Sequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure...

Lassa virus (LASV) remains a major public health threat in West Africa, with recurrent outbreaks, exported cases, and no licensed vaccine. LASV lineages are geographically separated and differ in immunogenicity and pathogenicity; however, the fundamental biophysical properties that may explain these differences remain poorly defined. Here, we analyse LASV protein properties at the population scale across lineages, focusing on the glycoprotein (GP), the principal target of humoral immunity. Across hundreds of curated sequences, protein length variation is driven primarily by short indels, with pronounced variation in the RNA polymerase and a recurrent one-amino-acid difference in GP. In parallel, population-scale analyses reveal subtle lineage- and protein-specific differences in amino-acid composition across the LASV proteins. Despite co-circulation in Nigeria, S-segment-encoded proteins from lineage III are consistently heavier than those from lineage II. An integrative framework combining random forest feature importance, Manhattan-distance profiling, Pearson correlation, and amino-acid composition analyses reveals that lineage III GPs are ~180 Da heavier on average, driven by shifts toward the use of heavier residues at specific sites. Population-scale computational structural modelling and flow-cytometric assays indicate that the N-terminal GP1 indel is structurally and functionally tolerated. Together, these findings define lineage-specific biophysical patterns in LASV and provide a catalogue of GP structures to inform vaccine and therapeutic design.