Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles
Abstract
:Simple Summary
Abstract
1. Introduction
2. Methods and Materials
2.1. Tissue Sampling
2.2. DNA Isolation, Library Preparation and Sequencing from Tissue and eDNA Samples
2.3. Quality Control and Read Trimming
2.4. Read Alignment
2.5. Consensus Sequence Generation
2.6. Nucleotide and Gene Diversity Analysis
2.7. Phylogenetic/Phylogenomic Analysis
2.8. Patient “Yucca” Whole Genome Phylogenomics
3. Results
3.1. Sequence/Nucleotide Diversity
3.2. Phylogenomics Reveals Clustering of ChHV5 by Geographic Trends
3.3. Phylogenetics Highlights Close Relatedness of Novel Sequences and ChHV5 Florida Variants A–C
3.4. Patient “Yucca” Whole Genome Phylogenomics: Do Separate Tumours in the Same Individual Harbour Differing ChHV5 Variants?
4. Discussion
4.1. Nucleotide Diversity of ChHV5
4.2. ChHV5 Phylogenomics
4.3. ChHV5 Phylogenetics
4.4. Within-Host Viral Diversity
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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Sample | Stranding Location | Species | Tissue Type | Sequencing Strategy | Total Reads | % ChHV5 Alignment | Total ChHV5 Aligning Reads | ChHV5 RPTM | Genome Coverage |
---|---|---|---|---|---|---|---|---|---|
27L1Fdna | Ormond Beach, east Florida | Cm | Lung tumour | No enrichment (host and viral DNA) | 6.88 × 108 | 0.038 | 257,692.5 | 3843 | 584.6× |
fISCEYFdna | South Carolina | Cm | External eye tumour | No enrichment (host and viral DNA) | 1.31 × 108 | 0.011 | 13,627 | 1064 | 30.9× |
fISCINFdna | External tumour | No enrichment (host and viral DNA) | 1.52 × 108 | 0.03 | 45,272 | 3031 | 102.7× | ||
poSCTFdna | South Carolina | Cm | External tumour | No enrichment (host and viral DNA) | 1.52 × 108 | 0.012 | 18,133 | 1224 | 41.1× |
yuLIRSFdna | Halifax Harbour, east Florida | Cm | External tumour | No enrichment (host and viral DNA) | 6.21 × 108 | 0.021 | 128,132 | 2119 | 290.7× |
yuRERFdna | External tumour | No enrichment (host and viral DNA) | 6.53 × 108 | 0.02 | 125,910 | 1976 | 285.7× | ||
yuRIRSFdna | External tumour | No enrichment (host and viral DNA) | 7.93 × 108 | 0.012 | 93,086 | 1198 | 211.2× | ||
yuRKTGFdna | Kidney tumour | No enrichment (host and viral DNA) | 7.25 × 108 | 0.021 | 152,495 | 2143 | 346.0× | ||
yuRKTMFdna | Kidney tumour | No enrichment (host and viral DNA) | 7.07 × 108 | 0.031 | 216,336 | 3127 | 490.8× | ||
yuRKTW1Fdna | Kidney tumour | No enrichment (host and viral DNA) | 6.30 × 108 | 0.011 | 65,453 | 1063 | 148.5× | ||
yuTSFdna | External tumour | No enrichment (host and viral DNA) | 8.59× 108 | 0.017 | 141,446 | 1682 | 320.9× | ||
TABT-Cm | Anchorage Marina, east Florida | Cm | Bladder tumour | No enrichment (host and viral DNA) | 1.69 × 108 | 0.03 | 43,563 | 2573 | 98.8× |
liRRF4dna | Marineland Beach, east Florida | Cm | External tumour | No enrichment (host and viral DNA) | 4.27 × 108 | 0.01 | 38,503 | 391 | 58.2× |
LoTXFdna | Texas | Lo | External tumour (deceased) | No enrichment (host and viral DNA) | 1.59 × 108 | 0.002 | 3018 | 192 | 6.9× |
LkNEFdna | New England, Cape Cod, Massachusetts | Lk | External tumour | No enrichment (host and viral DNA) | 1.12 × 108 | 0.01 | 9062 | 811 | 20.6× |
LkFLMCKFdna | Cape Romano, SW Florida | Lk | External tumour | No enrichment (host and viral DNA) | 1.50 × 108 | 0.01 | 14,929 | 992 | 33.9× |
20170226AFA | Mustang Island, Texas | Lk | External tumour | Viral enrichment | 3.45 × 107 | 14.61 | 4,222,944 | 1,461,284 | 9580.7× |
LLE-419 | Padre Island, Texas | Lk | External tumour | Viral enrichment | 1.46 × 107 | 2.2 | 301,155 | 219,649 | 683.2× |
MCK2015011701 | West Coast, Florida | Lk | External tumour | Viral enrichment | 5.89 × 107 | 13.1 | 6,527,585 | 1,309,565 | 14,809.3× |
NMFS14_313 | Florida Bay, Florida | Lk | External tumour | Viral enrichment | 3.69 × 107 | 23.2 | 7,180,057 | 2,320,447 | 16,289.6× |
Gene | ChHV5 Genome Position | Tajima’s D Statistic | Predicted Feature |
---|---|---|---|
F-UL37 | 98894–102139 | 1.31 | Tegument protein |
F-UL36 | 91944–98897 | 0.84 | VP1/2 tegument protein |
F-UL25 | 72184–73857 | 0.81 | 99% ID with gb|AAU93323.1 minor capsid protein |
HP17 | 57297–57764 | 0.79 | Hypothetical protein (HP) |
F-US8 | 12220–13842 | 0.77 | Glycoprotein e (gE) |
F-UL8 | 43118–45361 | 0.77 | Herpesvirus DNA helicase/primase complex associated protein |
HP16 | 50429–51067 | 0.66 | HP; predicted bipartite NLS |
F-UL15B | 55718–56788 | 0.61 | Probable DNA packing protein, C-terminus |
F-UL41 | 104719–105897 | 0.56 | Close similarity to gb|AER28066.1. Tegument host shutoff protein |
F-US4 | 14752–15549 | 0.51 | Similar to glycoprotein D (gD) |
HP34 | 126003–126476 | −1.64 | HP |
F-UL35 | 91561–91926 | −1.65 | VP26 basic phosphorylated capsid protein |
F-UL10 | 47779–49044 | −1.94 | Glycoprotein M (gM) |
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Whitmore, L.; Yetsko, K.; Farrell, J.A.; Page-Karjian, A.; Daniel, W.; Shaver, D.J.; Frandsen, H.R.; Walker, J.S.; Crowder, W.; Bovery, C.; et al. Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles. Animals 2021, 11, 2489. https://doi.org/10.3390/ani11092489
Whitmore L, Yetsko K, Farrell JA, Page-Karjian A, Daniel W, Shaver DJ, Frandsen HR, Walker JS, Crowder W, Bovery C, et al. Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles. Animals. 2021; 11(9):2489. https://doi.org/10.3390/ani11092489
Chicago/Turabian StyleWhitmore, Liam, Kelsey Yetsko, Jessica A. Farrell, Annie Page-Karjian, Whitney Daniel, Donna J. Shaver, Hilary R. Frandsen, Jennifer Shelby Walker, Whitney Crowder, Caitlin Bovery, and et al. 2021. "Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles" Animals 11, no. 9: 2489. https://doi.org/10.3390/ani11092489
APA StyleWhitmore, L., Yetsko, K., Farrell, J. A., Page-Karjian, A., Daniel, W., Shaver, D. J., Frandsen, H. R., Walker, J. S., Crowder, W., Bovery, C., Rollinson Ramia, D., Burkhalter, B., Ryan, E., & Duffy, D. J. (2021). Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles. Animals, 11(9), 2489. https://doi.org/10.3390/ani11092489