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Explore our COVID-19 sequencing tools and resources
Getting the Complete Picture
Protecting global health is best accomplished through comprehensive surveillance, complete genomic information, and accurate tracking. Tremendous progress has been made since technology first enabled the routine sequencing of pathogenic microbes.
The advent of Single Molecule, Real-Time (SMRT) Sequencing has radically increased the understanding of microbial genomics, pathogenicity, and antimicrobial resistance. The PacBio Systems deliver the most comprehensive genetic information available, and with SMRT Sequencing, federal agencies, healthcare centers, and other public health organizations have the ability to:
- Generate complete genome assemblies and gain a deeper understanding of community-acquired and hospital associated infections and transmission.
- Use microbial epigenetics to further characterize global outbreaks, pandemics, and epidemics.
- Inform local and global preparedness and response to seasonal and annual infections by rapidly resolving viral populations.
- Characterize complex populations to support surveillance and tracking of foodborne pathogens.
Learn how other scientist have used SMRT Sequencing to advance public heath:
- A Living Legacy of Microbiology Celebrates 100 Years
- Keeping a Close Eye on MRSA: Lessons Learned from PacBio Sequencing Surveillance
- The Antibiotic Arms Race: Tracking K. pneumoniae in a Hospital Setting
- For Pandemic Surveillance, Labcorp Scientists Sequence Thousands of SARS-CoV-2 Samples with HiFi Reads
- NARMS Scientists Track Antibiotic Resistance in Foodborne Bacteria Using SMRT Sequencing
- TB Study Finds Some Previously Reported Virulence Variants Were Sequencing Errors
- Scientists Investigate Minor Influenza Strains in Pandemic, Revealing New Clues in Flu Transmission
Spotlight: HiFi reads reveal emergence of SARS-CoV-2 minor variants during acute infection
A longitudinal study of a person who ultimately recovered showed that spike variants resistant to autologous neutralizing antibodies arose transiently before being displaced by the original strain ahead of virus clearance. Application of the method to more diverse cohorts may reveal circumstances under which variants capable of immune escape emerge and persist.
Ko, S. H., et al. (2021) High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19. PLOS Pathogens. 17(4): e1009431.
Spotlight: Long-reads shed light on the genetics of antibiotic resistance
Scientists interrogated the mobilome of drug resistant bacteria to understand their capacity for adaptation. This research showed that replicative transposons and homologous recombination are driving forces in rearrangements and evolution of resistance plasmids. Explore this research further:
He, S. et al., 2016. Mechanisms of evolution in high-consequence drug resistance plasmids. mBio, 7(6), pp.e01987–16.
Selected Resources
- Li, Yang et al. (2020) Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions Virus Genes
- Callahan, Benjamin J et al. (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic acids research
- Martijn, Joran et al. (2019) Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environmental microbiology
- Forde, Brian M et al. (2019) SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Scientific reports
- Murphy, Timothy F et al. (2019) Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. The Journal of infectious diseases
- Beaulaurier, John et al. (2019) Deciphering bacterial epigenomes using modern sequencing technologies. Nature reviews. Genetics
- Sullivan, Mitchell J et al. (2019) Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events BioRxiv
- Liang, Quanhui et al. (2019) Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Frontiers in microbiology
- Beaulaurier, John et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature biotechnology
- Fallon, Timothy R et al. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human molecular genetics
- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular therapy
- Xin, Tianyi et al. (2018) Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta pharmaceutica Sinica. B
- Vincent, Antony T et al. (2018) Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing. Genome
- Haig, Sarah-Jane et al. (2018) A high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and Mycobacterium avium. mBio
- Weingarten, Rebecca A et al. (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio
- Phelan, Jody et al. (2018) Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific reports
- Acuña-Amador, Luis et al. (2018) Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC genomics
- Pfeiffer, Friedhelm et al. (2018) The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC genomics
- Revez, Joana et al. (2017) Survey on the use of whole-genome sequencing for infectious diseases surveillance: Rapid expansion of European national capacities, 2015-2016. Frontiers in public health
- Perraudeau, Fanny et al. (2017) Accurate determination of bacterial abundances in human metagenomes using full-length 16S sequencing reads BioRxiv
- Zautner, Andreas E et al. (2017) Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing. The Journal of antimicrobial chemotherapy
- Hazen, Tracy H et al. (2017) Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli and Shigella. Antimicrobial agents and chemotherapy
- Vale-Silva, Luis et al. (2017) Comparative genomics of two sequential Candida glabrata clinical isolates. G3
- Zhao, J et al. (2017) Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. European journal of clinical microbiology & infectious diseases
- Stoesser, N et al. (2017) Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Scientific reports
- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human cell
- Pasini, Erica M et al. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome open research
- Tate, Heather et al. (2017) Comparative analysis of extended-spectrum-ß-lactamase CTX-M-65-producing Salmonella enterica serovar Infantis isolates from humans, food animals, and retail chickens in the United States. Antimicrobial agents and chemotherapy
- van Boheemen, Sander et al. (2017) Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname. Scientific reports
- Elghraoui, Afif et al. (2017) SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC genomics
- Diaz, Maureen H et al. (2017) Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PloS one
- Karl, Julie A et al. (2017) Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics
- Weigand, Michael R et al. (2017) The history of Bordetella pertussis genome evolution includes structural rearrangement. Journal of bacteriology
- Poster: Harting, John et al. (2021) Resolving Complex Pathogenic Alleles using HiFi Long-Range Amplicon Data and a New Clustering Algorithm
- Poster: Harting, John et al. (2021) Resolving Complex Pathogenic Alleles using HiFi Long-Range Amplicon Data and a New Clustering Algorithm
- Poster: Sovic, Ivan et al. (2020) Improving long-read assembly of microbial genomes and plasmids
- Poster: Boitano, M. et al. (2018) Full-length cDNA sequencing of prokaryotic transcriptome and metatranscriptome samples
- Poster: Heiner, Cheryl et al. (2018) Multiplexed complete microbial genomes on the Sequel System
- Poster: Lambert, C. et al. (2017) Multiplexing strategies for microbial whole genome sequencing using the Sequel System
- Poster: Seetin, M. et al. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome using long-read sequencing
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Oh, S. et al. (2016) Minimization of chimera formation and substitution errors in full-length 16S PCR amplification
- Poster: Heiner, C. et al. (2016) WGS SMRT Sequencing of patient samples from a fecal microbiota transplant trial
- Poster: Hall, R. et al. (2016) Workflow for processing high-throughput, Single Molecule, Real-Time Sequencing data for analyzing the microbiome of patients undergoing fecal microbiota transplantation
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Baybayan, Primo et al. (2016) Application specific barcoding strategies for SMRT Sequencing
- Poster: Seetin, Matthew et al. (2016) Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements
- Poster: Heiner, Cheryl et al. (2016) Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis
- Poster: Hall, Richard et al. (2016) Profiling the microbiome in fecal microbiota transplantation using circular consensus and Single Molecule, Real-Time Sequencing
- Stone, Jennifer (2021) HiFi Sequencing: See What You’ve Been Missing
- Ashby, Meredith; Bickhart, Derek, and Portik, Dan (2021) Revealing Mechanisms of Bacterial Virulence and Adaptation with PacBio SMRT Sequencing
- Ashby, Meredith and Brown, Candice and Driscoll, Mark and Leung, Elaine (2021) Identifying Key Players in Host-Microbiome Interactions with High Resolution 16S Sequencing
- Ashby, Meredith; and Boritz, Eli (2021) Resolving Viral Evolution and Quasispecies Diversity with HiFi Sequencing
- Ashby, Meredith; Bickhart, Derek, and Portik, Dan (2021) Optimizing for Information: What Richer Data and Better Assemblies Reveal About Metagenome Structure and Function
- Levy, Shawn and Heiner, Cheryl and Aro, Lori (2021) Transformative Drug Research and Development via Accurate and Scalable Long-Read Sequencing Services
- Blethrow, Justin and Smith, Melissa L. and Vinnere Pettersson, Olga (2021) Webinar: Unleashing the Power of HiFi Sequencing – How the Sequel IIe System Removes Barriers and Empowers Life Scientists
- Miller, Dave and Hernandez, Alvaro (2021) Creating Core Demand with HiFi Sequencing
- Wenger, Aaron (2021) Not All Long Reads Are Equal – High Accuracy Sets PacBio Apart
- Miller, David and Smith, Melissa Laird (2021) The Long and Short of Sequencing – Why HiFi Reads are the Future
- Becker, Aaron and Ekholm, Jenny and Harris, Charlotte and Kingham, Brewster and Vinnere Pettersson, Olga (2021) SMRT Sequencing as a Service – How to Bring Long-Read Technology to Your Core Lab
- (2020) Introduction to highly accurate long-read sequencing (HiFi Sequencing)
- (2020) Video: HiFi Sequencing – Unlock your next great discovery
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research
- Ashby, Meredith and Ma, Bing and Weinstock, George (2020) Webinar: A HiFi View – Sequencing the gut microbiome with highly accurate long reads
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Ashby, Meredith (2019) Webinar: Long-read sequencing and infectious disease: New insights into longstanding challenges
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Auvignen, Petra (2017) AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria
- Matthews, Ben (2017) PAG PacBio Workshop: Genome assembly and molecular genetics of the dengue, yellow fever, and zika vector Aedes aegypti
- Application Brief: Microbial whole genome sequencing – Best Practices (2021)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2021)
- Application Brief: Metagenomic sequencing with HiFi reads – Best Practices (2021)
- Product Brochure: Sequel IIe System – Sequencing evolved (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- PacBio Certified Service Providers (2020)
- Case Study: Sequencing an historic bacterial collection for the future (2019)
- Infographic: A brief history of microbiology (2019)