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Kourout M, Espich S, Fisher C, Tiper I, Purkayastha A, Smith S, Santana-Quintero L, Duncan R. Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform. Front Mol Biosci 2024; 11:1419213. [PMID: 38966129 PMCID: PMC11222771 DOI: 10.3389/fmolb.2024.1419213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/23/2024] [Indexed: 07/06/2024] Open
Abstract
Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.
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Affiliation(s)
- Moussa Kourout
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Scott Espich
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Carolyn Fisher
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Irina Tiper
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | | | - Sean Smith
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Luis Santana-Quintero
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Robert Duncan
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
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Liu D, Wang Z, Mao M, Zhang Z, Ding X, Zheng H, Li S, Zhang Z, Tian Z. Application of whole-genome tiling array at Shanghai port, China: An alternative method for SARS-CoV-2 surveillance. J Med Virol 2023; 95:e29222. [PMID: 37964661 DOI: 10.1002/jmv.29222] [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: 08/28/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the critical role of genomic surveillance in tracking rapidly spreading viruses and their evolving lineages. The emergence of the SARS-CoV-2 tiling array, a comprehensive tool capable of capturing the entire viral genome, has presented a promising avenue for variants. This study introduces the SARS-CoV-2 tiling array as a novel method for port inspection. Using next-generation sequencing as a benchmark, 35 positive samples underwent sequencing through both methodologies, including the Alpha variant (B.1.1.7), Delta variants (AY.120, AY.122, AY.23.1), and Omicron variants (BA.1, BA.2, BA.2.75, BA.4, BA.5, BE.1, BF.7, BN.1, BQ.1, XBB.1) within the sample set. The whole-genome tiling array demonstrated successful identification of various sublineages of SARS-CoV-2. The average sequencing coverage rates were 99.22% (96.82%-99.92%) for the whole-genome tiling array and 98.56% (92.81%-99.59%) for Illumina sequencing, respectively. The match rates of these two methods ranged from 92.81%-99.59%, with an average rate of 98.56%. Among the benefits of the whole-genome tiling array are its cost-effectiveness and equipment simplification, making it particularly suitable for identifying SARS-CoV-2 variants in the front-line inspection department. The aforementioned findings provide valuable insights into the surveillance of COVID-19 and present a pragmatic solution for improving quarantine measures at entry points.
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Affiliation(s)
- Danlei Liu
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhiyi Wang
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
| | - Mao Mao
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
| | - Zilei Zhang
- Inspection and Quarantine Technology Communication Department, Shanghai Customs College, Shanghai, China
| | - Xun Ding
- Centrillion Technologies, Palo Alto, California, USA
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
| | - Zilong Zhang
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai Customs District PR China, Shanghai, China
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Warmt C, Broweleit LM, Fenzel CK, Henkel J. An experimental comparison between primer and nucleotide labelling to produce RPA-amplicons used for multiplex detection of antibiotic resistance genes. Sci Rep 2023; 13:15734. [PMID: 37735542 PMCID: PMC10514322 DOI: 10.1038/s41598-023-42830-7] [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: 05/18/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Direct labelling of amplification products using isothermal amplification is currently done most frequently by incorporating previously labelled primer. Although this method is well proven and widely used, it is not a universal solution due to some weaknesses. Alternatively, labelled nucleotides could be used, whose application and functionality have been already partially demonstrated. It remains to be determined how this method performs in comparison to traditional labelling, in particular combined with isothermal amplification methods. In this work, we show a detailed analysis of the labelling efficiency under different conditions and compare the results with the traditional primer-labelling method in the context of RPA amplification. Impressively, our results showed that using Cy5-labelled dUTPs can achieve much more efficient labelling for fragments above 200 bp, while using them for smaller fragments does not bring any relevant disadvantages, but also no major benefit. Furthermore, this work successfully demonstrate for the first time a quadruplex microarray for the detection of resistance genes using RPA and direct labelling with Cy5-dUTP as a potential application scenario. The sensitivities achieved here extend to SNP discovery for the detection of the proper blaKPC variant.
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Affiliation(s)
- Christian Warmt
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Lisa-Marie Broweleit
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Carolin Kornelia Fenzel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
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Ko K, Takahashi K, Ito N, Sugiyama A, Nagashima S, Miwata K, Kitahara Y, Okimoto M, Ouoba S, Akuffo GA, E B, Akita T, Takafuta T, Tanaka J. Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification. BMC Med Genomics 2023; 16:199. [PMID: 37620887 PMCID: PMC10463848 DOI: 10.1186/s12920-023-01633-5] [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: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer. METHODS Using 241 stocked saliva samples collected from confirmed COVID-19 patients between November 2020 and March 2022 in Hiroshima, SARS-CoV-2 spike gene sequencing (nt22735-nt23532) was performed by nested RT-PCR and Sanger platform using in-house primers. The same samples underwent full-genome sequencing by NGS using Illumina NextSeq2000. RESULTS Among 241 samples, 147 were amplified by both the Sanger and the Illumina NextSeq2000 NGS, 86 by Sanger only, and 8 were not amplified at all. The overall amplification rates of Illumina NextSeq2000 NGS and Sanger were 61% and 96.7%, respectively. At low viral titer (< 103 copies/mL), Illumina NextSeq2000 NGS provided 19.2% amplification, while Sanger was 89.7% (p < 0.0001). Both platforms identified 38 wild type, 54 Alpha variants, 84 Delta variants, and 57 Omicron variants. CONCLUSIONS Our study provided evidence to expand the capacity of Sanger-based SARS-CoV-2 spike gene sequencing for variants identification over full-genome by Illumina NextSeq2000 NGS for mass screening. Therefore, the feasible and simple Sanger-based SARS-CoV-2 spike gene sequencing is practical for the initial variants screening, which might reduce the gap between the rapid evolution of SARS-CoV-2 and its molecular surveillance.
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Affiliation(s)
- Ko Ko
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kazuaki Takahashi
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Noriaki Ito
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | - Aya Sugiyama
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shintaro Nagashima
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kei Miwata
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | | | - Mafumi Okimoto
- Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | - Serge Ouoba
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
- Unité de Recherche Clinique de Nanoro (URCN), Institut de Recherche en Science de La Santé (IRSS), Nanoro, Burkina Faso
| | - Golda Ataa Akuffo
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Bunthen E
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
- Payment Certification Agency (PCA), Ministry of Health, Phnom Penh, Cambodia
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | | | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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Qi R, Wang G, Wang X, Li C, Huang L, Xiao W, Shao B, Zhou C, Ding X, Li F, Zhou W. A full genome tiling array enhanced the inspection and quarantine of SARS-CoV-2. Virol J 2023; 20:42. [PMID: 36872317 PMCID: PMC9985699 DOI: 10.1186/s12985-023-02000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/24/2023] [Indexed: 03/07/2023] Open
Abstract
As the worldwide spreading epidemic of SARS-CoV-2, quick inspection and quarantine of passengers for SARS-CoV-2 infection are essential for controlling the spread of SARS-CoV-2, especially the cross-border transmission. This study reports a SARS-CoV-2 genome sequencing method based on a re-sequencing tiling array successfully used in border inspection and quarantine. The tiling array chip has four cores, with one core of 240,000 probes dedicated to the whole genome sequencing of the SAR-CoV-2 genome. The assay protocol has been improved to reduce the detection time to within one day and can detect 96 samples in parallel. The detection accuracy has been validated. This fast and simple procedure is also of low cost and high accuracy, and it is particularly suitable for the rapid tracking of viral genetic variants in custom inspection applications. Combining these properties means this method has significant application potential in the clinical investigation and quarantine of SARS-CoV-2. We used this SARS-CoV-2 genome re-sequencing tiling array to inspect and quarantine China's entry and exit ports in the Zhejiang Province. From November 2020 to January 2022, we observed the gradual shift of SARS-CoV-2 variants from the D614G type to the Delta Variant, and then to the dominance of the Omicron variant recently, consistently with the global emergency pattern of the new SARS-CoV-2 variant.
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Affiliation(s)
- Runzi Qi
- Hangzhou Xiaoshan Airport Customs of the People's Republic of China, Hangzhou, 311241, China.
| | - Gang Wang
- Hangzhou International Travel Healthcare Center, Hangzhou, 310061, China
| | - Xu Wang
- Centrillion Technology (Hangzhou) Co., Ltd, Hangzhou, 310053, China
| | - Cheng Li
- Hangzhou Customs Logistics Management Center, Hangzhou, 310005, China
| | - Lei Huang
- Zhoushan International Travel Healthcare Center Clinic, Zhoushan, 316004, China
| | - Weixi Xiao
- Centrillion Technology (Hangzhou) Co., Ltd, Hangzhou, 310053, China
| | - Bing Shao
- Centrillion Technology (Hangzhou) Co., Ltd, Hangzhou, 310053, China
| | - Chunya Zhou
- Hangzhou Xiaoshan Airport Customs of the People's Republic of China, Hangzhou, 311241, China
| | - Xun Ding
- Centrillion Technologies, Palo Alto, CA, 94303, USA
| | - Feng Li
- Centrillion Technology (Hangzhou) Co., Ltd, Hangzhou, 310053, China
| | - Wei Zhou
- Centrillion Technologies, Palo Alto, CA, 94303, USA
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Warmt C, Fenzel CK, Henkel J, Bier FF. Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes. Sci Rep 2021; 11:20137. [PMID: 34635776 PMCID: PMC8505619 DOI: 10.1038/s41598-021-99774-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1% Cy5-dUTP and 99% unlabelled dTTP we were able to detect the blaCTX-M15 gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.
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Affiliation(s)
- Christian Warmt
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Carolin Kornelia Fenzel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.,Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Frank Fabian Bier
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Institute for Molecular Diagnostics and Bioanalysis, IMDB, 16761, Hennigsdorf, Germany
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Bardajee GR, Zamani M, Sharifi M. Efficient and Versatile Application of Fluorescence DNA-Conjugated CdTe Quantum Dots Nanoprobe for Detection of a Specific Target DNA of SARS Cov-2 Virus. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10223-10232. [PMID: 34379978 DOI: 10.1021/acs.langmuir.1c01687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Regarding the outbreak of the SARS Cov-2 virus pandemic worldwide, it seems necessary to provide new diagnostic methods to combat the virus. A fluorescence CdTe quantum dots-DNA (QDs-DNA) nanosensor was prepared for efficient detection of a specific target complementary DNA or RNA from the SARS Cov-2 virus using FRET experiment via forming a classic "sandwich" structure. The sequence of the complementary DNA (target DNA) is planned based on a substantial part of the SARS Cov-2 virus genome, and oligonucleotides of QDs-DNA nanoprobe are designed to complement it. The water-soluble CdTe QDs-DNA was prepared by replacing the thioglycolic acid (TGA) on the surface of QDs with capture DNA (thiolated DNA) through a ligand-exchange method. Subsequently, with the addition of complementary (target DNA) and quencher DNA (BHQ2-labeled DNA) into the QDs-DNA conjugates, sandwiched hybrids were formed. The resulting assembly brings the BHQ2-labeled DNA (as the acceptor), and the QDs (as the donor) into proximity, leading to quenching of fluorescence emission from the donor QDs through the FRET mechanism. In other words, a simple, highly sensitive, selective, and rapid approach was introduced to detect complementary DNA sequence from a specific part of the SARS Cov-2 virus genome with a detection limit of 2.52 × 10-9 mol L-1. Furthermore, the planned nanosensor was well used for the detection of RNA from SARS Cov-2 viruses in real samples with satisfactory analytical results, and the outcomes were compared with RT-PCR (Reverse Transcription Polymerase Chain Reaction) as the well-known standard method.
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Affiliation(s)
| | - Mohammadreza Zamani
- Department of Plant Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, P.O. Box 14155-6343, I.R. of Iran
| | - Mahdieh Sharifi
- Department of Chemistry, Payame Noor University, PO BOX 19395-3697, Tehran, Iran
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Shimada R, Alden EN, Hoff K, Ding X, Sun J, Halasz AM, Zhou W, Edwards JS. SARS-CoV-2 Variant Identification Using a Genome Tiling Array and Genotyping Probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.11.443659. [PMID: 34013279 PMCID: PMC8132287 DOI: 10.1101/2021.05.11.443659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With over three million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. We previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome when compared to traditional short read sequencing methods which can be time consuming and costly. Herein we present the addition of genotyping probes to our DNA chip which target known SARS-CoV-2 variants. The incorporation of the genotyping probe sets along with the advent of a moving average filter have improved our sequencing coverage and accuracy of the SARS-CoV-2 genome.
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