Abstract
Background Lassa virus (LASV) is a single-negative strand RNA Arenavirus (genus Mammarenavirus ), oriented in both negative and positive senses. Due to the increase in fatality rate of deadly disease LASV caused (Lassa fever), widespread of LASV in Nigeria has been a subject of interest. Following the upsurge of LASV endemicity in 2012, another marked incidence were recorded in Nigeria, 2018, with 394 confirmed cases in 19 states, and estimated 25% cases led to death. This study aimed at acquiring the genetic variation of LASV ancestral evolution with evolvement of new strains in different lineage and its geographical distributions within specific time of outbreaks through Bayesian inference, using genomic sequence across affected states in Nigeria. Results From the result, we were able to establish the relationship of Lassa mamarenavirus and other arenaviruses by classifying them into distinct monophyletic groups, i.e. the old world arenaviruses, new world arenaviruses, and Reptarenaviruses. Corresponding promoter sites for genetic expression of the viral genome were analyzed based on Transcription Starting Site (TSS), the S_Segment (MK291249.1) is about 2917–2947 bp and L_Segment (MH157036.1), is about1863–1894 bp long. LASV sequence obtained from different part of Nigeria were genetically related. Benue, Imo, and Bauchi states represent the host etiology of the LASV. Spread across other neighboring states were based on genetic pedigree dated to previous outbreaks as at year 2008 to 2012. Phylogeography of recent transmission from year 2017 to 2019 indicates vectors were fast spreading LASV from Ondo states to Delta, Edo, and Kogi states, while spread across north eastern states suggests a vector origin from Bauchi state. Conclusions The study evidently outlined the path of transmission based on genetic homology of the sampled LASV sequences in affected geographical locations. we suggests, federal government should initiate a vector surveillance program to curtails further spread of LASV, especially, states bordering with north western states and north central Nigeria. Keywords Genomic, Lassa Virus, Phylogeography, Spatiotemporal and Nigeria