The Essential Guide to ARTIC Primers for SARS-CoV-2 Sequencing

Understanding the genomic makeup of the SARS-CoV-2 virus has been critical during the COVID-19 pandemic. By sequencing viral samples taken from infected individuals, researchers can track mutations and identify new variants as they emerge. However, sequencing the roughly 30,000 base pairs that make up the SARS-CoV-2 genome requires specialized protocols and reagents. ARTIC primers have become an essential tool enabling labs around the world to sequence SARS-CoV-2.

What Are ARTIC Primers and Why Are They Importa

ARTIC stands for the Artic Network, a coalition of public hent?alth and academic groups working to coordinate and standardize genomic epidemiology across institutions. When the COVID-19 pandemic hit, ARTIC quickly mobilized to develop a set of PCR primers that could amplify the entire SARS-CoV-2 genome for sequencing.

These ARTIC SARS-CoV-2 primers consist of primer pairs tiling across the viral genome in roughly 400 base pair segments. This allows for PCR amplification of the full 30 kb genome using widely available high-throughput sequencing platforms from Illumina and Oxford Nanopore.

The standardization provided by ARTIC primers has made SARS-CoV-2 sequencing more accessible for labs, enabling critical real-time surveillance:

  • Tracking viral evolution and emerging variants
  • Monitoring vaccine effectiveness
  • Tracing infection clusters and outbreak sources
  • Informing public health policy and responses

For sequencing-based SARS-CoV-2 genomic epidemiology, ARTIC primers have become an essential part of the toolkit.

8

ARTIC Primer Versions and Updates

The ARTIC network has iterated through several versions of their SARS-CoV-2 primer schemes:

Version Key Improvements
v1 First version
v2 Fixed specificity issues
v3 Balanced coverage, new tiling scheme optimized for Nanopore and Illumina
v4 Adapted for ONT Rapid Barcoding kits
v4.1 Fixed detections issues in ORF1a

The latest scheme as of late 2022 is ARTIC v5, which continues improving amplification uniformity and genome coverage.

Each version aims to address limitations and optimize performance. For example, v2 primers fixed issues related to detecting other coronavirus strains, while newer 4.1 primers improve coverage problems in certain genomic regions.

ARTIC makes their primers freely available to the community under an open license. Researchers are also encouraged to suggest further optimizations at the ARTIC primer GitHub repository.

How Do ARTIC SARS-CoV-2 Primers Work?

ARTIC primers turn a 30 kb viral genome into a series of amplicons compatible with high-throughput sequencing. This process involves:

Viral RNA extraction

First viral RNA must be extracted from patient samples using an optimized protocol to preserve integrity.

Multiplexed RT-PCR

The ARTIC scheme uses two primer pools with 494 primers total to tile across the genome. Reverse transcription converts the RNA to cDNA.

Library prep and sequencing

The amplicons then undergo library preparation and sequencing using Illumina or Oxford Nanopore devices.

This amplicon approach allows the entire SARS-CoV-2 genome to be reconstructed bioinformatically from the individual sequence reads.

The latest v5 primer scheme has 98 primer pairs separated into two pools optimized to balance amplification across the viral genome.

81

Real-World Applications and Adoption

Since their initial release in early 2020, ARTIC primers have been rapidly adopted by sequencing labs and public health networks around the world.

Analyses show that sequences submitted to GISAID by contributors using ARTIC primers account for >60% as of 2022. Their impact and ubiquity is further evidenced by the >12,000 citations for the foundational 2020 ARTIC paper.

The ability to share protocols across labs has been invaluable. As Dr. Thomas Peacock, a key developer behind the primers remarked:

“It’s allowed groups to very quickly get up and running, and also allowed them to compare their data with other groups’ data very quickly as well.”

The ARTIC network also provides detailed documentation and community support to lower barriers for new adopters.

Their primers have enabled crucial genomic epidemiology investigations like:

  • The emergence of Alpha, Delta and other major variants
  • Transmission chains in superspreader events
  • Monitoring vaccine escape mutations

Challenges and Considerations

While adoption has exploded, researchers have also noted some downsides of the amplification-based approach:

Primer bias

  • Certain genomic regions can be preferentially amplified, skewing coverage
  • Requires balancing and optimization across many primer pairs

Contamination risks

  • SARS-CoV-2 PCR amplicons must be strictly contained
  • Can confound sequencing results if carryover occurs

Bioinformatics complexity

  • Reconstructing genomes from tiled amplicons requires specialized computational workflows

Despite these caveats, ARTIC primers enable the high-throughput sequencing needed for timely public health genomic surveillance. Ongoing optimizations also aim to improve performance and accuracy.

82

Frequently Asked Questions

What are some key benefits of the ARTIC SARS-CoV-2 primers?

Some major benefits include:

  • Standardization across labs
  • Enables high-throughput, affordable sequencing
  • Compatible with Illumina and Nanopore
  • Tiles entire 30 kb genome
  • Rapid protocol iteration and optimization

How can I access the latest ARTIC primers?

The primers are freely available at the ARTIC Network GitHub. Documentation on usage is provided, and researchers can get community support for implementing the protocol.

Why sequence SARS-CoV-2 genomes for public health surveillance?

Sequencing provides key genetic information on emerging variants, transmission patterns, and virus evolution. This guides policy decisions and control measures. Genome sequencing has been a vital tool throughout the COVID-19 pandemic.

What other resources does ARTIC provide beyond primers?

Other resources include detailed sample and library prep protocols optimized for SARS-CoV-2, bioinformatics pipelines for analyzing sequence data, training materials, and community networking support.

What might future updates to ARTIC primers aim to improve?

The ongoing iterative updates try to address issues like primer efficiency, specificity, uniformity of coverage across the genome, and accuracy in detecting variants. Further optimizations likely relate to these technical parameters as sequencing platforms also evolve.

In summary, key points about ARTIC primers for SARS-CoV-2:

  • Enable standardized high-throughput sequencing for genomic epidemiology tracking
  • Originally released early 2020, have gone through multiple optimization iterations
  • Two primer pools tile across the ~30 kb genome in ~400 bp segments
  • Adopted widely – account for >60% of sequences in GISAID
  • Balance amplification uniformity remains an area of optimization
  • Open access resources, community maintained and supported

References

  1. Quick, Joshua. “NCoV-2019 Sequencing Protocol V3.” Protocol Exchange, 25 Mar. 2020, https://www.nature.com/articles/s41596-020-0330-8.
  2. “ARTIC Network.” ARTIC Network, https://artic.network/.
  3. “Artic-Ncov2019/Artic-Ncov2019.” GitHub, https://github.com/artic-network/artic-ncov2019.
  4. Peacock, Thomas. “Artic Primers Have Supported Russell Viper Sequence Efforts.” This Week in Virology, 4 Aug. 2020, https://www.virology.ws/2020/08/04/twiv-640-artics-first/.
  5. “SARS-CoV-2 Coronavirus NGS Reagents.” Integrated DNA Technologies, https://www.idtdna.com/pages/landing/coronavirus-research-reagents/ngs-assays.
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