TABLE 1.
Major differences in ORF sizes between VACV-IOC clonesa
| Gene or gene fragmentb | Description/putative function | Ortholog(s)c | Length of genes or gene fragments (bp) |
||||
|---|---|---|---|---|---|---|---|
| B141 | B388 | VACV-WR | VACV-Cop | Other OPVd | |||
| IOC_001/255 | Hypothetical protein | VARV-Gar_1966-209/HSPV-001 | 255 | 429 (VARV)/219 (HSPV) | |||
| IOC_002/254 | Hypothetical protein | HSPV-001 | 147 | 147 | 219 (HSPV) | ||
| IOC_003/253 | Chemokine-binding protein | Cop-C23L/WR-001 | 681 | 711 | 735 | 735 | 747 (HSPV) |
| IOC_004/252 | TNF-α receptor | WR-002 | 192 | 186 | 1,050 (HSPV) | ||
| IOC_005/251 | TNF-α receptor | WR-002 | 105 | 105 | 186 | ||
| IOC_006/250 | TNF-α receptor | Cop-C22L/WR-004 | 360 | 342 | 369 | 369 | 1,050 (HSPV) |
| IOC_008/248 | Ankyrin-like protein | Cop-C21L/WR-006 | 201 | 201 | 195 | 342 | 1,764 (HSPV) |
| IOC_009/247 | Ankyrin-like protein | Cop-C21L/WR-006 | 141 | 141 | |||
| IOC_010/246 | Ankyrin-like protein | Cop-C18L/WR-007 | 186 | 186 | 330 | 453 | 2,019 (CPXV-GRI) |
| IOC_011/245 | Ankyrin-like protein | Cop-C17L | 318 | 318 | 1,161 | 1,194 (HSPV) | |
| IOC_012/244 | Ankyrin-like protein | Cop-C17L | 192 | 192 | |||
| IOC_013/243 | Ankyrin-like protein | Cop-C17L | 702 | 702 | |||
| IOC_014/242 | Predicted Bcl-2 protein | Cop-C16L | 531 | 522 | 546 | 462 (HSPV) | |
| IOC_015 | Hypothetical protein | HSPV-228 | 123 | 123 | 204 (HSPV) | ||
| IOC_016 | Hypothetical protein | Cop-C15L | 258 | 258 | 276 | ||
| IOC_019 | IL-1 receptor antagonist; binds to (PHD)2 protein; DNA-PK binding protein | Cop-C10L/WR-010 | 279 | 279 | 996 | 996 | 996 (HSPV) |
| IOC_020 | IL-1 receptor antagonist; binds to (PHD)2 protein; DNA-PK binding protein | Cop-C10L/WR-010 | 573 | 573 | |||
| IOC_021 | Ubiquitin ligase | WR-011 | 252 | 252 | 546 | 729 (CPX-GRI) | |
| IOC_023 | Interleukin-18-binding protein | WR-013 | 363 | 381 | 381 | 381 (HSPV) | |
| IOC_024 | Ankyrin-like protein | WR-014 | 273 | 273 | 714 | 2,007 (CPXV-GRI) | |
| IOC_025 | Ankyrin-like protein | WR-014 | 525 | 414 | |||
| IOC_027 | Ankyrin-like protein | WR-016 and WR-017 | 747 | 384 | 234 and 216 | 1,179 (VARV) | |
| IOC_028 | Ankyrin-like protein | Cop-C9L/WR-019 | 924 | 924 | 1,905 | 1,905 | 1,905 (HSPV) |
| IOC_029 | Ankyrin-like protein | Cop-C9L/WR-019 | 153 | 153 | |||
| IOC_030 | Ankyrin-like protein | Cop-C9L/WR-019 | 207 | ||||
| IOC_031 | Ankyrin-like protein | Cop-C9L/WR-019 | 684 | 495 | |||
| IOC_035 | Predicted Bcl-2 protein; IRF3 inhibitor | Cop-C6L/WR-022 | 270 | 261 | 456 | 456 | 468 (HSPV) |
| IOC_036 | Predicted Bcl-2 protein; IRF3 inhibitor | Cop-C6L/WR-022 | 126 | 126 | |||
| IOC_038 | Putative IL-1 receptor antagonist; NF-kB inhibitor | Cop-C4L/WR-024 | 189 | 189 | 951 | 951 | 951 (VARV) |
| IOC_039 | Putative IL-1 receptor antagonist; NF-kB inhibitor | Cop-C4L/WR-024 | 231 | 231 | |||
| IOC_040 | Putative IL-1 receptor antagonist; NF-kB inhibitor | Cop-C4L/WR-024 | 123 | 123 | |||
| IOC_041 | Putative IL-1 receptor antagonist; NF-kB inhibitor | Cop-C4L/WR-024 | 120 | 120 | |||
| IOC_042 | Secreted complement C3b/C4b-binding protein | Cop-C3L/WR-025 | 393 | 792 | 792 | 792 (HSPV) | |
| IOC_043 | Secreted complement C3b/C4b-binding protein | Cop-C3L/WR-025 | 189 | 786 | |||
| IOC_044 | POZ/BTB kelch domain protein | Cop-C2L/WR-026 | 105 | 105 | 1,539 | 1,539 | 1,539 (HSPV) |
| IOC_045 | POZ/BTB kelch domain protein | Cop-C2L/WR-026 | 534 | 534 | |||
| IOC_046 | POZ/BTB kelch domain protein | Cop-C2L/WR-026 | 813 | 813 | |||
| IOC_049 | Predicted Bcl-2 protein; IRF3 inhibitor | Cop-N2L/WR-029 | 513 | 513 | 528 | 528 | 534 (VARV) |
| IOC_050 | Ankyrin-like protein | Cop-M1L/WR-030 | 198 | 198 | 1,419 | 1,419 | 1,341 (VARV) |
| IOC_051 | Ankyrin-like protein | Cop-M1L/WR-030 | 645 | 645 | |||
| IOC_052 | Ankyrin-like protein | Cop-M1L/WR-030 | 474 | 474 | |||
| IOC_055 | Serine protease inhibitor-3 (SPI-3) | Cop-K2L/WR-033 | 1,095 | 1,095 | 1,110 | 1,110 | 1,122 (HSPV) |
| IOC_056 | eIF2 alpha-like PKR inhibitor | Cop-K3L/WR-034 | 183 | 267 | 267 | 267 (HSPV) | |
| IOC_057 | eIF2 alpha-like PKR inhibitor | Cop-K3L/WR-034 | 183 | 267 | |||
| IOC_063 | Predicted Bcl-2 protein; apoptosis inhibitor | Cop-F1L/WR-040 | 462 | 462 | 681 | 681 | 765 (HSPV) |
| IOC_064 | Predicted Bcl-2 protein; apoptosis inhibitor | Cop-F1L/WR-040 | 207 | 204 | |||
| IOC_093 | Involved in sustained ERK1/2 activation | Cop-O1L/WR-068 | 1,992 | 1,992 | 2,001 | 2,001 | 2,001 (HSPV) |
| IOC_134 | Virion core protein | Cop-D3R/WR-108 | 702 | 702 | 714 | 714 | 714 (HSPV) |
| IOC_149 | 39-kDa core protein | Cop-A4L/WR-123 | 840 | 822 | 846 | 846 | 852 (CPXV-GRI) |
| Cowpox A-type inclusion protein | Cop A25L/WR-145 | 198 | 198 | 213 (HSPV) | |||
| IOC_171 | Cowpox A-type inclusion protein | WR-146 | 180 | 180 | 465 | 612 (HSPV) | |
| IOC_185 | WV transmembrane phosphoprotein | Cop-A36R/WR-159 | 639 | 630 | 666 | 666 | 672 (HSPV) |
| IOC_189 | Semaphorin-like protein | Cop-A39R/WR-163 | 681 | 642 | 888 | 1,212 | 981 (HSPV) |
| IOC_190 | Semaphorin-like protein | Cop-A39R/WR-164 | 258 | 258 | 429 | ||
| IOC_191 | Semaphorin-like protein | Cop-A39R/WR-164 | 123 | 123 | |||
| IOC_193 | Chemokine binding protein | Cop-A41L/WR-166 | 639 | 639 | 660 | 660 | 657 (VARV) |
| IOC_204 | associates with and stabilizes ubiquitin | Cop-A51R/WR-177 | 210 | 210 | 1,005 | 1,005 | 1,005 (VARV) |
| IOC_205 | Associates with and stabilizes ubiquitin | Cop-A51R/WR-177 | 540 | 540 | |||
| IOC_208 | Secreted TNF-receptor-like protein; CrmC | Cop-A53R/WR-179 | 303 | 303 | 312 | 312 | 969 (CPX-GRI) |
| IOC_209 | kelch-like protein | Cop-A55R/WR-180 | 255 | 255 | 1,695 | 1,695 | 1,695 (HSPV) |
| IOC_210 | kelch-like protein | Cop-A55R/WR-180 | 1,416 | 1,416 | |||
| IOC_211 | Hemagglutinin | Cop-A56R/WR-181 | 927 | 927 | 945 | 948 | 945 (CPXV-GRI) |
| IOC_216 | schlafen-like protein | Cop-B3R/WR-185 | 183 | 183 | 504 | 375 | 375 (HSPV) |
| IOC_227 | Serine protease inhibitor (SPI-2/CrmA) | Cop-B13R/WR-195 | 351 | 351 | 1,038 | 351 | 1,038 (HSPV) |
| IOC_228 | Serine protease inhibitor (SPI-2/CrmA) | Cop-B14R/WR-195 | 144 | 144 | 669 | ||
| IOC_229 | Serine protease inhibitor (SPI-2/CrmA) | Cop-B14R/WR-195 | 534 | 534 | |||
| IOC_235 | Ankyrin-like protein | Cop-B20R/WR-202/WR-203 | 162 | 162 | 384 | 2,376 (HSPV) | |
| 930 | |||||||
| IOC_236 | IL-1 receptor antagonist; DNA-PK binding protein; binds to (PHD)2 protein | Cop-C10L/WR-209 | 573 | 996 | 996 | 996 (HSPV) | |
| IOC_237 | IL-1 receptor antagonist; DNA-PK binding protein; binds to (PHD)2 protein | Cop-C10L/WR-209 | 279 | ||||
| IOC_238 | Secreted epidermal growth factor-like | Cop-C11R/WR-009; WR-210 | 423 | 423 | 429 | 423 (HSPV) | |
| IOC_239 | Serine protease inhibitor (Serpin)-1 (SPI-1) | Cop-C12L/WR-205 | 1,062 | 1,062 | 1,074 (HSPV) | ||
a
The table lists only major differences in ORF length among VACV-IOC clones B141, B388, and other orthopoxviruses. The complete list of ORFs annotated in the genomes of B141 and B388 is shown in Table S2 in the supplemental material.
b
ORFs located in both ITRs (ITR paralogs) are indicated after a slash. ORFs in boldface are full-length or near-full-length genes in either one or both IOC clones. All other ORFs correspond to truncated genes or gene fragments.
c
Orthologs in VACV-Cop and VACV-WR are indicated. In the absence of those, the best matching sequence is indicated.
d
ORF size in other Orthopoxvirus (OPV) members is indicated for comparison with full-length (or near-full-length) genes. VARV, variola virus; CPXV-GRI, cowpox virus strain GRI.