Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Retrospective Analysis of Rehabilitation Cases and Stranding Data
2.2. Sample Collection—Blood and Tumors
2.3. DNA Extraction and qPCR for ChHV5 F-UL30 with Sequence Confirmation
2.4. Whole-Genome Shotgun Sequencing of Tumor Samples
2.4.1. Viral Phylogenetics
2.4.2. Kemp’s Ridley Mitochondrial Genome Analysis
3. Results
3.1. Retrospective Case Series Analysis
Case Report of Fibropapillomatosis in a Stranded Kemp’s Ridley Turtle in Massachusetts
3.2. qPCR for ChHV5 DNA
3.3. TPM Normalization
3.4. Viral Phylogenetics
4. Discussion
4.1. Epidemiology of FP in Kemp’s Ridley Turtles
4.2. Molecular Diagnostics for ChHV5
4.3. ChHV5 Phylogenetics
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Turtle ID | Year | Age Class | Sex | How Encountered | Location | FP Tumor Score | # Tumors | Tumor Location(s) |
---|---|---|---|---|---|---|---|---|
Lk1 | 2006 | Juvenile | Undetermined | Stranded, rehabilitation | Florida | 3 | 8 | Neck, LF and LH flippers, carapace, plastron, tail |
Lk2 | 2006 | Juvenile | Undetermined | Stranded, rehabilitation | Florida | 1 | 1 | LF flipper |
Lk3 | 2011 | Juvenile | Undetermined | Stranded, rehabilitation | Georgia | 1 | 8 | L/R inguinal regions, tail base |
Lk4 | 2011 | Juvenile | Undetermined | Incidental capture, rehabilitation | Georgia | 1 | 2 | LF and RF flippers |
Lk5 | 2012 | Adult | Female | Nesting, rehabilitation | Texas | 2 | 1 | R inguinal region |
Lk6a,c | 2014 | Adult | Female | Stranded dead | Florida | 3 | 9 | Neck, carapace, R inguinal region, tail, skeletal muscle, L/R lungs |
Lk7 | 2014 | Juvenile | Undetermined | Stranded, rehabilitation | North Carolina | 1 | 1 | Tail |
Lk8 | 2014 | Juvenile | Undetermined | Incidental capture, rehabilitation | North Carolina | 1 | 1 | LF flipper |
Lk9a,c | 2015 | Juvenile | Female | Stranded dead | Florida | 2 | 8 | Neck, LF and RF flippers, carapace |
Lk10 | 2015 | Adult | Female | Stranded, rehabilitation | Florida | 3 | 11 | R eye, neck, LF and RF flippers, R inguinal region, L/R lungs |
Lk11a,c | 2017 | Juvenile | Undetermined | Stranded dead | Texas | 1 | 1 | L inguinal region |
Lk12 | 2017 | Adult | Female | Stranded dead | Texas | 2 | 10 | Neck, LF and RF flipper bases |
Lk13a | 2019 | Adult | Female | Incidental capture, rehabilitation | Texas | 1 | 2 | Neck, RF flipper base |
Lk14a,c | 2019 | Adult | Female | Stranded dead | Florida | 1 | 2 | Neck |
Lk15a,c | 2019 | Juvenile | Undetermined | Stranded, rehabilitation | Massachusetts | 2 | 7 | Neck, RF flipper, RF and LH flipper bases, R inguinal region |
Lk16a,c | 2019 | Juvenile | Female | Stranded dead | Florida | 1 | 2 | Neck, LF flipper |
Lk17a,b,c | 2019 | Adult | Female | Nesting | Texas | 1 | 1 | LF flipper * |
Lk18a | 2020 | Adult | Female | Nesting | Texas | 1 | 2 | Neck |
Lk19a,b | 2020 | Adult | Female | Nesting | Texas | 1 | 1 | Neck |
Lk20a,b | 2020 | Adult | Female | Nesting | Texas | 1 | 2 | L eye, neck |
Lk21a | 2020 | Adult | Female | Stranded, rehabilitation | North Carolina | 1 | 2 | RF flipper base |
Lk22a | 2020 | Adult | Female | Stranded dead | Florida | 3 | 4 | L shoulder, L/R lungs |
Sample Type | N | Positive for ChHV5 DNA N (Prevalence) | Mean (± SD) ChHV5 DNA Copy Number (Range) |
---|---|---|---|
Whole blood | 51 | 4 (7.8%) | 649 ± 516 (210–2393) |
FP tumors | 12 | 11 (91.7%) | 6,809,552 ± 5,446,113 (50–17,261,001) |
Sample | Location | Viral Enrichment (VE) | Total Reads | % ChHV5 Alignment | Total ChHV5 Aligning Reads | ChHV5 Reads per 10 Million Total Reads | ChHV5 Genome Coverage (x) | Number of SNPs | Sample Acquisition |
---|---|---|---|---|---|---|---|---|---|
Lk11 FP Tumor 1 | Mustang Island, TX | VE | 34,533,962 | 14.61 | 4,222,944 | 1,461,284 | 9580.69 | 106 | Necropsy |
Lk17 FP Tumor 2 | N. Padre Island, TX | VE | 14,641,416 | 2.20 | 301,155 | 219,649 | 683.24 | 88 | Nesting |
Lk9 FP Tumor 3 | Marco Island, SW FL | VE | 58,980,497 | 13.10 | 6,527,585 | 1,309,565 | 14,809.28 | 438 | Necropsy |
Lk6 FP Tumor 4 | Florida Bay, SW FL | VE | 36,964,405 | 23.20 | 7,180,057 | 2,320,447 | 16,289.56 | 341 | Necropsy |
Lk15 FP Tumor 5 | Brewster, MA | VE | 111,730,494 | 0.01 | 9062 | 811 | 20.56 | 2223 | Surgery |
Lk16-1 FP Tumor 6 | Sanibel, SW FL | Non-VE | 129,584,639 | <0.01 | 140 | 11 | 0.31 | N/A | Necropsy |
Lk16-2 FP Tumor 7 | Sanibel, SW FL | Non-VE | 197,167,284 | <0.01 | 30 | 2 | 0 | N/A | Necropsy |
Lk14 FP Tumor 8 | Cape Romano, SW FL | Non-VE | 150,443,070 | 0.01 | 14,929 | 992 | 33.87 | 2284 | Necropsy |
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Page-Karjian, A.; Whitmore, L.; Stacy, B.A.; Perrault, J.R.; Farrell, J.A.; Shaver, D.J.; Walker, J.S.; Frandsen, H.R.; Rantonen, E.; Harms, C.A.; Norton, T.M.; Innis, C.; Yetsko, K.; Duffy, D.J. Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii). Animals 2021, 11, 3076. https://doi.org/10.3390/ani11113076
Page-Karjian A, Whitmore L, Stacy BA, Perrault JR, Farrell JA, Shaver DJ, Walker JS, Frandsen HR, Rantonen E, Harms CA, Norton TM, Innis C, Yetsko K, Duffy DJ. Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii). Animals. 2021; 11(11):3076. https://doi.org/10.3390/ani11113076
Chicago/Turabian StylePage-Karjian, Annie, Liam Whitmore, Brian A. Stacy, Justin R. Perrault, Jessica A. Farrell, Donna J. Shaver, J. Shelby Walker, Hilary R. Frandsen, Elina Rantonen, Craig A. Harms, Terry M. Norton, Charles Innis, Kelsey Yetsko, and David J. Duffy. 2021. "Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)" Animals 11, no. 11: 3076. https://doi.org/10.3390/ani11113076