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Wang M, Liang H, Yan Y, Bian R, Huang W, Zhang X, Nie J. Distribution of HPV types among women with HPV-related diseases and exploration of lineages and variants of HPV 52 and 58 among HPV-infected patients in China: A systematic literature review. Hum Vaccin Immunother 2024; 20:2343192. [PMID: 38745409 DOI: 10.1080/21645515.2024.2343192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
To summarize the distribution of types of human papillomavirus (HPV) associated with HPV-related diseases and investigate the potential causes of high prevalence of HPV 52 and 58 by summarizing the prevalence of lineages, sub-lineages, and mutations among Chinese women. We searched PubMed, EMBASE, CNKI, and WanFang from January, 2012 to June, 2023 to identify all the eligible studies. We excluded patients who had received HPV vaccinations. Data were summarized in tables and cloud/rain maps. A total of 102 studies reporting HPV distribution and 15 studies reporting HPV52/HPV58 variants were extracted. Among Chinese women, the top five prevalent HPV types associated with cervical cancer (CC) were HPV16, 18, 58, 52, and 33. In patients with vaginal cancers and precancerous lesions, the most common HPV types were 16 and 52 followed by 58. For women with condyloma acuminatum (CA), the most common HPV types were 11 and 6. In Chinese women with HPV infection, lineage B was the most prominently identified for HPV52, and lineage A was the most common for HPV58. In addition to HPV types 16, which is prevalent worldwide, our findings revealed the unique high prevalence of HPV 52/58 among Chinese women with HPV-related diseases. HPV 52 variants were predominantly biased toward lineage B and sub-lineage B2, and HPV 58 variants were strongly biased toward lineage A and sub-lineage A1. Further investigations on the association between the high prevalent lineage and sub-lineage in HPV 52/58 and the risk of cancer risk are needed. Our findings underscore the importance of vaccination with the nine-valent HPV vaccine in China.
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Affiliation(s)
- Meng Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Haoyu Liang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Yue Yan
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Rui Bian
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Xingxing Zhang
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
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Yuan H, Yan Z, Gan J, Di X, Qiu Y, Xu H. Phylogenetic analysis and antigenic epitope prediction for E6 and E7 of Alpha-papillomavirus 9 in Taizhou, China. BMC Genomics 2024; 25:507. [PMID: 38778248 PMCID: PMC11110188 DOI: 10.1186/s12864-024-10411-1] [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: 01/15/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Alpha-papillomavirus 9 (α-9) is a member of the human papillomavirus (HPV) α genus, causing 75% invasive cervical cancers worldwide. The purpose of this study was to provide data for effective treatment of HPV-induced cervical lesions in Taizhou by analysing the genetic variation and antigenic epitopes of α-9 HPV E6 and E7. METHODS Cervical exfoliated cells were collected for HPV genotyping. Positive samples of the α-9 HPV single type were selected for E6 and E7 gene sequencing. The obtained nucleotide sequences were translated into amino acid sequences (protein primary structure) using MEGA X, and positive selection sites of the amino acid sequences were evaluated using PAML. The secondary and tertiary structures of the E6 and E7 proteins were predicted using PSIPred, SWISS-MODEL, and PyMol. Potential T/B-cell epitopes were predicted by Industrial Engineering Database (IEDB). RESULTS From 2012 to 2023, α-9 HPV accounted for 75.0% (7815/10423) of high-risk HPV-positive samples in Taizhou, both alone and in combination with other types. Among these, single-type-positive samples of α-9 HPV were selected, and the entire E6 and E7 genes were sequenced, including 298 HPV16, 149 HPV31, 185 HPV33, 123 HPV35, 325 HPV52, and 199 HPV58 samples. Compared with reference sequences, 34, 12, 10, 2, 17, and 17 nonsynonymous nucleotide mutations were detected in HPV16, 31, 33, 35, 52, and 58, respectively. Among all nonsynonymous nucleotide mutations, 19 positive selection sites were selected, which may have evolutionary significance in rendering α-9 HPV adaptive to its environment. Immunoinformatics predicted 57 potential linear and 59 conformational B-cell epitopes, many of which are also predicted as CTL epitopes. CONCLUSION The present study provides almost comprehensive data on the genetic variations, phylogenetics, positive selection sites, and antigenic epitopes of α-9 HPV E6 and E7 in Taizhou, China, which will be helpful for local HPV therapeutic vaccine development.
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Affiliation(s)
- Haobo Yuan
- School of Medicine, Shaoxing University, Shaoxing, Zhejiang, 312000, P. R. China
| | - Ziyi Yan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China
| | - Jun Gan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, Zhejiang, 317000, P. R. China
| | - Xinghong Di
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China
| | - Yi Qiu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China
| | - Huihui Xu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China.
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, Zhejiang, 317000, P. R. China.
- Scientific Research Department, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, P. R. China.
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Yan ZY, Di XH, Qiu Y, Ying YY, Gan J, Xu HH. Cervical carcinogenesis risk association of HPV33 E6 and E7 genetic variations in Taizhou, Southeast China. Virol J 2023; 20:156. [PMID: 37468974 DOI: 10.1186/s12985-023-02125-9] [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: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) 33 belongs to the Alphapapillomavirus 9 (α-9 HPV) species group, which also contains types 16, 31, 35, 52, 58 and 67. The purpose of this study was to investigate the genetic variations of HPV33 and to explore its carcinogenicity among women in Taizhou, Southeast China. METHODS Exfoliated cervical cells were collected for HPV genotyping. Only single HPV33 infection cases were selected, and their E6 and E7 genes were sequenced using the ABI 3730xl sequencer and then analysed using MEGA X. RESULTS From 2014 to 2020, a total of 185 single HPV33-positive specimens were successfully amplified. We obtained 15 distinct HPV33 E6/E7 variants, which were published in GenBank under accession numbers OQ672665-OQ672679. Phylogenetic analysis revealed that all HPV33 E6/E7 variants belonged to lineage A, of which 75.7% belonged to lineage A1. Compared with CIN1, the proportion of sublineage A1 in CIN2/3 was higher, but there was no significant difference (76.5% vs. 80.6%, P > 0.05). Altogether, 20 single nucleotide substitutions were identified, of which 6 were novel substitutions, including T196G (C30G), A447T, G458T (R117L), G531A, A704A, and C740T. In addition, no significant trends were observed between the nucleotide substitutions of HPV33 E6/E7 variants and the risk of cervical lesions. CONCLUSION This study provides the most comprehensive data on genetic variations, phylogenetics and carcinogenicity of HPV33 E6/E7 variants in Southeast China to date. The data confirmed that cervical lesions among women in Taizhou are attributable to HPV33, which may be due to the high infection rate of sublineage A1 in the population.
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Affiliation(s)
- Zi-Yi Yan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Xing-Hong Di
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Yi Qiu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Yuan-Yuan Ying
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Jun Gan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, Zhejiang, China
| | - Hui-Hui Xu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China.
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, Zhejiang, China.
- Scientific Research Department, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China.
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Gyöngyösi E, László B, Szalmás A, Kónya J, Veress G. Transcriptional activity of the long control region in human papillomavirus type 33 intratype variants. Virol J 2023; 20:152. [PMID: 37461035 DOI: 10.1186/s12985-023-02114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND High-risk human papillomaviruses (HPVs) are responsible for the development of cervical and other anogenital cancers. Intratype sequence variants of certain high-risk HPV types (e.g. 16, 18 and 31) are thought to have different oncogenic potential, partly due to nucleotide sequence variation in the viral long control region (LCR). The LCR has an important role in the regulation of viral replication and transcription. The purpose of this study was to explore sequence variation in the LCR of HPV 33 intratype variants in Hungary and to see whether there are differences in the transcriptional activities of the variants. METHODS The complete HPV 33 LCR was amplified from HPV 33 positive cervical samples. After sequencing the LCR variants, multiple sequence alignment and phylogenetic analyses were carried out. Representative HPV 33 LCR sequence variants were selected for cloning and functional analysis. After transient transfection of HeLa cells, luciferase reporter assays were used to analyse the transcriptional activities of different LCR variants. RESULTS Altogether 10 different variants were identified by sequence analysis of the HPV 33 LCR. The results of phylogenetic analysis showed that 3 variants belonged to sublineage A1, while the other 7 variants clustered with sublineage A2. Variants belonging to sublineage A2 had significantly lower transcriptional activities than variants belonging to sublineage A1. Within sublineage A2, the two variants analysed had significantly different transcriptional activities, which was shown to be caused by the A7879G variation. CONCLUSIONS Nucleotide variation in the HPV 33 LCR can result in altered transcriptional activity of the intratype variants. Our results can help to understand the correlation between LCR polymorphism and the oncogenic potential of HPV 33 variants.
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Affiliation(s)
- Eszter Gyöngyösi
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Brigitta László
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Anita Szalmás
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - József Kónya
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - György Veress
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
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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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Yu M, Wu S, Wang S, Cui C, Lu Y, Sun Z. Polymorphism of E6 and E7 Genes in Human Papillomavirus Types 31 and 33 in Northeast China. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:9338294. [PMID: 36950084 PMCID: PMC10027458 DOI: 10.1155/2023/9338294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/04/2023] [Accepted: 01/30/2023] [Indexed: 03/14/2023]
Abstract
Persistent infection with human papillomavirus (HPV) types 31 and 33 is an important causative factor for cervical cancer. The E6/E7 genes are key oncogenes involved in the immortalization and transformation of human epithelial cells. Genetic polymorphism may lead to differences in the virus' carcinogenic potential, the immune reaction of the host, and the potencies of vaccines. Few studies on HPV31/33 E6/E7 genetic polymorphism have been carried out. To study the genetic polymorphism of HPV31 and HPV33 E6/E7 genes in northeast China, these genes (HPV31 E6/E7, n = 151; HPV33 E6/E7, n = 136) were sequenced and compared to reference sequences (J04353.1, M12732.1) using BioEdit. Phylogenetic trees were constructed by the neighbor-joining method using MegaX. The diversity of the secondary structure was estimated using the PSIPred server. The positively selected sites were analyzed using PAML4.9. The major histocompatibility complex (MHC) class I and MHCII epitopes were predicted using the ProPred-I server and ProPredserver. B-cell epitopes were predicted using the ABCpred server. In the 151 HPV31E6 sequences, 25 (25/450) single-nucleotide mutations were found, 14 of which were synonymous mutations and 11 were nonsynonymous. In the 151 HPV31E7 sequences, 8 (8/297) nucleotide mutations were found, 3 of which were synonymous mutations and 5 were nonsynonymous. In the 136 HPV33E6 sequences, 17 (17/450) nucleotide mutations were observed, 7 of which were synonymous mutations and 10 were nonsynonymous. C14T/G (T5I/S) was a triallelic mutation. Finally, in the 136 HPV33E7 sequences, 9 (9/294) nucleotide mutations were observed, 3 of which were synonymous mutations and 6 were nonsynonymous. C134T/A (A45V/E) and C278G/A (T93S/N) were triallelic mutations. Lineage A was the most common lineage in both HPV31 and HPV33. In all of the sequences, we only identified one positively selected site, HPV33 E6 (K93N). Most nonsynonymous mutations were localized at sites belonging to MHC and/or B-cell predicted epitopes. Data obtained in this study should contribute to the development and application of detection probes, targeted drugs, and vaccines.
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Affiliation(s)
- Miao Yu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Si Wu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shuang Wang
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Changwan Cui
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiping Lu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengrong Sun
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Ferraz MVF, Viana IFT, Coêlho DF, da Cruz CHB, de Arruda Lima M, de Luna Aragão MA, Lins RD. Association strength of E6 to E6AP/p53 complex correlates with HPV‐mediated oncogenesis risk. Biopolymers 2022; 113:e23524. [DOI: 10.1002/bip.23524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Matheus Vitor Ferreira Ferraz
- Aggeu Magalhães Institute Oswaldo Cruz Foundation Recife Brazil
- Department of Fundamental Chemistry Federal University of Pernambuco Recife Brazil
| | | | - Danilo Fernandes Coêlho
- Aggeu Magalhães Institute Oswaldo Cruz Foundation Recife Brazil
- Department of Fundamental Chemistry Federal University of Pernambuco Recife Brazil
| | | | | | | | - Roberto Dias Lins
- Aggeu Magalhães Institute Oswaldo Cruz Foundation Recife Brazil
- Department of Fundamental Chemistry Federal University of Pernambuco Recife Brazil
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Li S, Ye M, Chen Y, Gong Q, Mei B. Genetic variation of E6 and E7 genes of human papillomavirus 52 from Central China. J Med Virol 2021; 93:3849-3856. [PMID: 33230866 DOI: 10.1002/jmv.26690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/07/2020] [Accepted: 11/20/2020] [Indexed: 12/26/2022]
Abstract
Cervical cancer is the fourth most common malignant tumor in women worldwide and is closely related to human papillomavirus (HPV). Women have the highest susceptibility to HPV-52 type in Jingzhou, China. In this study, E6-E7 sequences of 183 HPV-52 positive samples were amplified by a polymerase chain reaction and sequenced. HPV-52 E6-E7 gene variations were analyzed. The phylogenetic tree was constructed using the Kimura 2-parameter method. The secondary structure of the protein was analyzed. The selective pressure to E6-E7 genes was estimated using PAML. In addition, the B cell epitopes of the E6-E7 sequences in HPV-52 were predicted by the ABCpred server. In E6 sequences, 15 single nucleotide variants were observed, including 6 nonsynonymous variants and 9 synonymous variants. In E7 sequences, 19 single nucleotide variants occurred, including 10 nonsynonymous variants and 9 synonymous variants. Six amino acid variants, including 3 nonconservative substitutions, were found in sequences encoding the alpha helix. Eight amino acid variants, including three nonconservative substitutions, occurred in sequences encoding the strand. Through phylogenetic analysis, the E6-E7 sequences were mainly distributed in B lineage. In HPV-52 E6-E7 sequences, no positively selected site was found. The nonconservative substitutions, such as K93R, K93E in E6, T37I, and D38N in E7, affected multiple hypothetical epitopes in the B cell. This study provides information for the investigation of HPV epidemic characters. The discovery of new variants of HPV-52 may lay the basis for the development of the virus diagnosis, further study of cervical cancer, and vaccine design in Central China.
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Affiliation(s)
- Shuo Li
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Mengxia Ye
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Yonglin Chen
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China
| | - Bing Mei
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, China
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de Sousa E, Ligeiro D, Lérias JR, Zhang C, Agrati C, Osman M, El-Kafrawy SA, Azhar EI, Ippolito G, Wang FS, Zumla A, Maeurer M. Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Int J Infect Dis 2020; 98:454-459. [PMID: 32693089 PMCID: PMC7368421 DOI: 10.1016/j.ijid.2020.07.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic factors such as the HLA type of patients may play a role in regard to disease severity and clinical outcome of patients with COVID-19. Taking the data deposited in the GISAID database, we made predictions using the IEDB analysis resource (TepiTool) to gauge how variants in the SARS-CoV-2 genome may change peptide binding to the most frequent MHC-class I and -II alleles in Africa, Asia and Europe. We caracterized how a single mutation in the wildtype sequence of of SARS-CoV-2 could influence the peptide binding of SARS-CoV-2 variants to MHC class II, but not to MHC class I alleles. Assuming the ORF8 (L84S) mutation is biologically significant, selective pressure from MHC class II alleles may select for viral varients and subsequently shape the quality and quantity of cellular immune responses aginast SARS-CoV-2. MHC 4-digit typing along with viral sequence analysis should be considered in studies examining clinical outcomes in patients with COVID-19.
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Affiliation(s)
- Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal.
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation (Instituto Português do Sangue e Transplantação, IPST, Lisbon, Portugal.
| | - Joana R Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal.
| | - Chao Zhang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
| | - Chiara Agrati
- National Institute for Infectious Diseases, Lazzaro Spallanzani, Rome, Italy.
| | - Mohamed Osman
- York Biomedical Research Institute, University of York, United Kingdom and Emerging and Re-Emerging Diseases, University of Khartoum, Sudan.
| | - Sherif A El-Kafrawy
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases, Lazzaro Spallanzani, Rome, Italy.
| | - Fu-Sheng Wang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK.
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal; I Medical Clinical, University of Mainz, Germany.
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Dong D, Zhu Y, Aili Z, Chen Z, Ding J. Bioinformatics analysis of HPV-68 E6 and E7 oncoproteins for designing a therapeutic epitope vaccine against HPV infection. INFECTION GENETICS AND EVOLUTION 2020; 81:104266. [PMID: 32114254 DOI: 10.1016/j.meegid.2020.104266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
The incidence and mortality of cervical cancer, which mainly results from the infection of human papillomavirus (HPV) is significantly increasing in Xinjiang. According to the previous research, the incidence of HPV-68 in cervical cancer patients in Xinjiang is significantly higher than in other parts of China. HPV E6 and E7 oncoproteins play a crucial role in cervical cancer, and can be used as ideal targets for therapeutic vaccines. Therefore, we analyzed and identified the possible T-cell and B-cell dominant epitopes and various aspects of HPV-68 E6 and E7 oncoproteins, including the physicochemical properties, secondary and tertiary structures using a bioinformatic approach, which provided a basis for designing an effective HPV infection therapeutic vaccine. The results showed that E6 oncoproteins was an unstable and hydrophilic protein, while E7 oncoproteins was unstable and hydrophilic protein. The secondary structure of the E6 oncoproteins consisted of 45.57% alpha helixes, 14.56% extended strands, 4.43% beta turns and 35.44% random coils. The secondary structure of E7 oncoproteins consisted of 35.45% alpha helixes, 17.27% extended strands, 0.91% beta turns and 46.36% random coils. Moreover, our results identified 5 dominant T-cell epitopes and 6 dominant B-cell epitopes in the E6 oncoproteins structure and 5 dominant T-cell epitopes and 3 dominant B-cell epitopes in E7 oncoproteins. In conclusion, this study provides comprehensive biological information about the HPV-68 E6 and E7 oncoproteins, which will lay a theoretical foundation for multi-epitope vaccines against HPV infection.
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Affiliation(s)
- Di Dong
- Department of Gynecology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Yuejie Zhu
- Center of Reproductive Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Zufeiya Aili
- Department of Gynecology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Zhifang Chen
- Department of Gynecology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China.
| | - Jianbing Ding
- Department of Immunology, Xinjiang Medical University, Urumqi, Xinjiang 830011, China.
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Zhao J, Zhan Q, Guo J, Liu M, Ruan Y, Zhu T, Han L, Li F. Phylogeny and polymorphism in the E6 and E7 of human papillomavirus: alpha-9 (HPV16, 31, 33, 52, 58), alpha-5 (HPV51), alpha-6 (HPV53, 66), alpha-7 (HPV18, 39, 59, 68) and alpha-10 (HPV6, 44) in women from Shanghai. Infect Agent Cancer 2019; 14:38. [PMID: 31832087 PMCID: PMC6873513 DOI: 10.1186/s13027-019-0250-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
Background Persistent infection with human papillomaviruses (HPVs) has been associated with cervical intraepithelial neoplasia (CIN) and cervical cancer. However, why only a fraction of HPV cases progress to cancer is still unclear. Methods We focused on the heterogeneity, classification, evolution and dispersal of variants for 14 common HPV types in 262 HPV-positive patients with cervical lesions. The E6 and E7 genes of HPV were sequenced and compared with the HPV reference for sequence analysis. Phylogenetic trees were constructed using the neighbour-joining tree method with MEGA 7.0. Results In this study, 233 E6 and 212 E7 sequences were successfully amplified by PCR, and these sequences were divided into 5 species groups: alpha-9 (HPV16, 31, 33, 52, 58), alpha-5 (HPV51), alpha-6 (HPV53, 66), alpha-7 (HPV18, 39, 59, 68) and alpha-10 (HPV6, 44). The incidence of high-grade squamous intraepithelial lesion (HSIL) in patients infected with alpha-9 HPV was significantly increased compared with other groups (P < 0.0001), especially HPV16 (P < 0.0001). Strikingly, E7 had significantly fewer nonsynonymous variants in the HSIL compared to <HSIL groups (P = 3.17× 10- 4). The A388C (K93 N) variation in HPV58 E6 can significantly reduce the risk of HSIL (P = 0.015). However, T7220G (D32E) variation in HPV16 E6 and A7689G (N29S) in HPV16 E7 increased the incidence of HSIL compared to the <HSIL group (P = 0.036 and 0.022). Conclusions Strict conservation of E7 is important for HPV carcinogenicity, especially N29 of HPV16. The findings in this work provide preventative/therapeutic interventions for HPV infections and CIN.
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Affiliation(s)
- Junwei Zhao
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Qin Zhan
- 2Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204 China
| | - Junhan Guo
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Min Liu
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Yetian Ruan
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Tailin Zhu
- 3School of Physics HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Lingfei Han
- 2Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204 China
| | - Fang Li
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
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12
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Chen Z, Li Q, Huang Q, Liu H, Jiang H, Chen Z, An Z, Luo Q. Characteristics of human papillomaviruses distribution in Guizhou Province, China. Virol J 2019; 16:123. [PMID: 31665045 PMCID: PMC6819633 DOI: 10.1186/s12985-019-1239-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV) is one of the most common sexually transmitted viruses. Data about HPV infection in Guizhou is limited. METHODS 56,768 cervical samples were collected and genotyped for 15 main high risk and 6 main low risk HPV types. RESULTS 16.95% (9623/56768) of samples were HPV positive; 90.70% (8728/9623) of HPV positive women were infected by high risk HPV. High risk and high risk mix infection (1458; 70.85%) was the most common mix HPV infection type. The highest HPV detection rate was found in age group 41-45 years old (detection rate = 17.89%) (χ2 = 204.77; P < 0.001); the highest within-group HPV infection rates were found in the ≤20 (25.62%) and ≥ 61 (24.67%) years old age groups, the lowest within-group HPV infection rate was found in the 31-35 years old age group (15.02%). The highest mix infection proportions were found in the ≥61 (36.06%) and ≤ 20 (33.63%) years old age groups (χ2 = 111.21; P < 0.001), the lowest mix infection proportion was found in the 41-45 (17.42%) years old age group. The highest high risk infection proportions were found in the 26-30 (92.98%), ≥61 (92.68%), and 36-40 (92.16%) years old age groups (χ2 = 31.72; P < 0.001), the lowest high risk infection proportion was found in the ≤20 (84.96%) years old age group. HPV infection rates varied with seasons in Guizhou. CONCLUSIONS Characteristics of HPV distribution in Guizhou were identified. There were significant differences in HPV distribution among age groups, prevention strategies should be adjusted according to the characteristics.
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Affiliation(s)
- Zuyi Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Qiongyao Li
- Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Qiong Huang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Huaqing Liu
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Hongwu Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
- Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Zehui Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Zhengyuan An
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
| | - Qingfang Luo
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou People’s Republic of China
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13
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Chen Z, Li Q, Huang J, Li J, Yang F, Min X, Chen Z. E6 and E7 gene polymorphisms in human papillomavirus Type-6 identified in Southwest China. Virol J 2019; 16:114. [PMID: 31511025 PMCID: PMC6740006 DOI: 10.1186/s12985-019-1221-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomavirus type-6 (HPV6) is the major etiological agent of anogenital warts both men and women. The present study aimed to characterize the genetic diversity among HPV6 in Southwest China, and to investigate the origin of, selective pressure experienced by, and impact of the resultantly identified genetic variants on the HPV6 secondary structure. METHODS Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by 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 Phylogenetic Analyses by Maximum Likelihood version 4.8 software. RESULTS HPV6 was the most prevalent low risk HPV type in southwest China. In total, 143 E6 and E7 gene sequences of HPV6 isolated from patients were sequenced and compared to GenBank HPV6 reference sequence X00203. The results of these analyses revealed that both the HPV6 E6 and E7 were highly conserved within the analyzed patient samples, and comprised only 3 types of variant sequence, respectively. Furthermore, the analysis of HPV6 E6 and E7 sequences revealed seven/five single-nucleotide mutations, two/four and five/one of which were non-synonymous and synonymous, respectively. The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. CONCLUSIONS HPV6 (detection rate = 13.10%) was very prevalent in southwest China, both the HPV6 E6 and E7 sequences were highly conserved within the analyzed patient samples in southwest China, indicating that the low risk HPV6 can adapt to the environment well without much evolution.
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Affiliation(s)
- Zuyi Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China
| | - Qiongyao Li
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China.,Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jian Huang
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jin Li
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Feng Yang
- Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Xun Min
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.
| | - Zehui Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
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14
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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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15
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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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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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Correction: E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China. PLoS One 2017; 12:e0181475. [PMID: 28700689 PMCID: PMC5507315 DOI: 10.1371/journal.pone.0181475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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