1
|
Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic surveillance of SARS-CoV-2 using long-range PCR primers. Front Microbiol 2024; 15:1272972. [PMID: 38440140 PMCID: PMC10910555 DOI: 10.3389/fmicb.2024.1272972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). Methods In this study we used a set of seven long-range PCR primer pairs to sequence clinical isolates of SARS-CoV-2 on Oxford Nanopore sequencer. These long-range primers generate seven amplicons approximately 4500 bp that covered whole genome of SARS-CoV-2. One of these regions includes the full-length S-gene by using a set of flanking primers. We also evaluated the performance of these long-range primers with Midnight primers by sequencing 94 clinical isolates in a Nanopore flow cell. Results and discussion Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias. The key finding of this study is that long range primers can be used in single-molecule sequencing of RNA viruses in surveillance of emerging variants. We also show that by designing primers flanking the S-gene, we can obtain reliable identification of SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Ashton K. Ingold
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Grace A. Turner
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Joshua L. Kennedy
- Arkansas Children's Research Institute, Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David W. Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|
2
|
Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
Collapse
|
3
|
Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers. bioRxiv 2023:2023.07.10.548464. [PMID: 37502853 PMCID: PMC10369864 DOI: 10.1101/2023.07.10.548464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence the ~30,000 nucleotide SARS-CoV-2 genome that use a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). This study uses seven long-range PCR primers with an amplicon size of ~4500 bp to tile across the complete SARS-CoV-2 genome. One of these regions includes the full-length S-gene by using a set of flanking primers. Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias.
Collapse
Affiliation(s)
- Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 782), Little Rock, AR 72205, USA
| | - Susanna L. Hartzell
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Ashton K. Ingold
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Grace A. Turner
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Joshua L. Kennedy
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David W. Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 782), Little Rock, AR 72205, USA
| |
Collapse
|
4
|
Diagne MM, Ndione MHD, Mencattelli G, Diallo A, Ndiaye EH, Di Domenico M, Diallo D, Kane M, Curini V, Top NM, Marcacci M, Mbanne M, Ancora M, Secondini B, Di Lollo V, Teodori L, Leone A, Puglia I, Gaye A, Sall AA, Loucoubar C, Rosà R, Diallo M, Monaco F, Faye O, Cammà C, Rizzoli A, Savini G, Faye O. Novel Amplicon-Based Sequencing Approach to West Nile Virus. Viruses 2023; 15:1261. [PMID: 37376561 DOI: 10.3390/v15061261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
West Nile virus is a re-emerging arbovirus whose impact on public health is increasingly important as more and more epidemics and epizootics occur, particularly in America and Europe, with evidence of active circulation in Africa. Because birds constitute the main reservoirs, migratory movements allow the diffusion of various lineages in the world. It is therefore crucial to properly control the dispersion of these lineages, especially because some have a greater health impact on public health than others. This work describes the development and validation of a novel whole-genome amplicon-based sequencing approach to West Nile virus. This study was carried out on different strains from lineage 1 and 2 from Senegal and Italy. The presented protocol/approach showed good coverage using samples derived from several vertebrate hosts and may be valuable for West Nile genomic surveillance.
Collapse
Affiliation(s)
| | | | - Giulia Mencattelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
- Centre Agriculture Food Environment, University of Trento, 38010 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - El Hadji Ndiaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Diawo Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Ndeye Marieme Top
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Maïmouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Alessandra Leone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Alioune Gaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Roberto Rosà
- Centre Agriculture Food Environment, University of Trento, 38010 San Michele all'Adige, Italy
| | - Mawlouth Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Federica Monaco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar BP220, Senegal
| |
Collapse
|
5
|
Zeghbib S, Kemenesi G, Jakab F. The importance of equally accessible genomic surveillance in the age of pandemics. Biol Futur 2023:10.1007/s42977-023-00164-5. [PMID: 37199870 DOI: 10.1007/s42977-023-00164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.
Collapse
Affiliation(s)
- Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary.
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
| |
Collapse
|
6
|
Koskela von Sydow A, Lindqvist CM, Asghar N, Johansson M, Sundqvist M, Mölling P, Stenmark B. Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization. Sci Rep 2023; 13:6461. [PMID: 37081087 PMCID: PMC10116481 DOI: 10.1038/s41598-023-33168-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/07/2023] [Indexed: 04/22/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
Collapse
Affiliation(s)
- Anita Koskela von Sydow
- Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Carl Mårten Lindqvist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Naveed Asghar
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Johansson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paula Mölling
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bianca Stenmark
- Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Clinical Genomics, Science for Life Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
7
|
Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
Collapse
Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| |
Collapse
|
8
|
Nicot F, Trémeaux P, Latour J, Jeanne N, Ranger N, Raymond S, Dimeglio C, Salin G, Donnadieu C, Izopet J. Whole-genome sequencing of SARS-CoV-2: Comparison of target capture and amplicon single molecule real-time sequencing protocols. J Med Virol 2022; 95:e28123. [PMID: 36056719 PMCID: PMC9539136 DOI: 10.1002/jmv.28123] [Citation(s) in RCA: 2] [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] [Received: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS-CoV-2.
Collapse
Affiliation(s)
- Florence Nicot
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | | | - Justine Latour
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Nicolas Jeanne
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Noémie Ranger
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Stéphanie Raymond
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Chloé Dimeglio
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Gérald Salin
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Cécile Donnadieu
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Jacques Izopet
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| |
Collapse
|