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Qu W, Hua C, Wang Y, Wang Y, Zhang L, Wang Z, Shi W, Chen F, Wu Z, Wang Q, Lu L, Jiang S, Sui L, Li Y. Lineage Replacement and Genetic Changes of Four HR-HPV Types during the Period of Vaccine Coverage: A Six-Year Retrospective Study in Eastern China. Vaccines (Basel) 2024; 12:411. [PMID: 38675793 PMCID: PMC11053858 DOI: 10.3390/vaccines12040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE This study aimed to provide clinical evidence for lineage replacement and genetic changes of High-Risk Human Papillomavirus (HR-HPV) during the period of vaccine coverage and characterize those changes in eastern China. METHODS This study consisted of two stages. A total of 90,583 patients visiting the Obstetrics and Gynecology Hospital of Fudan University from March 2018 to March 2022 were included in the HPV typing analysis. Another 1076 patients who tested positive for HPV31, 33, 52, or 58 from November 2020 to August 2023 were further included for HPV sequencing. Vaccination records, especially vaccine types and the third dose administration time, medical history, and cervical cytology samples were collected. Viral DNA sequencing was then conducted, followed by phylogenetic analysis and sequence alignment. RESULTS The overall proportion of HPV31 and 58 infections increased by 1.23% and 0.51%, respectively, while infection by HPV33 and 52 decreased by 0.42% and 1.43%, respectively, within the four-year vaccination coverage period. The proportion of HPV31 C lineage infections showed a 22.17% increase in the vaccinated group, while that of the HPV58 A2 sublineage showed a 12.96% increase. T267A and T274N in the F-G loop of HPV31 L1 protein, L150F in the D-E loop, and T375N in the H-I loop of HPV58 L1 protein were identified as high-frequency escape-related mutations. CONCLUSIONS Differences in epidemic lineage changes and dominant mutation accumulation may result in a proportional difference in trends of HPV infection. New epidemic lineages and high-frequency escape-related mutations should be noted during the vaccine coverage period, and regional epidemic variants should be considered during the development of next-generation vaccines.
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Affiliation(s)
- Wenjie Qu
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Chen Hua
- Shanghai Institute of Infection Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai 200032, China; (C.H.)
| | - Yaping Wang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Yan Wang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
- Qingpu Branch of the Yangtze River Delta Integrated Demonstration Zone, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200090, China
| | - Lu Zhang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Zhiheng Wang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
- Qingpu Branch of the Yangtze River Delta Integrated Demonstration Zone, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200090, China
| | - Wenqian Shi
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Fang Chen
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Zhiyong Wu
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
- Qingpu Branch of the Yangtze River Delta Integrated Demonstration Zone, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200090, China
| | - Qian Wang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai 201508, China
| | - Lu Lu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai 201508, China
| | - Shibo Jiang
- Shanghai Institute of Infection Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai 200032, China; (C.H.)
| | - Long Sui
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
| | - Yanyun Li
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China; (W.Q.)
- Qingpu Branch of the Yangtze River Delta Integrated Demonstration Zone, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200090, China
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Wang Y, Gong Y, Zhou Q, Qu W, Chen F, Wang Y, Mo J, Zhang H, Lin L, Bi T, Wang X, Gu J, Xu C, Li Y. Genetic variability analysis of human papillomavirus 58: Novel sublineage identification and persistent infection association. J Med Virol 2023; 95:e29262. [PMID: 38037452 DOI: 10.1002/jmv.29262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/20/2023] [Accepted: 11/12/2023] [Indexed: 12/02/2023]
Abstract
This study aims to characterize the genetic variability of HPV58, identify novel lineages and sublineages, and explore the association between persistent/multiple HPV58 infections and genetic variation. In this study, samples from 124 women with HPV58 infection in Eastern China were collected and 81 isolates of E6 and L1 full-length genes were successfully amplified from 55 samples. We evaluated the diversity of genetic variants and performed correlation analyses between genetic variability and pathology, vaccination, multiple infections, and persistent infections. Among the E6 and L1 gene sequences collected, the dominant prevailing sublineages were A1 (46.2%) and A2 (23.1%). In addition, we found two potential novel sublineages denoted as the A4 and A5 sublineage. A total of 50 nucleotide substitutions, including 28 synonymous substitutions and 22 nonsynonymous substitutions, were observed in the E6 and L1 genes. Among them, variants with A388C/K93N substitutions in the E6 gene correlated with persistent infection (≥1 and ≥2 years) (p < 0.005), and C307T/C66C was associated with persistent infection (≥2 years) (p < 0.005). Notably, two mutations above were detected in the isolate from the patient with breakthrough vaccine infection. Our study found two novel sublineages and sites of genetic variability in multiple and persistent infection variants. In addition, we identified two mutational sites associated with persistent infection. This study provides new insight into the clinical characteristics of HPV 58 genetic variations and offers new ideas for research on next-generation vaccines in Eastern China.
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Affiliation(s)
- Yan Wang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Yingxin Gong
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qi Zhou
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Wenjie Qu
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Fang Chen
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yaping Wang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jiayin Mo
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hongwei Zhang
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lin Lin
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Tianyi Bi
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Xujie Wang
- Department of Gynecology and Obstetrics, Shanghai Changning Maternity and Infant Health Hospital, Shanghai, China
| | - Jiashi Gu
- Department of Gynecology and Obstetrics, Shanghai Pudong Hospital, Fudan University, Shanghai, China
| | - Congjian Xu
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yanyun Li
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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Qu W, Sui L, Li Y. Vaccine escape challenges virus prevention: The example of two vaccine-preventable oncogenic viruses. J Med Virol 2023; 95:e29184. [PMID: 37943176 DOI: 10.1002/jmv.29184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Over the years, the pace of developing vaccines for HBV and HPV has never stopped. After more than 30 years of application, the HBV vaccine has reduced 80% of hepatocellular carcinoma (HCC). However, vaccine escape variants occur under selective pressure induced by widespread vaccination and antiviral therapy, which results in fulminant infection and horizontal transmission. Several mechanisms have been studied to explain HBV vaccine escape, including vaccine escape mutations (VEMs) in the major hydrophilic region, which leads to a decrease in the binding ability to neutralize antibodies and is the primary escape mechanism, protein conformational and N-linked glycosylation sites changes caused by VEMs, differences in genotype distribution, gene recombination, and some temporarily unknown reasons. However, effective solutions are still being explored. The HPV vaccine has also been proven to prevent 70%-90% of cervical cancer worldwide. Cases of HPV infection after being vaccinated have been observed in clinical practice. However, few researchers have paid attention to the mechanism of HPV vaccine escape. Thus, we reviewed the literature on vaccine escape of both HBV and HPV to discuss the mechanism of the virus escaping from vaccine protection and possible solutions to this problem. We analyzed the gap between studies of HPV and HBV and made prospects for further research in HPV vaccine escape.
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Affiliation(s)
- Wenjie Qu
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai, China
| | - Long Sui
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanyun Li
- Department of Gynecology and Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Yang Z, Zhang C, Luo P, Sun F, Mei B. Genetic diversity and functional implication of the long control region in human papillomavirus types 52, 58, and 16 from Central China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105447. [PMID: 37217029 DOI: 10.1016/j.meegid.2023.105447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 03/22/2023] [Indexed: 05/24/2023]
Abstract
OBJECT High-risk human papillomavirus (HR-HPV) is a main reason for cervical cancer. The long control region (LCR) of the genome plays a variety of roles in the transcription of the virus. METHODS LCR sequences were amplified by polymerase chain reaction (PCR) and confirmed by DNA sequencing. MEGA 11.0 software and NCBI blast were used to analyze the sequences and construct the Neighbor-Joining tree. In addition, the JASPAR database was used to predict the potential transcription factor binding sites (TFBS). RESULTS For HPV-52 LCR, 68 single nucleotide polymorphisms (SNPs), 8 deletions, and 1 insertion were found, 17 of which were novel variations. Most of the variants were clustered in B2 sub-lineage (96.22%). For HPV-58 LCR, 25.43% of samples were prototype. 49 SNPs, 2 deletions, and 1 insertion were observed in the remaining samples. A1 sub-lineage was the most frequent (64.16%). For HPV-16 LCR, 75 SNPs and 2 deletions were identified, 13 of which were newly identified. A total of 55.68% of the variants were distributed in A4 sub-lineage. The JASPAR results suggested that multiple variations occurred in TFBSs, which might affect the function of transcription factors. CONCLUSIONS This study provides experimental data for further studies on the epidemiology and biological function of LCR. Various LCR mutational data may prove useful for exploring the carcinogenic mechanism of HPV.
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Affiliation(s)
- ZhiPing Yang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Chunlin Zhang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Ping Luo
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Fenglan Sun
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Bing Mei
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China.
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Characteristics of human papillomavirus infection among females and the genetic variations of HPV18 and HPV58 in Henan province, China. Sci Rep 2023; 13:2252. [PMID: 36755053 PMCID: PMC9908864 DOI: 10.1038/s41598-022-24641-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/17/2022] [Indexed: 02/10/2023] Open
Abstract
The present study aims to investigate the genotype distribution of Human papillomavirus (HPV) and variations of HPV18 and HPV58 infection among 6538 females in Luoyang city during 2019-2021. The overall positive rate of females with HPV infection was 12.34%, with 9.74% were infected with single HPV and 2.60% with multiple HPVs. The prevalent rate of high-risk HPV (HR-HPV) was 9.85% and the top five HR-HPV genotypes were HPV52 (1.94%), HPV16 (1.93%), HPV58 (1.48%), HPV51 (1.02%) and HPVV39 (0.99%). Two peaks of HPV infections rates were observed in females aged ≤ 20 and 61-65 years old. To characterize mutations, 39 HPV18 and 56 HPV58 L1, E6 and E7 genes were sequenced and submitted to GenBank. In the HPV18 E6-E7-L1 sequences, 38 nucleotides changes were observed with 10/38 were non-synonymous mutations (5 in E6 gene, 1 in E7 gene and 4 in L1 gene). In the HPV58 E6-E7-L1 sequences, 53 nucleotides changes were observed with 23/53 were non-synonymous mutations (3 in E6 gene, 5 in E7 gene and 15 in L1 gene). Phylogenetic analysis based on L1 gene showed that 92.3% (36/39) of HPV18 isolates fell into sublineage A1 and 7.7% (3/39) belonged to A5. For HPV58, 75.0% (42/56) isolates belonged to sublineage A1 and 25.0% (14/56) were sublineage A2. There was no association between amino mutation and cervical lesions. The present study provides basic information about the distribution, genotypes and variations of HPV among females population in Luoyang city, which would assist in the formulation of HPV screening and vaccination programs and preventive strategies for HPV-attributable cancer in this region.
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Yang Z, Zhang C, Luo P, Ye M, Gong Q, Mei B. Genetic variability of E6 and E7 genes of human papillomavirus type 58 in Jingzhou, Hubei Province of central China. Virol J 2022; 19:71. [PMID: 35459244 PMCID: PMC9034476 DOI: 10.1186/s12985-022-01801-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cervical cancer is a common malignant tumor in women, with a high mortality rate, has great harm to women's health. Long-term and persistent infection of high-risk human papillomavirus (HR-HPV) is the main reason of the occurrence and development of cervical cancer. METHODS The infection rate of HPV-58 is higher in the Jingzhou area. In this study, 172 complete HPV-58 E6-E7 sequences were amplified by polymerase chain reaction (PCR), the amplified products were sequenced, and the gene variations of HPV-58 E6-E7 were analyzed. A Neighbor-Joining phylogenetic tree was constructed by MEGA 11. The secondary structure of E6 and E7 protein was investigated. PAML X was used to analyze the selective pressure. The B cell epitopes of E6 and E7 proteins in HPV-58 were predicted by ABCpred server. RESULTS In E6 sequences, 10 single nucleotide variants were observed, including 7 synonymous and 3 non-synonymous variants. In E7 sequences, 12 single nucleotide variants were found, including 3 synonymous variants and 9 non-synonymous variants. There are 5 novel variants. The phylogenetic analysis showed that all the E6-E7 sequences were distributed in A lineage. No positively selected site was found in E6 sequence, but G63 in E7 sequences was identified as positively selected site. Some amino acid substitutions affected multiple B cell epitopes. CONCLUSION Various E6 and E7 mutational data may prove useful for development of better diagnostic and vaccines for the region of Jingzhou, Hubei province of central China.
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Affiliation(s)
- Zhiping Yang
- Department of Laboratory Medicine, Jingzhou Hospital, Yangtze University, Jingzhou, 434020, China
| | - Chunlin Zhang
- Department of Laboratory Medicine, Jingzhou Hospital, Yangtze University, Jingzhou, 434020, China
| | - Ping Luo
- Department of Laboratory Medicine, Jingzhou Hospital, Yangtze University, Jingzhou, 434020, China
| | - Mengxia Ye
- Department of Laboratory Medicine, Jingzhou Hospital, Yangtze University, Jingzhou, 434020, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China
| | - Bing Mei
- Department of Laboratory Medicine, Jingzhou Hospital, Yangtze University, Jingzhou, 434020, China.
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Oumeslakht L, Ababou M, Badaoui B, Qmichou Z. Worldwide genetic variations in high-risk human papillomaviruses capsid L1 gene and their impact on vaccine efficiency. Gene 2021; 782:145533. [PMID: 33636291 DOI: 10.1016/j.gene.2021.145533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Human papillomavirus is the most common sexually transmitted infection. It is associated with different cancers, mainly cervical cancer, which remains the fourth most frequent cancer among women worldwide; it is also related to anogenital (anus, vulvar, vagina, and penis) and oropharyngeal cancers. Vaccination against HPV infection is the major way of prevention, and it has demonstrated impressive efficacy in reducing cervical cancer incidence. Nowadays, all the licensed HPV recombinant vaccines were designed based on HPV major capsid L1 protein. However, some variations in the HPV L1 gene sequence may induce structural changes within the L1 protein, which may alter the affinity and interaction of monoclonal antibodies (MAbs) with L1 protein epitopes, and influence host immune response and recognition. Hence, the importance of accuracy in delineating epitopes relevant to vaccine design and defining genetic variations within antigenic regions in the L1 gene to predict its impact on prophylactic vaccine efficiency. The present review reports the sequence variations in HR-HPV L1 gene isolates from different countries around the world, which may help to understand the effect of HPV L1 gene variations on vaccine efficiency. METHODS Research studies were retrieved from PubMed, Google Scholar, Science direct, and the National Center for Biotechnology Information (NCBI) database. A total of 31 articles describing genetic variations within the major capsid L1 gene and conducted in Africa, Europe, America and Asia were found. Only 26 studies conducted on HPV16, 18, 31, 33, 58, 45 and 52 which are the targets of HPV prophylactic vaccines, and which reported genetic variations within the L1 gene, were selected and evaluated in this review. FINDINGS We found a total of 87, 49, 11, 7, 22, 3, and 17 non-synonymous single nucleotide polymorphisms (SNPs) within HPV16, HPV18, HPV31, HPV58, HPV45, and HPV52 L1 gene, respectively. Four mutations were frequently observed in HPV16 L1 sequences: T353P in the HI loop, H228D in the EF loop, T266A in the FG loop, and T292A in the FG loop. Two mutations in HPV58 L1 sequences: T375N in the HI loop and L150F in the DE loop. Three mutations in HPV33 L1 sequences: T56N in the BC loop, G133S in the DE loop, T266K in the FG loop. Other mutations were found in HPV18, HPV45, and HPV52 L1 sequences. Some were found in different countries, and others were specific to a given population. Furthermore, some variations were located on peptide binding epitopes and lead to a modification of epitopes, which may influence MAbs interactions. Others need further investigations due to the lack of studies. CONCLUSION This study investigated the major capsid L1 genetic diversity of HPV16, 18, 31, 33, 58, 45, and 52 circulating in different populations around the world. Further investigations should be conducted to confirm their effect on immunogenicity and prophylactic vaccine efficiency.
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Affiliation(s)
- Loubna Oumeslakht
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research, MAScIR, Rabat, Morocco; Laboratory of Biodiversity, Ecology and Genome, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat, Morocco
| | - Mouna Ababou
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat, Morocco
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat, Morocco
| | - Zineb Qmichou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research, MAScIR, Rabat, Morocco.
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Genetic signatures for lineage/sublineage classification of HPV16, 18, 52 and 58 variants. Virology 2020; 553:62-69. [PMID: 33238224 DOI: 10.1016/j.virol.2020.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022]
Abstract
Increasing evidences indicate that high-risk HPV variants are heterogeneous in carcinogenicity and ethnic dispersion. In this work, we identified genetic signatures for convenient determination of lineage/sublineage of HPV16, 18, 52 and 58 variants. Using publicly available genomes, we found that E2 of HPV16, L2 of HPV18, L1 and LCR of HPV52, and L2, LCR and E1 of HPV58 contain the proper genetic signature for lineage/sublineage classification. Sets of hierarchical signature nucleotide positions were further confirmed for high accuracy (>95%) by classifying HPV genomes obtained from Chinese females, which included 117 HPV16 variants, 48 HPV18 variants, 117 HPV52 variants and 89 HPV58 variants. The circulation of HPV variants posing higher cancer risk in Eastern China, such as HPV16 A4 and HPV58 A3, calls for continuous surveillance in this region. The marker genes and signature nucleotide positions may facilitate cost-effective diagnostic detections of HPV variants in clinical settings.
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Wu E, An G, Wu R, Tang Y, Li Q, Wang J, Ling Y, You J. Prevalence of human papillomavirus in archival head and neck cancer in the eastern Inner Mongolian Autonomous Region, China. TUMORI JOURNAL 2020; 106:369-377. [PMID: 32066343 DOI: 10.1177/0300891620901768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To investigate the prevalence of human papillomavirus (HPV) in archival head and neck cancer (HNC) collected from the Tong-Liao area, which is located in east Inner Mongolia, China. METHODS The presence of HPV in 54 HNCs and 25 benign biopsies was detected and the sequence variation of the E6 gene in HPV-positive samples was analyzed to determine their lineage/sublineage classification. RESULTS HPV was detected in only 4 out of 54 HNCs and no benign biopsies were found to be HPV-positive. After further p16INK4a immunostaining, only 3 cases of HNC were positive for both HPV and p16INK4a. Phylogenetic analysis of the isolated E6 gene shows that the HPV 16, HPV 31, and HPV 58 isolated in this study belong to lineage A. CONCLUSIONS The prevalence of HPV in HNC from this area is very low. The lineage/sublineage classification of the 3 HPV types in HNC in this area is consistent with the previous reported data of HPV lineage distribution in cervical cancer within China.
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Affiliation(s)
- Enqi Wu
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
| | - Guangwen An
- Department of Pharmacy, No. 984 Hospital of the PLA, Beijing, China
| | - Ritu Wu
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
| | - Yuanyu Tang
- Department of Pathology, The First People's Hospital of Hkorchin, Hkorchin, China
| | - Qing Li
- Department of Pathology, Beijing Chaoyang Hospital, Capital University of Medical Sciences, Beijing, China
| | - Jinhua Wang
- Department of Pathology, Inner Mongolia University for Nationalities Affiliated Hospital, Inner Mongolia, China
| | - Yaqin Ling
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
| | - Jia You
- Biotherapy Center, The Seventh Medical Center of PLA General Hospital, Beijing, China
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He J, Yang Y, Chen Z, Liu Y, Bao S, Zhao Y, Ding X. Identification of variants and therapeutic epitopes in HPV-33/HPV-58 E6 and E7 in Southwest China. Virol J 2019; 16:72. [PMID: 31138240 PMCID: PMC6537359 DOI: 10.1186/s12985-019-1168-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/22/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) E6 and E7 oncoproteins play a crucial role in HPV-related diseases, such as cervical cancer, and can be used as ideal targets for therapeutic vaccines. Human leukocyte antigen (HLA) participates in the immune response to block HPV infection and invasion by its target/recognition function. HPV-33 and HPV-58 are highly prevalent among Chinese women. Therefore, it is of great significance to study the E6 and E7 region-specific gene polymorphisms of HPV-33 and HPV-58 in Southwest China and to identify ideal epitopes for vaccine design. Both HPV-33 and HPV-58 belong to α-9 genus HPV and are highly homologous, so their correlations are included in our research. METHODS To study the E6 and E7 variations and polymorphisms of HPV-33 and HPV-58 in Southwest China, we collected samples, extracted and sequenced DNA, and identified variants. Nucleotide sequences were translated into amino acids by Mega 6.0 software. The physical/chemical properties, amino acid-conserved sequences and secondary structure of protein sequences were analysed by the Protparam server, ConSurf server and PSIPRED software. The T and B cell epitopes of the E6/E7 reference and variant sequences in HPV-33 and HPV-58 were predicted by the Immune Epitope Database (IEDB) analysis server and the ABCpred server, respectively. RESULTS Five and seven optimal HLA-I restricted T cell epitopes were selected from HPV-33 and HPV-58 E6, respectively, and these optimal epitopes are mainly located in 41-58EVYDFAFADLTVVYREGN of HPV-33 E6 and 40-60SEVYDFVFADLRIVYRDGNPF of HPV-58 E6. Six optimal HLA-I-restricted T cell epitopes were selected from HPV-33 and HPV-58 E7, and these epitopes are mainly located in 77-90RTIQQLLMGTVNIV of HPV-33 E7 and 78-91RTLQQLLMGTCTIV of HPV-58 E7. CONCLUSIONS HPV-33/HPV-58 E6/E7 gene polymorphisms and T/B cell epitopes of their reference and variant sequences were studied, and candidate epitopes were selected by bioinformatics techniques for therapeutic vaccine design for people in Southwest China. This study was the first to investigate the correlation of epitopes between HPV-33 and HPV-58. After experimental validation, these selected epitopes will be employed to induce a wide range of immune responses in heterogeneous HLA populations.
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Affiliation(s)
- Jiaoyu He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yasi Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Zuyi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Shanfei Bao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xianping Ding
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China. .,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China. .,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China.
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11
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Yu JH, Shi WW, Zhou MY, Liu JM, Han QY, Xu HH. Genetic variability and oncogenic risk association of human papillomavirus type 58 E6 and E7 genes in Taizhou area, China. Gene 2018; 686:171-176. [PMID: 30471332 DOI: 10.1016/j.gene.2018.11.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023]
Abstract
It is well recognized that the association of human papillomavirus (HPV) and cervical carcinogenesis is based on the presence of HPV DNA sequence. The E6 and E7 oncoproteins encoded by high-risk HPV types play a key role in carcinogenesis. HPV58 type accounts for a larger share of cervical disease in China, whereas data on HPV58 genetic variability in China is limited. We aimed to evaluate the diversity of HPV58 genetic variants by sequencing the entire E6 and E7 genes. Phylogenetic trees were constructed by Maximum likelihood method by MEGA 5.05 software. In this study, the overall HPV infection rate was 22.6% (2891/12780) in Southeast China and the prevalence of HPV58 infection rate was 2.6% (335/12780). 26 nucleotides substitutions were observed in E6 and E7 genes with 10 novel substitutions and 17 non-synonymous substitutions. We obtained 25 distinct variation patterns which the accession GenBank numbers as MH348918-MH348942. All of HPV58 variants belong to lineage A, while no lineage B, C and D were detected in Taizhou area, Southeast China. The sublineage A1, A2, and A3 variants were found in 136 (68.3%), 39 (19.6%), and 24 (12.1%) of HPV58 isolates, respectively. The sublineage A3 variants with T20I/G63S substitutions at E7 oncoprotein carried a significantly higher risk for high-grade cervical intraepithelial neoplasia (CIN2 or worse, CIN2+) when compared with other HPV58 variants (odds ratio = 4.41, P < 0.05). Nevertheless, there was no association between HPV58 (sub) lineages and cervical lesions. These data provide the critical characteristics of HPV58 variants to assist further investigation of carcinogenic association and the development of next generation vaccines and diagnostic assays in China.
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Affiliation(s)
- Jun-Hui Yu
- Department of Gynecology and Obstetrics, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Wei-Wu Shi
- Laboratory of Gynecologic Oncology, Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Mei-Ying Zhou
- Laboratory of Gynecologic Oncology, Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Jia-Mei Liu
- Laboratory of Gynecologic Oncology, Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Qiu-Yue Han
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Hui-Hui Xu
- Laboratory of Gynecologic Oncology, Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China.
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12
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Xi J, Chen J, Xu M, Yang H, Wen S, Pan Y, Wang X, Ye C, Qiu L, Sun Q. The polymorphisms of LCR, E6, and E7 of HPV-58 isolates in Yunnan, Southwest China. Virol J 2018; 15:76. [PMID: 29695285 PMCID: PMC5918753 DOI: 10.1186/s12985-018-0986-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/16/2018] [Indexed: 02/07/2023] Open
Abstract
Backgroud Variations in HPV LCR/E6/E7 have been shown to be associated with the viral persistence and cervical cancer development. So far, there are few reports about the polymorphisms of the HPV-58 LCR/E6/E7 sequences in Southwest China. This study aims to characterize the gene polymorphisms of the HPV-58 LCR/E6/E7 sequences in women of Southwest China, and assess the effects of variations on the immune recognition of viral E6 and E7 antigens. Methods Twelve LCR/E6/E7 of the HPV-58 isolates were amplified and sequenced. A neighbor-joining phylogenetic tree was constructed by MEGA 7.0, followed by the secondary structure prediction of the related proteins using PSIPRED v3.3. The selection pressure acting on the HPV-58 E6 and E7 coding regions was estimated by Bayes empirical Bayes analysis of PAML 4.8. Meanwhile, the MHC class-I and II binding peptides were predicted by the ProPred-I server and ProPred server. The transcription factor binding sites in the HPV-58 LCR were analyzed using the JASPAR database. Results Twenty nine SNPs (20 in the LCR, 3 in the E6, 6 in the E7) were identified at 27 nucleotide sites across the HPV-58 LCR/E6/E7. From the most variable to the least variable, the nucleotide variations were LCR > E7 > E6. The combinations of all the SNPs resulted in 11 unique sequences, which were clustered into the A lineage (7 belong to A1, 2 belong to A2, and 2 belong to A3). An insertion (TGTCAGTTTCCT) was found between the nucleotide sites 7280 and 7281 in 2 variants, and a deletion (TTTAT) was found between 7429 and 7433 in 1 variant. The most common non-synonymous substitution V77A in the E7 was observed in the sequences encoding the α-helix. 63G in the E7 was determined to be the only one positively selected site in the HPV-58 E6/E7 sequences. Six non-synonymous amino acid substitutions (including S71F and K93 N in the E6, and T20I, G41R, G63S/D, and V77A in the E7) were affecting multiple putative epitopes for both CD4+ and CD8+ T-cells. In the LCR, C7265G and C7266T were the most variable sites and were the potential binding sites for the transcription factor SOX10. Conclusion These results provide an insight into the intrinsic geographical relatedness and biological differences of the HPV-58 variants, and contribute to further research on the HPV-58 epidemiology, carcinogenesis, and therapeutic vaccine development. Electronic supplementary material The online version of this article (10.1186/s12985-018-0986-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China
| | - Miaoling Xu
- The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, People's Republic of China
| | - Hongying Yang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Provincial Tumor Hospital, Kunming, 650118, People's Republic of China
| | - Songjiao Wen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China
| | - Xiaodan Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China
| | - Chao Ye
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China.,Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Lijuan Qiu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China.,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China.,Institute of Pediatric Disease Research in Yunnan, the Affiliated Children's Hospital of Kunming Medical University, Kunming, 650228, People's Republic of China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming, 650118, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, 650118, People's Republic of China. .,Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Pu'er, 665000, People's Republic of China.
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13
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Liu J, Lu Z, Wang G, Wang W, Zhou W, Yang L, Liu C, Wang B, Miao Y, Sun Z, Ruan Q. Viral load and integration status of HPV58 associated with cervical lesion severity in women of Northeast China. Jpn J Clin Oncol 2017; 47:123-129. [PMID: 28173077 DOI: 10.1093/jjco/hyw166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/09/2016] [Accepted: 10/19/2016] [Indexed: 12/29/2022] Open
Abstract
Objective We aimed to evaluate the viral load and integration status of human papillomavirus 58 in women with different grades of cervical lesions to determine whether viral load and integration status are related to malignant transformation in HPV58-infected women. Methods A total of 212 cervical specimens were collected from women in Northeast China who had undergone human papillomavirus genotyping and were HPV58-positive. The HPV58 viral load was determined using real-time polymerase chain reaction, and the integration status was discriminated using the ratio of HPV58 E2 gene copy number to E6 gene copy number. Results The median HPV58 viral load in women with normal cervix or cervicitis, low-grade squamous cell intraepithelial lesion, high-grade squamous cell intraepithelial lesion and cervical cancer was 352.12, 864.21, 1199.75 and 693.04 copies/genome, respectively. High significance was obtained when comparing the viral load of infected women presenting normal/cervicitis with that of the women either with precancerous cervical lesions or cervical cancer (P < 0.05). The HPV58 genome was in the episomal form in 35 samples (16.5%), mixed episomal and integrated forms in 165 (77.8%) samples, and completely integrated into the host genome in 12 (5.7%) samples. The HPV58 E2/E6 copy number ratio in the cervical cancer group was significantly lower than that in the other groups (P < 0.01). Conclusions The HPV58 viral load in patients with precancerous cervical lesions or cervical cancer increases significantly with disease progression. The HPV58 E2/E6 copy number ratio in patients with cervical cancer is lower than that for less severe cervical lesions, suggesting a high degree of viral integration may be a considerable risk factor for cervical cancer.
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Affiliation(s)
- Jianhua Liu
- Department of Clinical Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Zhitao Lu
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Guili Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Wei Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Weiqiang Zhou
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Lianxia Yang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Chao Liu
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Bo Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Ye Miao
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Zhengrong Sun
- Biobank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
| | - Qiang Ruan
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, P.R. China
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14
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Chen Z, Jing Y, Wen Q, Ding X, Wang T, Mu X, Chenzhang Y, Cao M. E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China. PLoS One 2017; 12:e0171140. [PMID: 28141822 PMCID: PMC5283733 DOI: 10.1371/journal.pone.0171140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/16/2017] [Indexed: 11/18/2022] Open
Abstract
Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV). The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216) and HPV-58 (E6, E7: n = 405) E6 and E7 genes were sequenced and compared to others submitted to GenBank. Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by PAML 4.8 (Phylogenetic Analyses by Maximun Likelihood version4.8) software. The positive sites of HPV-33 and HPV-58 E6/E7 were contrasted by ClustalX 2.1. Among 216 HPV-33 E6 sequences, 8 single nucleotide mutations were observed with 6/8 non-synonymous and 2/8 synonymous mutations. The 216 HPV-33 E7 sequences showed 3 single nucleotide mutations that were non-synonymous. The 405 HPV-58 E6 sequences revealed 8 single nucleotide mutations with 4/8 non-synonymous and 4/8 synonymous mutations. Among 405 HPV-58 E7 sequences, 13 single nucleotide mutations were observed with 10/13 non-synonymous mutations and 3/13 synonymous mutations. The selective pressure analysis showed that all HPV-33 and 4/6 HPV-58 E6/E7 major non-synonymous mutations were sites of positive selection. All variations were observed in sites belonging to major histocompatibility complex and/or B-cell predicted epitopes. K93N and R145 (I/N) were observed in both HPV-33 and HPV-58 E6.
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Affiliation(s)
- Zuyi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Yaling Jing
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Qiang Wen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
- * E-mail:
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Xuemei Mu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Yuwei Chenzhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Man Cao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
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15
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Xu WX, Wang J, Tang HP, He YP, Zhu QX, Gupta SK, Gu SH, Huang Q, Ji CN, Liu LF, Li GL, Xu CJ, Xie Y. Epitomics: IgG-epitome decoding of E6, E7 and L1 proteins from oncogenic human papillomavirus type 58. Sci Rep 2016; 6:34686. [PMID: 27708433 PMCID: PMC5052575 DOI: 10.1038/srep34686] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/06/2016] [Indexed: 01/31/2023] Open
Abstract
To enable rational multi-epitope vaccine and diagnostic antigen design, it is imperative to delineate complete IgG-epitome of the protein. Here, we describe results of IgG-epitome decoding of three proteins from high-risk (HR-) oncogenic human papillomavirus type 58 (HPV58). To reveal their entire epitomes, employing peptide biosynthetic approach, 30 precise linear B-cell epitopes (BCEs) were mapped on E6, E7 and L1 proteins using rabbits antisera to the respective recombinant proteins. Using sequence alignment based on BCE minimal motif, the specificity and conservativeness of each mapped BCE were delineated mainly among known HR-HPVs, including finding 3 broadly antibody cross-reactive BCEs of L1 that each covers almost all HR-HPVs. Western blots revealed that 13 of the 18 BCEs within L1-epitome were recognized by murine antisera to HPV58 virus-like particles, suggesting that these are antibody accessible BCEs. Also, a highly conserved epitope (YGD/XTL) of E6 was found to exist only in known common HR-HPVs, which could be used as the first peptide reference marker for judging HR-HPVs. Altogether, this study provides systemic and exhaustive information on linear BCEs of HR-HPV58 that will facilitate development of novel multi-epitope diagnostic reagents/chips for testing viral antibodies and ‘universal’ preventive HPV peptide vaccine based on L1 conserved BCEs.
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Affiliation(s)
- Wan-Xiang Xu
- Division of Reproductive Immunology, Key Lab of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, China
| | - Jian Wang
- Division of Reproductive Immunology, Key Lab of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, China
| | - Hai-Ping Tang
- Division of Reproductive Immunology, Key Lab of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, China
| | - Ya-Ping He
- Division of Reproductive Immunology, Key Lab of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, China
| | - Qian-Xi Zhu
- Division of Reproductive Immunology, Key Lab of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, China
| | - Satish K Gupta
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Shao-Hua Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chao-Neng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ling-Feng Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gui-Ling Li
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
| | - Cong-Jian Xu
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
| | - Yi Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
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16
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Wu H, Wu E, Ma L, Zhang G, Shi Y, Huang J, Zha X. Lineage distribution and E2 sequence variation of high-risk human papillomavirus types isolated from patients with cervical cancer in Sichuan province, China. Arch Virol 2015; 160:2845-55. [PMID: 26303138 DOI: 10.1007/s00705-015-2559-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 07/27/2015] [Indexed: 11/27/2022]
Abstract
To explore the nucleotide sequence variability of the E2 gene in high-risk HPV types in cervical cancer patients from Sichuan province, China, the E2 genes of eight high-risk HPV types were amplified and sequenced. Several novel nucleotide substitutions and deletions were observed. The lineages to which the isolates belonged were determined by phylogenetic analysis, employing the sequence of the representative lineages/sublineages in the coherent classification and nomenclature system as references. This study updates the lineage distribution data on high-risk HPV types in Southwest China and helps broaden understanding of the polymorphism of the E2 gene.
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Affiliation(s)
- Haijing Wu
- Department of Gynecol Oncology, Sichuan Cancer Hospital, Chengdu, 610041, China.
| | - Enqi Wu
- State Nationalities Affairs Commission and Department of Educational Key Lab of Minority Traditional Medicine, Minzu University of China, Beijing, 100081, China.
| | - Lin Ma
- Health Science Center, Temple University, Philadelphia, PA, 19140, USA.
| | - Guonan Zhang
- Department of Gynecol Oncology, Sichuan Cancer Hospital, Chengdu, 610041, China.
| | - Yu Shi
- Department of Gynecol Oncology, Sichuan Cancer Hospital, Chengdu, 610041, China.
| | - Jianming Huang
- Department of Molecular Pharmacology, Sichuan Cancer Hospital, Chengdu, 610041, China.
| | - Xiao Zha
- Department of Molecular Pharmacology, Sichuan Cancer Hospital, Chengdu, 610041, China.
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17
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Prevalence of microorganisms co-infections in human papillomaviruses infected women in Northern China. Arch Gynecol Obstet 2015; 293:595-602. [PMID: 26280325 DOI: 10.1007/s00404-015-3826-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/21/2015] [Indexed: 01/19/2023]
Abstract
PURPOSE Due to scarce data on the prevalence of genital microorganism infections among individuals with human papillomavirus (HPV) infections, the present study aimed to evaluate microorganism co-infections and associated risk factors in HPV-infected women in Northern China. METHODS Cervical samples of 4290 enrolled female patients were collected to detect HPV, bacterial and yeast infections in gynecologic outpatients. Serum samples collected were analyzed for the presence of serological markers for human immunodeficiency virus (HIV), hepatitis B (HBV) and hepatitis C (HCV) and Treponema pallidum infections. HPV typing was carried out by polymerase chain reaction and flow-through hybridization on cervical brush specimens. Chlamydia trachomatis was identified by strand displacement amplification, and other microorganisms were detected by conventional methods. Odds ratio of co-infection was assessed between HPV-positive and -negative patients. RESULTS Overall, co-infections among HPV-infected patients showed a trend for risk compared with HPV-negative patients. In this cross-sectional study on 4290 female outpatients, statistical analyses revealed a significant association between HPV and detection of anti-HBV antibodies, bacterial vaginosis, C. trachomatis and Ureaplasma urealyticum; no correlation was found between HPV infection and anti-HIV, anti-HCV, T. pallidum, Trichomonas vaginalis and Neisseria gonorrhoeae, which were detected only in few cases among either HPV-positive or -negative patients. CONCLUSION The study demonstrated a significant association between HPV and HBV, bacterial vaginosis, C. trachomatis and U. urealyticum. The study results suggest that it may be important to screen for the simultaneous presence of different microorganism co-infections with HPV that may have synergistic pathological effects.
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18
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Prevalence of human papillomavirus variants and genetic diversity in the L1 gene and long control region of HPV16, HPV31, and HPV58 found in North-East Brazil. BIOMED RESEARCH INTERNATIONAL 2015; 2015:130828. [PMID: 25793187 PMCID: PMC4352477 DOI: 10.1155/2015/130828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/08/2015] [Indexed: 02/06/2023]
Abstract
This study showed the prevalence of human papillomavirus (HPV) variants as well as nucleotide changes within L1 gene and LCR of the HPV16, HPV31, and HPV58 found in cervical lesions of women from North-East Brazil.
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Yang L, Yang H, Chen J, Huang X, Pan Y, Li D, Ding X, Wu K, Shi X, Fu J, Shi H, Ma S, Sun Q. Genetic variability of HPV-58 E6 and E7 genes in Southwest China. INFECTION GENETICS AND EVOLUTION 2013; 21:395-400. [PMID: 24368255 DOI: 10.1016/j.meegid.2013.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/04/2013] [Accepted: 12/17/2013] [Indexed: 01/18/2023]
Abstract
HPV accounts for most of incidence of cervical cancer. Genetic variations of E6 and E7 may be associated with the development of cervical cancer in specific geographic regions. HPV-58 has been found to be a relatively prevalent high-risk HPV among southwest Chinese women. To explore gene intratypic variations and polymorphisms of HPV-58 E6 and E7 genes originating in Southwest China, a total of 2000 scraped cell samples were collected for DNA extraction and HPV typing. Then, the E6 and E7 genes of HPV-58 (n=22) were sequenced and compared to others submitted to GenBank, followed by an analysis of the diversity of secondary structure by DNASTAR software. Phylogenetic trees were then constructed by Neighbor-Joining and the Kimura 2-parameters methods, followed by an analysis of selection pressures acting on the E6/E7 genes by PAML software. 22 were HPV-58 positive among 215 high-risk types' samples. The nucleotide variation rate of E6 was 86.36% (19/22) among the 22 HPV-58 E6 sequences studied. 4 single nucleotide changes were identified among the E6 sequences with 3/4 synonymous mutations (C187T, A260C, C307T) and 1/4 non-synonymous mutations (A388C, from Lys to Asn, in alpha helix). The most common mutations of E6 genes are the C307T and A388C. 8 single nucleotide changes were identified among the HPV-58 E7 sequences with 2/8 synonymous mutations (T726C, T744G) and 6/8 non-synonymous mutations (G599A, C632T, G694A, G760A, G761A, T803C). The nucleotide variation rate of E7 was 72.73% (17/22). The most common mutations of E7 genes are C632T, G694A, T744G, G760A (from Gly to Ser, in turn), G761A and T803C. The phylogenetic analyses demonstrate that all HPV-58 E6/E7 variants identified belonged to the Southeast Asia lineage. There was no evidence of positive selection in the sequence alignment of HPV-58 E6 and E7 genes.
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Affiliation(s)
- Lijuan Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Hongying Yang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Provincial Tumor Hospital, Kunming 650118, PR China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xinwei Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Duo Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xiaojie Ding
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Kun Wu
- The First Affiliated Hospital of Kunming Medical University, Kunming 650032, PR China
| | - Xinan Shi
- Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi 562400, PR China
| | - Juanjuan Fu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Haijing Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Shaohui Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
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