Genomic epidemiology analysis of lassa virus from infected small rodents suggests bidirectional movement of the virus across human and animals

Lassa Fever (LF) is a viral haemorrhagic fever that continues to pose a persistent public health threat in Nigeria and almost all West African countries. LASV circulation is maintained in the environment by several rodent reservoirs. Studies on the genomic characterization of the LASV in the rodent reservoir have been carried out with only a few rodent LASV sequences available in the GenBank. This leaves a huge gap necessary for understanding transmission, diversity and development of countermeasures. We sampled 1189 small rodents from two LF endemic states in southern Nigeria (Ondo and Ebonyi) and tested for LASV using RT-qPCR. We recorded an overall 61.6% positivity. Ondo State had a significantly higher LASV rodents compared to Ebonyi State. In Ebonyi State, LASV PCR Ct values were significantly higher than in Ondo State suggesting host resistance in Ebonyi than Ondo. We also measured and compared rodent immune response to LASV in 269 small rodents using the ReLASV® Lassa NP and Pf- GP-specific IgM and IgG ELISA and obtained an overall 45% seropositivity. While the IgM and IgG were both measured in almost all rodents tested positive, indicating failure in Ig class switch, IgM antibody response against the LASV NP and Pf-GP detection was significantly higher compared with IgG NP and GP in both states. Using Nextera XT metagenomic sequencing protocol, we produced 53 partial and full length genomes from rodents sampled which clustered within sub-lineage 2g. Additionally, we found that our sequences from Ondo were interspersed across ten well-supported phylogenetic clusters and two singletons in the subtree annotated as sub-lineage 2g. Our sequences from Ebonyi State (2019 - 2020) were closely related to sequences sampled in Owo (2019 - 2022) in Sub-lineage 2g across both segments, despite a greater physical distance. We also looked at the diversity of the virus among rodent samples in two states in Southern Nigeria about 900 km apart. Additionally, using phylogeography we suggested the free movement of the virus across states in Nigeria and across human and various animal taxa, suggestive of anthropo and zooanthropozoonotic transmission. LASV sequences generated from this study reveals that LASV lineages variation is based on location and not host. This is essential for pandemic preparedness, further research, and development of countermeasures against Lassa Fever outbreaks.

Importance: We present the highest number of LASV whole genomes from small rodent reservoirs ever recorded and the first detection of LASV sublineage 2g in Ebonyi State. In this study the isolates collected from rodents are interspersed with previous isolates collected from both rodent and non-rodent hosts with probable free inter-hosts transmission of the virus. Consequently, it may be a potential pandemic threat. It is interesting to note that this study found IgM and IgG co-circulating in rodents and IgM antibody responses to be significantly higher than the IgG responses in rats and mice, suggesting persistent and active immune responses and failure of immunoglobulin class switch. Genomic data from this study reveals that LASV sub-lineage is a function of location but not host, inferring that countermeasures and diagnosis may need to consider the location of the virus origin and not one-size fits all.