Abstract

Lassa virus is the cause of morbidity and mortality in Ekpoma Nigeria. Recently, two new strains of the virus were identified. The genes were sequenced and deposited in the GenBank. We presume that genes of similar sequence will code for protein of similar function. Hence any vaccine produced using this protein could protect against any other similar virus due to conservation of active and functional regions. The gene codes for a glycoprotein which could be antigenic and stimulate the production of antibody. This is however if the protein could be made non virulence. It then becomes important to have a proper molecular knowledge and function of the protein. Determination of the function of the protein was first by global sequence alignment using blastp with different parameters. However, not all the parameters used produced hits even when e- values were adjusted. Pairwise alignment and multiple sequence alignment (MSA) of the two newly identified proteins were carried out but full analysis of only one of the protein (strain) was done. Other tools used in determining the function of the protein included hydrophobicity, leader sequence, transmembrane helices, Pfam using different tools from expasy and PHD tools. Prints and blocks databases were also searched, but the block database gave no hit. The hidden Markov’s model structure was also done before searching for the 3D structure at PDB using phyre at expasy. The pairwise alignment and MSA were done with clustal W. This study gives a clear function of the lassa virus glycoprotein, and also confirms the stability and antigenicity of the protein so long as multiple domain repeats are carried out before synthesis which will help increase the molecular weight while preserving protein function.

Key words: Lassa virus, multiple sequence alignment, glycoprotein, protein structure, vaccine.