Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling and Virus Enrichment
2.2. RNA Preparation and Illumina Sequencing
2.3. Sequence Data Processing and Sequence Analyses
3. Results
3.1. Noda-like Viruses
3.2. Reo-like Viruses
3.3. Bunya-like Viruses
3.4. Birna-like Viruses
3.5. Permutotetra-like Viruses
3.6. Nido-like Viruses
3.7. Flavivirus Supergroup
3.8. Nege-like Virus
3.9. Rhabdoviridae
3.10. Chuviridae
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Capsid Protein | RdRp Superfamily | Examples |
---|---|---|
Viral coat protein S-domain (pfam00729) | RdRp1 (pfam00729) | Plasmopara halstedii virus A, Sclerophthora macrospora virus A, Beijing sediment noda-like virus1, Beihai noda-like virus 5, Ripothoz virus TC-noda-LV–11, –16 |
RdRp3 (pfam00998) | Tombusviridae (except Luteovirus), Tombunodavirus | |
RdRp4 (pfam02123) | Sobemovirus, Polemovirus | |
permuted RdRp | Inari permutotetravirus, Beihai sphaeromadae virus 4, TC-permutotetra-LV–2, –7 | |
Nodavirus capsid protein VNN (pfam11729) | RdRp1 (pfam00680) | Betanodavirus, Orsay nodavirus, Le Blanc nodavirus, Santeuil nodavirus |
RdRp3 (pfam00998) | Wufeng shrew carmotetravirus 1 | |
Luteovirus coat protein(pfam00894) | RdRp1 (pfam00729) | Craigies Hill virus |
RdRp3 (pfam00998) | Luteovirus | |
RdRp4 (pfam02123) | Enamovirus, Polerovirus | |
Peptidase A6 (pfam01829) | RdRp1 (pfam00680) | Alphanodavirus, Ripothip virus, TC-noda-LV–92 |
RdRp2 (pfam00978) | H-hepe-LV–5, TC-hepe-LV–20 | |
RdRp3 (pfam00998) | TC-tombus-LV–336, –339, –340, H-tombus-LV–4, –6, –15, Shahe isopoda virus 5 | |
RdRp4 (pfam02123) | H-solemo-LV–4, –6, –10, –15, TC-solemo-LV–11 | |
permuted RdRp | TC-hepe-LV–22, –24 | |
Peptidase A21 (pfam03566) | RdRp1 (pfam00680) | Sinhaliviridae, Lutzomyia nodavirus |
RdRp2 (pfam00978) | Alphatetraviridae, Hubei hepe-like virus 2, TC-hepe-LV–30 | |
RdRp3 (pfam00998) | Carmotetraviridae, TC-tombus-LV–87, –337, Sichuan mosquito tombus-like virus | |
permuted RdRp | Permutotetraviridae, Permutotetraviridae sp. 174-k141_43091, Hubei permutotetra-like virus 6 |
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Zell, R.; Groth, M.; Selinka, L.; Selinka, H.-C. Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses. Microorganisms 2024, 12, 2361. https://doi.org/10.3390/microorganisms12112361
Zell R, Groth M, Selinka L, Selinka H-C. Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses. Microorganisms. 2024; 12(11):2361. https://doi.org/10.3390/microorganisms12112361
Chicago/Turabian StyleZell, Roland, Marco Groth, Lukas Selinka, and Hans-Christoph Selinka. 2024. "Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses" Microorganisms 12, no. 11: 2361. https://doi.org/10.3390/microorganisms12112361
APA StyleZell, R., Groth, M., Selinka, L., & Selinka, H.-C. (2024). Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses. Microorganisms, 12(11), 2361. https://doi.org/10.3390/microorganisms12112361