|
1
|
Chau VQ, Kolb AW, Miller DL, Yannuzzi NA, Brandt CR. Phylogenetic and Genomic Characterization of Whole Genome Sequences of Ocular Herpes Simplex Virus Type 1 Isolates Identifies Possible Virulence Determinants in Humans. Invest Ophthalmol Vis Sci 2023; 64:16. [PMID: 37450309 DOI: 10.1167/iovs.64.10.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Purpose There are limited data on the prevalence and genetic diversity of herpes simplex virus type 1 (HSV-1) virulence genes in ocular isolates. Here, we sequenced 36 HSV-1 ocular isolates, collected by the Bascom Palmer Eye Institute, a university-based eye hospital, from three different ocular anatomical sites (conjunctiva, cornea, and eyelid) and carried out a genomic and phylogenetic analyses. Methods The PacBio Sequel II long read platform was used for genome sequencing. Phylogenetic analysis and genomic analysis were performed to help better understand genetic variability among common virulence genes in ocular herpetic disease. Results A phylogenetic network generated using the genome sequences of the 36 Bascom Palmer ocular isolates, plus 174 additional strains showed that ocular isolates do not group together phylogenetically. Analysis of the thymidine kinase and DNA polymerase protein sequences from the Bascom Palmer isolates showed multiple novel single nucleotide polymorphisms, but only one, BP-K14 encoded a known thymidine kinase acyclovir resistance mutation. An analysis of the multiple sequence alignment comprising the 51 total ocular isolates versus 159 nonocular strains detected several possible single nucleotide polymorphisms in HSV-1 genes that were found significantly more often in the ocular isolates. These genes included UL6, gM, VP19c, VHS, gC, VP11/12, and gG. Conclusions There does not seem to be a specific genetic feature of viruses causing ocular infection. The identification of novel and common recurrent polymorphisms may help to understand the drivers of herpetic pathogenicity and specific factors that may influence the virulence of ocular disease.
Collapse
Affiliation(s)
- Viet Q Chau
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Aaron W Kolb
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, United States
| | - Darlene L Miller
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Nicolas A Yannuzzi
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Curtis R Brandt
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Wisconsin, United States
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, United States
| |
Collapse
|
|
2
|
Whitmore L, Yetsko K, Farrell JA, Page-Karjian A, Daniel W, Shaver DJ, Frandsen HR, Walker JS, Crowder W, Bovery C, Rollinson Ramia D, Burkhalter B, Ryan E, Duffy DJ. 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 (Basel) 2021; 11:2489. [PMID: 34573455 PMCID: PMC8465875 DOI: 10.3390/ani11092489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/05/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
The spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth's ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2035 single nucleotide polymorphisms (SNPs), 1.54% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific, with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic virus.
Collapse
Affiliation(s)
- Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
- Department of Biological Sciences, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
| | - Jessica A. Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Annie Page-Karjian
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL 34946, USA;
| | - Whitney Daniel
- South Carolina Aquarium, 100 Aquarium Wharf, Charleston, SC 29401, USA;
| | - Donna J. Shaver
- Division of Sea Turtle Science and Recovery, Padre Island National Seashore, Corpus Christi, TX 78480, USA; (D.J.S.); (H.R.F.); (J.S.W.)
| | - Hilary R. Frandsen
- Division of Sea Turtle Science and Recovery, Padre Island National Seashore, Corpus Christi, TX 78480, USA; (D.J.S.); (H.R.F.); (J.S.W.)
| | - Jennifer Shelby Walker
- Division of Sea Turtle Science and Recovery, Padre Island National Seashore, Corpus Christi, TX 78480, USA; (D.J.S.); (H.R.F.); (J.S.W.)
| | - Whitney Crowder
- Gumbo Limbo Nature Center, Boca Raton, FL 33432, USA; (W.C.); (C.B.)
| | - Caitlin Bovery
- Gumbo Limbo Nature Center, Boca Raton, FL 33432, USA; (W.C.); (C.B.)
| | - Devon Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
| | - Elizabeth Ryan
- Department of Biological Sciences, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
| | - David J. Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; (K.Y.); (J.A.F.); (D.R.R.); (B.B.); (D.J.D.)
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|