Background <p>Whole blood samples are often used to generate whole genome sequences, which provide valuable insights into the genetic make-up of viruses. However, the collection and management present significant challenges, particularly in remote and resource-limited communities, where maintaining a cold chain is often difficult and costly. The use of dry blood spots (DBS) is gradually increasing to overcome these logistical barriers with reduced biosafety constraints. We propose an alternative approach using native DBS Lassa virus (LASV)-positive samples as a substitute for whole blood.</p> Findings <p>Next-generation sequencing (NGS) was performed on RNA extracted from whole blood and DBS samples using Illumina technology. RNA concentration, cycle threshold (Ct) values and sequence read counts were statistically compared. A total of 78 samples from 39 LASV-positive <i>Mastomys atalensis</i> were analysed. Whole blood had significantly higher mean RNA concentration (26.5 ± 1.9) than DBS (3.4 ± 0.3), <i>P</i> &lt; 0.05. Mean Ct values in whole blood were significantly lower than in DBS (<i>P</i> = 0.0001). Log mean sequence reads and NGS coverage for both S and L segments were significantly higher in whole blood (<i>P</i> = 0.0001). RNA concentration showed no association with sequence coverage (<i>P</i> = 0.382), while Ct values showed a strong association (<i>P</i> = 0.0001).</p> Conclusions <p>Our study demonstrates that DBS is a viable alternative for whole genome sequencing of LASV, although whole blood samples consistently outperform DBS in terms of RNA concentration, Ct values and NGS coverage.</p> Graphical Abstract <p></p>