Background The introduction of multiple avian influenza virus (AIV) subtypes into Nigeria has resulted in several poultry outbreaks purportedly linked to trade and wild birds. The role of wild birds in perpetuating AIV in Nigeria was, therefore, elucidated. Methods A cross-sectional study was conducted among wild aquatic bird species at the Hadejia-Nguru wetlands in northeastern Nigeria between March and April 2022. A total of 452 swabs (226 cloacae and 226 oropharyngeal swabs) were collected using a mist net to capture the birds. These samples were tested by RT-qPCR, followed by sequencing. Results Highly pathogenic AIV of the H5N1 subtype was identified in clinically healthy wild bird species, namely African jacana, ruff, spur-winged goose, squared-tailed nightjar, white-faced whistling ducks, and white stork. A prevalence of 11.1% (25/226) was recorded. Phylogenetic analysis of the complete HA gene segment indicated the presence of clade 2.3.4.4b. However, these H5N1 viruses characterized from these wild birds cluster separately from the H5N1 viruses characterized in Nigerian poultry since early 2021. Specifically, the viruses form two distinct genetic groups both linked with the Eurasian H5N1 gene pool but likely resulting from two distinct introductions of the virus in the region. Whole genome characterization of the viruses reveals the presence of the mammalian adaptive marker E627K in two Afro-tropical resident aquatic ducks. This has zoonotic potential. Conclusion Our findings highlight the key role of surveillance in wild birds to monitor the diversity of viruses in this area, provide the foundations of epidemiological understanding, and facilitate risk assessment.

Crimean - Congo haemorrhagic fever virus (CCHFV) is a tick-borne viral haemorrhagic febrile disease that is highly pathogenic in humans with enzootic cycle between tick vectors and animal hosts. Human infection with CCHFV takes the clinical form of viral haemorrhagic disease, a major health condition but with limited testing in Nigeria. In this study, blood samples were collected from 333 pastoralists’ cattle in North Central Nigeria and 1,470 ticks were picked from the animals. For serology, Enzyme Linked Immuno Sorbent Assay (ELISA) was performed using a double antigen multi species ELISA kit with sensitivity and specificity of 98.9% and 95% respectively at 95% confidence interval to detect IgG antibody to CCHFV in plasma. RT-qPCR virological technique was used to identify viral antigen in ticks that were pooled based on location and genus. Four species of ticks were morphologically identified to parasitize cattle in the sampled location namely; Rhipicephalus ( Boophilus) decoloratus (34.6%), Hyalomma truncatum (32.9%), Amblyomma variegatum (24.6%) and Rhipicephalus sanguineus (8%). The seroprevalence of CCHFV was found to be 67%. In Kaduna state, 85 of 108 plasma samples tested positive (78.7%) while in Plateau state 138 of 225 plasma samples tested positive (61.3%). Of the 41 pools of tick tested for CCHF, one (1) pool of 35 Rhipicephalus ( Boophilus) ticks (2.4%) was positive for CCHF virus with qPCR cycle threshold of 31.88. Although Hyalomma spp. is documented to be the main vector of CCHFV, in the present investigation, Rhipicephalus ( Boophilus) species was identified to play a role as reservoir of CCHF. The high seroprevalence of CCHF in livestock underscores the public health risk associated with CCHFV at the human-animal interface in Nigeria.