An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe
BMC Biology volume 23, Article number: 179 (2025 ) Cite this article
From 1918 to 1920, the largest influenza A virus (IAV) pandemic known to date spread globally causing between 20 to 100 million deaths. Historical records have captured critical aspects of the disease dynamics, such as the occurrence and severity of the pandemic waves. Yet, other important pieces of information such as the mutations that allowed the virus to adapt to its new host can only be obtained from IAV genomes. The analysis of specimens collected during the pandemic and still preserved in historical pathology collections can significantly contribute to a better understanding of its course. However, efficient RNA processing protocols are required to work with such specimens.
Here, we describe an alternative protocol for efficient ancient RNA sequencing and evaluate its performance on historical samples, including a published positive control. The phenol/chloroform-free protocol efficiently recovers ancient viral RNA, especially small fragments, and maintains information about RNA fragment directionality through incorporating fragments by a ligation-based approach. One of the assessed historical samples allowed for the recovery of the first 1918 IAV genome from Switzerland. This genome, derived from a patient deceased during the beginning of the first pandemic wave in Switzerland, already harbours mutations linked to human adaptation.
