Table 2.
Main findings from studies reporting (A) HPV phylogenetic variants distribution in head and neck tumors from 2000 to 2023, including those exploring also (B) specific SNPs in E6 and E7 viral oncogenes.
| (A) | |||||||
|---|---|---|---|---|---|---|---|
| Variant Classification System |
Reference | Year | Country | Typing Method | HPV16 Gene | HPV16 Lineages and Number (n) of Cases |
Cancer Specimen and Total Sample Size Number (n) |
| Geographical | [27] | 2000 | USA | Sanger sequencing |
E6 | European prototype (n = 39) Asian (n = 9) North American (n = 2) African 1 (n = 2) |
HNSCC (n = 253) |
| Geographical | [28] | 2007 | Italy | Sanger sequencing |
E6 | European-German (n = 9) African 2 (n = 2) Asian American (n = 1) Unclassified (n = 1) |
HNSCC (n = 115) |
| Geographical | [29] | 2008 | USA | Sanger sequencing |
E6 | European (n = 13) Asian (n = 1) |
HNSCC (n = 135) |
| Geographical | [30] | 2014 | Italy | Sanger sequencing |
L1 | European (n = 41) African (n = 10) |
OPSC (n = 81) |
| Geographical | [31] | 2016 | Brazil | Sanger Sequencing |
LCR-E6 | European (n = 12) Asian American (n = 9) |
HNSCC (n = 186) |
| Geographical | [32] | 2018 | USA | Sanger Sequencing |
E6-E7 | European (n = 77) Asian (n = 6) African 1A (n = 1) African 2A (n = 1) African 2B (n = 1) North American (n = 2) Asian American 1 (n = 2) Asian American 2 (n = 2) |
OPSCC (n = 226) |
| Alphanumeric | [24] | 2021 | Japan | Sanger sequencing |
LCR-E6 | A4 (n = 12) A1/A2/A3 (n = 8) D (n = 2) A5 (n = 2) |
OPSCC (n = 91) |
| Alphanumeric | [33] | 2021 | USA | NGS | WG | A1 (n = 112) A2 (n = 63) A3 (n = 3) A4 (n = 14) C (n = 1) D1 (n = 1) D3 (n = 13) D4 (n = 2) |
OPC (n = 259) |
| Alphanumeric | [34] | 2022 | USA | NGS | WG | A1 (n = 215) A2 (n = 107) A3 (n = 3) A4 (n = 22) B1 (n = 1) C1 (n = 6) D1 (n = 1) D2 (n = 2) D3 (n = 25) D4 (n = 2) |
OPSCC (n = 460) |
| Alphanumeric | [35] | 2022 | Greece | Sanger sequencing | E6 | A3 (n = 34) D1 (n = 6) |
HNSCC (n = 40) |
| Alphanumeric | [36] | 2023 | Canada | Sanger sequencing | E6 | A1 (n = 38) A2 (n = 54) D2-D3 (n = 2) |
HNSCC (n = 94) |
| (B) | |||||||
| Reference | Year | Country | Typing Method | HPV16 Gene |
E6 and E7 SNPs
AA Change and Number (n) of Cases |
Cancer
Specimen and Total Sample Size Number (n) |
|
| [37] | 2004 | Germany | Sanger sequencing |
E6-E7 | 350T (n = 6) T350G (L83V) (n = 8) A131G (R10G)/C712A (H51N) (n = 7) |
HNSCC (n = 24) | |
| [29] | 2008 | USA | Sanger sequencing |
E6 | E-350T (n = 6) E-350G (L83V) (n = 4) E-T131G (R10G) (n = 2) |
HNSCC (n = 135) | |
| [38] | 2009 | Italy | Sanger sequencing |
E6 | T350G (L83V) (n = 5) | UADT (n = 77) |
|
| [39] | 2012 | Sweden | Sanger sequencing |
E6 | E-A131G (R10G) (n = 21) E-T350G (L83V) (n = 43) |
TSCC (n = 108) | |
| [40] | 2015 | Japan | Sanger sequencing |
E6 | E-350T (n = 2) E-350G (L83V) (n = 8) |
TSCC (n = 24) | |
| [32] | 2018 | USA | Sanger sequencing |
E6-E7 | 7392G (L90V) (n = 12) 7173G (R17G) (n = 4) 7754A (H51N) (n = 2) |
OPSCC (n = 226) |
|
| [35] | 2022 | Greece | Sanger sequencing |
E6 | T350G (L83V) (n = 33) | HNSCC (n = 40) | |
| [36] | 2023 | Canada | Sanger sequencing |
E6 | 350T (n = 33) 350G (L83V) (n = 40) |
HNSCC (n = 94) |
|
HNSCC: head and neck squamous cell carcinoma; UADT: upper aerodigestive tract; OPC: oropharyngeal cancer; OPSCC: oropharyngeal squamous cell carcinoma; TSCC: tonsillar squamous cell carcinoma.; WG: whole genome; NGS: next generation sequening.