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 Immune Escape and Basal Core Promoter/Precore Gene Mutations in Hepatitis B Virus Isolated from Asymptomatic Hospital Attendees in Two Southwestern States in Nigeria.

Several mutations in the surface (S), basal core promoter (BCP), and precore (PC) genes of the hepatitis B virus have been linked to inaccurate diagnosis and the development of immune escape mutants (IEMs) of the infection, which can lead to chronic infection. Understanding the prevalence and spread of these mutations is critical in the global effort to eliminate HBV. Blood samples were collected from 410 people in Osun and Ekiti states, southwest Nigeria, between 2019 and 2021. Participants were drawn from a group of asymptomatic people who were either blood donors, outpatients, or antenatal patients with no record of HBV infection at the medical outpatients' unit of the hospital. DNA was extracted from plasma using a Qiagen DNEasy kit, followed by nested PCR targeting HBV S and BCP/PC genes. The Sanger sequencing method was used to sequence the positive PCR amplicons, which were further analyzed for IEMs, BCP, and PC mutations. HBV-DNA was detected in 12.4% (51/410) of individuals. After DNA amplification and purification, 47.1% (24) of the S gene and 76.5% (39) of the BCP/PC gene amplicons were successfully sequenced. Phylogenetic analysis showed that all the HBV sequences obtained in this study were classified as HBV genotype E. Mutational analysis of the major hydrophilic region (MHR) and a-determinant domain of S gene sequences revealed the presence of three immune escape mutations: two samples harbored a T116N substitution, six samples had heterogenous D144A/N/S/H substitution, and one sample had a G145E substitution, respectively. The BCP/PC region analysis revealed a preponderance of major BCP mutants, with the prevalence of BCP double substitutions ranging from 38.5% (A1762T) to 43.6% (G1764A). Previously reported classical PC mutant variants were observed in high proportion, including G1896A (33.3%) and G1899A (12.8%) mutations. This study confirms the strong presence of HBV genotype E in Nigeria, the ongoing circulation of HBV IEMs, and a high prevalence of BCP/PC mutants in the cohorts. This has implications for diagnosis and vaccine efficacy for efficient management and control of HBV in the country.

Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria.

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria.

Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.

Seroprevalence, co-infection and risk of transmission of Hepatitis B and D virus among hospital attendees in two South-western states in Nigeria.

Infection with both Hepatitis B (HBV) and D (HDV) virus causes more severe liver damage than HBV alone. Superinfections among chronic HBV infected cohorts often lead to HDV persistence with rapid progression to cirrhosis, necessitating continuous surveillance to determine their prevalence and relative contribution to liver pathology. A cross-sectional study among hospital outpatients in Ekiti and Osunstates was conducted using random sampling technique. Blood samples were collected from 410 participants and tested for HBV serological markers. All samples positive for HBsAg samples were tested for Hepatitis D virus antigen (HDAg), serum anti-HDV IgM, and serum anti-HDV IgG using enzyme-linked immunosorbent assay kits. The prevalence of HBV infection among the 410 samples was 12.4% (CI 9.5-15.9). Past HBV exposure was detected in 120 (29.2%), while 147(35.8%) were susceptible to HBV infection. Among the HBsAg positive individuals, 9.8% were hepatitis D antigen (HDAg) positive, while 3.9% and 1.9% were positive for IgG anti-HDV and IgM anti-HDV, respectively. Risk factors associated with HBV infections in this study were multiple sexual partners and sharing of sharp objects. Our investigation has verified the endemicity of HBV in Nigeria and revealed that HBV- HDV co-infection is highly prevalent in south-west Nigeria.

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.

Metagenomic sequencing characterizes a wide diversity of viruses in field mosquito samples in Nigeria.

Mosquito vectors are a tremendous public health threat. One in six diseases worldwide is vector-borne transmitted mainly by mosquitoes. In the last couple of years, there have been active Yellow fever virus (YFV) outbreaks in many settings in Nigeria, and nationwide, entomological surveillance has been a significant effort geared towards understanding these outbreaks. In this study, we used a metagenomic sequencing approach to characterize viruses present in vector samples collected during various outbreaks of Yellow fever (YF) in Nigeria between 2017 and 2020. Mosquito samples were grouped into pools of 1 to 50 mosquitoes, each based on species, sex and location. Twenty-five pools of Aedes spp and one pool of Anopheles spp collected from nine states were sequenced and metagenomic analysis was carried out. We identified a wide diversity of viruses belonging to various families in this sample set. Seven different viruses detected included: Fako virus, Phasi Charoen-like virus, Verdadero virus, Chaq like-virus, Aedes aegypti totivirus, cell fusing agent virus and Tesano Aedes virus. Although there are no reports of these viruses being pathogenic, they are an understudied group in the same families and closely related to known pathogenic arboviruses. Our study highlights the power of next generation sequencing in identifying Insect specific viruses (ISVs), and provide insight into mosquito vectors virome in Nigeria.

Cross-sectional community-based assessment of knowledge, attitude and practices on tuberculosis in Osun State, South-west, Nigeria.

Tuberculosis (TB) has continued to be a global public health issue, especially in developing countries, where Nigeria accounts for 4% of the global TB burden. However, to achieve the Sustainable Development Goals targets for 2030, there is a need for adequate and robust awareness campaigns to ensure that individuals in the communities are aware of the total TB program package. This study assessed the knowledge, attitudes and practices (KAP) towards TB of the residents of two communities affected by the TB scourge in Osun State, Nigeria. An interviewer-administered, semi-structured questionnaire adapted from the WHO-KAP study guide was employed, and the data generated were analysed using the SPSS statistical package. A total of 280 respondents participated in the study comprising 162 (57.9%) males and 118 (42.1%) females, a large percentage of the respondents (273/97.5%) know about TB and know that anybody can be infected (63.6%). However, in this study, we obtained the following KAP scores: overall good knowledge of TB: 60% (Iwo- 54.7% and Ikire-65.2%), overall good attitude towards TB: 50% (Iwo- 53.3% and Ikire- 46.7%) and overall good TB preventive practices 65.2% (Iwo- 66.6% and Ikire- 63.8%). Ikire respondents were significantly more knowledgeable than Iwo respondents (p = .002), while Iwo respondents had better TB attitudes than Ikire respondents (p = .03). Predictors of good KAP scores were accommodation type, education, age and main source of income of respondents. This study assessed the level of community TB-KAP and reinforced the need for a more robust awareness campaign for better TB health service utilisation.

Epidemiology of HIV and Tuberculosis in pregnant women, South West Nigeria.

BACKGROUND: Pregnant women remain the most vulnerable high-risk population to the devastating impact of the on-going human immunodeficiency virus (HIV) generalized epidemic and co-infection with Tuberculosis in Nigeria. By the end of 2017, the country ranked the second highest in adult HIV-infected individuals and the highest population of orphans due to AIDS in sub-Saharan Africa. We assessed the epidemiology of HIV among pregnant women across ten facilities in south-west Nigeria. METHODS: This is a cross-sectional study design in which 353 pregnant women randomly selected across ten health care facilities in two states in south west Nigeria. This study was conducted between January and May 2015. HIV testing was conducted and active tuberculosis screening was implemented using the fluorescence microscopy. In addition, a structured questionnaire was administered to elicit risk factors of HIV infection and syndromic Tuberculosis in the study population. RESULTS: We found a 5.1% (18/353:95% CI:3.0%-8.0%) rate of HIV and 0% active tuberculosis in the study population. HIV positive pregnant women were 6 times more likely to have blood transfusion with greater odds of infection found in pregnant women with history of blood transfusion in the previous three months (OR:3.27, 95% CI:0.44-24.36). Pregnant women who tested HIV negative had 70% reduction in odds of infection (OR:0.21:95% CI:0.06-0.77). CONCLUSIONS: This study suggests a possible strong epidemiological link between HIV infection and recent blood transfusion among pregnant women attending ante-natal clinics in south west Nigeria. We therefore recommend further study to develop a more robust estimate of blood transfusion and the risk of HIV in pregnant women in Nigeria.

Epidemiology and bacterial colonization of burn injuries in Blantyre.

Forty-nine patients from the Burns Unit at the QECH had swabs taken from various sites in order to determine the bacterial profile and antibiotic susceptibilities in burn wounds colonized by bacteria. The mean age was 16 years (range 1-70 years); 27 (55 %) of the study population were female and 22 (45%) were male. Twenty-four (49%) patients were epileptic. Open fire (41%) was the most common cause of burn injuries among epileptics while hot water burns (29%) were commonest among non-epileptics. Burn injury and percentage total burn surface area (% TBSA) injuries decreased with age, and the upper and lower limbs, trunk, head and neck were the most commonly affected sites. Staphylococcus aureus was the commonest isolate (23%), followed by Proteus mirabilis (22.7%), Streptococci spp (15.9%), Pseudomonas aeruginosa (4.5%) and 3.4% for Escherichia coli, Salmonella and Klebsiella spp. There was a significant trend of bacterial growth with increasing % TBSA (p<0.001). Bacterial growth was significantly more common in more recent burns of less than 20 days compared to burns of longer duration (OR 4.1 [95% CI 1.58-10.99]). Broad-spectrum antibiotics are required as first-line therapy for burns-related sepsis but there is need for surveillance of antibiotic susceptibility to help determine appropriate therapy.

Epidemiology and Bacterial Colonization of Burn Injuries in Blantyre

Forty-nine patients from the Burns Unit at the QECH had swabs taken from various sites in order to determine the bacterial profile and antibiotic susceptibilities in burn wounds colonized by bacteria. The mean age was 16 years (range 1-70 years); 27 (55 ) of the study population were female and 22 (45) were male. Twenty-four (49) patients were epileptic. Open fire (41) was the most common cause of burn injuries among epileptics while hot water burns (29) were commonest among non-epileptics. Burn injury and percentage total burn surface area (TBSA) injuries decreased with age; and the upper and lower limbs; trunk; head and neck were the most commonly affected sites. Staphylococcus aureus was the commonest isolate (23); followed by Proteus mirabilis (22.7); Streptococci spp (15.9); Pseudomonas aeruginosa (4.5) and 3.4 for Escherichia coli; Salmonella and Klebsiella spp. There was a significant trend of bacterial growth with increasing CI 1.58-10.99]). Broad-spectrum antibiotics are required as first-line therapy for burns-related sepsis but there is need for surveillance of antibiotic susceptibility to help determine appropriate therapy

Etiology and incidence of chronic ulcers in Blantyre, Malawi.

BACKGROUND: Little information is available on the incidence and etiology of chronic ulcers in the tropics. Therefore, the incidence and etiology of chronic skin ulcers were assessed in out-patients at the Department of Dermatology and in in-patients at the Departments of Dermatology, Surgery, Medicine, and Pediatrics, Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi. METHOD: In a 10-week study period, 44 patients (31 males, 70%) with chronic skin ulcers were diagnosed from 6292 patients seen by the departments involved. RESULTS: The mean age of patients with ulcers was 38 years (range, 9 months to 82 years). The most frequent cause of ulcers was bacterial infection (n=22), followed by malignancy (n=11) and trauma (n=7). CONCLUSION: In contrast with developed countries, venous and diabetic ulcers were uncommon. In addition to bacterial infections, a surprisingly large number of malignancies were found in this study. We speculate that human immunodeficiency virus (HIV) infection, which is seen with a high prevalence at QECH, is a contributing factor. Because of the large number of malignancies, we recommend early histopathologic investigation of chronic ulcers in this part of Africa.