Table 3.
Recurring endogenous retrovirus-like sequences in bovine CNAs
| No. of non-infected animals (no. of total sequence occurrences) | No. of infected animals (no. of total sequence occurrences) | Best homology | Best murine homology | CNA contains stop codon in-frame | Present in bovine genome (>95% DNA ID) | |
|---|---|---|---|---|---|---|
| (a) | 0 (0) | 5 (12) | 10−47 gag/pol protein (Populus trichocarpa) | 10−14 putative gag-pro-pol polyprotein (xenotropic murine leukemia virus) | No | No |
| (b) | 5 (5) | 0 (0) | 10−18 predicted pol polyprotein from transposon 297, partial (Canis familiaris) | 10−11 pol protein (Recombinant M-MuLV/RaLV retrovirus) | No | Truncated match |
| 5 (5) | 3 (3) | 10−29 predicted protein (Homo sapiens) | 10−23 polymerase (murine leukemia virus) | No | Truncated match | |
| 2 (2) | 5 (4) | 10−37 gag protein (Bos taurus) | 10−10 gag polyprotein (xenotropic murine leukemia virus) | No | Yes | |
| (c) | 2 (4) | 4 (5) | 10−23 pol protein (human endogenous retrovirus HCML-ARV) | 10−19 gag-pol polyprotein (murine leukemia virus) | Yes | Truncated match |
| 5 (7) | 8 (10) | 10−49 polyprotein (multiple sclerosis associated retrovirus) | 10−34 pol polypeptide (murine leukemia virus) | Yes | Yes | |
| 2 (2) | 3 (3) | 10−8 pol protein (human endogenous retrovirus HCML-ARV) | 10−6 pol polypeptide (murine leukemia virus) | Yes | Yes |
(a) One pol-like sequence was found exclusively in (5 of 16) infected animals, but may not be endogenous to cattle as it is not found in the current version of the draft bovine genome (13 September 2007). (b) One pol-like sequence was found exclusively in non-infected animals (5 of 13). (c) One gag-like and four pol-like sequences are recurrent in both PrPres-infected and non-infected populations, indicating that some endogenous retrovirus sequences are consistently detectable regardless of prion exposure.