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Dass M, Ghai M. Development of a multiplex PCR assay and quantification of microbial markers by ddPCR for identification of saliva and vaginal fluid. Forensic Sci Int 2024; 362:112147. [PMID: 39067179 DOI: 10.1016/j.forsciint.2024.112147] [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: 04/12/2024] [Revised: 06/11/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
The identification of biological fluids at crime scenes contributes to crime scene reconstruction and provides investigative leads. Traditional methods for body fluid identification are limited in terms of sensitivity and are mostly presumptive. Emerging methods based on mRNA and DNA methylation require high quality template source. An exploitable characteristic of body fluids is their distinct microbial profiles allowing for the discrimination of body fluids based on microbiome content. Microbial DNA is highly abundant within the body, robust and stable and can persist in the environment long after human DNA has degraded. 16S rRNA sequencing is the gold standard for microbial analysis; however, NGS is costly, and requires intricate workflows and interpretation. Also, species level resolution is not always achievable. Based on the current challenges, the first objective of this study was to develop a multiplex conventional PCR assay to identify vaginal fluid and saliva by targeting species-specific 16S rRNA microbial markers. The second objective was to employ droplet digital PCR (ddPCR) as a novel approach to quantify bacterial species alone and in a mixture of body fluids. Lactobacillus crispatus and Streptococcus salivarius were selected because of high abundance within vaginal fluid and saliva respectively. While Fusobacterium nucleatum and Gardnerella vaginalis, though present in healthy humans, are also frequently found in oral and vaginal infections, respectively. The multiplex PCR assay detected L. crispatus and G. vaginalis in vaginal fluid while F. nucleatum and S. salivarius was detected in saliva. Multiplex PCR detected F. nucleatum, S. salivarius and L. crispatus in mixed body fluid samples while, G. vaginalis was undetected in mixtures containing vaginal fluid. For samples exposed at room temperature for 65 days, L. crispatus and G. vaginalis were detected in vaginal swabs while only S. salivarius was detected in saliva swabs. The limit of detection was 0.06 copies/µl for F. nucleatum (2.5 ×10-9 ng/µl) and S. salivarius (2.5 ×10-6 ng/µl). L. crispatus and G. vaginalis had detection limits of 0.16 copies/µl (2.5 ×10-4 ng/µl) and 0.48 copies/µl (2.5 ×10-7 ng/µl). All 4 bacterial species were detected in mixtures and aged samples by ddPCR. No significant differences were observed in quantity of bacterial markers in saliva and vaginal fluid. The present research reports for the first time the combination of the above four bacterial markers for the detection of saliva and vaginal fluid and highlights the sensitivity of ddPCR for bacterial quantification in pure and mixed body fluids.
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Affiliation(s)
- Mishka Dass
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal - Westville Campus, Private Bag X 54001, Durban, KwaZulu Natal, South Africa.
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal - Westville Campus, Private Bag X 54001, Durban, KwaZulu Natal, South Africa.
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2
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Yin X, Luo H, Zhou H, Zhang Z, Lan Y, Feng Z, Chen W, Zheng H. A rapid isothermal CRISPR-Cas13a diagnostic test for genital herpes simplex virus infection. iScience 2024; 27:108581. [PMID: 38213624 PMCID: PMC10783623 DOI: 10.1016/j.isci.2023.108581] [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: 07/26/2023] [Revised: 10/02/2023] [Accepted: 11/23/2023] [Indexed: 01/13/2024] Open
Abstract
Prompt diagnosis is essential for managing herpes simplex virus types 1 and 2 (HSV-1/2). Existing diagnostic methods are not widely available that required expensive or additional equipment for conducting examinations and result readouts, which can limit their utility in resource-constrained settings. We successfully developed a CRISPR-Cas13a-based assay for the detection and genotyping of HSV. Our assay demonstrated a high sensitivity of 96.15% and 95.15% for HSV-1 and HSV-2, respectively, with a specificity of 100% compared to a commercial qPCR assay when tested on 194 clinical samples. Remarkably, the assay enables a limit of detection of 1 copy/μL of viral DNA, facilitated by an enhanced input of RPA product and is designed for both mobile app integration and colorimetric interpretation, allowing for semiquantitative readings. These findings highlight the excellent performance of our CRISPR-based diagnostic in detecting HSV and its potential for point-of-care testing in resource-constrained settings.
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Affiliation(s)
- Xiaona Yin
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Hao Luo
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Han Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Ziyan Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Yinyuan Lan
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Zhanqin Feng
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
| | - Wentao Chen
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou 510091, China
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3
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Huang L, Hong Y, Fu X, Tan H, Chen Y, Wang Y, Chen D. The role of the microbiota in glaucoma. Mol Aspects Med 2023; 94:101221. [PMID: 37866106 DOI: 10.1016/j.mam.2023.101221] [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: 06/03/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
Glaucoma is a common irreversible vision loss disorder because of the gradual loss of retinal ganglion cells (RGCs) and the optic nerve axons. Major risk factors include elder age and high intraocular pressure (IOP). However, high IOP is neither necessary nor sufficient to cause glaucoma. Some non-IOP signaling cascades can mediate RGC degeneration. In addition, gender, diet, obesity, depression, or anxiety also contribute to the development of glaucoma. Understanding the mechanism of glaucoma development is crucial for timely diagnosis and establishing new strategies to improve current IOP-reducing therapies. The microbiota exerts a marked influence on the human body during homeostasis and disease. Many glaucoma patients have abnormal compositions of the microbiota (dysbiosis) in multiple locations, including the ocular surface, intraocular cavity, oral cavity, stomach, and gut. Here, we discuss findings in the last ten years or more about the microbiota and metabolite changes in animal models, patients with three risk factors (aging, obesity, and depression), and glaucoma patients. Antigenic mimicry and heat stress protein (HSP)-specific T-cell infiltration in the retina may be responsible for commensal microbes contributing to glaucomatous RGC damage. LPS-TLR4 pathway may be the primary mechanism of oral and ocular surface dysbiosis affecting glaucoma. Microbe-derived metabolites may also affect glaucoma pathogenesis. Homocysteine accumulation, inflammatory factor release, and direct dissemination may link gastric H. pylori infection and anterior chamber viral infection (such as cytomegalovirus) to glaucoma. Potential therapeutic protocols targeting microbiota include antibiotics, modified diet, and stool transplant. Later investigations will uncover the underlying molecular mechanism connecting dysbiosis to glaucoma and its clinical applications in glaucoma management.
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Affiliation(s)
- Ling Huang
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yiwen Hong
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiangyu Fu
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haishan Tan
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongjiang Chen
- The School of Optometry and Vision Science, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada
| | - Yujiao Wang
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Danian Chen
- The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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4
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Joseph DM, Lim LL, Samalia PD, Wells JM, McCluskey PJ, Paul E, Hall AJ. Long term outcome and prognostic indicators in Posner Schlossman syndrome. Clin Exp Ophthalmol 2023; 51:781-789. [PMID: 37700734 DOI: 10.1111/ceo.14292] [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: 01/30/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Posner Schlossman syndrome is a well-defined uveitis entity that is characterised by relapsing remitting unilateral anterior uveitis with markedly raised intraocular pressure. The aim of this study was to determine the risk factors for progression in patients with Posner Schlossman syndrome. METHODS Ninety-eight patients were enrolled in a retrospective case series. Progression was defined as a composite endpoint of any of development of permanent glaucoma (in patients with no evidence of glaucomatous loss on presentation), corneal failure, or chronic inflammation. Relapse was defined as a resolving episode of inflammation not meeting the criteria for progression. RESULTS Seventy seven percent of patients relapsed on average each 2.2 years. Forty percent of patients progressed. On univariate analysis, increased age at enrolment, immunocompromise at enrolment, the presence of glaucomatous optic neuropathy at enrolment, the performance of an anterior chamber tap and a positive anterior chamber tap were all associated with increased risk of progression. On multivariate analysis, age at enrolment, immunocompromise at enrolment, the performance of an anterior chamber tap, and the presence of glaucomatous optic neuropathy at enrolment were independently associated with increased risk of disease progression. CONCLUSIONS Posner Schlossman syndrome is not a benign uveitis entity and risk of both relapse and progression are high. Older patients, immunocompromised patients, patients with glaucomatous optic neuropathy at enrolment and those with a positive anterior chamber tap are all at increased risk of progression.
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Affiliation(s)
| | - Lyndell L Lim
- Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, The University of Melbourne, Melbourne, Victoria, Australia
| | - Priya D Samalia
- Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jane M Wells
- Ophthalmology Unit, Canberra Hospital, Canberra, Australian Capital Territory, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Peter J McCluskey
- Sydney Eye Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine & Health, Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Eldho Paul
- Department of Ophthalmology, Alfred Hospital, Melbourne, Victoria, Australia
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Anthony J Hall
- Department of Ophthalmology, Alfred Hospital, Melbourne, Victoria, Australia
- Department of Surgery, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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5
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Mitkova-Hristova V, Stoyanova N, Atanassov M. Trabeculectomy with ExPress - an effective solution to Posner-Schlossman syndrome. Folia Med (Plovdiv) 2023; 65:675-680. [PMID: 37655390 DOI: 10.3897/folmed.65.e84894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/10/2022] [Indexed: 09/02/2023] Open
Abstract
Posner-Schlossman syndrome (PSS) is a unilateral ocular disease, characterized by recurrent non-granulomatous anterior uveitis and increased intraocular pressure (IOP), leading to chronic secondary glaucoma.
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Ye Z, Yang Y, Ke W, Li Y, Wang K, Chen M. Overview and update on cytomegalovirus-associated anterior uveitis and glaucoma. Front Public Health 2023; 11:1117412. [PMID: 36935679 PMCID: PMC10014866 DOI: 10.3389/fpubh.2023.1117412] [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: 12/06/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023] Open
Abstract
Cytomegalovirus anterior uveitis is the most common ocular inflammatory disease caused by cytomegalovirus infection. It mainly occurs in middle-aged males with competent immunologic function, and the incidence is higher in Asia. The clinical manifestations vary from Posner-Schlossman syndrome and corneal endotheliitis to Fuchs uveitis syndrome, and are often accompanied by intraocular hypertension. Secondary glaucoma is a potentially blinding ocular complication with a pathogenesis that includes complicated immunological factors, intraocular inflammation, different types of angle abnormalities, and the administration of steroids, which may result in physical discomfort and visual impairment. Diagnostic tests, such as the polymerase chain reaction, optical coherence tomography, ocular microscopy, and confocal microscopy, might help in identifying anterior uveitis caused by other viruses. Combinations of antiviral medications and anti-inflammatory agents are effective treatments. If pharmacological therapy cannot reduce intraocular pressure or slow the progression of glaucomatous optic neuropathy, surgical intervention is required as a last resort.
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Affiliation(s)
- Zifan Ye
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yumei Yang
- Shangyu People's Hospital of Shaoxing, Shaoxing, China
| | - Weishaer Ke
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yuhang Li
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Kaijun Wang
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
- Kaijun Wang
| | - Min Chen
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
- *Correspondence: Min Chen
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7
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HSP70 and TNF Loci Polymorphism Associated with the Posner-Schlossman Syndrome in a Southern Chinese Population. J Immunol Res 2022; 2022:5242948. [DOI: 10.1155/2022/5242948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
Previous studies have shown that HLA gene polymorphisms are associated with the pathogenesis of the Posner-Schlossman syndrome (PSS). This study was aimed at evaluating the associations between HLA-III gene polymorphisms and PSS in a southern Chinese Han population. A total of 150 PSS patients and 183 healthy controls were included in this study. Twenty-one single nucleotide polymorphisms (SNPs) of HLA-III genes (including HSP70-1, HSP70-2, HSP70-hom, TNF-α, TNF-β, C2, and CFB) were genotyped using the SNaPshot technique. Our study showed that the frequencies of G allele at rs909253, A allele at rs1041981, and G allele at rs2844484 of TNF-β in the patient group were significantly higher than those in healthy controls (Corrected
,
;
,
;
,
, respectively). The frequency of T allele at rs12190359 of HSP70-1 was significantly lower in PSS patients than those in healthy controls (
and
). The frequencies of the CCT haplotype of HSP70-1 gene (rs1008438-rs562047-rs12190359) and the ACCCTTT haplotype of HSP70 gene (rs2227956-rs1043618-rs1008438-rs562047-rs12190359-rs2763979-rs6457452) were significantly lower in PSS patients than those in healthy controls (
,
;
,
, respectively). In conclusion, the G allele at rs909253, A allele at rs1041981, and G allele at rs2844484 of TNF-β gene might be risk factors for PSS, while the T allele at rs12190359 of HSP70-1 gene and specific haplotypes of the HSP70-1 and HSP70 genes might be protective factors for PSS.
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8
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The Viral Load of Human Cytomegalovirus Infection in Children following Hematopoietic Stem Cell Transplant by Chip Digital PCR. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2786841. [PMID: 36300166 PMCID: PMC9592232 DOI: 10.1155/2022/2786841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/16/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022]
Abstract
Objective To detect viral load in human cytomegalovirus (HCMV) infection children after hematopoietic stem cell transplant (HSCT) by chip digital PCR (cdPCR). Methods The plasmid pUC57-UL83 containing the HCMV-UL83 gene and HCMV AD169 strain were used to evaluate the sensitivity of cdPCR. Either HSV-1, HSV-2, VZV, EBV, HHV-6, or HHV-7 was used to evaluate the specificity of HCMV cdPCR. The cdPCR was compared with quantitative PCR (qPCR) by detecting HCMV infection in 125 children's whole blood samples following HSCT. Results The limit of detection (LOD) of HCMV cdPCR was 103 copies/ml and the qPCR LOD was 297 copies/ml for plasmid pUC57-UL83. The result of HCMV cdPCR was 146 copies/ml for the HCMV AD169 strain, indicating that the sensitivity of cdPCR was higher than that of qPCR. There is no cross-reaction between HCMV cdPCR and other herpes viruses. The incidence of HCMV infection was 30.40% in 125 children following HSCT by cdPCR. The range of the HCMV viral load was from 107 copies/ml to 6600 copies/ml by cdPCR. Conclusions cdPCR is more sensitive than qPCR for detecting HCMV viral load. Furthermore, the cdPCR could be used to detect the viral load of HCMV infection before or after HSCT in children.
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Wang K, Li B, Guo Y, Wu Y, Li Y, Wu W. An integrated digital PCR system with high universality and low cost for nucleic acid detection. Front Bioeng Biotechnol 2022; 10:947895. [PMID: 36061433 PMCID: PMC9437218 DOI: 10.3389/fbioe.2022.947895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Digital PCR is the most advanced PCR technology. However, due to the high price of the digital PCR analysis instrument, this powerful nucleic acid detection technology is still difficult to be popularized in the general biochemistry laboratory. Moreover, one of the biggest disadvantages of commercial digital PCR systems is the poor versatility of reagents: each instrument can only be used for a few customized kits. Herein, we built a low-cost digital PCR system. The system only relies on low-cost traditional flat-panel PCR equipment to provide temperature conditions for commercial dPCR chips, and the self-made fluorescence detection system is designed and optically optimized to meet a wide range of reagent requirements. More importantly, our system not only has a low cost (<8000 US dollars) but also has a much higher universality for nucleic acid detection reagents than the traditional commercial digital PCR system. In this study, several samples were tested. The genes used in the experiment were plasmids containing UPE-1a fragment, TP53 reference DNA, hepatitis B virus DNA, leukemia sample, SARS-COV-2 DNA, and SARS-COV-2 RNA. Under the condition that DNA can be amplified normally, the function of the dPCR system can be realized with simpler and low-price equipment. Some DNA cannot be detected by using the commercial dPCR system because of the special formula when it is configured as the reaction solution, but these DNA fluorescence signals can be clearly detected by our system, and the concentration can be calculated. Our system is more applicable than the commercial dPCR system to form a new dPCR system that is smaller and more widely applicable than commercially available machinery.
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Affiliation(s)
- Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Bin Li
- Institute of Microbiology Chinese Academy of Sciences, Beijing, China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou, China
| | - Yanqi Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, China
| | - Yan Li
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Wenming Wu,
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Zhu X, Liu P, Lu L, Zhong H, Xu M, Jia R, Su L, Cao L, Sun Y, Guo M, Sun J, Xu J. Development of a multiplex droplet digital PCR assay for detection of enterovirus, parechovirus, herpes simplex virus 1 and 2 simultaneously for diagnosis of viral CNS infections. Virol J 2022; 19:70. [PMID: 35443688 PMCID: PMC9020426 DOI: 10.1186/s12985-022-01798-y] [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: 12/26/2021] [Accepted: 04/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Enterovirus (EV), parechovirus (HPeV), herpes simplex virus 1 and 2 (HSV1/2) are common viruses leading to viral central nervous system (CNS) infections which are increasingly predominant but exhibit deficiency in definite pathogen diagnosis with gold-standard quantitative PCR method. Previous studies have shown that droplet digital PCR (ddPCR) has great potential in pathogen detection and quantification, especially in low concentration samples. Methods Targeting four common viruses of EV, HPeV, HSV1, and HSV2 in cerebrospinal fluid (CSF), we developed a multiplex ddPCR assay using probe ratio-based multiplexing strategy, analyzed the performance, and evaluated it in 97 CSF samples collected from patients with suspected viral CNS infections on a two-channel ddPCR detection system. Results The four viruses were clearly distinguished by their corresponding fluorescence amplitude. The limits of detection for EV, HPeV, HSV1, and HSV2 were 5, 10, 5, and 10 copies per reaction, respectively. The dynamic range was at least four orders of magnitude spanning from 2000 to 2 copies per reaction. The results of 97 tested clinical CSF specimens were identical to those deduced from qPCR/qRT-PCR assays using commercial kits. Conclusion The multiplex ddPCR assay was demonstrated to be an accurate and robust method which could detect EV, HPeV, HSV1, and HSV2 simultaneously. It provides a useful tool for clinical diagnosis and disease monitoring of viral CNS infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01798-y.
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Affiliation(s)
- Xunhua Zhu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yameng Sun
- Shanghai Bio-Chain Biological Technology Co., Ltd, Shanghai, China
| | - Meijun Guo
- Shanghai Bio-Chain Biological Technology Co., Ltd, Shanghai, China
| | - Jianyue Sun
- Department of Pediatrics, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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Yi J, Wang N, Wu J, Tang Y, Zhang J, Zhu L, Rui X, Guo Y, Xu Y. Development of a Droplet Digital Polymerase Chain Reaction for Sensitive Detection of Pneumocystis jirovecii in Respiratory Tract Specimens. Front Med (Lausanne) 2021; 8:761788. [PMID: 35004733 PMCID: PMC8727342 DOI: 10.3389/fmed.2021.761788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Background:Pneumocystis jirovecii is a human-specific opportunistic fungus that causes Pneumocystis pneumonia (PCP), a life-threatening opportunistic lung infection that affects immunocompromised patients. P. jirovecii colonization may be linked to the transmission of the infection. The detection of P. jirovecii in immunocompromised patients is thus especially important. The low fungal load and the presence of PCR inhibitors limit the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of P. jirovecii in specimens. Droplet digital PCR (ddPCR), however, presents a methodology that allows higher sensitivity and accuracy. Here, we developed a ddPCR method for detecting P. jirovecii DNA in respiratory specimens, and evaluated its sensitivity against qPCR. Materials and Methods: One bronchoalveolar fluid (BALF) sample each was collected from 82 patients with potential PCP to test the presence of P. jirovecii DNA using both ddPCR and qPCR, and samples with inconsistent results between the two methods were further tested by metagenomic next generation sequencing (mNGS). In addition, 37 sputum samples from 16 patients diagnosed with PCP, as well as continuous respiratory tract specimens from nine patients with PCP and treated with sulfonamides, were also collected for P. jirovecii DNA testing using both ddPCR and qPCR. Results: ddPCR and qPCR gave the same results for 95.12% (78/82) of the BALF samples. The remaining four specimens tested positive using ddPCR but negative using qPCR, and they were found to be positive by mNGS. Detection results of 78.37% (29/37) sputum samples were consistent between ddPCR and qPCR, while the other eight samples tested positive using ddPCR but negative using qPCR. The P. jirovecii load of patients with PCP decreased to undetectable levels after treatment according to qPCR, but P. jirovecii was still detectable using ddPCR. Conclusions: ddPCR was more sensitive than qPCR, especially at detecting low-pathogen-load P. jirovecii. Thus, ddPCR represents a useful, viable, and reliable alternative to qPCR in P. jirovecii testing in patients with immunodeficiency.
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Affiliation(s)
- Jie Yi
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wang
- Human Genetic Resource Center, National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Jie Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yueming Tang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjia Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | | | - Xiao Rui
- TargetingOne Corporation, Beijing, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- Yong Guo
| | - Yingchun Xu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yingchun Xu
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12
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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13
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Zhai R, Wang Z, Sheng Q, Fan X, Kong X, Sun X. Polymorphisms of the cytomegalovirus glycoprotein B genotype in patients with Posner-Schlossman syndrome. Br J Ophthalmol 2021; 106:1240-1244. [PMID: 33753409 PMCID: PMC9411906 DOI: 10.1136/bjophthalmol-2020-318284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/16/2021] [Accepted: 03/07/2021] [Indexed: 02/05/2023]
Abstract
Aims The aim of this observational study was to report the distribution of glycoprotein B (gB) genotypes in the eyes of cytomegalovirus (CMV) positive patients with Posner-Schlossman syndrome (PSS), and to investigate their clinical characteristics and outcomes. Methods We collected aqueous humour samples from 165 patients clinically diagnosed with PSS between 2017 and 2019. PCR was performed to analyse the CMV DNA and identify the gB genotypes in the samples. Clinical characteristics and responses to antiviral treatment were compared among patients with different gB genotypes. Results CMV DNA was detected in 94 (56.97%) of the 165 aqueous humour specimens analysed. Owing to the quantity requirement for CMV gB genotype analysis, results could be obtained from only 14 specimens. CMV gB type 1 was detected in 11 samples (78.6%), whereas CMV gB type 3 was detected in three samples (21.4%). No other gB genotypes or mixed genotypes were detected. Overall, 9.1% (1/11) of the patients in the gB type 1 group and 66.7% (2/3) of the patients in the gB type 3 group had bilateral attacks (p=0.093). The concentration of anti-CMV immunoglobulin G (IgG) in the type 1 group was 0.94±0.79 s/co (ratio of aqueous humour CMV IgG/serum CMV IgG to aqueous humour albumin concentration/serum albumin concentration), whereas that in the type 3 group was 0.67±0.71 s/co. Conclusion Genotype 1 was the most prevalent genotype in the aqueous humour of CMV-infected patients with PSS. Bilateral attack was predominant among patients with gB genotype 3. CMV gB gene may be related to the pathogenicity of CMV virus strain in patients with PSS.
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Affiliation(s)
- Ruyi Zhai
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China.,Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Zhujian Wang
- Department of Clinical Laboratory, Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Qilian Sheng
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China.,Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xintong Fan
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China.,Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xiangmei Kong
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Fudan University, Shanghai, China .,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China.,Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xinghuai Sun
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China.,Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science,Fudan University, Shanghai, China
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14
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Chen B, Jiang Y, Cao X, Liu C, Zhang N, Shi D. Droplet digital PCR as an emerging tool in detecting pathogens nucleic acids in infectious diseases. Clin Chim Acta 2021; 517:156-161. [PMID: 33662358 DOI: 10.1016/j.cca.2021.02.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
The microbial infectious diseases (infectious diseases) represent the leading global public health problem, and the effective treatment depends on rapid and accurate detection of pathogens. Droplet digital PCR (ddPCR), a new assay that combines microfluidics technology with TaqMan-based PCR, provides absolute quantification without the need of the standard curves. With the development of ddPCR, it has become an ideal tool for microorganism detection. In this review, we summarized the major literature with regard to the application of ddPCR in detecting the pathogenic microorganisms of infectious diseases, including bacteria, fungi, and virus. The ddPCR method has the advantages of detecting the targeted DNA of infectious microorganisms, with high sensitivity, high precision, and absolute quantification. Thus, ddPCR has emerged as a promising and reliable tool in detecting pathogenicmicroorganisms.
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Affiliation(s)
- Biao Chen
- Postdoctoral of Shandong University of Traditional Chinese Medicine, Jinan 210355, China; The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining 272111, China
| | - Yufeng Jiang
- Postdoctoral of Shandong University of Traditional Chinese Medicine, Jinan 210355, China; Department of Medical Laboratory, Jining No. 1 People's Hospital, Jining 272111, China
| | - Xiaohua Cao
- Intensive Care Unit, Jining No. 1 People's Hospital, Jining 272111, China
| | - Chen Liu
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining 272111, China
| | - Ning Zhang
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining 272111, China
| | - Dongmei Shi
- The Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining 272111, China; Department of Dermatology, Jining No. 1 People's Hospital, Jining, Shandong Province, China.
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15
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Murata K, Ishida K, Ozawa K, Sawada A, Mochizuki K, Yamamoto T. The characteristics of Posner-Schlossman syndrome: A comparison in the surgical outcome between cytomegalovirus-positive and cytomegalovirus-negative patients. Medicine (Baltimore) 2019; 98:e18123. [PMID: 31770242 PMCID: PMC6890343 DOI: 10.1097/md.0000000000018123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This retrospective observational study aims to report the clinical characteristics and surgical results in eyes with Posner-Schlossman syndrome (PSS), and compare these outcomes between cytomegalovirus (CMV)-positive and -negative eyes.We reviewed the medical records of 21 consecutive immunocompetent patients clinically diagnosed with PSS between the years 2010 and 2018. Aqueous humor was collected from all the affected eyes to detect if CMV was present, and polymerase chain reaction (PCR) was performed using the herpesvirus family primers.The average period between the initial PSS attack and aqueous humor sampling at our institute was 9.3 years. Out of the 21 patients, 62% were CMV-positive. Regardless of CMV status, the mean intraocular pressure (IOP), mean deviation (MD), and central corneal endothelium cell (CEC) density, at the initial examination at our institute were already significantly worse in the affected eyes than in the unaffected eyes (all P values < .05). The average visual acuity (VA) was only significantly worse in the CMV-positive group (P = .02). Out of all the patients, those that were CMV-positive had undergone more glaucoma surgeries (P = .056). Fourteen patients underwent either a trabeculectomy (TRAB) or a trabeculotomy (LOT), and their IOP significantly reduced following surgery (P < .001). In 85.7% of those that had surgery, their IOP was successfully lowered to less than 20 mm Hg.Long-lasting PSS causes a decrease in VA, MD, and the CEC density. A prompt diagnosis is required, and an appropriate treatment plan should be formulated. In those patients with PSS that develop uncontrolled glaucoma, both TRAB and LOT may be effective in controlling IOP.
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Affiliation(s)
- Kazuhiro Murata
- Department of Ophthalmology, Gifu University Graduate School of Medicine
| | - Kyoko Ishida
- Department of Ophthalmology, Toho University Ohashi Medical Center, Japan
| | - Kenji Ozawa
- Department of Ophthalmology, Gifu University Graduate School of Medicine
| | - Akira Sawada
- Department of Ophthalmology, Gifu University Graduate School of Medicine
| | - Kiyofumi Mochizuki
- Department of Ophthalmology, Gifu University Graduate School of Medicine
| | - Tetsuya Yamamoto
- Department of Ophthalmology, Gifu University Graduate School of Medicine
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16
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Kimura H, Kwong YL. EBV Viral Loads in Diagnosis, Monitoring, and Response Assessment. Front Oncol 2019; 9:62. [PMID: 30809508 PMCID: PMC6379266 DOI: 10.3389/fonc.2019.00062] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/22/2019] [Indexed: 12/26/2022] Open
Abstract
The quantification of circulating Epstein Barr virus (EBV) DNA loads has played an important role in the diagnosis and management of EBV-associated lymphoid malignancies. Viral load measurement is particularly useful for monitoring EBV-DNA in hematopoietic stem cell transplant patients, and for assessing the prognosis or response to therapy of EBV-associated intractable lymphomas like extranodal NK/T-cell lymphoma, nasal type. Cell-free EBV-DNA in plasma can be used as a biomarker for estimating the severity or prognosis of these lymphomas. In addition to plasma, whole blood has been used for the management of transplant patients. Although measuring EBV-DNA has been useful, there is a lack of standardization and the optimal specimens for measuring viral loads are unknown. This can be attributed to the different forms of EBV-DNA that exist in peripheral blood and the different pathologies that result from diverse EBV disease states. As a result, guidelines for EBV diagnosis or the initiation of treatment are unclear. However, the newly established World Health Organization standard for EBV quantification will encourage collaborative studies across institutions and countries to establish proper guidelines for EBV diagnosis and the initiation of treatment.
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Affiliation(s)
- Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yok-Lam Kwong
- Department of Medicine, Queen Mary Hospital, Hong Kong, China
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