Variation in lineage 2 strain of Lassa fever virus in Nigeria

Abstract

Background: Nigeria is one of four countries endemic for Lassa fever (LF) in West Africa and harbours three of the four established lineages (strains) of LF. Lineages 2 and 3 occur dominantly in the southern and Northern regions of the country respectively. In the southern region, the South central (S.C) and South east (S.E) axes are most endemic for LF in the southern region. The disparity in complications, morbidity and subsequent mortality (CFR of 30% of S.C cases versus 48% of S.E cases) raised the question; Are there any variations in the LF strains in the SC and SE axes? Methods & Materials: Following the 2014 epidemic with fifteen positive cases in the SE axes, genomic studies elucidating their nucleic acid sequences were conducted in NUITM. A ten year study of nucleic acid sequences of lineage two strains of LF from Nigeria covering the period 2004-2014 gleaned from the GENBANK pool was conducted. To this was added the fifteen positive samples of 2014, totalling 79 LF glycoprotein precursor (GPC) gene sequences. Using MEGA 6 software, phylogenetic and BLAST analysis of the homologous identity of all the 79 strains were conducted. Results: Fifty of the 79 LF lineage two strains were of SC origin while 29 were of SE. Three distinct clades of the SE strain were observed and clustered around Nig 05-SE40, Nig 08-04 and Nig 11-186 strains. Diversity among the clades of the SE strains ranged between 18 – 21%. Perhaps there is a new clade developed every three years in the SE axis. The SC strains were essentially of one clade and exhibited good homologous identity of 97-100%. This suggests less diversity of the SC strains than the SE strains. The SC and SE strains strains exhibited diversity of up to 20%. Conclusion: The Lineage 2 strain has four clades, with 3 of the clades belonging to the strain from the SE axis. This may explain the worse CFR of LF cases in SE axes. The SC strains are essentially of one clade. There is need to evaluate for Ribavirin resistance and/or mutation among clades of SE origin