TABLE 2.
Sequence analysis of viral genomes
| Virus | Family | Genomeb
|
CpG motif deviation (%)a
|
CpG indexh | |||||
|---|---|---|---|---|---|---|---|---|---|
| Total CpGe | Consensus motifc
|
||||||||
| Methylated | Size (kb) | G+C (%) | CpG per kbd | Stimulatoryf | Inhibitoryg | ||||
| HHV1 (HSV-1) | Alpha | No | 152.3 | 68.3 | 235.4 | 100.9 | 104.9 | 94.8 | 24.0 |
| HHV2 (HSV-2) | Alpha | No | 154.7 | 70.4 | 262.1 | 105.8 | 106.2 | 96.9 | 25.8 |
| HHV3 (VZV) | Alpha | Noj | 124.9 | 46.0 | 120.2 | 113.5 | 126.8 | 123.3 | 4.8 |
| HHV4 (EBV) | Gamma | Yes | 172.3 | 59.9 | 107.4 | 59.8 | 56.4 | 71.0 | −9.4i |
| HHV5 (HCMV) | Beta | Yes/no | 229.4 | 57.2 | 194.2 | 118.9 | 138.3 | 101.9 | 84.0 |
| HVS | Gamma | Yes | 112.9 | 34.5 | 19.6 | 33.0 | 43.3 | 26.7 | 1.1 |
| BHV-1 | Alpha | No | 135.3 | 72.4 | 311.9 | 118.9 | 134.1 | 94.0 | 148.7 |
| Adenovirus (serotype 5) | No | 35.9 | 55.2 | 134.4 | 88.2 | 88.3 | 80.9 | 8.8 | |
| Adenovirus (serotype 12) | No | 34.1 | 46.5 | 87.9 | 81.2 | 116.6 | 74.4 | 30.1 | |
Deviations in specified motif occurrences relative to those expected based on genomic G+C content.
GenBank accession numbers for genomes analyzed are HSV-1, GI9629378; HSV-2, GI9629267; VZV, GI9625875; EBV, GI9625578; human cytomegalovirus (HCMV), GI9625671; HVS, GI60230; hepatitis A virus type 5 (HAV-5), GI9626187; HAV-12, GI9626621; and BHV-1, GI2653291.
Consensus stimulatory and inhibitory CpG hexamer motifs are based on published analysis (31, 32). They are used in this table as indicators of the general frequencies of stimulatory and inhibitory CpG hexamer motifs in each genome.
Number of CpG hexamer motifs (NNCGNN) occurring in each genome normalized to 100 kb.
Total frequency of CpG hexamer motifs (NNCGNN); expected number based on nucleotide composition of the genome.
Frequency of consensus stimulatory hexamer motifs (RRCGYY).
Frequency of consensus inhibitory hexamer motifs (NCCGNN and NNCGRN).
Calculated from frequencies of stimulatory less inhibitory consensus hexamer motifs as an indicator of stimulation versus inhibition multiplied by total CpG number (normalized to 1 kb) and the overall frequency of CpG (NNCGNN). As an example, the CpG index for HSV-1 is (1.049-0.948) × 235.4 × 1.009 = 24.0.
The EBV CpG index is negative, since the frequency of inhibitory motifs exceeds the frequency of stimulatory motifs.
Presumed nonmethylated based on other alphaherpesviruses.