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Aldossary AM, Tawfik EA, Altammami MA, Alquait AA, Booq RY, Sendy BK, Alarawi MS, Gojobori T, Altamimi AM, Alaifan TA, Albarrag AM, Alyamani EJ. Development and Validation of Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) as a Simple and Rapid Diagnostic Tool for SARS-CoV-2 Detection. Diagnostics (Basel) 2022; 12:diagnostics12092232. [PMID: 36140632 PMCID: PMC9498013 DOI: 10.3390/diagnostics12092232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 12/23/2022] Open
Abstract
Since the COVID-19 pandemic outbreak in the world, many countries have searched for quick diagnostic tools to detect the virus. There are many ways to design diagnostic assays; however, each may have its limitations. A quick, sensitive, specific, and simple approach is essential for highly rapidly transmitted infections, such as SARS-CoV-2. This study aimed to develop a rapid and cost-effective diagnostic tool using a one-step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) approach. The results were observed using the naked eye within 30–60 min using turbidity or colorimetric analysis. The sensitivity, specificity, and lowest limit of detection (LoD) for SARS-CoV-2 RNA against the RT-LAMP assay were assessed. This assay was also verified and validated against commercial quantitative RT-PCR used by health authorities in Saudi Arabia. Furthermore, a quick and direct sampling from the saliva, or buccal cavity, was applied after simple modification, using proteinase K and heating at 98 °C for 5 min to avoid routine RNA extraction. This rapid single-tube diagnostic tool detected COVID-19 with an accuracy rate of 95% for both genes (ORF1a and N) and an LoD for the ORF1a and N genes as 39 and 25 copies/reaction, respectively. It can be potentially used as a high-throughput national screening for different respiratory-based infections within the Middle East region, such as the MERS virus or major zoonotic pathogens such as Mycobacterium paratuberculosis and Brucella spp., particularly in remote and rural areas where lab equipment is limited.
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Affiliation(s)
- Ahmad M. Aldossary
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Essam A. Tawfik
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Musaad A. Altammami
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Azzam A. Alquait
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Rayan Y. Booq
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Bandar K. Sendy
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Mohammed S. Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Asmaa M. Altamimi
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Taghreed A. Alaifan
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Ahmed M. Albarrag
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Essam J. Alyamani
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
- Correspondence:
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Altamimi AM, Obeid DA, Alaifan TA, Taha MT, Alhothali MT, Alzahrani FA, Albarrag AM. Assessment of 12 qualitative RT-PCR commercial kits for the detection of SARS-CoV-2. J Med Virol 2021; 93:3219-3226. [PMID: 33629747 PMCID: PMC8014669 DOI: 10.1002/jmv.26900] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/05/2023]
Abstract
The emergence of the novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in the late months of 2019 had the officials to declare a public health emergency leading to a global response. Public measurements rely on an accurate diagnosis of individuals infected with the virus by using real‐time reverse transcriptase‐polymerase chain reaction (RT‐PCR). The aim of our study is to relate the fundamental clinical and analytical performance of SARS‐CoV‐2 (RT‐PCR) commercial kits. A total of 94 clinical samples were selected. Generally, 400 µl of each respiratory specimen was subjected to extraction using ExiPrep 96 Viral RNA Kit. All kits master mix preparation, cycling protocol, thermocycler, and results interpretation were carried out according to the manufacturer's instructions of use and recommendations. The performance of the kits was comparable except for the LYRA kit as it was less sensitive (F = 67, p < .001). Overall, four kits scored a sensitivity of 100% including: BGI, IQ Real, Sansure, and RADI. For specificity, all the tested kits scored above 95%. The performance of these commercial kits by gene target showed no significant change in CT values which indicates that kits disparities are mainly linked to the oligonucleotide of the gene target. We believe that most of the commercially available RT‐PCR kits included in this study can be used for routine diagnosis of patients with SARS‐CoV‐2. We recommend including kits with multiple targets in order to monitor the virus changes over time. The aim of our study is to relate the fundamental clinical and analytical performance of SARS‐COV‐2 (RT‐PCR) commercial kits. Overall, four kits scored a sensitivity of 100% including: BGI, IQ Real, Sansure, and RADI. For specificity, all the tested kits scored above 95%. Whole‐genome sequencing was used to analysis the nucleotide and amino acid identity and the genetic diversity of G9P[8] RVAs in this study. The performance of these commercial kits by gene target showed no significant change in Ct values which indicates that kits disparities are mainly linked to the oligonucleotide of the gene target. We recommend including kits with multiple targets in order to monitor the virus changes over time.
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Affiliation(s)
- Asmaa M Altamimi
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Dalia A Obeid
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Taghreed A Alaifan
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Moroje T Taha
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Marwa T Alhothali
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Fahad A Alzahrani
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Ahmad M Albarrag
- Public Health Laboratories, Saudi Center for Disease Prevention and Control, Riyadh, Saudi Arabia.,Pathology Department, Medical Microbiology, King Saud University, Riyadh, Saudi Arabia
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Tamin A, Queen K, Paden CR, Lu X, Andres E, Sakthivel SK, Li Y, Tao Y, Zhang J, Kamili S, Assiri AM, Alshareef A, Alaifan TA, Altamimi AM, Jokhdar H, Watson JT, Gerber SI, Tong S, Thornburg NJ. Isolation and growth characterization of novel full length and deletion mutant human MERS-CoV strains from clinical specimens collected during 2015. J Gen Virol 2020; 100:1523-1529. [PMID: 31592752 PMCID: PMC7079693 DOI: 10.1099/jgv.0.001334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Middle East respiratory syndrome (MERS) is a viral respiratory illness first reported in Saudi Arabia in September 2012 caused by the human coronavirus (CoV), MERS-CoV. Using full-genome sequencing and phylogenetic analysis, scientists have identified three clades and multiple lineages of MERS-CoV in humans and the zoonotic host, dromedary camels. In this study, we have characterized eight MERS-CoV isolates collected from patients in Saudi Arabia in 2015. We have performed full-genome sequencing on the viral isolates, and compared them to the corresponding clinical specimens. All isolates were clade B, lineages 4 and 5. Three of the isolates carry deletions located on three independent regions of the genome in the 5'UTR, ORF1a and ORF3. All novel MERS-CoV strains replicated efficiently in Vero and Huh7 cells. Viruses with deletions in the 5'UTR and ORF1a exhibited impaired viral release in Vero cells. These data emphasize the plasticity of the MERS-CoV genome during human infection.
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Affiliation(s)
- Azaibi Tamin
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Krista Queen
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Clinton R Paden
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Xiaoyan Lu
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Erica Andres
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Senthilkumar K Sakthivel
- Batelle, Columbus, OH, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Yan Li
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Ying Tao
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Jing Zhang
- IHRC, Atlanta, GA, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Shifaq Kamili
- IHRC, Atlanta, GA, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Ali Alshareef
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | | | - Asmaa M Altamimi
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | - Hani Jokhdar
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | - John T Watson
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Susan I Gerber
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Suxiang Tong
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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