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Li J, Cheng R, Bian Z, Niu J, Xia J, Mao G, Liu H, Wu C, Hao C. Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants. Appl Microbiol Biotechnol 2024; 108:35. [PMID: 38183475 DOI: 10.1007/s00253-023-12941-2] [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: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 01/08/2024]
Abstract
Quick differentiation of current circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmissions. However, the widely applied gene sequencing method is time-consuming and costly especially when facing recombinant variants, because a large part or whole genome sequencing is required. Allele-specific reverse transcriptase real time RT-PCR (RT-qPCR) represents a quick and cost-effective method for SNP (single nucleotide polymorphism) genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 5 multiplex allele-specific RT-qPCR assays targeting 20 key mutations for quick differentiation of the Omicron subvariants (BA.1 to BA.5 and their descendants) and the recombinant variants (XBB.1 and XBB.1.5). Two parallel multiplex RT-qPCR reactions were designed to separately target the prototype allele and the mutated allele of each mutation in the allele-specific RT-qPCR assay. Optimal annealing temperatures, primer and probe dosage, and time for annealing/extension for each reaction were determined by multi-factor and multi-level orthogonal test. The variation of Cp (crossing point) values (ΔCp) between the two multiplex RT-qPCR reactions was applied to determine if a mutation occurs or not. SARS-CoV-2 subvariants and related recombinant variants were differentiated by their unique mutation patterns. The developed multiplex allele-specific RT-qPCR assays exhibited excellent analytical sensitivities (with limits of detection (LoDs) of 1.47-18.52 copies per reaction), wide linear detection ranges (109-100 copies per reaction), good amplification efficiencies (88.25 to 110.68%), excellent reproducibility (coefficient of variations (CVs) < 5% in both intra-assay and inter-assay tests), and good clinical performances (99.5-100% consistencies with Sanger sequencing). The developed multiplex allele-specific RT-qPCR assays in the present study provide an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants. KEY POINTS: • A panel of five multiplex allele-specific RT-qPCR assays for quick differentiation of 11 SARS-CoV-2 Omicron subvariants (BA.1, BA.2, BA.4, BA.5, and their descendants) and 2 recombinant variants (XBB.1 and XBB.1.5). • The developed assays exhibited good analytical sensitivities and reproducibility, wide linear detection ranges, and good clinical performances, providing an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants.
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China.
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Zixin Bian
- College of Life Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Guoli Mao
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Hulong Liu
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Chunyan Hao
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, People's Republic of China.
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2
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Promja S, Puenpa J, Achakulvisut T, Poovorawan Y, Lee SY, Athamanolap P, Lertanantawong B. Machine Learning-Assisted Real-Time Polymerase Chain Reaction and High-Resolution Melt Analysis for SARS-CoV-2 Variant Identification. Anal Chem 2023; 95:2102-2109. [PMID: 36633573 PMCID: PMC9843624 DOI: 10.1021/acs.analchem.2c05112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
Abstract
Since the declaration of COVID-19 as a pandemic in early 2020, multiple variants of the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) have been detected. The emergence of multiple variants has raised concerns due to their impact on public health. Therefore, it is crucial to distinguish between different viral variants. Here, we developed a machine learning web-based application for SARS-CoV-2 variant identification via duplex real-time polymerase chain reaction (PCR) coupled with high-resolution melt (qPCR-HRM) analysis. As a proof-of-concept, we investigated the platform's ability to identify the Alpha, Delta, and wild-type strains using two sets of primers. The duplex qPCR-HRM could identify the two variants reliably in as low as 100 copies/μL. Finally, the platform was validated with 167 nasopharyngeal swab samples, which gave a sensitivity of 95.2%. This work demonstrates the potential for use as automated, cost-effective, and large-scale viral variant surveillance.
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Affiliation(s)
- Sutossarat Promja
- Department
of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya 73170, Nakhon Pathom, Thailand
| | - Jiratchaya Puenpa
- Center
of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Titipat Achakulvisut
- Department
of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya 73170, Nakhon Pathom, Thailand
| | - Yong Poovorawan
- Center
of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Su Yin Lee
- Faculty
of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
| | - Pornpat Athamanolap
- Department
of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya 73170, Nakhon Pathom, Thailand
- Integrative
Computational BioScience (ICBS) Center, Mahidol University, Salaya 73170, Nakhon Pathom, Thailand
| | - Benchaporn Lertanantawong
- Department
of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya 73170, Nakhon Pathom, Thailand
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3
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Koshikawa T, Miyoshi H. High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2. Biochem Biophys Rep 2022; 31:101306. [PMID: 35791375 PMCID: PMC9247225 DOI: 10.1016/j.bbrep.2022.101306] [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: 06/05/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022] Open
Abstract
High-resolution melting (HRM) analysis was conducted to discriminate between SARS-CoV-2 Omicron variant BA.1 (B.1.1.529.1) and subvariant BA.2 (B.1.1.529.2). We performed two-step PCR consisting of the first PCR and the second nested PCR to prepare the amplicon for HRM analysis, which detected G339D, N440K, G446S and D796Y variations in the SARS-CoV-2 spike protein. The melting temperatures (Tms) of the amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 receptor binding domain (RBD) in spike protein were the same: 75.2 °C (G339D variation) and 73.4 °C (D796Y variation). These Tms were distinct from those of SARS-CoV-2 isolate Wuhan-Hu-1, and were specific to the Omicron variant. In HRM analyses that detected the N440K and G446S variations, the Tms of amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 RBDs were 73.0 °C (N440K and G446S variations) and 73.5 °C (G446S variation). This difference indicates that the SARS-CoV-2 Omicron variants BA.1 and BA.2 can be clearly discriminated. Our study demonstrates the usefulness of HRM analysis after two-step PCR for the discrimination of SARS-CoV-2 variants. SARS-CoV-2 Omicron variant-specific variations in the spike protein were analysed by HRM analysis after nested PCR. Tm of the amplicon of the SARS-CoV-2 Omicron BA.1 variant were clearly distinct from those of Omicron BA.2 subvariant. HRM analysis detected the N440K and G446S variations on the spike protein. HRM analysis can discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2.
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4
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Li J, Gao Z, Chen J, Cheng R, Niu J, Zhang J, Yang Y, Yuan X, Xia J, Mao G, Liu H, Dong Y, Wu C. Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:953027. [PMID: 36061868 PMCID: PMC9433905 DOI: 10.3389/fcimb.2022.953027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Quick differentiation of the circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmission. However, the widely used gene sequencing method is time-consuming and costly when facing the viral recombinant variants, because partial or whole genome sequencing is required. Allele-specific real time RT-PCR (qRT-PCR) represents a quick and cost-effective method in SNP genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 3 multiplex allele-specific qRT-PCR assays targeting 12 key differential mutations for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2). Two parallel multiplex qRT-PCR reactions were designed to separately target the protype allele and the mutated allele of the four mutations in each allele-specific qRT-PCR assay. The variation of Cp values (ΔCp) between the two multiplex qRT-PCR reactions was applied for mutation determination. The developed multiplex allele-specific qRT-PCR assays exhibited outstanding analytical sensitivities (with limits of detection [LoDs] of 2.97-27.43 copies per reaction), wide linear detection ranges (107-100 copies per reaction), good amplification efficiencies (82% to 95%), good reproducibility (Coefficient of Variations (CVs) < 5% in both intra-assay and inter-assay tests) and clinical performances (99.5%-100% consistency with Sanger sequencing). The developed multiplex allele-specific qRT-PCR assays in this study provide an alternative tool for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2).
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
| | - Zefeng Gao
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jing Chen
- Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan, China
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jialei Zhang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - You Yang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Ximei Yuan
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Guoli Mao
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Hulong Liu
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Yongkang Dong
- Administrative Office, the Fourth People's Hospital of Taiyuan, Taiyuan, China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
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5
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Miyoshi H, Ichinohe R, Koshikawa T. High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Biochem Biophys Res Commun 2022; 606:128-134. [PMID: 35349821 PMCID: PMC8942459 DOI: 10.1016/j.bbrc.2022.03.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/04/2023]
Abstract
High-resolution melting (HRM) analysis was performed to detect G339D and D796Y variations in the SARS-CoV-2 Omicron variant spike protein. We employed two-step PCR consisting of the first RT–PCR and the second nested PCR to prepare the amplicon for HRM analysis. The melting temperatures (Tm) of the amplicon from the cDNA of the Omicron variant receptor binding domain (RBD) were 73.1 °C (G339D variation) and 75.1 °C (D796Y variation), respectively. These Tm values were clearly distinct from those of SARS-CoV-2 isolate Wuhan-Hu-1. HRM analysis after the two-step PCR was conducted on Omicron variant-positive specimens. The HRM curve and Tm value obtained with the Omicron variant-positive specimen were coincident with those of the amplicon from cDNA of the Omicron variant RBD. Our study demonstrates the utility of HRM analysis after two-step PCR for the detection of mutations in SARS-CoV-2 gene.
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6
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Allen RA, Williams CL, Penrod Y, McCloskey C, Carpenter-Azevedo K, Huard RC, King E, Terence Dunn S. A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants. J Med Virol 2022; 94:3661-3668. [PMID: 35416308 PMCID: PMC9088475 DOI: 10.1002/jmv.27770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/18/2022] [Accepted: 04/09/2022] [Indexed: 11/25/2022]
Abstract
Next‐generation sequencing (NGS) is the primary method used to monitor the distribution and emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants around the world; however, it is costly and time‐consuming to perform and is not widely available in low‐resourced geographical regions. Pyrosequencing has the potential to augment surveillance efforts by providing information on specific targeted mutations for rapid identification of circulating and emerging variants. The current study describes the development of a reverse transcription (RT)‐PCR‐pyrosequencing assay targeting >65 spike protein gene (S) mutations of SARS‐CoV‐2, which permits differentiation of commonly reported variants currently circulating in the United States with a high degree of confidence. Variants typed using the assay included B.1.1.7 (Alpha), B.1.1.529 (Omicron), B.1.351 (Beta), B.1.375, B.1.427/429 (Epsilon), B.1.525 (Eta), B.1.526.1 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.621 (Mu), P1 (Gamma), and B.1.1 variants, all of which were confirmed by the NGS data. An electronic typing tool was developed to aid in the identification of variants based on mutations detected by pyrosequencing. The assay could provide an important typing tool for rapid identification of candidate patients for monoclonal antibody therapies and a method to supplement SARS‐CoV‐2 surveillance efforts by identification of circulating variants and novel emerging lineages.
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Affiliation(s)
| | - Christopher L Williams
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yvonne Penrod
- OU Health Laboratories, Oklahoma City, Oklahoma, USA
| | | | | | - Richard C Huard
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - Ewa King
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - S Terence Dunn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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7
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Castañeda-Mogollón D, Kamaliddin C, Fine L, Oberding LK, Pillai DR. SARS-CoV-2 variant detection with ADSSpike. Diagn Microbiol Infect Dis 2022; 102:115606. [PMID: 34963097 PMCID: PMC8608664 DOI: 10.1016/j.diagmicrobio.2021.115606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 coronavirus pandemic has been an unprecedented challenge to global pandemic response and preparedness. With the continuous appearance of new SARS-CoV-2 variants, it is imperative to implement tools for genomic surveillance and diagnosis in order to decrease viral transmission and prevalence. The ADSSpike workflow was developed with the goal of identifying signature SNPs from the S gene associated with SARS-CoV-2 variants through amplicon deep sequencing. Seventy-two samples were sequenced, and 30 mutations were identified. Among those, signature SNPs were linked to 2 Zeta-VOI (P.2) samples and one to the Alpha-VOC (B.1.17). An average depth of 700 reads was found to properlycorrectly identify all SNPs and deletions pertinent to SARS-CoV-2 mutants. ADSSpike is the first workflow to provide a practical, cost-effective, and scalable solution to diagnose SARS-CoV-2 VOC/VOI in the clinical laboratory, adding a valuable tool to public health measures to fight the COVID-19 pandemic for approximately $41.85 USD/reaction.
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8
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Aoki A, Mori Y, Okamoto Y, Jinno H. Simultaneous Screening of SARS-CoV-2 Omicron and Delta Variants Using High-Resolution Melting Analysis. Biol Pharm Bull 2022; 45:394-396. [DOI: 10.1248/bpb.b21-01081] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Yoko Mori
- Faculty of Pharmacy, Meijo University
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9
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Ferreira BIDS, da Silva-Gomes NL, Coelho WLDCNP, da Costa VD, Carneiro VCDS, Kader RL, Amaro MP, Villar LM, Miyajima F, Alves-Leon SV, de Paula VS, Leon LAA, Moreira OC. Validation of a novel molecular assay to the diagnostic of COVID-19 based on real time PCR with high resolution melting. PLoS One 2021; 16:e0260087. [PMID: 34807915 PMCID: PMC8608302 DOI: 10.1371/journal.pone.0260087] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/03/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of the COVID-19 pandemic resulted in an unprecedented need for RT-qPCR-based molecular diagnostic testing, placing a strain on the supply chain and the availability of commercially available PCR testing kits and reagents. The effect of limited molecular diagnostics-related supplies has been felt across the globe, disproportionally impacting molecular diagnostic testing in developing countries where acquisition of supplies is limited due to availability. The increasing global demand for commercial molecular diagnostic testing kits and reagents has made standard PCR assays cost prohibitive, resulting in the development of alternative approaches to detect SARS-CoV-2 in clinical specimens, circumventing the need for commercial diagnostic testing kits while mitigating the high-demand for molecular diagnostics testing. The timely availability of the complete SARS-CoV-2 genome in the beginning of the COVID-19 pandemic facilitated the rapid development and deployment of specific primers and standardized laboratory protocols for the molecular diagnosis of COVID-19. An alternative method offering a highly specific manner of detecting and genotyping pathogens within clinical specimens is based on the melting temperature differences of PCR products. This method is based on the melting temperature differences between purine and pyrimidine bases. Here, RT-qPCR assays coupled with a High Resolution Melting analysis (HRM-RTqPCR) were developed to target different regions of the SARS-CoV-2 genome (RdRp, E and N) and an internal control (human RNAse P gene). The assays were validated using synthetic sequences from the viral genome and clinical specimens (nasopharyngeal swabs, serum and saliva) of sixty-five patients with severe or moderate COVID-19 from different states within Brazil; a larger validation group than that used in the development to the commercially available TaqMan RT-qPCR assay which is considered the gold standard for COVID-19 testing. The sensitivity of the HRM-RTqPCR assays targeting the viral N, RdRp and E genes were 94.12, 98.04 and 92.16%, with 100% specificity to the 3 SARS-CoV-2 genome targets, and a diagnostic accuracy of 95.38, 98.46 and 93.85%, respectively. Thus, HRM-RTqPCR emerges as an attractive alternative and low-cost methodology for the molecular diagnosis of COVID-19 in restricted-budget laboratories.
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Affiliation(s)
- Beatriz Iandra da Silva Ferreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Natália Lins da Silva-Gomes
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | - Rafael Lopes Kader
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa Pimentel Amaro
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lívia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Fábio Miyajima
- Oswaldo Cruz Foundation (Fiocruz), Branch Ceará, Eusebio, Brazil
| | - Soniza Vieira Alves-Leon
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Luciane Almeida Amado Leon
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Otacilio Cruz Moreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
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10
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Lago J, Groot H, Navas D, Lago P, Gamboa M, Calderón D, Polanía-Villanueva DC. Genetic and Bioinformatic Strategies to Improve Diagnosis in Three Inherited Bleeding Disorders in Bogotá, Colombia. Genes (Basel) 2021; 12:genes12111807. [PMID: 34828413 PMCID: PMC8625804 DOI: 10.3390/genes12111807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/03/2022] Open
Abstract
Inherited bleeding disorders (IBDs) are the most frequent congenital diseases in the Colombian population; three of them are hemophilia A (HA), hemophilia B (HB), and von Willebrand Disease (VWD). Currently, diagnosis relies on multiple clinical laboratory assays to assign a phenotype. Due to the lack of accessibility to these tests, patients can receive an incomplete diagnosis. In these cases, genetic studies reinforce the clinical diagnosis. The present study characterized the molecular genetic basis of 11 HA, three HB, and five VWD patients by sequencing the F8, F9, or the VWF gene. Twelve variations were found in HA patients, four in HB patients, and 19 in WVD patients. From these variations a total of 25 novel variations were found. Disease-causing variations were used as positive controls for validation of the high-resolution melting (HRM) variant-scanning technique. This approach is a low-cost genetic diagnostic method proposed to be incorporated in developing countries. For the data analysis, we developed an accessible open-source code in Python that improves HRM data analysis with better sensitivity of 95% and without bias when using different HRM equipment and software. Analysis of amplicons with a length greater than 300 bp can be performed by implementing an analysis by denaturation domains.
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Affiliation(s)
- Juliana Lago
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Helena Groot
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Diego Navas
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Paula Lago
- Department of Basic Sciences, Kyushu Institute of Technology, Kitakyushu 804-8550, Japan;
| | - María Gamboa
- Laboratorio de Referencia en Hemostasia, Bogotá 110231, Colombia;
| | - Dayana Calderón
- Corporación Corpogen, Universidad Central, Bogotá 110311, Colombia;
| | - Diana C. Polanía-Villanueva
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
- Correspondence:
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11
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Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting. Diagnostics (Basel) 2021; 11:diagnostics11101788. [PMID: 34679489 PMCID: PMC8534650 DOI: 10.3390/diagnostics11101788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the past 18 months, numerous SARS-CoV-2 variants have emerged. Many of these variants are suggested to be more transmissible as well as less responsive to neutralization by vaccine-induced antibodies. Viral whole-genome sequencing is the current standard for tracking these variants. However, whole-genome sequencing is costly and the technology and expertise are limited to larger reference laboratories. Here, we present the feasibility of a fast, inexpensive methodology using snapback primer-based high-resolution melting to test for >20 high-consequence SARS-CoV-2 spike mutations. This assay can distinguish between multiple variant lineages and be completed in roughly 2 h for less than $10 per sample.
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12
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Gazali FM, Nuhamunada M, Nabilla R, Supriyati E, Hakim MS, Arguni E, Daniwijaya EW, Nuryastuti T, Haryana SM, Wibawa T, Wijayanti N. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Heliyon 2021; 7:e07936. [PMID: 34514180 PMCID: PMC8420086 DOI: 10.1016/j.heliyon.2021.e07936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Monitoring the spread of the G614 in specific locations is critical as this variant is highly transmissible and can trigger the emergence of other mutations. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. This study aims to analyze the potential use of the two-step Reverse Transcriptase quantitative polymerase chain reaction - high resolution melting analysis (RT-qPCR-HRM) to detect a specific mutation in the SARS-CoV-2 genome. METHODS Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. The primers are designed to target the specific Spike region containing the D614G mutation. The qPCR-HRM analysis was conducted simultaneously, and the identification of the SARS-CoV-2 variant was confirmed by conventional PCR and Sanger sequencing methods. RESULTS The results showed that the melting temperature (Tm) of the D614 variant was 79.39 ± 0.03 °C, which was slightly lower than the Tm of the G614 variant (79.62 ± 0.015 °C). The results of the HRM analysis, visualized by the normalized melting curve and the difference curve were able to discriminate the D614 and G614 variant samples. All samples were identified as G614 variants by qPCR-HRM assay, which was subsequently confirmed by Sanger sequencing. CONCLUSIONS This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology Study Program, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Diagnostic Laboratory of World Mosquito Program (WMP), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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