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

Paediatric brought-in-dead at a tertiary health facility in South western Nigeria: Patterns and drivers

Background: ‘Brought- in-dead’ (BID) refers to the demise of an individual before presentation to a health facility. This study assessed the pattern of paediatric BID cases seen at a tertiary health facility in southwest Nigeria. Method: A cross-sectional, descriptive study was done at the Children Emergency Ward (CEW) of the hospital between January 2014 and December 2018. The patterns of BID cases and presumed causes of death were determined using a standardized checklist adapted from the WHO verbal autopsy instrument. Results: Ninety-eight BID cases were seen during the study, constituting 2.5% of total patients seen during the period. The median (IQR) age of cases was 24.0 (8.75 – 63.0) months and 72.4% were under-fives. Most had symptoms related to the haematologic (36.7%), respiratory (24.5%) or digestive (20.4%) systems. Severe anaemia 31(31.6%), gastroenteritis 19 (19.4) and aspiration 17 (17.3%) were the most common causes of death. The median (IQR) duration of illness before presentation was 3.0 (1.0 – 7.0) days but most presented from 4 – 7 days of illness. A significant relationship was found between the duration of illness and whether or not pre-hospital treatment was received (p < 0.0001). Unprescribed drugs purchased over the counter were the most commonly used treatment in 79.1% of cases (p < 0.0001). Conclusion: This study has highlighted the prevalence and pattern of paediatric BID in a tertiary health facility in southwest Nigeria and the factors that were associated with it. More efforts need to be geared towards community sensitization and pediatric health care to prevent factors drivingits menace

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 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

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

First report of Wolbachia from field populations of Culex mosquitoes in south-western Nigeria

Recent reports on finding Wolbachia-strain infections in field mosquito species in some West African countries and the potential for developing these as disease vector biocontrol tools have prompted a search for Wolbachia in mosquitoes within the study area. Using a completely randomised design, mosquito traps were set at different locations in a rural and an urbanised community. One hundred and eighty (180) mosquitoes were trapped and pooled on the basis of genus, sex and site of collection, because there have been no earlier reports of Wolbachia isolated from Nigeria. Twenty pools, made up of not more than ten mosquitoes per pool, were homogenised and analysed for Wolbachia-specific DNA. Mosquitoes were trapped within Ede (urbanised community) and Akoda (rural community). Genomic DNA was extracted from trapped mosquito samples and used as a template in a PCR reaction. The Wolbachia sp. specific 16S rRNA gene was amplified, sequence analysis of PCR products was performed and a chromatogram of the sequence was subjected to Basic Local Alignment Search Tool analysis to identify the Wolbachia sp. This sequence was subsequently submitted to GenBank with accession number MK127541. The first evidence of the presence of the endosymbiont, Wolbachia in field-caught mosquitoes is hereby documented. The homology of this strain of Wolbachia bears similarities to those reported recently from other parts of West Africa and forms a single clade with a Wolbachia sp. from Mali, with a strong bootstrap support of 99%. This finding of a Wolbachia strain in mosquitoes at Ede could form the basis for more searches for diverse strains of Wolbachia in Nigeria.Keywords: 16S rRNA gene, Akoda, Ede, endosymbiont, gene sequence, homology, obligate bacteria, PCR amplificatio

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

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