Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer.

BACKGROUND

The COVID-19 pandemic exposed critical vulnerabilities in global laboratory supply chains, disrupting the availability of key reagents and jeopardising the continuity of genomic surveillance for epidemic response. Sustaining sequencing capacity during shortages requires locally accessible alternatives to commercial kits.

METHODS

We developed ARTIC HELP (Homebrew Enzymes for Library Preparation), an open-source adaptation of the ARTIC nanopore sequencing protocol for viral genomic surveillance. We described cost-effective, generic replacements for enzyme mixes used in tiling multiplex RT-PCR and the nanopore native barcoding workflow, including end-prep (EP), barcode ligation (BL), and adapter ligation (AL). Through systematic evaluation, we tested wild-type M-MLV reverse transcriptase and two types of proofreading DNA polymerases, (i) B-family Pfu-based polymerases fused to an Sso7d DNA-binding domain, and (ii) blends of A-family (Taq-based) and B-family (Pfu-based) polymerases, against standard reagents. We validated the workflow on clinical SARS-CoV-2 and Norovirus GII samples.

RESULTS

The HELP workflow delivered genome coverage comparable to the ARTIC LoCost protocol. For SARS-CoV-2 samples (Ct ≤28), wild-type M-MLV RT combined with selected Pfu or AB blend polymerases, alongside optimized HELP EP, BL, and AL mixes, achieved 84.0-99.6% genome coverage. For Norovirus GII samples (Ct ≤32), the HELP workflow enabled >85% coverage across six of eight genotypes tested. While some polymerases showed reduced performance at higher Ct values, they performed reliably at Ct <24, supporting their use as emergency alternatives when viral load is high and RNA quality sufficient.

CONCLUSIONS

ARTIC HELP provides a practical and flexible solution to maintain viral sequencing capacity when standard ARTIC LoCost reagents are inaccessible or unaffordable. Our cost analysis highlights global disparities in reagent pricing, likely influenced by import fees, supply barriers, and local procurement conditions, underscoring the need for more equitable pricing models and local sourcing strategies. By expanding reagent options, ARTIC HELP strengthens preparedness for future global health emergencies.