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Li T, Yang Z, Luo P, Yang Y, Lin Z, Mei B. Genetic variability of human papillomavirus type 18 based on E6, E7 and L1 genes in central China. Virol J 2024; 21:152. [PMID: 38970084 PMCID: PMC11227198 DOI: 10.1186/s12985-024-02424-9] [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: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND High-risk human papillomavirus (HR-HPV) infection is an important factor for the development of cervical cancer. HPV18 is the second most common HR-HPV after HPV16. METHODS In this study, MEGA11 software was used to analyze the variation and phylogenetic tree of HPV18 E6-E7 and L1 genes. The selective pressure to E6, E7 and L1 genes was estimated using pamlX. In addition, the B cell epitopes of L1 amino acid sequences and T cell epitopes of E6-E7 amino acid sequences in HPV18 were predicted by ABCpred server and IEDB website, respectively. RESULTS A total of 9 single nucleotide variants were found in E6-E7 sequences, of which 2 were nonsynonymous variants and 7 were synonymous variants. Twenty single nucleotide variants were identified in L1 sequence, including 11 nonsynonymous variants and 9 synonymous variants. Phylogenetic analysis showed that E6-E7 and L1 sequences were all distributed in A lineage. In HPV18 E6, E7 and L1 sequences, no positively selected site was found. The nonconservative substitution R545C in L1 affected hypothetical B cell epitope. Two nonconservative substitutions, S82A in E6, and R53Q in E7, impacted multiple hypothetical T cell epitopes. CONCLUSION The sequence variation data of HPV18 may lay a foundation for the virus diagnosis, further study of cervical cancer and vaccine design in central China.
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Affiliation(s)
- Ting Li
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China
| | - Zhiping Yang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China
| | - Ping Luo
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China
| | - Yang Yang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China
| | - Zicong Lin
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China
| | - Bing Mei
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434020, China.
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Hung TM, Son HX, Bang LVN, Van Duyet L. Characteristics of Cervical Cancer Caused by the Human Papillomavirus 18 and Its Genetic Variations in Vietnamese Women. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105546. [PMID: 38176603 DOI: 10.1016/j.meegid.2023.105546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND The involvement of HPV18 in cervical cancer pathogenesis, as well as its high oncogenic potential and influence on the variation of cervical cancer distribution in different geographical regions, makes assessing the characteristics of cervical cancer and its variants the basis for considering potential carcinogenic HPV18 sequence variations and vaccine strategies. METHODS A prospective study was conducted at Vietnam Central Obstetrics Hospital from January 1, 2019 to December 31, 2020. HPV18 infection was confirmed in cervical cancer patients using molecular diagnostics. Nucleotide sequences of the HPV18 E6, E7, and L1 genes were used to analyze genetic variations. The demographic, clinical, and laboratory data of the patients were collected and statistically analyzed. RESULTS Among 48 patients with HPV18-infected cervical cancer, 79.2% were between the ages of 35-54; while only 20.8% were < 35 and > 54 years old. 100% of patients have been pregnant at some point in their lives, with ≥3 pregnancies accounting for 83.3%. Patients with cervical cancer caused by HPV18 infection were predominantly in stages 0 and I, with no patients in stages II, III, or IV. A single HPV18 infection generates much more cervical cancer cases than multiple HPV18 infections. Symptoms such as lower abdomen pain, unusual anginal discharge, and vaginal bleeding were observed in both stages 0 and I; however, vaginal bleeding after sex was only detected in women with stage I cervical cancer. Cervicitis, cervical ectropion, and ulcers are reported in cervical status stages 0 and I; however, warts and ulcers were only present in stage I. Magnetic resonance imaging produces far superior outcomes than ultrasound. All cytology and pathology tests confirmed L/HSIL, SCC, AC, and CIS. On the other hand, a single HPV18 infection was associated with a significantly higher risk of L/HSIL, SCC, AC, and CIS than multiple HPV18 infections. Nulceotide sequences of the E6, E7, and L1 genes revealed 20 mutations, including three (E6), five (E7), and twelve (L1) mutations. High-frequency mutations (95.8%-100% of HPV18 samples had mutations) occur at the following positions: C287G - P61P (E6 gene), G5503A - R25Q, C5701G - P91R, C6460G - P344R, C6625G - P399R, and C6842G - P471R (L1 gene). A phylogenetic tree based on the E6/E7/L1 gene sequence revealed that 100% belonged to A lineage, with 97.9% belonging AA (Asian Amerindian - A1) and 2.1% belonging to the E (European - A5). CONCLUSION Patients with a single HPV18 infection have a higher risk of cervical cancer than those infected with HPV18 and other high-risk strains simultaneously. HPV18 single-infection, on the other hand, had considerably higher incidences of L/HSIL, SCC, AC, and CIS than HPV18 co-infection. The HPV18 strain that was found in Vietnam belonged to lineage A (A1 and A5), which contains several oncogene mutations.
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Affiliation(s)
- Than Manh Hung
- Emergency Department, National Hospital for Tropical Diseases, 78 Giai Phong, Dong Da, Hanoi, Viet Nam; Infectious Department, University of Medicine and Pharmacy, Vietnam National University, 144 Xuan Thuy, Cau Giay, Hanoi, Viet Nam
| | - Hoang Xuan Son
- Departments of obstetrics and gynecology, Cho Moi District General Hospital, Na Mo village, Dong Tam town, Cho Moi district, Bac Kan province, Viet Nam
| | - Le Van Nguyen Bang
- Luong The Vinh High School, 35 Dinh Nup, Trung Hoa, Cau Giay, Hanoi, Viet Nam
| | - Le Van Duyet
- Micobiology and Moclecular Biology Department, National Hospital for Tropical Diseases, 78 Giai Phong, Dong Da, Hanoi, Viet Nam.
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Santos GRBD, Cunha APA, Batista ZDS, Silva MACND, Figueiredo FVD, Santos FRBD, Fraga EDC, Barros MC, Vidal FCB, Nascimento MDDSB. HPV 18 variants in women with cervical cancer in Northeast Brazil. Braz J Infect Dis 2022; 27:102734. [PMID: 36587927 PMCID: PMC9871062 DOI: 10.1016/j.bjid.2022.102734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Human Papillomavirus (HPV) is the main etiological factor for the development of cervical cancer. HPV 18 is the second most frequent type, accounting for up to 65% of all cases. HPV intratypic variation may influence the potential for progression to invasive cancer. The aim of this study was to evaluate the prevalence of human papillomavirus 18 intratypic variants in cervical cancer samples from women in the state of Maranhão, Brazil. METHODS The study included 118 women over 18 years of age with a diagnosis of cervical cancer. Tumor fragments were collected and subjected to DNA extraction and Polymerase Chain Reaction (PCR) for HPV detection using the PGMY09/11 and GP+5/6 primers. Positive samples were submitted to automated sequencing for viral genotyping. To determine the HPV 18 lineages, positive samples were submitted to PCR, using specific primers to amplify the LCR and E6 regions of HPV 18 virus. RESULTS HPV was present in 88 women (73.3%). Of those, 48 (54%) were HPV 16, the most prevalent, followed by 12 (13.6%) HPV 18. Histologically, squamous cell carcinoma was predominant (79.1%). Among the HPV 18 variants identified, 10 (80%) belonged to lineage A, and sublineages A1, A2, A3, and A4. Two (29%) HPV 18 B variant was also detected, with the sublineages B1 and B2. In this study, the C variant was not found. There was no statistically significant association between the HPV 18 lineages found and sociodemographic and lifestyle variables (p > 0.05). CONCLUSIONS A higher frequency of HPV 16 and 18 were found in women with cervical cancer in the state of Maranhão, Brazil, with a high prevalence of the lineage A among women with HPV 18.
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Affiliation(s)
| | - Ana Paula Almeida Cunha
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | - Zulmira da Silva Batista
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | | | - Fábio Vidal de Figueiredo
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Saúde do Adulto, São Luís, MA, Brazil
| | | | - Elmary da Costa Fraga
- Centro de Estudos Superiores de Caxias (CESC), da Universidade Estadual do Maranhão (UEMA), Caxias, MA, Brazil
| | - Maria Claudene Barros
- Centro de Estudos Superiores de Caxias (CESC), da Universidade Estadual do Maranhão (UEMA), Caxias, MA, Brazil
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Kim N, Park JS, Kim JE, Park JH, Park H, Roh EY, Yoon JH, Shin S. Fifteen new nucleotide substitutions in variants of human papillomavirus 18 in Korea : Korean HPV18 variants and clinical manifestation. Virol J 2020; 17:70. [PMID: 32448303 PMCID: PMC7245819 DOI: 10.1186/s12985-020-01337-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 12/04/2022] Open
Abstract
High-risk human papillomavirus (HPV) infection is an essential factor for the development of cervical cancer. HPV18 is the second most common carcinogenic HPV type following HPV16, but the lineages of HPV18 have been less well studied than those of HPV 16. The purpose of this study was to analyze the nucleotide variants in the E6, E7, and L1 genes of HPV18, to assess the prevalence of HPV18 variants in Korea and to explore the relationship between HPV18 genetic variants and the risk for cervical cancer. A total of 170 DNA samples from HPV18-positive cervical specimens were collected from women admitted to a secondary referral hospital located in Seoul. Among them, the lineages of the 97 samples could be successfully determined by historical nomenclature. All the studied HPV 18 variants were lineage A. Sublineages A1 and A4 comprised 91.7% (89/97) and 1.0% (1/97), respectively. Sublineages other than A1 or A4 comprised 7.2% (7/97). We identified 15 new nucleotide substitutions among 44 nucleotide substitutions: C158T, T317G, T443G, A560G, A5467G, A5560C, A5678C, A6155G, G6462A, T6650G, G6701A, T6809C, A6823G, T6941C and T6953C. Among them, 6 substitutions at positions 317, 443, 5467, 5560, 6462, and 6823 resulted in amino acid changes (E6: F71L and N113K; L1: H13R, H44P, A345T, and N465S, respectively). The pathologic results were classified as normal in 25.8% (25/97) of the women, atypical squamous cells of undermined significance (ASCUS) in 7.2% (7/97), cervical intraepithelial neoplasia (CIN) 1 in 36.1% (35/97), CIN2/3 in 19.6% (18/97), and carcinoma in 12.4% (12/97). There was no significant association between the HPV18 sublineages and the severity of pathologic lesion or the disease progression. This study is the first to analyze the distribution of HPV18 variants in Korean and to associate the results with pathologic findings. Although the HPV18 variants had no significant effect on the degree and progression of the disease, the newly discovered nonsynonymous mutation in L1 might serve as a database to determine vaccine efficacy in Korean women.
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Affiliation(s)
- Namhee Kim
- Department of Laboratory Medicine, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong Su Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Gyeonggi-do, South Korea
| | - Ji Eun Kim
- Department of Pathology, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea.,Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University Metropolitan Government Boramae Medical Center, Seoul, South Korea. .,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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Human papillomavirus (HPV) 18 genetic variants and cervical cancer risk in Taizhou area, China. Gene 2018; 647:192-197. [PMID: 29331480 DOI: 10.1016/j.gene.2018.01.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/20/2017] [Accepted: 01/09/2018] [Indexed: 11/22/2022]
Abstract
Human papillomavirus (HPV) type 18 is predominantly associated with the development of cervical adenocarcinomas, whereas data on HPV18 genetic variability in China are limited. HPV18 genetic variants were formed phylogenetic tree, including lineages A, B, and C. We aimed to evaluate the diversity of HPV18 genetic variants by sequencing the entire E6, E7 and L1 genes. Between 2012 and 2015, a total of 138 (0.8%, 138/17669) women with single HPV18 infection were selected in this study. Finally, we observed 122 HPV18 isolates of the complete E6-E7-L1 sequences, and obtained 36 distinct variation patterns which the accession GenBank numbers as KY457805-KY457840. Except KY457805, KY457813, KY457819, KY457827, KY457829, the rest of HPV18 isolates (81.1%, 31/36) are novel variants. All of HPV18 variants belong to lineage A, while no lineage B, and C was found in our population of Taizhou region, Southeast China. Sublineage A1 was the most common variants (85.2%, 104/122), followed by sublineage A4, A3 and A5, while no sublineage A2 was obtained. Based on the tree topologies, there were three newly identified candidates' sublineages A6-A8. Out of 122 women, 67 (54.9%) had diagnosed by biopsy, including 49 women who diagnosed with cervicitis, 12 with cervical intraepithelial neoplasia (CIN)1, 4 with CIN2/3, and 2 with adenocarcinomas, respectively. Nevertheless, there was no association between HPV18 (sub) lineages and CIN1 or worse (CIN1+) lesions comparing with normal biopsies (P = .469). In conclusion, knowledge of the distribution of geographic/ethnical HPV18 genetic diversity provides critical information for developing diagnostic probes, epidemiologic correlate of cervical cancer risk and design of HPV vaccines for targeted populations.
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Chen AA, Gheit T, Franceschi S, Tommasino M, Clifford GM. Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide. J Virol 2015; 89:10680-7. [PMID: 26269181 PMCID: PMC4580183 DOI: 10.1128/jvi.01747-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/05/2015] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED Human papillomavirus 18 (HPV18) is the second most carcinogenic HPV type, after HPV16, and it accounts for approximately 12% of squamous cell carcinoma (SCC) as well as 37% of adenocarcinoma (ADC) of the cervix worldwide. We aimed to evaluate the worldwide diversity and carcinogenicity of HPV18 genetic variants by sequencing the entire long control region (LCR) and the E6 open reading frame of 711 HPV18-positive cervical samples from 39 countries, taking advantage of the International Agency for Research on Cancer biobank. A total of 209 unique HPV18 sequence variants were identified that formed three phylogenetic lineages (A, B, and C). A and B lineages each divided into four sublineages, including a newly identified candidate B4 sublineage. The distribution of lineages varied by geographical region, with B and C lineages found principally in Africa. HPV18 (sub)lineages were compared between 453 cancer cases and 236 controls, as well as between 81 ADC and 160 matched SCC cases. In region-stratified analyses, there were no significant differences in the distribution of HPV18 variant lineages between cervical cancer cases and controls or between ADC and SCC. In conclusion, our findings do not support the role of HPV18 (sub)lineages for discriminating cancer risk or explaining why HPV18 is more strongly linked with ADC than SCC. IMPORTANCE This is the largest and most geographically/ethnically diverse study of the genetic variation of HPV18 to date, providing a comprehensive reference for phylogenetic classification of HPV18 sublineages for epidemiological and biological studies.
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Affiliation(s)
- Alyce A Chen
- International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
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Wang X, Li Y, Ni T, Xie X, Zhu J, Zheng ZM. Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58. Cell Biosci 2014; 4:5. [PMID: 24410913 PMCID: PMC3903022 DOI: 10.1186/2045-3701-4-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/16/2013] [Indexed: 11/20/2022] Open
Abstract
Background Genome variations in human papillomaviruses (HPVs) are common and have been widely investigated in the past two decades. HPV genotyping depends on the finding of the viral genome variations in the L1 ORF. Other parts of the viral genome variations have also been implicated as a possible genetic factor in viral pathogenesis and/or oncogenicity. Results In this study, the HPV58 genome in cervical lesions was completely sequenced both by rolling-circle amplification of total cell DNA and deep sequencing (RCA-seq) and by long PCR template cloning and sequencing. By comparison of three HPV58 genome sequences decoded from three clinical samples to reference HPV-58, we demonstrated that RCA-seq is much more accurate than long-PCR template cloning and sequencing in decoding HPV58 genome. Three HPV58 genomes decoded by RCA-seq displayed a total of 52 nucleotide substitutions from reference HPV58, which could be verified by long PCR template cloning and sequencing. However, the long PCR template cloning and sequencing led to additional nucleotide substitutions, insertions, and deletions from an authentic HPV58 genome in a clinical sample, which vary from one cloned sequence to another. Because the inherited error-prone nature of Tgo DNA polymerase used in preparation of the long PCR templates of HPV58 genome from the clinical samples, the measurable error rate in incorporation of nucleotide into an elongating DNA template was about 0.149% ±0.038% in our studies. Conclusions Since PCR template cloning and sequencing is widely used in identification of single nucleotide polymorphism (SNP), our data indicate that a serious caution should be taken in finding of true SNPs in various genetic studies.
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Affiliation(s)
| | | | | | | | | | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Co NNC, Chu LO, Chow JKF, Tam JWO, Ng EKO. HPV Prevalence and Detection of Rare HPV Genotypes in Hong Kong Women from Southern China with Cytological Abnormalities. ACTA ACUST UNITED AC 2013. [DOI: 10.5402/2013/312706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human papillomavirus (HPV) has been identified as the primary cause of cervical squamous intraepithelial lesion and invasive cervical cancer. The emergence of various commercial HPV genotyping kits with different characteristics facilitates the detection of most high-risk and low-risk HPV genotypes, but the rare HPV types are usually underdiagnosed. In the present study, HPV detection was performed using the GenoFlow HPV Array Test kit (DiagCor Bioscience), which can identify 33 HPV subtypes by specific probes. Besides, a HPV consensus probe (universal probe) was designed to capture not only the 33 genotypes but also rare subtypes. Of the 1643 Southern Chinese women tested between 2012 and 2013, the HPV prevalence was 42.3%, with HPV 52 (139/1643, 8.5%), HPV 81 (89/1643, 5.4%), and HPV 16 (63/1643, 3.8%) being the most frequent subtypes detected. Among all 695 HPV-positive cases, 56 (8.1%) cases were only detected by the universal probe, in which 5 were either ASCUS or LSIL cases. Sequencing results confirmed HPV types 30, 91, and 74, and the intratypic variants of HPV 72 and 82 were present in the 5 cases. The result suggests that some rare HPV subtypes might be involved in cervical lesions.
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Affiliation(s)
- Ngai Na Chloe Co
- Molecular Diagnostics Division, DiagCor Bioscience Incorporation Ltd, Hong Kong SAR, Hong Kong
| | - Lai-On Chu
- Molecular Diagnostics Division, DiagCor Bioscience Incorporation Ltd, Hong Kong SAR, Hong Kong
| | - Joseph K. F. Chow
- Molecular Diagnostics Division, DiagCor Bioscience Incorporation Ltd, Hong Kong SAR, Hong Kong
| | - Joseph W. O. Tam
- Molecular Diagnostics Division, DiagCor Bioscience Incorporation Ltd, Hong Kong SAR, Hong Kong
| | - Enders K. O. Ng
- Molecular Diagnostics Division, DiagCor Bioscience Incorporation Ltd, Hong Kong SAR, Hong Kong
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