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Hasan MS, Rahman MS, Das PK, Ul Alam AR, Islam OK, Al-Emran HM, Hossain MA, Jahid IK. Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology. MethodsX 2024; 12:102646. [PMID: 38524302 PMCID: PMC10957433 DOI: 10.1016/j.mex.2024.102646] [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: 11/12/2022] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.
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Affiliation(s)
- Md. Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Prosanto Kumar Das
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - A.S.M. Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Hassan M. Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Anwar Hossain
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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2
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Lu M, Sun X, Zhao Y, Zheng L, Lin J, Tang C, Chao K, Chen Y, Li K, Zhou Y, Xiao J. Low cycle number multiplex PCR: A novel strategy for the construction of amplicon libraries for next-generation sequencing. Electrophoresis 2024. [PMID: 38533931 DOI: 10.1002/elps.202300160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Multiplex PCR is a critical step when preparing amplicon library for next-generation sequencing. However, there are several challenges related to multiplex PCR including poor uniformity, nonspecific amplification, and primer-dimers. To address these issues, we propose a novel solution strategy that involves using a low cycle number (<10 cycles) in multiplex PCR and then employing carrier DNAs and magnetic beads for the selection of targeted products. This technique improves the amplicon uniformity while also reducing primer-dimers and PCR artifacts. To evaluate our technique, we initially utilized 120 DNA fragments from mouse genome containing single nucleotide polymorphism (SNP) sites. Sequencing results demonstrated that with only 7 cycles of multiplex PCR, 95.8% of the targeted SNP sites were mapped, with a coverage of at least 1×. The average sequencing depth of all amplicons was 1705.79 ± 1205.30×; 87% of them reached a coverage depth that exceeded 0.2-fold of the average sequencing depth. Our method had a greater uniformity (87%) when compared to Hi-Plex PCR (53.3%). Furthermore, we validated our strategy by randomly selecting 90 primer pairs twice from the initial set of 120 primer-pairs. Next, we used the same protocol to prepare amplicon libraries. The two groups had an average sequencing depth of 1013.30 ± 585.57× and 219.10 ± 158.27×, respectively; over 84% of the amplicons had a sequencing depth that exceeded 0.2-fold of average depth. These results suggest that the use of a low cycle number in multiplex PCR is a cost-effective and efficient approach for the preparation of amplicon libraries.
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Affiliation(s)
- Meng Lu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Xiuxiu Sun
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxin Zhao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Chen Tang
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Kaiyue Chao
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Ye Chen
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
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3
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Gonzalez-Alba JM, Rojo-Alba S, Perez-Martinez Z, Boga JA, Alvarez-Arguelles ME, Gomez J, Herrero P, Costales I, Alba LM, Martin-Rodriguez G, Campo R, Castelló-Abietar C, Sandoval M, Abreu-Salinas F, Coto E, Rodriguez M, Rubianes P, Sanchez ML, Vazquez F, Antuña L, Álvarez V, Melón García S. Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain. Access Microbiol 2023; 5:000573.v4. [PMID: 37841093 PMCID: PMC10569657 DOI: 10.1099/acmi.0.000573.v4] [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: 01/30/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Mutational analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can quantify the relative importance of variants over time, enable dominant mutations to be identified, and facilitate near real-time detection, comparison and tracking of evolving variants. SARS-CoV-2 in Asturias, an autonomous community of Spain with a large ageing population, and high levels of migration and tourism, was monitored and tracked from the beginning of the pandemic in February 2020 until its decline and stabilization in August 2021, and samples were characterized using whole genomic sequencing and single nucleotide polymorphisms. Data held in the GISAID database were analysed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1 % of the population with SARS-CoV-2 were found, identifying ten major variants worldwide (seven arose before January 2021), 19 regional and one local. In Asturias only 17 different variants were found. After vaccination, no further regional major variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures such as rapid diagnosis, isolation and vaccination were efficient.
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Affiliation(s)
- Jose Maria Gonzalez-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Susana Rojo-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Zulema Perez-Martinez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Jose A. Boga
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Elena Alvarez-Arguelles
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Juan Gomez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Pablo Herrero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Isabel Costales
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luz Maria Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gabriel Martin-Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rainer Campo
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Cristian Castelló-Abietar
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Sandoval
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fátima Abreu-Salinas
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Eliecer Coto
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Mercedes Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Rubianes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Maria Luisa Sanchez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fernando Vazquez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Antuña
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Victoria Álvarez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Santiago Melón García
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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4
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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5
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Romagnoli A, D'Agostino M, Pavoni E, Ardiccioni C, Motta S, Crippa P, Biagetti G, Notarstefano V, Rexha J, Perta N, Barocci S, Costabile BK, Colasurdo G, Caucci S, Mencarelli D, Turchetti C, Farina M, Pierantoni L, La Teana A, Al Hadi R, Cicconardi F, Chinappi M, Trucchi E, Mancia F, Menzo S, Morozzo Della Rocca B, D'Annessa I, Di Marino D. SARS-CoV-2 multi-variant rapid detector based on graphene transistor functionalized with an engineered dimeric ACE2 receptor. NANO TODAY 2023; 48:101729. [PMID: 36536857 PMCID: PMC9750890 DOI: 10.1016/j.nantod.2022.101729] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/14/2022] [Accepted: 12/11/2022] [Indexed: 05/14/2023]
Abstract
Reliable point-of-care (POC) rapid tests are crucial to detect infection and contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The emergence of several variants of concern (VOC) can reduce binding affinity to diagnostic antibodies, limiting the efficacy of the currently adopted tests, while showing unaltered or increased affinity for the host receptor, angiotensin converting enzyme 2 (ACE2). We present a graphene field-effect transistor (gFET) biosensor design, which exploits the Spike-ACE2 interaction, the crucial step for SARS-CoV-2 infection. Extensive computational analyses show that a chimeric ACE2-Fragment crystallizable (ACE2-Fc) construct mimics the native receptor dimeric conformation. ACE2-Fc functionalized gFET allows in vitro detection of the trimeric Spike protein, outperforming functionalization with a diagnostic antibody or with the soluble ACE2 portion, resulting in a sensitivity of 20 pg/mL. Our miniaturized POC biosensor successfully detects B.1.610 (pre-VOC), Alpha, Beta, Gamma, Delta, Omicron (i.e., BA.1, BA.2, BA.4, BA.5, BA.2.75 and BQ.1) variants in isolated viruses and patient's clinical nasopharyngeal swabs. The biosensor reached a Limit Of Detection (LOD) of 65 cps/mL in swab specimens of Omicron BA.5. Our approach paves the way for a new and reusable class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.
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Affiliation(s)
- Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Eleonora Pavoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Chiara Ardiccioni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paolo Crippa
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giorgio Biagetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Valentina Notarstefano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Jesmina Rexha
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Nunzio Perta
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simone Barocci
- Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Davide Mencarelli
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Claudio Turchetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Marco Farina
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luca Pierantoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Richard Al Hadi
- Alcatera Inc., 1401 Westwood Blvd Suite 280, Los Angeles, CA 90024, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Blasco Morozzo Della Rocca
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ilda D'Annessa
- Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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6
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Li Y, Shi X, Zuo Y, Li T, Liu L, Shen Z, Shen J, Zhang R, Wang S. Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes. Microbiol Spectr 2022; 10:e0229722. [PMID: 36287061 PMCID: PMC9769626 DOI: 10.1128/spectrum.02297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.
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Affiliation(s)
- Yiming Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaomin Shi
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zuo
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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7
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Repurposing Positive SARS-CoV-2 Antigen Test Devices for Variant Tracking. Curr Microbiol 2022; 79:272. [PMID: 35881313 PMCID: PMC9315323 DOI: 10.1007/s00284-022-02973-8] [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: 11/12/2021] [Accepted: 07/11/2022] [Indexed: 12/18/2022]
Abstract
From the very beginning of the SARS-CoV-2 pandemic, one of the very few common opinions was that to control the expansion of the virus as many as the possible test had to be done. Antigen tests, being affordable and easy and fast to use, represented a great opportunity to expand the testing capacities of many healthcare systems. However, in 2021 with the appearance of the new SARS-CoV-2 variants, variant tracking strategies had to be implemented, which often included needing a second test to determine the variant of the patients diagnosed with antigen tests or not taking these samples into consideration at all. Therefore, we proposed recovering the positive antigen test devices to include them in our routine variant tracking strategy. The recovered positive antigen test devices obtained from 1st April 2021 to 15the January 2022 were analysed following the variant tracking protocol in force. The results obtained were compared to the positive samples detected by RT-PCR which were processed for variant tracking during the same period. 21,304 samples were processed, 6297 from the recovered positive antigen devices and 15,007 from the standard nasopharyngeal swabs. Only 773 (3.63%) samples were no conclusive, 104 (1.65%) from the recovered antigen devices and 669 (4.46%) from the RT-PCR positive group. This difference was statistically significant (p < 0.01). Taking this into account the proposed method is suitable and very recommendable, as it is an important measure to have a better and immediate picture of the circulating variants in every community.
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8
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains. Viruses 2022; 14:v14061230. [PMID: 35746701 PMCID: PMC9227152 DOI: 10.3390/v14061230] [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: 03/22/2022] [Revised: 05/14/2022] [Accepted: 06/04/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.
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De novo emergence of the mutation E484K in a SARS-CoV-2 B.1.1.7 lineage variant. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:520-522. [PMID: 35729053 PMCID: PMC9174144 DOI: 10.1016/j.eimce.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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11
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Colleluori G, Graciotti L, Pesaresi M, Di Vincenzo A, Perugini J, Di Mercurio E, Caucci S, Bagnarelli P, Zingaretti CM, Nisoli E, Menzo S, Tagliabracci A, Ladoux A, Dani C, Giordano A, Cinti S. Visceral fat inflammation and fat embolism are associated with lung’s lipidic hyaline membranes in subjects with COVID-19. Int J Obes (Lond) 2022; 46:1009-1017. [PMID: 35082385 PMCID: PMC8790008 DOI: 10.1038/s41366-022-01071-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
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12
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Use of the Ct difference between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for SARS-CoV-2 variants with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay: Searching the N in Variants. J Virol Methods 2022; 301:114463. [PMID: 35051443 PMCID: PMC8763412 DOI: 10.1016/j.jviromet.2022.114463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/02/2022]
Abstract
Purpose With the rise of the different Variants of Concern (VOC) and Variants of Interest (VOI) in order to control the SARS-CoV-2 pandemic, strategies for accurately tracking these different variants have been developed. While most of these strategies rely heavily on specific PCRs targeting the characteristic mutations of some lineages, several approaches using the alterations at the cycle threshold (Ct) of different commercial PCR diagnostic tests have been described. The objective of this study is to analyse the use of the Ct difference at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Seegene, Korea) between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for variant tracking. Methods The samples analysed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay from 1st of March 2021 to 26th of December 2021 were selected. The Ct values for N, S, RdRP were collected, and the differences between N and S (ΔS) and N and RdRP (ΔRdRP) were calculated. Using ΔS and ΔRdRP a diagnostic test was designed and these results were compared to the routine Variant assessment. Results The mean ΔS and ΔRdRP were characteristic for Alpha and Delta. This difference was statistically significant. For Every analysed Variant the diagnostic test achieved a higher than 90% sensitivity with a noteworthy performance with the Omicron variant (97% sensitivity and 90% specificity). Conclusions The analysis of the Ct alterations at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay may be a suitable method for an early approach to SARS-CoV-2 variant assessment.
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Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: an IDSA/ASM Consensus Review Document. J Clin Microbiol 2021; 60:e0165921. [PMID: 34731022 PMCID: PMC8769737 DOI: 10.1128/jcm.01659-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with more than 2 million genomes sequenced at the time of writing. The rise of more transmissible variants of concern that impact vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, and clinical reporting for laboratories, as well as emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretells a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.
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14
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Greninger AL, Dien Bard J, Colgrove RC, Graf EH, Hanson KE, Hayden MK, Humphries RM, Lowe CF, Miller MB, Pillai DR, Rhoads DD, Yao JD, Lee FM. Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document. Clin Infect Dis 2021; 74:1496-1502. [PMID: 34731234 PMCID: PMC8689887 DOI: 10.1093/cid/ciab761] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Indexed: 11/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert C Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Harvard School of Medicine
| | - Erin H Graf
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, USA
| | - Kimberly E Hanson
- Department of Internal Medicine and Pathology, University of Utah, Salt Lake City, UT, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine and Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Romney M Humphries
- Division of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, Providence Health Care, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Melissa B Miller
- Clinical Microbiology Laboratory, University of North Carolina Hospitals and Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Dylan R Pillai
- Department of Pathology and Laboratory Medicine and Microbiology & Infectious Diseases, University of Calgary, Alberta, Canada
| | - Daniel D Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Francesca M Lee
- Division of Infectious Diseases and Geographic Medicine, Department of Pathology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Caucci S, Corvaro B, Tiano SML, Valenza A, Longo R, Marinelli K, Ferreri ML, Spiridigliozzi P, Salvoni G, Bagnarelli P, Menzo S. Weak Cross-Lineage Neutralization by Anti SARS-CoV-2 Spike Antibodies after Natural Infection or Vaccination Is Rescued by Repeated Immunological Stimulation. Vaccines (Basel) 2021; 9:1124. [PMID: 34696232 PMCID: PMC8537215 DOI: 10.3390/vaccines9101124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
After over one year of evolution, through billions of infections in humans, SARS-CoV-2 has evolved into a score of slightly divergent lineages. A few different amino acids in the spike proteins of these lineages can hamper both natural immunity against reinfection, and vaccine efficacy. In this study, the in vitro neutralizing potency of sera from convalescent COVID-19 patients and vaccinated subjects was analyzed against six different SARS-CoV-2 lineages, including the latest B.1.617.2 (or Delta variant), in order to assess the cross-neutralization by anti-spike antibodies. After both single dose vaccination, or natural infection, the neutralizing activity was low and fully effective only against the original lineage, while a double dose or a single dose of vaccine, even one year after natural infection, boosted the cross-neutralizing activity against different lineages. Neither binding, nor the neutralizing activity of sera after vaccination, could predict vaccine failure, underlining the need for additional immunological markers. This study points at the importance of the anamnestic response and repeated vaccine stimulations to elicit a reasonable cross-lineage neutralizing antibody response.
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Affiliation(s)
- Sara Caucci
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Benedetta Corvaro
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Sofia Maria Luigia Tiano
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Anna Valenza
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Roberta Longo
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Katia Marinelli
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Monica Lucia Ferreri
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Patrik Spiridigliozzi
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Giovanna Salvoni
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Patrizia Bagnarelli
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
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Jacot D, Pillonel T, Greub G, Bertelli C. Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants. J Clin Microbiol 2021; 59:e0094421. [PMID: 34319802 PMCID: PMC8451431 DOI: 10.1128/jcm.00944-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only a few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low-quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over 10 tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for 11 selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low-frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations, or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low-frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose 11 metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which are cycle thresholds, mean depth, proportion of genome covered at least 10×, and the number of low-frequency variants combined with mutation prevalence data.
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Affiliation(s)
- Damien Jacot
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Diepenbroek M, Bayer B, Anslinger K. Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing. Genes (Basel) 2021; 12:genes12091362. [PMID: 34573344 PMCID: PMC8466929 DOI: 10.3390/genes12091362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping.
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18
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Urrutikoetxea-Gutierrez M, Ugalde Zarraga E, Gallego Rodrigo M, Díaz de Tuesta Del Arco JL. De novo emergence of the mutation E484K in a SARS-CoV-2 B.1.1.7 lineage variant. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00225-1. [PMID: 34400021 PMCID: PMC8363242 DOI: 10.1016/j.eimc.2021.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/24/2021] [Accepted: 07/04/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Mikel Urrutikoetxea-Gutierrez
- Hospital Universitario Basurto, Servicio de Microbiología Clínica, Bizkaia, España; Grupo de Microbiología y Control Infección, Instituto Biocruces Bizkaia, Bizkaia, España.
| | - Estibaliz Ugalde Zarraga
- Hospital Universitario Basurto, Servicio de Microbiología Clínica, Bizkaia, España; Grupo de Microbiología y Control Infección, Instituto Biocruces Bizkaia, Bizkaia, España
| | - Mikel Gallego Rodrigo
- Hospital Universitario Cruces, Servicio de Microbiología Clínica, Bizkaia, España; Grupo de Microbiología y Control Infección, Instituto Biocruces Bizkaia, Bizkaia, España
| | - Jose Luis Díaz de Tuesta Del Arco
- Hospital Universitario Basurto, Servicio de Microbiología Clínica, Bizkaia, España; Grupo de Microbiología y Control Infección, Instituto Biocruces Bizkaia, Bizkaia, España
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Fabiani M, Margiotti K, Viola A, Mesoraca A, Giorlandino C. Mild Symptomatic SARS-CoV-2 P.1 (B.1.1.28) Infection in a Fully Vaccinated 83-Year-Old Man. Pathogens 2021; 10:pathogens10050614. [PMID: 34067881 PMCID: PMC8156209 DOI: 10.3390/pathogens10050614] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/15/2021] [Indexed: 11/16/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) and the associated coronavirus disease 2019 (COVID-19) continue to spread throughout the world, causing more than 120 million infections. Several variants of concern (VOCs) have emerged and spread with implications for vaccine efficacy, therapeutic antibody treatments, and possible reinfections. On 17 March 2021, several VOCs were detected, including lineage B.1.1.7, first identified in the UK, B.1.351 in South Africa, Lineage P.1 (B.1.1.28.1) in Brazil, and novel Sub-Lineage A (A.23.1), reported in Uganda, and B.1.525, reported in Nigeria. Here, we describe an 83-year-old man infected with the SARS-CoV-2 P.1 variant after two doses of the BNT162b2 mRNA COVID-19 vaccine.
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Affiliation(s)
- Marco Fabiani
- Human Genetics Lab, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.V.); (A.M.); (C.G.)
| | - Katia Margiotti
- Human Genetics Lab, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.V.); (A.M.); (C.G.)
- Correspondence: ; Tel.: +39-06-850-5805; Fax: +39-06-850-5815
| | - Antonella Viola
- Human Genetics Lab, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.V.); (A.M.); (C.G.)
| | - Alvaro Mesoraca
- Human Genetics Lab, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.V.); (A.M.); (C.G.)
| | - Claudio Giorlandino
- Human Genetics Lab, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.V.); (A.M.); (C.G.)
- Department of Biochemistry, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy
- Department of Prenatal Diagnosis, Fetal-Maternal Medical Centre, ALTAMEDICA, Viale Liegi 45, 00198 Rome, Italy
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Ouadghiri M, Aanniz T, Essabbar A, Seffar M, Kabbaj H, El Amin G, Zouaki A, Amzazi S, Belyamani L, Ibrahimi A. Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. Microbiol Resour Announc 2021; 10:e00240-21. [PMID: 33888505 PMCID: PMC8063648 DOI: 10.1128/mra.00240-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.
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Affiliation(s)
- Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Myriam Seffar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Hakima Kabbaj
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Ghizlane El Amin
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Amal Zouaki
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
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Telwatte S, Martin HA, Marczak R, Fozouni P, Vallejo-Gracia A, Kumar GR, Murray V, Lee S, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts. Methods 2021; 201:15-25. [PMID: 33882362 PMCID: PMC8105137 DOI: 10.1016/j.ymeth.2021.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The replication of SARS-CoV-2 and other coronaviruses depends on transcription of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and multiple different subgenomic mRNAs (sgRNAs) encompassing fragments arising from discontinuous transcription. Recent studies have aimed to characterize the expression of subgenomic SARS-CoV-2 transcripts in order to investigate their clinical significance. Here, we describe a novel panel of reverse transcription droplet digital PCR (RT-ddPCR) assays designed to specifically quantify multiple different subgenomic SARS-CoV-2 transcripts and distinguish them from transcripts that do not arise from discontinuous transcription at each locus. These assays can be applied to samples from SARS-CoV-2 infected patients to better understand the regulation of SARS-CoV-2 transcription and how different sgRNAs may contribute to viral pathogenesis and clinical disease severity.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States
| | - Holly Anne Martin
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States
| | - Ryan Marczak
- University of California, Santa Barbara, CA, United States
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States
| | - Albert Vallejo-Gracia
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States
| | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States
| | - Victoria Murray
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Sulggi Lee
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States
| | - Joseph K Wong
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States
| | - Steven A Yukl
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States.
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First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. Microbiol Resour Announc 2021; 10:10/11/e00027-21. [PMID: 33737349 PMCID: PMC7975867 DOI: 10.1128/mra.00027-21] [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] [Indexed: 11/21/2022] Open
Abstract
We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys). We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys).
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Cotten M, Lule Bugembe D, Kaleebu P, V.T. Phan M. Alternate primers for whole-genome SARS-CoV-2 sequencing. Virus Evol 2021; 7:veab006. [PMID: 33841912 PMCID: PMC7928614 DOI: 10.1093/ve/veab006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43 per cent of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.
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Affiliation(s)
- Matthew Cotten
- MRC/UVRI & London School of Hygiene and Tropical Medicine, 51-59 Nakiwoggo Road, Entebbe, Uganda
- UK Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Dan Lule Bugembe
- MRC/UVRI & London School of Hygiene and Tropical Medicine, 51-59 Nakiwoggo Road, Entebbe, Uganda
| | - Pontiano Kaleebu
- MRC/UVRI & London School of Hygiene and Tropical Medicine, 51-59 Nakiwoggo Road, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - My V.T. Phan
- MRC/UVRI & London School of Hygiene and Tropical Medicine, 51-59 Nakiwoggo Road, Entebbe, Uganda
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