Understand the Evolving Pandemic with PacBio Sequencing
The spread of new variants has made whole genome sequencing a newly critical part of the global SARS-CoV-2 response. In this new phase of the pandemic, PacBio is committed to supporting government, academic, and commercial labs in their efforts to increase virus surveillance.
Targeted Sequencing for SARS-CoV-2 Surveillance
HiFi reads from the Sequel IIe System provide a reliable, cost effective, high-throughput solution for sequencing SARS-CoV-2 quickly and easily.
HiFiViral for SARS-CoV-2 Workflow
Amplify and barcode up to 900 SARS-CoV-2 samples for multiplexing in a single library
Use the Sequel II or Sequel IIe Systems to generate >99.9% accurate HiFi reads
Assemble genomes and call all variants with our efficient analytical software tools and standard file formats.
Protocol: HiFiViral for SARS-CoV-2 Workflow – Multiplexing 1.2 kb Amplicons for Full-Viral Genome Sequencing
This protocol describes a workflow for multiplexing 1.2 kb amplicons for full-viral genome sequencing of SARS-CoV-2 samples on the Sequel II or Sequel IIe Systems for genome assembly or variant calling.
Sequences for the 29 pairs of M13-tailed primers are available using this oligo ordering sheet.
Learn More about the SARS-CoV-2 Analysis Application
Use this application in SMRT Link to analyze multiplexed viral surveillance samples for SARS-CoV-2. For each sample, this analysis provides:
- Amplicon coverage (CSV)
- Variant calls (VCF)
- Consensus sequence (FASTA)
- Aligned reads (BAM)
The application supports the full range of throughput options and is intended to identify variants and call a single consensus sequence per sample. The output consensus sequence is based on the dominant variants observed at each position.
How it Works:
Benefits of this Protocol for SARS-CoV-2 Research
With only 29 amplicons, primers anneal to just 4.5% of the viral genome compared to 17-40% with other assays, lowering the chance that viral mutations will cause dropouts due to primer mismatches
Easier Primer Balancing
The use of 1.2 kb amplicons optimizes for even and complete genome coverage by balancing multiplex PCR simplification against the challenge of sample-quality variability
Call All Variants
Using >99.9% accurate HiFi reads you can detect both SNPs and indels up to 300 bp in length with only 4-fold coverage
LabCorp: Geographic and Temporal Mapping of SARS-CoV-2 Pandemic
Watch this video to learn how LabCorp is using HiFi sequencing and the Sequel II System in their population-scale surveillance of SARS-CoV-2 mutants in the United States.
Learn More about LabCorp’s Surveillance Efforts
Advantages of HiFi Sequencing on the Sequel IIe System:
- Better data for superior results with lower coverage, from a single technology
- Less time spent on data processing and analysis for faster answers
- Cost savings at every step of your sequencing pipeline
- Reliable high-throughput sequencing for a broad range of applications
In this video Jonas Korlach, PacBio Chief Scientific Officer, describes the benefits of the HiFiViral for SARS-CoV-2 Workflow for delivering complete viral genomes as well as variant detection successes made to date using the workflow.
In the News
Relevant Publications on Viral Sequencing
- 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.
- Le Nouën, C., et al. (2021) Rescue of codon-pair deoptimized respiratory syncytial virus by the emergence of genomes with very large internal deletions that complemented replication. PNAS. 118(13).
- Greaney, A. J., et al. (2021) Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host & Microbe. 29(2): 44-57.
- Gonzalez-Reiche, A. S., et al. (2020) Introductions and early spread of SARS-CoV-2 in the New York City area. Science. 369(6501): 297-301.
- Starr, N. T. et al., (2020) Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell.
- Djiking, A., and Spiro, D. (2009) Advancing full length genome sequencing for human RNA viral pathogens. Future Virology. 4(1): 47–53.
- Betz-Stablein, B. D., et al. (2016) Single-molecule sequencing reveals complex genomic variation of hepatitis B virus during 15 years of chronic infection following liver transplantation. Journal of Virology, 90, 7171–7183.
- Brese, R. L., et al. (2018) Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues. Journal of Neurovirology, 24(4), 439–453.
- Tao, Y., et al. (2017) Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology, 91(5), e01953–16.
- Lu, X., et al. (2017) Spike gene deletion quasispecies in serum of patient with acute MERS-CoV infection. Journal of Medical Virology, 89(3), 542–545.
- Le Nouën, C., et al. (2017) Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure. PNAS, 114(3), E386–E395.
- Li, Y., et al (2020) Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions. Virus Genes.
Connect with a PacBio Scientist
If you are working on coronavirus or COVID-19 and would like to learn more about protocols or service providers, please contact us.