Molecular detection and characterization of Rift Valley fever virus in humans and domestic ruminants in Nigeria

Rift Valley fever virus (RVFV) causes a zoonotic mosquito-borne disease of domestic livestock, wildlife and humans majorly in Africa and the Arabian Peninsula. The virus is a Phlebovirus belonging to the Family Phenuiviridae and constitutes a threat to both human and animal health. Although there has been serological evidence of RVFV in humans and animals in Nigeria, reports on its molecular detection and characterization are absent. Blood samples (n = 1101) were collected between January 2019 and March 2021 from humans, cattle and sheep in four States of Nigeria. The harvested plasma samples were tested using a commercial ELISA kit. All the ELISA-positive, ‘-doubtful’ and some ‘-negative’ samples (n = 436) were further analyzed using nested reverse transcriptase-polymerase chain reaction (nRT-PCR). Eight samples (humans, n = 1; cattle, n = 6; sheep, n = 1) that gave the expected band size of approximately 668 base pairs following gel electrophoresis were sequenced by Sanger method. The sequence data were edited using BioEdit software and RVFV was successfully identified in all of them. Nucleotide sequence and phylogenetic analyses revealed that these eight RVFV strains were 98.3–99.9% identical and clustered with the Ugandan Smithburn strain. Genotyping showed that they belonged to Lineage K. This report, which is the first molecular detection and characterization of RVFV in Nigeria, confirms the circulation of the virus in the country. It also highlights the need for large-scale surveillance for RVFV in Nigeria, including among mosquito vectors, to provide better understanding of its spatiotemporal epidemiology, and thus, aid in preventing potential RVF outbreaks in the country.