Metagenomic Detection and Genetic Characterization of Human Sapoviruses among Children with Acute Flaccid Paralysis in Nigeria.

Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six complete genome sequences and two partial genome sequences. Several SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1), and GI (GI.2 and GI.7). To our knowledge, this is the first description of SaV infections and complete genomes from Nigeria. Pairwise identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks with associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were seen in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria. Future studies in different populations are, therefore, recommended.

Detection of Alpha- and Betacoronaviruses in Frugivorous and Insectivorous Bats in Nigeria.

The rise of bat-associated zoonotic viruses necessitates a close monitoring of their natural hosts. Since the detection of severe acute respiratory syndrome coronavirus (SARS-CoV), it is evident that bats are vital reservoirs of coronaviruses (CoVs). In this study, we investigated the presence of CoVs in multiple bat species in Nigeria to identify viruses in bats at high-risk human contact interfaces. Four hundred and nine bats comprising four bat species close to human habitats were individually sampled from five states in Nigeria between 2019 and 2021. Coronavirus detection was done using broadly reactive consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene of CoVs. Coronavirus RNA was detected in 39 samples (9.5%, CI 95%: [7.0, 12.8]), of which 29 were successfully sequenced. The identified CoVs in Nigerian bats were from the unclassified African alphacoronavirus lineage and betacoronavirus lineage D (Nobecovirus), with one sample from Hipposideros ruber coinfected with alphacoronavirus and betacoronavirus. Different bat species roosting in similar or other places had CoVs from the same genetic lineage. The phylogenetic and evolutionary dynamics data indicated a high CoV diversity in Nigeria, while host switching may have contributed to CoV evolution. Robust sentinel surveillance is recommended to enhance our knowledge of emerging and re-emerging coronaviruses.

Serologic evidence of silent Rift Valley fever virus infection among occupationally exposed persons in northern Nigeria.

INTRODUCTION: Rift Valley fever (RVF) is a zoonotic disease caused by RVF virus (RVFV) and transmitted primarily by mosquitoes and contact with fluids and tissues of infected animals. First described in Kenya, it has spread to many African countries and beyond. In humans, it is sometimes misdiagnosed because the symptoms resemble those of influenza and/or malaria. Butchers, abattoir workers, and livestock keepers have the highest risk of infection. METHODOLOGY: In this study, serum samples collected between February and September 2019 from 196 individuals comprising of butchers (n = 121), abattoir/slaughterhouse workers (n = 55), and livestock keepers (n = 20) in Benue, Sokoto, and Borno States of northern Nigeria were screened using a commercial ELISA that detected anti-RVFV IgM and IgG alike (i.e., without discrimination). Data from administered questionnaires and the ELISA results were statistically analyzed. RESULTS: Thirty-nine (19.9%) of the 196 samples were positive for RVFV antibodies. The distribution by states showed that 17.4% (8/46), 21.7% (15/69), and 19.8% (16/81) of samples from Benue, Sokoto, and Borno States were seropositive, respectively. Additionally, 21.5% (26/121) butchers, 16.4% (9/55) abattoir workers, and 20% (4/20) livestock keepers were seropositive. CONCLUSIONS: These findings provide serological evidence for exposure of occupationally at-risk individuals in northern Nigeria to RVFV. The higher seropositivity obtained in Sokoto and Borno states could be due to contact of these individuals with infected animal blood/tissues, aborted fetuses, and unhindered transboundary movement of animals and animal products into these states which share international borders with Niger, Chad, and Cameroon where evidences of RVFV infections were recently reported.

Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E.

Introduction. Hepatitis B virus (HBV) infection is the leading cause of hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). HBV genotype E (HBV/E) is the predominant genotype in West Africa and has been linked epidemiologically with chronic and occult HBV infections as well as development of HCC. Mutations in the surface and polymerase genes of HBV have been associated with occult infection, drug resistance, vaccine escape, as well as HCC.Hypothesis/Gap Statement. There is limited data on the occurrence and patterns of mutations associated with occult infection, drug resistance, vaccine escape and HCC for HBV/E.Aim. This study characterized amino acid (aa) substitutions in the major hydrophilic (MHR) and reverse transcriptase (RT) regions of the surface and polymerase genes respectively of HBV sequences from a group of Nigerians with genotype E infection. The CpG islands of the PreC/C and PreS/S regions of these sequences were also described.Methodology. HBV surface and polymerase genes were detected using PCR techniques. Occurrence of new and previously described mutations in these genes were analysed using phylogenetic techniques.Results. Overall 13 HBV isolates were each sequenced for polymerase and surface genes mutations. Thirteen and nine PreS/S and PreC/C HBV genes respectively were analysed for CpG islands. Mutations in the MHR and a-determinants region of the S protein were discovered in eleven and nine of the 13 tested isolates respectively. These mutations were concomitant with aa changes in the RT functional domains of the isolates. Mutations associated with vaccine escape, occult infection and poor HCC prognosis were identified in HBV/E isolated in this study. Furthermore, all the isolates had at least one putative nucleotide analogue resistance mutations. Drug resistance mutations had the highest association with CpG islands.Conclusion. The results of this study contribute to further understanding of HBV variability in Nigeria and the West African region. This will aid the planning of adequate HBV immunization and treatment programmes for the countries in the region.

Laboratory diagnosis of a new outbreak of acute African swine fever in smallholder pig farms in Jos, Nigeria.

African swine fever (ASF) is a highly contagious fatal infectious disease of pigs and wild suids. The disease has a worldwide occurrence and significant impact on pig production. Two adult intensively raised large white boars from two farms in Jos with a history of sudden death were diagnosed of ASF between July and August 2019. Post-mortem examination of carcasses grossly showed splenomegaly, haemorrhagic lymphadenitis and hepatomegaly with severe congestion. The kidneys were enlarged and had generalized petechiae and blood clot in the pelvis. The heart was moderately enlarged. Microscopic examination of the spleen and lymph nodes revealed severe lymphocytic depletion, haemorrhage and severe haemosiderosis. The liver was severely congested with focal coagulative necrosis of the hepatocytes. The kidneys were severely congested and showed renal tubular necrosis with few tubular protein casts. Tissue samples were confirmed to be positive for African swine fever virus (ASFV) by polymerase chain reaction (PCR) assay, and phylogenetic analysis revealed that the isolate belonged to genotype I.