Evidence of a Possible Viral Host Switch Event in an Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling, Virus Isolation and Genome Sequencing
2.2. Genome Assembly and Annotation
2.3. Comparative Genomics
2.4. Phylogenetic Analyses
3. Results
3.1. Genome of Albatrosspox Virus 2 (ALPV2)
3.2. Genome Annotation and Comparative Analyses of ALPV2
3.3. Core/Conserved ORFs
3.4. Multigene Families
3.5. Evolutionary Relationships of ALPV2
4. Discussion
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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Virus | Abbreviation | Year of Isolation | GenBank Accession Number | Reference |
---|---|---|---|---|
Albatrosspox virus 2 | ALPV2 | 1997 | OK348853 | This study |
Albatrosspox virus | ALPV | 1997 | MW365933 | [29] |
Canarypox virus | CNPV | 1948, 2015 | AY318871, MG760432 | [43,44] |
Cheloniidpox virus 1 | ChePV1 | 2018 | MT799800 | [26] |
Fowlpox virus | FWPV | 2012, 2000 *, 2010 *, 2015, 2016, 2018 *, 2011 #, 2018, 2010 # | MW142017, AF198100 *, AJ581527 *, MH734528, MH719203, MF766430-32, MH709124-25 *, MG702259 #, OK558608-09, KX196452 # | [45,46,47,48,49] |
Flamingopox virus | FGPV | 2008 | MF678796 | [24] |
Magpiepox virus | MPPV | 2018 | MK903864 | [32] |
Magpiepox virus 2 | MPPV2 | 1956 | MW485973 | [50] |
Mudlarkpox virus | MLPV | 2019 | MT978051 | [41] |
Penguinpox virus | PEPV | 1992 | KJ859677 | [51] |
Penguinpox virus 2 | PEPV2 | 1997 | MW296038 | [18] |
Pigeonpox virus | FeP2 | 1992 | KJ801920 | [51] |
Saltwater crocodilepox virus 1 | SwCRV1 | 2017 | MG450915 | [52,53] |
Shearwaterpox virus 1 | SWPV1 | 2015 | KX857216 | [30] |
Shearwaterpox virus 2 | SWPV2 | 2015 | KX857215 | [30] |
Turkeypox virus | TKPV | 2011 | NC_028238 | [54] |
Teiidae poxvirus 1 | TePV-1 | 2019 | MT712273 | [27] |
Avipoxvirus (Abbreviation) | GenBank Accession Number | Genome Identity (%) | Genome Length (kbp) | A+T Content (%) | Number of ORFs | Reference |
---|---|---|---|---|---|---|
Albatrosspox virus 2 (ALPV2) | OK348853 | 286 | 69.1 | 359 | This study | |
Albatrosspox virus (ALPV) | MW365933 | 48.8 | 352 | 71.2 | 336 | [29] |
Canarypox virus (CNPV) | AY318871 | 48.0 | 360 | 69.6 | 328 | [43] |
Fowlpox virus (FWPV) | AF198100 | 99.3 | 289 | 69.1 | 260 | [45] |
Flamingopox virus (FGPV) | MF678796 | 75.0 | 293 | 70.5 | 285 | [24] |
Magpiepox virus (MPPV) | MK903864 | 51.1 | 293 | 70.4 | 301 | [32] |
Magpiepox virus 2 (MPPV2) | MW485973 | 50.8 | 298 | 70.5 | 419 | [50] |
Mudlarkpox virus (MLPV) | MT978051 | 49.0 | 343 | 70.2 | 352 | [41] |
Penguinpox virus (PEPV) | KJ859677 | 76.6 | 307 | 70.5 | 285 | [51] |
Penguinpox virus 2 (PEPV2) | MW296038 | 49.0 | 350 | 69.9 | 327 | [18] |
Pigeonpox virus (FeP2) | KJ801920 | 73.1 | 282 | 70.5 | 271 | [51] |
Shearwaterpox virus 1 (SWPV1) | KX857216 | 52.2 | 327 | 72.4 | 310 | [30] |
Shearwaterpox virus 2 (SWPV2) | KX857215 | 48.4 | 351 | 69.8 | 312 | [30] |
Turkeypox virus (TKPV) | KP728110 | 40.3 | 189 | 70.2 | 171 | [54] |
ALPV2 | FWPV | MPPV2 | MPPV | SWPV2 | SWPV1 | CNPV | PEPV | FeP2 | FGPV | TKPV | Function |
---|---|---|---|---|---|---|---|---|---|---|---|
33 | 16 | 44 | 34 | 28 | 24 | 32 | 19 | 19 | 11 | 001.1a | Ig-like domain |
34 | 17 | 45 | 35 | 29 | 25 | 33 | 20 | 20 | 12 | 2 | V-type Ig domain |
40 | 20 | 53 | 41 | 34 | 28 | 38 | 24 | 24 | 17 | 5 | C4L/C10L protein |
41 | 21 | 54 | 42 | 35 | 29 | 39 | 25 | 25 | 18 | 6 | GPCR |
42 | 22 | 55 | 43 | 36 | 30 | 40 | 26 | 26 | 19 | 7 | Ankyrin repeat |
43 | 23 | 57 | 44 | 37 | 31 | 41 | 27 | 27 | 20 | 8 | Ankyrin repeat |
44 | 24 | 58 | 45 | 38 | 32 | 42 | 28 | 28 | 21 | 9 | Ankyrin repeat |
53 | 30 | 66 | 52 | 44 | 38 | 48 | 35 | 35 | 29 | 12 | Alkaline phosphodiesterase |
54 | 31 | 69 | 55 | 46 | 40 | 50 | 36 | 36 | 30 | 13 | Ankyrin repeat |
60 | 35 | 72 | 58 | 49 | 44 | 53 | 40 | 38 | 34 | 16 | Hypothetical protein |
62 | 37 | 74 | 60 | 51 | 46 | 55 | 41 | 39 | 36 | 17 | Hypothetical protein |
64 | 39 | 77 | 63 | 54 | 49 | 58 | 43 | 41 | 38 | 20 | B-cell lymphoma 2 (Bcl-2) |
65 | 40 | 78 | 64 | 55 | 50 | 59 | 44 | 42 | 39 | 21 | Serpin |
69 | 43 | 81 | 66 | 57 | 52 | 61 | 46 | 44 | 41 | 22 | DNA ligase |
70 | 44 | 82 | 67 | 58 | 53 | 62 | 47 | 45 | 42 | 23 | Serpin family |
71 | 46 | 83 | 68 | 59 | 54 | 63 | 48 | 46 | 43 | 24 | Hydroxysteroid dehydrogenase |
73 | 47 | 87 | 71 | 61 | 56 | 65 | 49 | 47 | 44 | 25 | Semaphorin |
76 | 48 | 92 | 75 | 64 | 59 | 68 | 50 | 48 | 45 | 26 | GNS1/SUR4 |
82 | 54 | 103 | 83 | 72 | 66 | 76 | 56 | 54 | 51 | 32 | mutT motif |
96 | 65 | - | - | 83 | 78 | 88 | 67 | 65 | 64 | 40 | Hypothetical protein |
100 | 68 | 128 | 98 | 87 | 82 | 92 | 70 | 68 | 67 | 42 | Hypothetical protein |
102 | 70 | 130 | 100 | 89 | 84 | 94 | 72 | 70 | 69 | 44 | T10-like protein |
104 | 71 | - | 104 | 92 | 87 | 97 | 75 | 72 | 72 | 46 | Hypothetical protein |
109 | 75 | 140 | 110 | 98 | 92 | 103 | 78 | 77 | 76 | 50 | N1R/p28 |
120 | 86 | 150 | 120 | 108 | 102 | 113 | 89 | 87 | 87 | 60 | Thymidine kinase |
126 | 91 | 156 | 126 | 113 | 107 | 118 | 95 | 93 | 93 | 65 | Hypothetical protein |
127 | 92 | 157 | 127 | 114 | 108 | 119 | 96 | 94 | 94 | 66 | Hypothetical virion core protein |
142 | 104 | 169 | 139 | 126 | 120 | 131 | 108 | 106 | 106 | 75 | Hypothetical protein |
143 | 105 | 170 | 140 | 127 | 121 | 132 | 109 | 107 | 107 | 76 | Hypothetical protein |
149 | 110 | 175 | 145 | 132 | 126 | 137 | 114 | 112 | 112 | 80 | Hypothetical protein |
152 | 113 | 178 | 148 | 135 | 129 | 140 | 117 | 115 | 115 | 83 | Hypothetical protein |
196 | 145 | 243 | 199 | 179 | 167 | 191 | 153 | 146 | 151 | 109 | Hypothetical protein |
203 | 151 | 253 | 209 | 187 | 175 | 199 | 159 | 153 | 157 | 113 | Deoxycytidine kinase |
255 | 190 | 331 | 274 | 250 | 237 | 264 | 203 | 195 | 204 | 140 | A-type inclusion protein |
256 | 191 | 333 | 275 | 251 | 238 | 265 | 204 | 196 | 205 | 141 | A-type inclusion protein |
262 | 196 | 339 | 280 | 256 | 243 | 270 | 210 | 202 | 211 | 144 | Hypothetical protein |
267 | 201 | 343 | 284 | 259 | 247 | 273 | 215 | 207 | 216 | 149 | Hypothetical protein |
269 | 203 | 344 | 285 | 260 | 248 | 274 | 216 | 208 | 217 | 150 | Tyrosine kinase |
271 | 205 | 346 | 287 | 262 | 250 | 276 | 218 | 210 | 219 | 151 | Hypothetical protein |
273 | 207 | 348 | 289 | 264 | 252 | 278 | 220 | 212 | 221 | 151.1a | Hypothetical protein |
277 | 208 | 351 | 292 | 267 | 255 | 281 | 222 | 214 | 224 | 152 | Hypothetical protein |
280 | 211 | 355 | 296 | 271 | 259 | 285 | 225 | 216 | 227 | 153 | Epidermal Growth Factor |
281 | 212 | 356 | 297 | 272 | 260 | 286 | 226 | 217 | 228 | 154 | Serine/threonine protein kinase |
282 | 213 | 357 | 298 | 273 | 261 | 287 | 227 | 218 | 229 | 155 | Hypothetical protein |
284 | 214 | 361 | 300 | 275 | 263 | 289 | 228 | 219 | 230 | 156 | Putative 13.7 kDa protein |
293 | 219 | 370 | 308 | 282 | 272 | 296 | 234 | 226 | 238 | 161 | Ankyrin repeat |
312 | 232 | 394 | 327 | 290 | 283 | 304 | 248 | 238 | 251 | 164 | Ankyrin repeat |
Gene Family | ALPV2 | ALPV | FWPV | MPPV2 | MPPV | PEPV2 | CNPV | SWPV2 | MLPV | SWPV1 | FP9 | PEPV | FeP2 | TKPV | FGPV |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ankyrin Repeat | 33 | 48 | 31 | 78 | 62 | 49 | 51 | 46 | 47 | 50 | 22 | 33 | 26 | 16 | 45 |
B22R | 6 | 6 | 6 | 9 | 7 | 6 | 6 | 7 | 7 | 6 | 5 | 5 | 4 | 1 | 4 |
N1R/p28 | 12 | 28 | 10 | 20 | 24 | 24 | 26 | 20 | 25 | 20 | 8 | 11 | 11 | 3 | 13 |
C4L/C10L | 3 | 3 | 3 | 4 | 2 | 3 | 3 | 3 | 3 | 2 | 3 | 2 | 2 | 2 | 2 |
CC chemokine | 4 | 5 | 4 | 7 | 4 | 5 | 5 | 5 | 5 | 6 | 4 | 1 | 4 | 2 | 6 |
C-type lectin | 8 | 14 | 9 | 11 | 10 | 11 | 11 | 11 | 13 | 13 | 6 | 7 | 4 | 2 | 4 |
G protein-coupled receptor | 3 | 4 | 3 | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 2 | 3 | 2 | 2 | 3 |
HT motif | 6 | 5 | 6 | 5 | 5 | 5 | 5 | 4 | 5 | 4 | 6 | 5 | 4 | 1 | 7 |
Ig-like domain | 6 | 9 | 5 | 13 | 10 | 9 | 9 | 8 | 8 | 9 | 4 | 6 | 4 | 3 | 9 |
Serpin | 6 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 4 | 4 | 3 | 5 |
EFc | 3 | 2 | 3 | 3 | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 1 | 1 | 1 | 1 |
TGF-β | 1 | 5 | 1 | 5 | 4 | 5 | 5 | 4 | 6 | 3 | 1 | 1 | 1 | 1 | 1 |
β-NGF | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 0 | 0 | 2 | 3 |
IL-18 BP | 2 | 3 | 1 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 1 | 1 | 0 | 2 | 0 |
TOTAL | 95 | 139 | 89 | 169 | 144 | 133 | 137 | 124 | 134 | 129 | 71 | 80 | 67 | 41 | 103 |
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Sarker, S.; Bowden, T.R.; Boyle, D.B. Evidence of a Possible Viral Host Switch Event in an Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi). Viruses 2022, 14, 302. https://doi.org/10.3390/v14020302
Sarker S, Bowden TR, Boyle DB. Evidence of a Possible Viral Host Switch Event in an Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi). Viruses. 2022; 14(2):302. https://doi.org/10.3390/v14020302
Chicago/Turabian StyleSarker, Subir, Timothy R. Bowden, and David B. Boyle. 2022. "Evidence of a Possible Viral Host Switch Event in an Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)" Viruses 14, no. 2: 302. https://doi.org/10.3390/v14020302
APA StyleSarker, S., Bowden, T. R., & Boyle, D. B. (2022). Evidence of a Possible Viral Host Switch Event in an Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi). Viruses, 14(2), 302. https://doi.org/10.3390/v14020302