Facilitating Cross-border Viral Sequencing Through Nucleic Acid Sample Transport Using Dry Cards

TL;DR

This study shows that using FTA cards to transport viral DNA samples allows for effective sequencing in areas with limited resources, improving disease monitoring.

Contribution

The study introduces a practical method for transporting amplified nucleic acids using FTA cards in resource-limited settings.

Findings

FTA cards achieved a 9.6% recovery rate for amplicons, sufficient for viral genome sequencing.

71.7% of transported samples yielded high-quality SARS-CoV-2 genomic sequences with coverage exceeding 100X.

Higher Ct values in original samples significantly reduced sequencing coverage and depth.

Abstract

(1) Background: A safe and effective nucleic acid sample transportation method was developed that is suitable for underdeveloped areas which lack advanced sequencing capabilities, specifically for virus genomic sequencing and infectious disease monitoring. (2) Methods: This study evaluated the use of Flinders Technology Associates (FTA) cards for transporting amplified whole-genome DNA from 120 SARS-CoV-2-positive nasopharyngeal swab samples in Sierra Leone. Nucleic acid extraction and whole-genome amplification were conducted at a local laboratory. Amplified products were applied to FTA Elute cards for room temperature shipment to China CDC for elution and sequencing. (3) Results: The FTA card method achieved a 9.6% recovery rate for amplicons, sufficient for viral genome sequencing. In total, 86 (71.7%) high-quality SRAS-CoV-2 genomic sequences were obtained, with the majority reaching depths exceeding 100X. Sequence analysis revealed co-circulation of Delta, Omicron, and B.1 lineages. Higher Ct values in the original sample significantly reduced coverage and depth, with Ct ≤ 27; 73.6% of samples yielded effective sequences. (4) Conclusions: Transportation of amplified nucleic acid samples using FTA cards enables virus genomic sequencing in resource-limited areas. This approach can potentially improve local virus surveillance and outbreak response capabilities. Further optimizations could improve sequence recovery rate. Implementing this method could significantly enhance sequencing accessibility in underdeveloped regions.

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