Table 4.
Classification of low-risk complete HPV genomes sequenced in our study.
| Species | HPV Type | Genomes Sequenced | No. of Genomes on NCBI 1 | No. of Genomes Used 2 | Genome Size 3 | GC Content (%) | Existing Lineage/Sublineage Sequenced | Novel Lineage/Sublineage Proposed |
|---|---|---|---|---|---|---|---|---|
| α-10 | HPV6 | 4 | 214 | 4 | 8020–8032 | 40 | B1, B3 | – |
| α-6 | HPV30 | 2 | 17 | 6 | 7843–7881 | 40 | A2–A3 | – |
| α-11 | HPV34 | 4 | 17 | 5 | 7668–7788 | 37–38 | A2, C2 | D |
| α-8 | HPV40 | 3 | 4 | 4 | 7905–7909 | 43 | – | A2–A4 |
| α-1 | HPV42 | 21 | 8 | 8 | 7901–7920 | 39 | A1, A2 | A3, B, C |
| α-8 | HPV43 | 2 | 2 | 2 | 7986–8007 | 40 | – | B1–B2 |
| α-10 | HPV44 | 3 | 6 | 6 | 7822–7837 | 40–41 | A, B | – |
| α-6 | HPV53 | 21 | 29 | 7 | 7859–7864 | 40 | A, C, D1–D2 | – |
| α-13 | HPV54 | 6 | 12 | 5 | 7760–7776 | 41 | A2 | D |
| α-3 | HPV61 | 1 | 12 | 4 | 7989 | 46 | – | A3 |
| α-3 | HPV62 | 3 | 4 | 4 | 8092–8092 | 45–46 | A1 | A2 |
| α-9 | HPV67 | 12 | 12 | 3 | 7806–7809 | 38 | B1 | B2 |
| α-11 | HPV73 | 7 | 16 | 3 | 7694–7716 | 36 | A2, B | C |
| α-7 | HPV70 | 2 | 10 | 2 | 7905–7911 | 40 | A | – |
| α-10 | HPV74 | 3 | 1 | 1 | 7893–7902 | 40–41 | – | B, C |
| α-5 | HPV82 | 2 | 22 | 10 | 7868–7874 | 40 | A3, B1 | – |
| α-3 | HPV84 | 2 | 1 | 1 | 7956–7974 | 46 | – | B1–B2 |
| α-3 | HPV87 | 4 | 4 | 4 | 7998–8001 | 45 | A1 | – |
| α-3 | HPV89 | 1 | 4 | 4 | 8072 | 45 | A2 | – |
| α-14 | HPV90 | 7 | 3 | 8016–8032 | 46 | A1 | A3, B | |
| α-8 | HPV91 | 4 | 1 | 1 | 7959–7959 | 40 | – | A2 |
| γ-6 | HPV101 | 2 | 1 | 1 | 7258–7259 | 43 | – | B, C |
| γ-6 | HPV103 | 1 | 1 | 1 | 7263 | 41 | – | – |
| γ-6 | HPV108 | 4 | 1 | 1 | 7158–7158 | 42 | – | B |
| γ-6 | HPV214 | 1 | 1 | 1 | 7357 | 41 | – | – |
| γ-6 | HPV226 | 2 | 1 | 1 | 7313–7315 | 42 | B | |
| γ-13 | HPV213 | 1 | - | 7096 | 39 | – | – |
GC Content, guanine-cytosine content. 1 Total number of complete genomes available on NCBI/GenBank. 2 Number of genomes downloaded from NCBI for the analysis. 3 Size of genomes sequenced in the study. For genotypes with established lineages/sublineages in PaVE only reference variants were used. For genotypes with no established lineages/sublineages in PaVE all complete genomes available in NCBI were used. See Supplementary Table S2 for the list of downloaded genomes.