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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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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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Kombe Kombe AJ, Li B, Zahid A, Mengist HM, Bounda GA, Zhou Y, Jin T. Epidemiology and Burden of Human Papillomavirus and Related Diseases, Molecular Pathogenesis, and Vaccine Evaluation. Front Public Health 2021; 8:552028. [PMID: 33553082 PMCID: PMC7855977 DOI: 10.3389/fpubh.2020.552028] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022] Open
Abstract
Diagnosed in more than 90% of cervical cancers, the fourth deadliest cancer in women, human papillomavirus (HPV) is currently the most common pathogen responsible for female cancers. Moreover, HPV infection is associated with many other diseases, including cutaneous and anogenital warts, and genital and upper aerodigestive tract cancers. The incidence and prevalence of these pathologies vary considerably depending on factors including HPV genotype, regional conditions, the study population, and the anatomical site sampled. Recently, features of the cervicovaginal microbiota are found to be associated with the incidence of HPV-related diseases, presenting a novel approach to identify high-risk women through both blood and cervical samples. Overall, the HPV repartition data show that HPV infection and related diseases are more prevalent in developing countries. Moreover, the available (2-, 4-, and 9-valent) vaccines based on virus-like particles, despite their proven effectiveness and safety, present some limitations in terms of system development cost, transport cold chain, and oncogenic HPV variants. In addition, vaccination programs face some challenges, leading to a considerable burden of HPV infection and related diseases. Therefore, even though the new (9-valent) vaccine seems promising, next-generation vaccines as well as awareness programs associated with HPV vaccination and budget reinforcements for immunization are needed.
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Affiliation(s)
- Arnaud John Kombe Kombe
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Gabonese Scientific Research Consortium, Libreville, Gabon
| | - Bofeng Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ayesha Zahid
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hylemariam Mihiretie Mengist
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Guy-Armel Bounda
- Gabonese Scientific Research Consortium, Libreville, Gabon.,Department of Clinical Pharmacy, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Sinomedica Co., Ltd., Mong Kok, Hong Kong
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Chinese Academy of Science Center for Excellence in Molecular Cell Science, Shanghai, China
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Evidence for Missing Positive Results for Human Papilloma Virus 45 (HPV-45) and HPV-59 with the SPF 10-DEIA-LiPA 25 (Version 1) Platform Compared to Type-Specific Real-Time Quantitative PCR Assays and Impact on Vaccine Effectiveness Estimates. J Clin Microbiol 2020; 58:JCM.01626-20. [PMID: 32907991 PMCID: PMC7587105 DOI: 10.1128/jcm.01626-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/01/2020] [Indexed: 11/29/2022] Open
Abstract
Human papillomavirus (HPV) epidemiological and vaccine studies require highly sensitive HPV detection systems. The widely used broad-spectrum SPF10-DEIA-LiPA25 (SPF10 method) has reduced sensitivity toward HPV-45 and -59. Therefore, anogenital samples from the PASSYON study were retrospectively analyzed with type-specific (TS) HPV-45 and -59 real-time quantitative PCR (qPCR) assays. The SPF10 method missed 51.1% of HPV-45 and 76.1% of HPV-59 infections that were detected by the TS qPCR assays. Human papillomavirus (HPV) epidemiological and vaccine studies require highly sensitive HPV detection systems. The widely used broad-spectrum SPF10-DEIA-LiPA25 (SPF10 method) has reduced sensitivity toward HPV-45 and -59. Therefore, anogenital samples from the PASSYON study were retrospectively analyzed with type-specific (TS) HPV-45 and -59 real-time quantitative PCR (qPCR) assays. The SPF10 method missed 51.1% of HPV-45 and 76.1% of HPV-59 infections that were detected by the TS qPCR assays. The viral copy number (VCn) of SPF10-missed HPV-45 and -59 was significantly lower than SPF10-detected HPV-45 and -59 (P < 0.0001 for both HPV types). Sanger sequencing showed no phylogenetic distinction between SPF10-missed and SPF10-detected HPV-59 variants, but variants bearing the A6562G single-nucleotide polymorphism (SNP) in the SPF10 target region were more likely to be missed (P = 0.0392). HPV cooccurrence slightly influenced the detection probability of HPV-45 and -59 with the SPF10 method. Moreover, HPV-59 detection with the SPF10 method was hampered more in nonvaccinated women than vaccinated women, likely due to a stronger masking effect by increased HPV cooccurrence in the former group. Consequently, the SPF10 method led to a strong negative vaccine effectiveness (VE) of –84.6% against HPV-59, while the VE based on TS qPCR was 3.1%. For HPV-45, the relative increase in detection in nonvaccinated women compared vaccinated women was more similar, resulting in comparable VE estimates. In conclusion, this study shows that HPV-45 and -59 detection with the SPF10 method is dependent on factors including VCn, HPV cooccurrence, and vaccination, thereby showing that knowledge of the limitations of the HPV detection method used is of great importance.
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Chan WS, Chan TL, Au CH, Leung CP, To MY, Ng MK, Leung SM, Chan MKM, Ma ESK, Tang BSF. An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping. Diagn Pathol 2020; 15:45. [PMID: 32375813 PMCID: PMC7203875 DOI: 10.1186/s13000-020-00964-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022] Open
Abstract
Background Human papillomavirus (HPV) testing has been employed by several European countries to augment cytology-based cervical screening programs. A number of research groups have demonstrated potential utility of next-generation sequencing (NGS) for HPV genotyping, with comparable performance and broader detection spectrum than current gold standards. Nevertheless, most of these NGS platforms may not be the best choice for medium sample throughput and laboratories with less resources and space. In light of this, we developed a Nanopore sequencing assay for HPV genotyping and compared its performance with cobas HPV Test and Roche Linear Array HPV Genotyping Test (LA). Methods Two hundred and one cervicovaginal swabs were routinely tested for Papanicolaou smear, cobas HPV Test and LA. Residual DNA was used for Nanopore protocol after routine testing. Briefly, HPV L1 region was amplified using PGMY and MGP primers, and PCR-positive specimens were sequenced on MinION flow cells (R9.4.1). Data generated in first 2 h were aligned with reference sequences from Papillomavirus Episteme database for genotyping. Results Nanopore detected 96 HPV-positive (47.76%) and 95 HPV-negative (47.26%) specimens, with 10 lacking β-globin band and not further analyzed (4.98%). Substantial agreement was achieved with cobas HPV Test and LA (κ: 0.83–0.93). In particular, Nanopore appeared to be more sensitive than cobas HPV Test for HPV 52 (n = 7). For LA, Nanopore revealed higher concordance for high-risk (κ: 0.93) than non-high risk types (κ: 0.83), and with similar high-risk positivity in each cytology grading. Nanopore also provided better resolution for HPV 52 in 3 specimens co-infected with HPV 33 or 58, and for HPV 87 which was identified as HPV 84 by LA. Interestingly, Nanopore identified 5 additional HPV types, with an unexpected high incidence of HPV 90 (n = 12) which was reported in North America and Belgium but not in Hong Kong. Conclusions We developed a Nanopore workflow for HPV genotyping which was economical (about USD 50.77 per patient specimen for 24-plex runs), and with comparable or better performance than 2 reference methods in the market. Future prospective study with larger sample size is warranted to further evaluate test performance and streamline the protocol.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chin Pang Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Yan To
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - May Kwok Mei Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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Mane A, Patil L, Limaye S, Nirmalkar A, Kulkarni‐Kale U. Characterization of major capsid protein (L1) variants of
Human papillomavirus
type 16 by cervical neoplastic status in Indian women: Phylogenetic and functional analysis. J Med Virol 2020; 92:1303-1308. [DOI: 10.1002/jmv.25675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/10/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Arati Mane
- Division of MicrobiologyICMR‐National AIDS Research InstitutePune India
| | - Linata Patil
- Division of MicrobiologyICMR‐National AIDS Research InstitutePune India
| | - Sanket Limaye
- Bioinformatics CentreSavitribai Phule Pune UniversityPune India
| | - Amit Nirmalkar
- Division of Data Management, Biostatistics and ITICMR‐National AIDS Research InstitutePune India
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Li H, Zhang L, Ren H, Hu P. Higher baseline viral diversity correlates with lower HBsAg decline following PEGylated interferon-alpha therapy in patients with HBeAg-positive chronic hepatitis B. Infect Drug Resist 2018; 11:671-680. [PMID: 29765238 PMCID: PMC5939877 DOI: 10.2147/idr.s163765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Viral diversity seems to predict treatment outcomes in certain viral infections. The aim of this study was to evaluate the association between baseline intra-patient viral diversity and hepatitis B surface antigen (HBsAg) decline following PEGylated interferon-alpha (Peg-IFN-α) therapy. Patients and methods Twenty-six HBeAg-positive patients who were treated with Peg-IFN-α were enrolled. Nested polymerase chain reaction (PCR), cloning, and sequencing of the hepatitis B virus S gene were performed on baseline samples, and normalized Shannon entropy (Sn) was calculated as a measure of small hepatitis B surface protein (SHBs) diversity. Multiple regression analysis was used to estimate the association between baseline Sn and HBsAg decline. Results Of the 26 patients enrolled in the study, 65.4% were male and 61.5% were infected with hepatitis B virus genotype B. The median HBsAg level at baseline was 4.5 log10 IU/mL (interquartile range: 4.1–4.9) and declined to 3.0 log10 IU/mL (interquartile range: 1.7–3.9) after 48 weeks of Peg-IFN-α treatment. In models adjusted for baseline alanine aminotransferase (ALT) and HBsAg, the adjusted coefficients (95% CI) for ΔHBsAg and relative percentage HBsAg decrease were −1.3 (−2.5, −0.2) log10 IU/mL for higher SHBs diversity (Sn≥0.58) patients and −26.4% (−50.2%, −2.5%) for lower diversity (Sn<0.58) patients. Further analysis showed that the “a” determinant upstream flanking region and the first loop of the “a” determinant (nucleotides 341–359, 371–389, and 381–399) were the main sources of higher SHBs diversity. Conclusion Baseline intra-patient SHBs diversity was inverse to HBsAg decline in HBeAg-positive chronic hepatitis B (CHB) patients receiving Peg-IFN-α monotherapy. Also, more sequence variations within the “a” determinant upstream flanking region and the first loop of the “a” determinant were the main sources of the higher SHBs diversity.
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Affiliation(s)
- Hu Li
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Li Zhang
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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8
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Sait K, Turki R, Abuzenadah AM, Jiffiri OH, Bohmaidah A, Sohrab SS. Genetic diversity and phylogenetic analysis of HPV 16 & 18 variants isolated from cervical specimens of women in Saudi Arabia. Saudi J Biol Sci 2018; 26:317-324. [PMID: 31485171 PMCID: PMC6717139 DOI: 10.1016/j.sjbs.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/20/2018] [Accepted: 05/01/2018] [Indexed: 12/31/2022] Open
Abstract
Human papillomavirus (HPV) are well known to be associated with the development of cervical cancer. HPV16 and HPV 18 are known as high-risk types and reported to be predominantly associated with cervical cancer. The prevalence and genetic diversity of HPV have been well documented globally but, in the Kingdom of Saudi Arabia, data on HPV genetic diversity are lacking. In this study, we have analyzed the genetic diversity of both HPV16 and HPV18 based on their L1 gene sequence because L1 gene is a major capsid protein gene and has been utilized to develop a prophylactic vaccine. In January 2011-2012, a total of forty samples from cervical specimens of women in Saudi Arabia were collected. The association of HPV16, HPV18 was detected by polymerase chain reaction, sequenced and submitted to GenBank. The sequences identity matrix and the phylogenetic relationship were analyzed with selected HPVs. The highest sequence identity (99.5%) for HPV16 and (99.3%) for HPV was observed with selected HPVs. The phylogenetic analysis results showed that HPVs from Saudi Arabia formed a closed cluster with African, Asian, East Asian as well as American HPVs distributed into multiple linages from various geographical locations. The results provided the valuable information about genetic diversity, but there is an urgent need to generate full genome sequence information which will provide a clearer picture of the genetic diversity and evolution of HPVs in Saudi Arabia. In conclusion, the generated data will be highly beneficial for developing molecular diagnostic tools, analyzing and correlating the epidemiological data to determine the risk of cervical cancer and finally to develop a vaccine for Saudi Arabian population.
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Affiliation(s)
- Khalid Sait
- Faculty of Medicine, Department of Obstetrics and Gynecology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rola Turki
- Faculty of Medicine, Department of Obstetrics and Gynecology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel Mohammed Abuzenadah
- Faculty of Applied Medical Sciences, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osama H Jiffiri
- Faculty of Medicine, Department of Obstetrics and Gynecology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulbaset Bohmaidah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Faculty of Applied Medical Sciences, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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van der Weele P, Meijer CJLM, King AJ. High Whole-Genome Sequence Diversity of Human Papillomavirus Type 18 Isolates. Viruses 2018; 10:v10020068. [PMID: 29414918 PMCID: PMC5850375 DOI: 10.3390/v10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
Background: The most commonly found human papillomavirus (HPV) types in cervical cancer are HPV16 and HPV18. Genome variants of these types have been associated with differential carcinogenic potential. To date, only a handful of studies have described HPV18 whole genome sequencing results. Here we describe HPV18 variant diversity and conservation of persistent infections in a longitudinal retrospective cohort study. Methods: Cervical self-samples were obtained annually over four years and genotyped on the SPF10-DEIA-LiPA25 platform. Clearing and persistent HPV18 positive infections were selected, amplified in two overlapping fragments, and sequenced using 32 sequence primers. Results: Complete viral genomes were obtained from 25 participants with persistent and 26 participants with clearing HPV18 infections, resulting in 52 unique HPV18 genomes. Sublineage A3 was predominant in this population. The consensus viral genome was completely conserved over time in persistent infections, with one exception, where different HPV18 variants were identified in follow-up samples. Conclusions: This study identified a diverse set of HPV18 variants. In persistent infections, the consensus viral genome is conserved. The identification of only one HPV18 infection with different major variants in follow-up implies that this is a potentially rare event. This dataset adds 52 HPV18 genome variants to Genbank, more than doubling the currently available HPV18 information resource, and all but one variant are unique additions.
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Affiliation(s)
- Pascal van der Weele
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, 3721 MA Bilthoven, The Netherlands.
- Department of Pathology, Vrije Universiteit-University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands.
| | - Chris J L M Meijer
- Department of Pathology, Vrije Universiteit-University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands.
| | - Audrey J King
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, 3721 MA Bilthoven, The Netherlands.
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El-Aliani A, Alaoui MAE, Chaoui I, Ennaji MM, Attaleb M, Mzibri ME. Naturally occurring capsid protein variants L1 of human papillomavirus genotype 16 in Morocco. Bioinformation 2017; 13:241-248. [PMID: 28959092 PMCID: PMC5609288 DOI: 10.6026/97320630013241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022] Open
Abstract
HPV L1 protein is a corner stone in HPV structure, it's involved in the formation of the viral capsid; widely used as a systematic material and considered as the main component in vaccines development and production. The present study aims to characterize genetic variation of L1 gene of HPV 16 specimens and to evaluate in silico the impact of major variants on the epitope change affecting its conformational structure. A fragment of L1 gene from 35 HPV 16 confirmed specimens were amplified by PCR and sequenced. Overall, five amino acids residues changes were reported: T390P in 16 specimens, M425I and M431I in 2 cases, insertion of Serine at 460 and aspartic acid deletion at position 477 in all analyzed cases. The 3D generated model showed that T389P amino acid substitution is located in the H-I loop; the two substitutions M424I and M430I are both located in the H2 helice. The Serine insertion and aspartic acid deletion are located in the H4 helice and B-C loop, respectively. Superimposition of sequences' structures showed that they share a very similar conformation highlighting that the reported amino acids variations don't affect the structure of the L1 protein. However T389P, located in the H-I loop identified as an immunogenetic region of L1 capsid, was reported in 51.4% of cases could interact with vaccines induced monoclonal antibodies suggesting a potential impact on the efficacy of available anti-HPV vaccines.
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Affiliation(s)
- Aissam El-Aliani
- Unit of Biology and Medical Research, National Centre Natuional de l´Energie, des Sciences et des techniques Nucléaires. Morocco
- Laboratory of Virology Microbiology, Quality, Biotechnologies/Eco-Toxicology and Biodiversity (LVMQB/ETB), Faculté des Sciences et Techniques Mohammedia, Morocco
| | | | - Imane Chaoui
- Unit of Biology and Medical Research, National Centre Natuional de l´Energie, des Sciences et des techniques Nucléaires. Morocco
| | - My Mustapha Ennaji
- Laboratory of Virology Microbiology, Quality, Biotechnologies/Eco-Toxicology and Biodiversity (LVMQB/ETB), Faculté des Sciences et Techniques Mohammedia, Morocco
| | - Mohammed Attaleb
- Unit of Biology and Medical Research, National Centre Natuional de l´Energie, des Sciences et des techniques Nucléaires. Morocco
| | - Mohammed El Mzibri
- Unit of Biology and Medical Research, National Centre Natuional de l´Energie, des Sciences et des techniques Nucléaires. Morocco
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King AJ, Sonsma JA, Vriend HJ, van der Sande MAB, Feltkamp MC, Boot HJ, Koopmans MPG. Correction: Genetic Diversity in the Major Capsid L1 Protein of HPV-16 and HPV-18 in the Netherlands. PLoS One 2016; 11:e0154977. [PMID: 27123932 PMCID: PMC4849751 DOI: 10.1371/journal.pone.0154977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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