A total of 86 samples was collected (Mytilus n = 43, Crassostrea n = 37, Ostrea n = 6).
2.2. RNA Extraction
2.3. RT-PCR Screening
2.4. Oxford Nanopore Technologies (ONT) Sequencing and Genome Detective Pipeline
2.5. Sequence and Phylogenetic Analyses
3. Results
3.1. RT-PCR Screening
3.2. ONT Sequencing
3.3. Phylogenetic Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Barcode | Nr Contig | Reads | Depth of Coverage | Identity to Reference Strains | |||
---|---|---|---|---|---|---|---|
Genus | Accession nr | FASTA Nucleotide | nt identity % | ||||
BR1 | 1a | 16,846 | 1870 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 60.1 |
BR2 | 2a | 6733 | 5255.6 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.4 |
2b | 566 | 482.6 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 63.5 | |
2c | 228 | 221.4 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 63.8 | |
BR3 | 3a | 5831 | 489.8 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.3 |
3b | 4208 | 3625.2 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.1 | |
3c | 1413 | 1151.6 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.6 | |
3d | 208 | 235.3 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.9 | |
3e | 57 | 51.6 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 58.0 | |
BR4 | 4a | 5417 | 13,488.9 | Unclassified | MG599895 | FAstV/CHN/2017/spearnose grenadier fish/XYHYC187426 | 60.2 |
4b | 67 | 142.8 | Mamastrovirus | KT894875 | MAstV/GER/2013/bat/B8 | 72.2 | |
BR5 | 5a | 1147 | 1474.7 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 59.9 |
5b | 3 | 5.9 | Avastrovirus | KY320405 | AAstV/SWE/2014/mallard/313 | 81.9 | |
5c | 3 | 4.9 | Avastrovirus | JX985678 | AAstV/HKG/2009/chicken/MPJ0111 | 63.7 | |
BR6 | 6a | 9727 | 19,702.3 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 59.7 |
6b | 5 | 6 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 62.2 | |
6c | 1 | 2 | Avastrovirus | KY320405 | AAstV/SWE/2014/mallard/313 | 80.1 | |
BR7 | 7a | 7566 | 809 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 57.6 |
7b | 425 | 450.3 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 67.5 | |
7c | 326 | 669.4 | Avastrovirus | KY320405 | AAstV/SWE/2014/mallard/313 | 92.5 | |
7d | 31 | 59.4 | Unclassified | MG599917 | RAstV/CHN/2017/gecko/LPXYC188631 | 69.3 | |
BR8 | 8a | 5065 | 540.5 | Avastrovirus | KY320405 | AAstV/SWE/2014/mallard/313 | 82.2 |
8b | 1861 | 1861 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 59.9 | |
8c | 897 | 1224.9 | Unclassified | MG599917 | RAstV/CHN/2017/gecko/LPXYC188631 | 67.9 | |
8d | 561 | 474 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 62.1 | |
8e | 149 | 161.1 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.2 | |
BR9 | 9a | 2659 | 3935 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 58.3 |
9b | 261 | 286.8 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 63.6 | |
9c | 105 | 120.1 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 63.1 | |
9d | 24 | 38.6 | Mamastrovirus | KY575664 | MAstV/MDG/2014/bat/UADBA SMG18894 | 68.4 | |
BR 10 | 10a | 40,150 | 6633.5 | Avastrovirus | MK189093 | AAstV/BRA/2010/ruddy turnstone/RT | 66.7 |
BR 11 | 11a | 64,214 | 67,410.2 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 58.2 |
BR 12 | 12a | 41,948 | 6639 | Unclassified | KX884564 | FAstV/CHN/2014/shrimp/BHWZXX13371 | 58.2 |
12b | 17 | 49.4 | Avastrovirus | HM029238 | AAstV/CHN/2009/chicken/Sichuan | 75.0 | |
BR 13 | 13a | 723 | 93.1 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 64.7 |
13b | 72 | 100.2 | Avastrovirus | KY320405 | AAstV/SWE/2014/mallard/313 | 80.2 | |
13c | 50 | 52.8 | Avastrovirus | KT946721 | AAstV/HKG/2015/white eye bird/D11-148.2 | 63.5 |
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Beikpour, F.; Pellegrini, F.; Lanave, G.; Camero, M.; Catella, C.; Di Martino, B.; Di Profio, F.; Masotti, C.; Battistini, R.; Serracca, L.; et al. Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing. Vet. Sci. 2023, 10, 175. https://doi.org/10.3390/vetsci10030175
Beikpour F, Pellegrini F, Lanave G, Camero M, Catella C, Di Martino B, Di Profio F, Masotti C, Battistini R, Serracca L, et al. Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing. Veterinary Sciences. 2023; 10(3):175. https://doi.org/10.3390/vetsci10030175
Chicago/Turabian StyleBeikpour, Farzad, Francesco Pellegrini, Gianvito Lanave, Michele Camero, Cristiana Catella, Barbara Di Martino, Federica Di Profio, Chiara Masotti, Roberta Battistini, Laura Serracca, and et al. 2023. "Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing" Veterinary Sciences 10, no. 3: 175. https://doi.org/10.3390/vetsci10030175