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Zhang Q, Qiao R, Niu J, Xiong X, Wang N, Zhang R, Luo S, Guo Y, Liu Z, Peng L, Zhang S, Tan G, Song K, Sun M, Xu L, Zhang R, Wu X. Evaluation of an identification method for the SARS-CoV-2 Delta variant based on the amplification-refractory mutation system. Front Cell Infect Microbiol 2023; 13:1180297. [PMID: 37475960 PMCID: PMC10354518 DOI: 10.3389/fcimb.2023.1180297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023] Open
Abstract
The Delta variant of SARS-CoV-2 dominated the COVID-19 pandemic due to its high viral replication capacity and immune evasion, causing massive outbreaks of cases, hospitalizations, and deaths. Currently, variant identification is performed mainly by sequencing. However, the high requirements for equipment and operators as well as its high cost have limited its application in underdeveloped regions. To achieve an economical and rapid method of variant identification suitable for undeveloped areas, we applied an amplification-refractory mutation system (ARMS) based on PCR for the detection of novel coronavirus variants. The results showed that this method could be finished in 90 min and detect as few as 500 copies/mL and not react with SARS-Coronavirus, influenza A H1N1(2009), and other cross-pathogens or be influenced by fresh human blood, α- interferon, and other interfering substances. In a set of double-blind trials, tests of 262 samples obtained from patients confirmed with Delta variant infection revealed that our method was able to accurately identify the Delta variant with high sensitivity and specificity. In conclusion, the ARMS-PCR method applied in Delta variant identification is rapid, sensitive, specific, economical, and suitable for undeveloped areas. In our future study, ARMS-PCR will be further applied in the identification of other variants, such as Omicron.
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Affiliation(s)
- Qin Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Runjie Qiao
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jiaojiao Niu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xia Xiong
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Nan Wang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ruixian Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Sha Luo
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuwan Guo
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Zhonghua Liu
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Li Peng
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Shaoduo Zhang
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Guolei Tan
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Keyu Song
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Mei Sun
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lulu Xu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Rong Zhang
- Research and Development Department, Jiangsu Bioperfectus Technologies Company Limited, Taizhou, Jiangsu, China
| | - Xuping Wu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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Multiplex Snapshot minisequencing for the detection of common PAH gene mutations in Iranian patients with Phenylketonuria. IRANIAN BIOMEDICAL JOURNAL 2023; 27:46-57. [PMID: 36624928 PMCID: PMC9971712 DOI: 10.52547/ibj.3856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Phenylketonuria is a common inborn defect of amino acid metabolism in the world. This failure is caused by an autosomal recessive insufficiency of the hepatic enzyme hyperphenylalaninemia (PAH), which catalyzes the irreversible hydroxylation of phenylalanine to tyrosine. More than 1,040 different disease-causing mutations have already been identified in the PAH gene. The most prominent complication of Phenylketonuria, if not diagnosed and treated, is severe mental retardation. Hence, early diagnosis and initiation of nutritional therapy are the most significant measures in preventing this mental disorder. Given these data, we developed a simple and rapid molecular test to detect the most frequent PAH mutations. Methods Multiplex assay was developed based on the SNaPshot minisequencing approach to simultaneously perform genotyping of the 10 mutations at the PAH gene. We optimized detection of these mutations in one multiplex PCR, followed by 10 single-nucleotide extension reactions. DNA sequencing assay was also used to verify genotyping results obtained by SNaPshot minisequencing. Result All 10 genotypes were determined based on the position and the fluorescent color of the peaks in a single electropherogram. Sequencing results of these frequent mutations showed that by using this method, a 100% detection rate could be achieved in the Iranian population. Conclusion SNaPshot minisequencing can be useful as a secondary test in neonatal screening for HPA in neonates with a positive screening test, and it is also suitable for carrier screening. The assay can be easily applied for accurate and time- and cost-efficient genotyping of the selected SNPs in various population.
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Yan Y, Jin X, Wang X, Zhang C, Zhang Q, Zheng L, Feng X, Hao S, Gao H, Ma X. Screening of PAH Common Mutations in Chinese Phenylketonuria Patients Using iPLEX MALDI-TOF MS. ACS OMEGA 2020; 5:1805-1812. [PMID: 32039316 PMCID: PMC7003239 DOI: 10.1021/acsomega.9b02955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previous research has identified some PAH mutation hotspots in Chinese patients with PKU. In this study, we introduce a novel MassArray panel for screening the 29 common PAH gene mutations in Chinese patients using iPLEX MALDI-TOF MS. 105 Patients with PKU and known PAH gene mutations were genotyped using this MassArray panel. All of the 29 mutations screened were detected, and MassArray panel results were consistent with those obtained by Sanger sequencing. Fifty patients newly diagnosed with PKU were recruited in the double-blind experiment. PAH gene variants were detected in these 50 patients using the MassArray panel, and the results were verified with Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) methods. Our results show that the mutation detection rate using the MassArray panel with 29 mutations is 74% (95% CI, 65-83%), and the clinical genetic diagnosis rate is 54% (95% CI, 40-68%). This panel can be used as a high throughput, low cost, and rapid method for screening and diagnosing PAH gene mutations. The establishment of this approach provides proof-of-concept for future large-scale PAH mutation carrier screening in areas with high rates of PKU.
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Affiliation(s)
- Yousheng Yan
- National
Research Institute for Family Planning, Beijing 100081, China
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
- Peking
University International Hospital, Beijing 102206, China
| | - Xiaohua Jin
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xing Wang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Chuan Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Qinhua Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Lei Zheng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Xuan Feng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Shengju Hao
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Huafang Gao
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xu Ma
- National
Research Institute for Family Planning, Beijing 100081, China
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