Entire genome characterization of human papillomavirus type 16 from infected Thai women with different cytological findings

Lurchachaiwong, Woradee; Junyangdikul, Pairoj; Payungporn, Sunchai; Chansaenroj, Jira; Sampathanukul, Pichet; Tresukosol, Damrong; Termrungruanglert, Wichai; Theamboonlers, Apiradee; Poovorawan, Yong

doi:10.1007/s11262-009-0363-0

Cited by 14 publications

(17 citation statements)

References 38 publications

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“…1 ). In contrast to existing data on HPV16 variants, HPV16 in Thailand was more closely related to the European than the Asian-American and the African types [17] . Thus, our study showed that HPV18 variants in Thailand related two distinct groups of HPV18 variants (European and Asian-American types).…”

Section: Hpv18 In Different Cytological Findingscontrasting

confidence: 99%

“…Hence, it does not affect the function of the L1 gene. In addition, the proteins displaying most nonsynonymous amino acids were detected in E2 and L2 as reported for HPV16 in a previous study [17] . López-Saavedra et al [19] indicated that the E2 viral protein is essential for regulating LCR activity and transcription of viral genes.…”

Section: Hpv18 In Different Cytological Findingssupporting

confidence: 77%

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Whole-Genome Sequence Analysis of Human Papillomavirus Type 18 from Infected Thai Women

Lurchachaiwong

Junyangdikul²,

Termrungruanglert³

et al. 2010

Intervirology

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Objective: The aim of this study was to attain molecular knowledge of human papillomavirus type 18 (HPV18) by sequencing the whole genome of HPV18 isolated from Thai women at various clinical stages of disease progression. Method: Our group analyzed 9 samples of whole-genome HPV18 in infected women ranging from normal to cervical cancer by PCR, a sequencing method and bioinformatics programs. Results: Phylogenetic analysis based on the whole genome showed that HPV18 samples were more closely related to the European and Asian-American type than the African type. The vaccine strain’s L1 nucleotide (US patent 5820870) showed a close relationship to the African type. However, our data cannot indicate the correlation between cytological data and nucleotide or amino acid variation. Conclusion: Our group cannot draw any inference between the clinical stage of disease progression and amino acid alterations as there were only 1 or 2 samples available for each clinical trial. However, we hope that these new data on the HPV genome, which are representative of the entire genome of HPV in Southeast Asia, can serve as basis data for future research on the pathogenesis of cervical cancer. Additionally, the second-generation HPV18 vaccines should be tested on both HPV18-L1 and HPV18-L2 for increasing potential protection.

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Section: Hpv18 In Different Cytological Findingscontrasting

confidence: 99%

Section: Hpv18 In Different Cytological Findingssupporting

confidence: 77%

Whole-Genome Sequence Analysis of Human Papillomavirus Type 18 from Infected Thai Women

Lurchachaiwong

Junyangdikul²,

Termrungruanglert³

et al. 2010

Intervirology

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“…However, the majority of variations of the whole genome found within the E1-1374 ∧ 63nt variants in this study were also found in four studies that sequenced the whole genomes of 7 [32], 12 [48], 62 [17] and 98 samples [15]. These four studies detected 20 of 29 variations found in the E1-1374 ∧ 63nt variant and the majority of variations were observed in all 4 studies.…”

Section: Discussionsupporting

confidence: 65%

Characterization and Whole Genome Analysis of Human Papillomavirus Type 16 E1-1374∧63nt Variants

et al. 2012

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Background The variation of the most common Human papillomavirus (HPV) type found in cervical cancer, the HPV16, has been extensively investigated in almost all viral genes. The E1 gene variation, however, has been rarely studied. The main objective of the present investigation was to analyze the variability of the E6 and E1 genes, focusing on the recently identified E1-1374 ∧ 63nt variant. Methodology/Principal Findings Variation within the E6 of 786 HPV16 positive cervical samples was analyzed using high-resolution melting, while the E1-1374 ∧ 63nt duplication was assayed by PCR. Both techniques were supplemented with sequencing. The E1-1374 ∧ 63nt duplication was linked with the E-G350 and the E-C109/G350 variants. In comparison to the referent HPV16, the E1-1374 ∧ 63nt E-G350 variant was significantly associated with lower grade cervical lesions (p = 0.029), while the E1-1374 ∧ 63nt E-C109/G350 variant was equally distributed between high and low grade lesions. The E1-1374 ∧ 63nt variants were phylogenetically closest to E-G350 variant lineage (A2 sub-lineage based on full genome classification). The major differences between E1-1374 ∧ 63nt variants were within the LCR and the E6 region. On the other hand, changes within the E1 region were the major differences from the A2 sub-lineage, which has been historically but inconclusively associated with high grade cervical disease. Thus, the shared variations cannot explain the particular association of the E1-1374 ∧ 63nt variant with lower grade cervical lesions. Conclusions/Significance The E1 region has been thus far considered to be well conserved among all HPVs and therefore uninteresting for variability studies. However, this study shows that the variations within the E1 region could possibly affect cervical disease, since the E1-1374 ∧ 63nt E-G350 variant is significantly associated with lower grade cervical lesions, in comparison to the A1 and A2 sub-lineage variants. Furthermore, it appears that the silent variation 109T>C of the E-C109/G350 variant might have a significant role in the viral life cycle and warrants further study.

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“…This variant has been identified also in other East Asian countries, such as China (8.0–14.5% of all HPV‐16 strains isolated in the reports), Korea (3.5–5.4%), and Hong Kong (3.1%), but very seldom in other areas [Chan et al, 2002; de Boer et al, 2004; Tornesello et al, 2004; Choi et al, 2007; Qiu et al, 2007; Lurchachaiwong et al, 2009; Lee et al, 2011]. The HPV‐16 European (Prototype) variant with E6 L83V, D113D, and E7 L28F was found only in Japan in the current study and has been reported in Thailand [Lurchachaiwong et al, 2009]. The HPV‐16 variant with E7 N29S, one of the essential mutations for the European (Asian) sublineages, was identified in 80.6% of Japanese HPV‐16 strains (n = 31).…”

Section: Discussionmentioning

confidence: 99%

“…The HPV‐16 variant with E7 N29S, one of the essential mutations for the European (Asian) sublineages, was identified in 80.6% of Japanese HPV‐16 strains (n = 31). This variant is prevalent mainly in East Asia in China (70.2%), Korea (53.2–73.0%), and Hong Kong (58.0%), followed by Indonesia (22.7%), Thailand (14.3%), and India (1.7–37.8%) [Chan et al, 2002; Tornesello et al, 2004; Chopjitt et al, 2009; Lurchachaiwong et al, 2009; Vrtačnik Bokal et al, 2010; Lee et al, 2011]. The European (Asian) sublineage with E6 D25E was found only in Vietnam in the current study.…”

Section: Discussionmentioning

confidence: 99%

E6 and E7 variants of human papillomavirus‐16 and ‐52 in Japan, the Philippines, and Vietnam

Ishizaki

Matsushita

Hoang

et al. 2013

Journal of Medical Virology

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Human papillomavirus (HPV) has several intragenotypic variants with different geographical and ethnic distributions. This study aimed to elucidate the distribution patterns of E6 and E7 (E6/E7) intragenotypic variants of HPV type 16 (HPV-16), which is most common worldwide, and HPV-52, which is common in Asian countries such as Japan, the Philippines, and Vietnam. In previous studies, genomic DNA samples extracted from cervical swabs were collected from female sex workers in these three countries and found to be positive for HPV-16 or HPV-52. Samples were amplified further for their E6/E7 genes using type-specific primers and analyzed genetically. Seventy-nine HPV-16 E6/E7 genes were analyzed successfully and grouped into three lineages: European (Prototype), European (Asian), and African-2. The prevalences of HPV-16 European (Prototype)/European (Asian) lineages were 19.4%/80.6% (n=31) in Japan, 75.0%/20.8% (n=24) in the Philippines, and 0%/95.8% (n=24) in Vietnam. The 109 HPV-52 E6/E7 genes analyzed successfully were grouped into four lineages, A to D; the prevalences of lineages A/B/C/D were respectively 5.1%/ 92.3%/0%/2.6% in Japan (n=39), 34.4%/62.5%/0%/3.1% in the Philippines (n=32), and 15.8%/73.7%/7.9%/2.6% in Vietnam (n=38).The distribution patterns of HPV-16 and HPV -52 lineages in these countries differed significantly (p<0.000001 and p=0.0048, respectively). There was no significant relationship between abnormal cervical cytology and either HPV-16 E6/E7 lineages or specific amino acid mutations, such as E6 D25E, E6 L83V, and E7 N29S. Analysis of HPV-16 and HPV-52 E6/E7 genes can be a useful molecular-epidemiological tool to distinguish geographical diffusion routes of these HPV types in Asia.3

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Entire genome characterization of human papillomavirus type 16 from infected Thai women with different cytological findings

Cited by 14 publications

References 38 publications

Whole-Genome Sequence Analysis of Human Papillomavirus Type 18 from Infected Thai Women

Whole-Genome Sequence Analysis of Human Papillomavirus Type 18 from Infected Thai Women

Characterization and Whole Genome Analysis of Human Papillomavirus Type 16 E1-1374∧63nt Variants

E6 and E7 variants of human papillomavirus‐16 and ‐52 in Japan, the Philippines, and Vietnam

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