Genomic Analysis of the First Virological Evidence of a Human Case of Crimean-Congo Haemorrhagic Fever Virus (CCHFV) in Nigeria

Abstract

Several studies in both humans and animals in Nigeria have presented evidence for the endemicity of CCHFV in Nigeria. In spite of the aforementioned, there has been no confirmed human case of CCHF infection in Nigeria. We present a study giving the first serologic and virological evidence of CCHF in a 15-year-old female, She was admitted in March 2012 into the female medical ward of the University of Maiduguri Teaching Hospital, a tertiary health facility in northeastern Nigeria with a 6 day history of fever, body pain, bloody diarrhoea, and epistaxis. She resides in a peri-urban settlement in old Maiduguri located not far from a major municipal abattoir in Maiduguri, the capital city of Borno state, Nigeria. The abattoir serves as the major animal slaughter house within Maiduguri city. Animals (Camel, Cattle, Goat and Sheep) are brought from within the Stat Borno), neighbouring states and mostly from neighbouring countries such as Cameroun, Chad, Niger, and as far as Sudan, Central Africa. The RNA extracted from this sample (N428) was further characterized by next generation sequencing (NGS) which resulted in complete S, M, and L viral RNA segment sequences. Phylogenetic analysis clustered the S-segment in the Africa 3 clade or phylogenetic group. The S-segment open-reading frame showed close homology with a previous isolate of CCHFV from Nigeria (IbAr10200), as well as isolates from Mauritania (ArD39554) and South Africa (SPU415/85 and SPU128/61/7). The M and L clustered closely with the Sudan ABI-2009 isolate and the Nigeria IbAr10200. The L, M, and S sequences were submitted to GenBank with accession numbers KX238956, KX238957 and KX238958 respectively. This genomic analysis provides the first published evidence of a human case of CCHFV in Nigeria and its phylogenetic context.