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Khan MYA, Dai D, Su X, Tian J, Zhou J, Ma L, Wang Y, Wen W, Zhang Y. Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet 2024; 55:457-464. [PMID: 38622758 DOI: 10.1111/age.13432] [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: 11/25/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
The common deleterious genetic defects in Holstein cattle include haplotypes 1-6 (HH1-HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single-tube multiplex fluorescent amplification-refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3' end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf-ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf-ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.
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Affiliation(s)
- Md Yousuf Ali Khan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | - Dongmei Dai
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Su
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia Tian
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Jiamin Zhou
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Liqin Ma
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wan Wen
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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2
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Fu Y, He X, Fang Q, Kong F, Zhang Y, Fu T, Chen L, Liu Y, Wang Z, Lyu J, Chen L. Rapid identification of SARS-CoV-2 variants using stable high-frequency mutation sites. APMIS 2024; 132:348-357. [PMID: 38488266 DOI: 10.1111/apm.13388] [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: 07/26/2023] [Accepted: 01/25/2024] [Indexed: 04/16/2024]
Abstract
Respiratory infectious viruses, including SARS-CoV-2, undergo rapid genetic evolution, resulting in diverse subtypes with complex mutations. Detecting and differentiating these subtypes pose significant challenges in respiratory virus surveillance. To address these challenges, we integrated ARMS-PCR with molecular beacon probes, allowing selective amplification and discrimination of subtypes based on adjacent mutation sites. The method exhibited high specificity and sensitivity, detecting as low as 104 copies/mL via direct fluorescence analysis and ~106 copies/mL using real-time PCR. Our robust detection approach offers a reliable and efficient solution for monitoring evolving respiratory infections, aiding early diagnosis and control measures. Further research could extend its application to other respiratory viruses and optimize its implementation in clinical settings.
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Affiliation(s)
- Yu Fu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Xiaobai He
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Quan Fang
- Department of laboratory, Physical Examination Center, Air Force Hangzhou Special Service Convalescence Center Zone 1, Hangzhou, China
| | - Fei Kong
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Yan Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Ting Fu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Liang Chen
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - YanXin Liu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Zhen Wang
- Center for Laboratory Medicine, Allergy center, Department of Transfusion medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Linjie Chen
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
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3
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Nawab M, Riaz SK, Ismail E, Ahamed A, Tariq A, Malik MFA, Qusty NF, Bantun F, Slama P, Umair M, Haque S, Bonilla-Aldana DK, Rodriguez-Morales AJ. Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR. Ann Clin Microbiol Antimicrob 2024; 23:11. [PMID: 38303011 PMCID: PMC10836012 DOI: 10.1186/s12941-023-00665-0] [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: 10/09/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.
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Affiliation(s)
- Maryam Nawab
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Eiman Ismail
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Alfar Ahamed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aaysha Tariq
- Molecular Diagnostic Unit, Clinical Pathology Department, PAEC General Hospital, Islamabad, Pakistan
| | | | - Naeem F Qusty
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, PO Box 7607, Makkah, Al Abdeyah, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, 61300, Czech Republic
| | - Massab Umair
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, 13306, United Arab Emirates
| | | | - Alfonso J Rodriguez-Morales
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Master Program on Clinical Epidemiology and Biostatistics, Faculty of Health Sciences, Universidad Científica del Sur, Lima, 15046, Peru
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4
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Xu X, Hu X, Ma G, Wang T, Wu J, Zhu X, Chen G, Zhao L, Chen J. Detecting fa leptin receptor mutation in Zucker rats with tetra-primer amplification-refractory mutation system (ARMS)-PCR. Heliyon 2023; 9:e20159. [PMID: 37809507 PMCID: PMC10559934 DOI: 10.1016/j.heliyon.2023.e20159] [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: 12/16/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Due to the genetic mutation (fa) in the gene encoding for leptin receptor, homozygous Zucker rats (fa-/-) develop excessive adiposity and become an experimental animal model in obesity and metabolic-related diseases research. Based on tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), we developed a method to quickly genotype Zucker rats with a mutated fa allele from their wildtype littermates. The three genotypes are clearly discriminated on 2.0% agarose gel. Our method can be used as a reliable tool to set up and maintain the breeding colony in animal facilities as well as assign animals to control and treatment groups based on their genotypes for animal studies.
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Affiliation(s)
- Xinyun Xu
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Xinge Hu
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Guodong Ma
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Tiannan Wang
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, The University of Tennessee Knoxville, TN, 37996, United States
| | - Xiaojuan Zhu
- Office of Information Technology, The University of Tennessee Knoxville, TN, 37996, United States
| | - Guoxun Chen
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Ling Zhao
- Department of Nutrition, The University of Tennessee Knoxville, TN, 37996, United States
| | - Jiangang Chen
- Department of Public Health, The University of Tennessee Knoxville, TN, 37996, United States
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Yu L, Tang Z, Sun Y, Yi H, Tang Y, Zhong Y, Dian D, Cong Y, Wang H, Xie Z, He S, Chen Z. A polyethylene glycol enhanced ligation-triggered self-priming isothermal amplification for the detection of SARS-CoV-2 D614G mutation. Talanta 2023; 262:124711. [PMID: 37244245 DOI: 10.1016/j.talanta.2023.124711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
We presented a polyethylene glycol (PEG) enhanced ligation-triggered self-priming isothermal amplification (PEG-LSPA) for the detection D614G mutation in S-glycoprotein of SARS-CoV-2. PEG was employed to improve the ligation efficiency of this assay by constructing a molecular crowding environment. Two hairpin probes (H1 and H2) were designed to contain 18 nt and 20 nt target binding site at their 3' end and 5' end, respectively. In presence of target sequence, it complemented with H1 and H2 to trigger ligation by ligase under molecular crowding condition to form ligated H1-H2 duplex. Then 3' terminus of the H2 would be extended by DNA polymerase under isothermal conditions to form a longer extended hairpin (EHP1). 5' terminus of EHP1 with phosphorothioate (PS) modification could form hairpin structure due to the lower Tm value. The resulting 3' end overhang would also fold back as a new primer to initiate the next round of polymerization, resulting in the formation of a longer extended hairpin (EHP2) containing two target sequence domains. In the circle of LSPA, long extended hairpin (EHPx) containing numerous target sequence domains was produced. The resulting DNA products can be monitored in real-time fluorescence signaling. Our proposed assay owns an excellent linear range from 10 fM to 10 nM with a detection limit down to 4 fM. Thus, this work provides a potential isothermal amplification method for monitoring mutations in SARS-CoV-2 variants.
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Affiliation(s)
- Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zibin Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuanzhong Sun
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Hai Yi
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuebiao Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yangqing Zhong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Dongchun Dian
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Yanguang Cong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Houqi Wang
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zhaoyang Xie
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Suhui He
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Zhangquan Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
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6
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Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern. Sci Rep 2023; 13:2342. [PMID: 36759632 PMCID: PMC9910272 DOI: 10.1038/s41598-023-28275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.
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7
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Yang W, Tao D, Xu B, Zheng Y, Zhao S. Detecting Melanocortin 1 Receptor Gene's SNPs by CRISPR/enAsCas12a. Genes (Basel) 2023; 14:genes14020394. [PMID: 36833321 PMCID: PMC9957350 DOI: 10.3390/genes14020394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, while the application of single nucleotide polymorphism (SNP) detection is limited. The MC1R SNPs were investigated by CRISPR/enAsCas12a and are not limited to the protospacer adjacent motif (PAM) sequence in vitro. Specifically, we optimized the reaction conditions, which proved that the enAsCas12a has a preference for divalent magnesium ion (Mg2+) and can effectively distinguish the genes with a single base difference in the presence of Mg2+, and the Melanocortin l receptor (MC1R) gene with three kinds of SNP sites (T305C, T363C, and G727A) was quantitatively detected. Since the enAsCas12a is not limited by PAM sequence in vitro, the method shown here can extend this extraordinary CRISPR/enAsCas12a detection system to other SNP targets, thus providing a general SNP detection toolbox.
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Affiliation(s)
- Wei Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yueting Zheng
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs and Key Laboratory of Animal Growth and Development of Henan Province, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (Y.Z.); (S.Z.)
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.Z.); (S.Z.)
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8
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Chen J, Xu X, Dalhaimer P, Zhao L. Tetra-Primer Amplification-Refractory Mutation System (ARMS)-PCR for Genotyping Mouse Leptin Gene Mutation. Animals (Basel) 2022; 12:ani12192680. [PMID: 36230421 PMCID: PMC9558987 DOI: 10.3390/ani12192680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 09/24/2022] [Indexed: 11/05/2022] Open
Abstract
Due to spontaneous deficiency in leptin, ob/ob mice are one of the most commonly used experimental animal models in diabetes research. In this study, we reported a quick and easy-to-conduct genotyping method using tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) to differentiate mice with a mutated allele from the wild-type genotype. The amplicon patterns of different genotypes are clearly visible and distinguishable on 1.5% agarose gel. This method can serve as a valuable tool to differentiate genotypes for breeding purposes, to maintain animal colonies, control the available space in the animal facility, and identify appropriate individuals for animal experiments.
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Affiliation(s)
- Jiangang Chen
- Department of Public Health, The University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (J.C.); (L.Z.)
| | - Xinyun Xu
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, USA
| | - Paul Dalhaimer
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN 37996, USA
| | - Ling Zhao
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (J.C.); (L.Z.)
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9
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Development and validation of cost-effective one-step multiplex RT-PCR assay for detecting the SARS-CoV-2 infection using SYBR Green melting curve analysis. Sci Rep 2022; 12:6501. [PMID: 35444203 PMCID: PMC9019801 DOI: 10.1038/s41598-022-10413-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 03/23/2022] [Indexed: 11/08/2022] Open
Abstract
TaqMan probe-based commercial real-time (RT) PCR kits are expensive but most frequently used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections needs to meet the challenge of testing more persons at a reasonable cost. This study developed a simple and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay targeting two virus-specific genes along with a host-specific internal control. A total of 180 randomly selected samples portioning into two subsets based on crude and high-quality RNA extraction were used to compare this assay with a nationwide available commercial kit (Sansure Biotech Inc., (Hunan, China)), so that we could analyze the variation and validity of this in-house developed method. Our customized-designed primers can specifically detect the viral RNA likewise Sansure. We separately optimized SYBR Green RT-PCR reaction of N, E, S, and RdRp genes based on singleplex melting curve analysis at the initial stage. After several rounds of optimization on multiplex assays of different primer combinations, the optimized method finally targeted N and E genes of the SARS-CoV-2 virus, together with the β-actin gene of the host as an internal control. Comparing with the Sansure commercial kit, our proposed assay provided up to 97% specificity and 93% sensitivity. The cost of each sample processing ranged between ~2 and ~6 USD depending on the purification level of extracted RNA template. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in low-income countries.
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10
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Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Microbiol Spectr 2022; 10:e0143821. [PMID: 34985323 PMCID: PMC8729772 DOI: 10.1128/spectrum.01438-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With the emergence and wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), such as the Delta variant (B.1.617.2 lineage and AY sublineage), it is important to track VOCs for sourcing of transmission. Currently, whole-genome sequencing is commonly used for detecting VOCs, but this is limited by the high costs of reagents and sophisticated sequencers. In this study, common mutations in the genomes of SARS-CoV-2 VOCs were identified by analyzing more than 1 million SARS-CoV-2 genomes from public data. Among them, mutations C1709A (a change of C to A at position 1709) and C56G, respectively, were found in more than 99% of the genomes of Alpha and Delta variants and were specific to them. Then, a method using the amplification refractory mutation system combined with quantitative reverse transcription-PCR (ARMS-RT-qPCR) based on the two mutations was developed for identifying both VOCs. The assay can detect as little as 1 copy/μL of the VOCs, and the results for identifying Alpha and Delta variants in clinical samples by the ARMS-RT-qPCR assay showed 100% agreement with the results using sequencing-based methods. The whole assay can be completed in 2.5 h using commercial fluorescent PCR instruments. Therefore, the ARMS-RT-qPCR assay could be used for screening the two highly concerning variants Alpha and Delta by normal PCR laboratories in airports and in hospitals and other health-related organizations. Additionally, based on the unique mutations identified by the genomic analysis, similar molecular assays can be developed for rapid identification of other VOCs. IMPORTANCE The current stage of the pandemic, led by SARS-CoV-2 variants of concern (VOCs), underscores the necessity to develop a cost-effective and rapid molecular diagnosis assay to differentiate the VOCs. In this study, over 1 million SARS-CoV-2 genomic sequences of high quality from GISAID were analyzed and a network of the common mutations of the lineages was constructed. The conserved unique mutations specific for SARS-CoV-2 VOCs were found. Then, ARMS-RT-qPCR assays based on the two unique mutations of the Alpha and Delta variants were developed for the detection of the two VOCs. Application of the assay in clinical samples demonstrated that the current method is a convenient, cost-effective, and rapid way to screen the target SARS-CoV-2 VOCs.
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Rosman N, Nawawi HM, Al-Khateeb A, Chua YA, Chua AL. Development of an Optimized Tetra-Amplification Refractory Mutation System PCR for Detection of 12 Pathogenic Familial Hypercholesterolemia Variants in the Asian Population. J Mol Diagn 2022; 24:120-130. [PMID: 35074074 DOI: 10.1016/j.jmoldx.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/03/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Early detection of genetic diseases such as familial hypercholesterolemia (FH), and the confirmation of related pathogenic variants, are crucial in reducing the risk for premature coronary artery disease. Currently, next-generation sequencing is used for detecting FH-related candidate genes but is expensive and time-consuming. There is a lack of kits suitable for the detection of the common FH-related variants in the Asia-Pacific region. Thus, this study addressed that need with the development of an optimized tetra-amplification mutation system (T-ARMS) PCR-based assay for the detection of 12 pathogenic variants of FH in the Asian population. The two important parameters for T-ARMS PCR assay performance-annealing temperature and the ratio of outer/inner primer concentrations-were optimized in this study. The optimal annealing temperature of all 12 T-ARMS PCR reactions was 64.6°C. The ideal ratios of outer/inner primer concentrations with each pathogenic variant were: A1, 1:2; A2, 1:4; L1, 1:10; L2, 1:1; L3, 1:2; L4, 1:8; L5, 1:1; L6, 1:2; L7, 1:8; L8, 1:8; L9, 1:2; and L10, 1:8. The lowest limit of detection using DNA extracted from patients was 0.1 ng. The present article highlights the beneficial findings on T-ARMS PCR as part of the development of a PCR-based detection kit for use in detecting FH in economically developing countries in Asia with a greater prevalence of FH.
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Affiliation(s)
- Norhidayah Rosman
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Hapizah M Nawawi
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Alyaa Al-Khateeb
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia; Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Yung-An Chua
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Ang-Lim Chua
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
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12
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Al-Emran HM, Hasan MS, Ahasan Setu MA, Rahman MS, Alam ARU, Sarkar SL, Islam MT, Islam MR, Rahman MM, Islam OK, Jahid IK, Hossain MA. Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh. J Infect Public Health 2021; 15:156-163. [PMID: 34952247 PMCID: PMC8688836 DOI: 10.1016/j.jiph.2021.12.002] [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: 08/05/2021] [Revised: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 11/21/2022] Open
Abstract
Background Bangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (12.8%) received either one or two dose of vaccination like other low-income countries. The COVID-19 infections were continued to roll all over the places although the information on genomic variations of SARS-CoV-2 between both immunized and unimmunized group was unavailable. The objective of this study was to compare the proportion of immune escaping variants between those groups. Methods A total of 4718 nasopharygeal samples were collected from March 1 until April 15, 2021, of which, 834 (18%) were SARS-CoV-2 positive. The minimum sample size was calculated as 108 who were randomly selected for telephone interview and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized groups was measured. A total of 63 spike protein sequences and 14 whole-genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared. Results A total of 40 respondents (37%, N = 108) received single-dose and 2 (2%) received both doses of ChAdOx1 nCoV-19 vaccine, which significantly reduce dry cough, loss of appetite and difficulties in breathing compared to none. There was no significant difference in hospitalization, duration of hospitalization or reduction of other symptoms like running nose, muscle pain, shortness of breathing or generalized weakness between immunized and unimmunized groups. Spike protein sequence assumed 21 (87.5%) B.1.351, one B.1.526 and two 20B variants in immunized group compared to 27 (69%) B.1.351, 5 (13%) B.1.1.7, 4 (10%) 20B, 2 B.1.526 and one B.1.427 variant in unimmunized group. Whole genome sequence analysis of 14 cases identified seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and the rest three 20B variants. Conclusion Our study observed that ChAdOx1 could not prevent the new infection or severe COVID-19 disease outcome with single dose while the infections were mostly caused by B.1.351 variants in Bangladesh.
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Affiliation(s)
- Hassan M Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Shazid Hasan
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Ali Ahasan Setu
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Asm Rubayet Ul Alam
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shovon Lal Sarkar
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Tanvir Islam
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Mir Raihanul Islam
- Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Dhaka, Bangladesh
| | - Mohammad Mahfuzur Rahman
- Department of Environmental Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Ovinu Kibria Islam
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Iqbal Kabir Jahid
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
| | - M Anwar Hossain
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh; Vice-Chancellor, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
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13
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Navarro A, Gómez L, Sanseverino I, Niegowska M, Roka E, Pedraccini R, Vargha M, Lettieri T. SARS-CoV-2 detection in wastewater using multiplex quantitative PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148890. [PMID: 34298359 PMCID: PMC8278834 DOI: 10.1016/j.scitotenv.2021.148890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 05/03/2023]
Abstract
A multiplex reverse transcription quantitative PCR (RT-qPCR)-based method was designed for the simultaneous detection of different SARS-CoV-2 genes. In this study, we used three target genes encoding for the nucleocapsid 1 and 3 (N1, N3), and the spike (S) proteins, all commonly used in the detection of SARS-CoV-2 in human and environmental samples. The performance of the multiplex assay, compared to the single assay was assessed for the standard calibration curve, required for absolute quantification, and then, for the real environmental samples to detect SARS-CoV-2. For this latter, four environmental samples were collected at a local wastewater treatment plant (WWTP). The results showed that the cycle threshold (Ct) values of the multiplex were comparable to the values obtained by the singleplex PCR. The amplification of the three target genes indicated the presence of SARS-CoV-2 in the four water samples with an increasing trend in February and these results were confirmed in the multiplex approach, showing the robustness of this method and its applicability for the relative abundance analysis among the samples. Overall, both the laboratory and field work results demonstrated that the multiplex PCR assay developed in this study could provide a method for SARS-CoV-2 detection as robust as the single qPCR, but faster and cost-effective, reducing by three times the number of reactions, and consequently the handling time and reagents.
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Affiliation(s)
- Anna Navarro
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Livia Gómez
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Isabella Sanseverino
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Magdalena Niegowska
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Eszter Roka
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | | | - Marta Vargha
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Teresa Lettieri
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy.
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14
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Afrin SZ, Paul SK, Begum JA, Nasreen SA, Ahmed S, Ahmad FU, Aziz MA, Parvin R, Aung MS, Kobayashi N. Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020. New Microbes New Infect 2021; 41:100889. [PMID: 33936746 PMCID: PMC8065242 DOI: 10.1016/j.nmni.2021.100889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
In Bangladesh, coronavirus disease 2019 (COVID-19) has been highly prevalent during late 2020, with nearly 500 000 confirmed cases. In the present study, the spike (S) protein of severe acute respiratory coronavirus 2 (SARS-CoV-2) circulating in Bangladesh was genetically investigated to elucidate the diversity of mutations and their prevalence. The nucleotide sequence of the S protein gene was determined for 15 SARS-CoV-2 samples collected from eight divisions in Bangladesh, and analysed for mutations compared with the reference strain (hCoV-19/Wuhan/WIV04/2019). All the SARS-CoV-2 S genes were assigned to B.1 lineage in G clade, and individual S proteins had 1-25 mutations causing amino acid substitution/deletion. A total of 133 mutations were detected in 15 samples, with D614G being present in all the samples; 53 were novel mutations as of January 2021. On the receptor-binding domain, 21 substitutions including ten novel mutations were identified. Other novel mutations were located on the N-terminal domain (S1 subunit) and dispersed sites in the S2 subunit, including two substitutions that remove potential N-glycosylation sites. A P681R substitution adjacent to the furin cleavage site was detected in one sample. All the mutations detected were located on positions that are functionally linked to host transition, antigenic drift, host surface receptor binding or antibody recognition sites, and viral oligomerization interfaces, which presumably related to viral transmission and pathogenic capacity.
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Affiliation(s)
- S Z Afrin
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - S K Paul
- Department of Microbiology, Netrokona Medical College, Netrokona, Bangladesh
| | - J A Begum
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - S A Nasreen
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - S Ahmed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - F U Ahmad
- Department of Microbiology, TMSS Medical College, Bogura, Bangladesh
| | - M A Aziz
- Department of Microbiology, Rangpur Medical College, Rangpur, Bangladesh
| | - R Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M S Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - N Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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