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Human papillomavirus type 16 long control region and E6 variants stratified by cervical disease stage.

Marongiu L, Godi A, Parry JV, Beddows S - Infect. Genet. Evol. (2014)

Bottom Line: Almost all samples (110/112; 98%) were assigned to the EUR lineage, one sample was classified as European-Asian (EAS) and another African (Afr1a).None of these sites, however, including the T350G non-synonymous (L83V) substitution in E6, alone or in combination, were found to be associated with cervical disease stage.Monitoring intra-lineage, site-specific variants, such as T350G, is unlikely to be of diagnostic value.

View Article: PubMed Central - PubMed

Affiliation: Virus Reference Department, Public Health England, London, UK.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic distribution of LCR–E6 variants. Radial neighbor-joining phylogenetic trees derived using the HPV16 LCR–E6 EUR variants from this study (n = 112) and (A) worldwide (n = 353) or (B) only background EUR variants (n = 145) (Cornet et al., 2012). The geographical source of each sequence is represented by colored dot, as indicated by the key. Variant lineages are indicated as follows: European (EUR), European-Asian (EAS), African 1 (Afr1a, Afr1b), African 2 (Afr2a, Afr2b), Asian-American (AA1 and AA2) and North-American (NA). EUR branches indicated in gray had less than 50% bootstrap support (500 iterations). Variant sites that form the majority of the sequences within each potential sub-cluster within the EUR variant lineage are indicated, with minority site-specific variants indicated in gray text.
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f0005: Phylogenetic distribution of LCR–E6 variants. Radial neighbor-joining phylogenetic trees derived using the HPV16 LCR–E6 EUR variants from this study (n = 112) and (A) worldwide (n = 353) or (B) only background EUR variants (n = 145) (Cornet et al., 2012). The geographical source of each sequence is represented by colored dot, as indicated by the key. Variant lineages are indicated as follows: European (EUR), European-Asian (EAS), African 1 (Afr1a, Afr1b), African 2 (Afr2a, Afr2b), Asian-American (AA1 and AA2) and North-American (NA). EUR branches indicated in gray had less than 50% bootstrap support (500 iterations). Variant sites that form the majority of the sequences within each potential sub-cluster within the EUR variant lineage are indicated, with minority site-specific variants indicated in gray text.

Mentions: LCR–E6 sequences were generated from 112 liquid-based cytology samples singly infected with HPV16. To ascertain the variant lineage of these sequences, we initially aligned the LCR fragment with 353 LCR sequences from a recent study on the global distribution of HPV16 variants (Cornet et al., 2012) (Fig. 1A). Almost all (110/112, 98%) sequences from this present study were of the European (EUR) variant lineage apart from one sequence that aligned with the EAS variant lineage and one sequence that aligned with the Afr1a variant lineage. These two sequences were removed from further analysis. The remaining 110 EUR LCR–E6 sequences were then aligned with 145 global EUR LCR–E6 sequences (Cornet et al., 2012), to identify any potential sub-lineages (Fig. 1B). Sub-clustering within the EUR lineage was only weakly supported, with bootstrap values ranging between 50% and 70%.


Human papillomavirus type 16 long control region and E6 variants stratified by cervical disease stage.

Marongiu L, Godi A, Parry JV, Beddows S - Infect. Genet. Evol. (2014)

Phylogenetic distribution of LCR–E6 variants. Radial neighbor-joining phylogenetic trees derived using the HPV16 LCR–E6 EUR variants from this study (n = 112) and (A) worldwide (n = 353) or (B) only background EUR variants (n = 145) (Cornet et al., 2012). The geographical source of each sequence is represented by colored dot, as indicated by the key. Variant lineages are indicated as follows: European (EUR), European-Asian (EAS), African 1 (Afr1a, Afr1b), African 2 (Afr2a, Afr2b), Asian-American (AA1 and AA2) and North-American (NA). EUR branches indicated in gray had less than 50% bootstrap support (500 iterations). Variant sites that form the majority of the sequences within each potential sub-cluster within the EUR variant lineage are indicated, with minority site-specific variants indicated in gray text.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4150919&req=5

f0005: Phylogenetic distribution of LCR–E6 variants. Radial neighbor-joining phylogenetic trees derived using the HPV16 LCR–E6 EUR variants from this study (n = 112) and (A) worldwide (n = 353) or (B) only background EUR variants (n = 145) (Cornet et al., 2012). The geographical source of each sequence is represented by colored dot, as indicated by the key. Variant lineages are indicated as follows: European (EUR), European-Asian (EAS), African 1 (Afr1a, Afr1b), African 2 (Afr2a, Afr2b), Asian-American (AA1 and AA2) and North-American (NA). EUR branches indicated in gray had less than 50% bootstrap support (500 iterations). Variant sites that form the majority of the sequences within each potential sub-cluster within the EUR variant lineage are indicated, with minority site-specific variants indicated in gray text.
Mentions: LCR–E6 sequences were generated from 112 liquid-based cytology samples singly infected with HPV16. To ascertain the variant lineage of these sequences, we initially aligned the LCR fragment with 353 LCR sequences from a recent study on the global distribution of HPV16 variants (Cornet et al., 2012) (Fig. 1A). Almost all (110/112, 98%) sequences from this present study were of the European (EUR) variant lineage apart from one sequence that aligned with the EAS variant lineage and one sequence that aligned with the Afr1a variant lineage. These two sequences were removed from further analysis. The remaining 110 EUR LCR–E6 sequences were then aligned with 145 global EUR LCR–E6 sequences (Cornet et al., 2012), to identify any potential sub-lineages (Fig. 1B). Sub-clustering within the EUR lineage was only weakly supported, with bootstrap values ranging between 50% and 70%.

Bottom Line: Almost all samples (110/112; 98%) were assigned to the EUR lineage, one sample was classified as European-Asian (EAS) and another African (Afr1a).None of these sites, however, including the T350G non-synonymous (L83V) substitution in E6, alone or in combination, were found to be associated with cervical disease stage.Monitoring intra-lineage, site-specific variants, such as T350G, is unlikely to be of diagnostic value.

View Article: PubMed Central - PubMed

Affiliation: Virus Reference Department, Public Health England, London, UK.

No MeSH data available.


Related in: MedlinePlus