Nucleotide sequence of the S RNA of Lassa virus (Nigerian strain) and comparative analysis of arenavirus gene products

Abstract

The nucleotide sequence of the small (S) genomic RNA of Lassa virus (strain GA391, of Nigerian origin) has been determined. The RNA has features which conform to those seen in most other arenavirus S RNAs which have been characterised, including conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. Comparison of the nucleotide sequence with that of the Josiah strain of Lassa virus (from Sierra Leone) reveals considerable nucleotide divergence in the third base of codons in the reading frames of all three proteins, although the resulting protein sequences are highly conserved, with 92, 94 and 91% identical residues for the mature glycoproteins G1 and G2 and the N protein, respectively. Sequence alignments of the available arenavirus structural proteins and dendrograms summarising the relationships between the viral proteins are presented.