Virology
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Item Circulation of hepatitis B virus genotype-E among outpatients in tertiary hospitals in the Niger-Delta region of Nigeria(African Journals Online (AJOL), 2022) Umego, C. F.; Mboto, C. I.; Asitok, A. D.; Osaji, L. C.; George, U. E.; Edet, U. O.; Mbim, E. N.; Faleye, T. O. C.; Adewumi, O. M.; Adeniji, J. A.Introduction: Hepatitis B virus (HBV) infection continues to be a significant public health challenge globally, with higher disease burden in developing countries. HBV genotypes are associated with different geographical regions and clinical outcomes. Limited information exists on epidemiology of HBV in the Niger-Delta region (South-South) of Nigeria. Consequently, this study was designed to characterise hepatitis B virus infection among outpatients in selected tertiary hospitals in the region. Methodology: Between June and August 2017, consenting nine hundred asymptomatic out-patients were enrolled and initially screened for HBV infection using one step Hepatitis B surface antigen (HBsAg) strip and subsequently re-tested using HBsAg and Hepatitis B core total antibody (anti-HBc) specific Enzyme-Linked Immunosorbent Assay (ELISA). Blood serum with detectable HBsAg were subsequently subjected to DNA extraction, S-gene amplification using a nested polymerase chain reaction (PCR) protocol, gel electrophoresis, sequencing and phylogenetic analysis. Results: Seroprevalence of HBsAg was 4.6% (95% CI 2.5-7.1) and anti-HBc was 10.1% (95% confidence interval (CI) 6.1-15.3). Of the 41 HBsAg positive samples subjected to DNA extraction and HBV S-gene specific PCR, only 6 (14.6%) yielded the expected ~408bp band. Phylogenetic analysis based on HBV pre-S/S sequences identified all six typable samples as genotype E, subtype ayw4 of the West African clade. Conclusion: Results of the study confirm the presence and circulation of HBV genotype-E in the Niger-Delta region of Nigeria, thus corroborating the inclusion of the country in the Genotype E crescent. The authors advocate value-added HBV intervention in the region and the country at large.Item Microbiological Assessment and Detection of Adenovirus in Sachet Water Sold In Abeokuta, Nigeria(Nigerian Society for Microbiology (NSM), 2021) Shittu, O. B.; Adekunle, O. T.; Olufemi, F. O.; Faleye, T. O. C.; Adewumi, M. O.; Adeniji, J. A.Microbiological safety of sachet water remains a public health problem in Nigeria. This study was aimed at investigating some packaged sachet water sold in Abeokuta, South-West Nigeria for the microbiological safety including some of the enteric viruses on contaminant candidate list. Sachet water samples from five different producers were obtained over three month’s period. Bacterial and fungal analyses were conducted with standard culture method. Targeted protozoans were investigated by microscopic examination of sediments obtained after centrifugation. Nested and semi-nested polymerase chain reaction (PCR) techniques targeting specific genes in adenovirus, norovirus and rotavirus were used for viral analyses. Results were presented in presence-absence score. Contingency table was used to establish relationship between viruses, Escherichia coli and protozoans. Out of a total twenty pooled samples analysed, adenovirus had a prevalence rate of 10% across the study period, whereas rotavirus and norovirus were absent. Giardia cysts and Cryptosporidium oocysts were also absent. Escherichia coli was present in 40% of the brands. Other bacteria identified were Salmonella enterica serovar Typhi, Shigella dysentariae, and Pseudomonas aeruginosa. Aspergillus sp, Mucor and Rhizopus sp. were present in some samples collected. Adenovirus was detected by PCR in a pooled sample of sachet water thattested negative for Escherichia coli, Cryptosporidium oocysts and Giardia cysts. There is need for microbiological screening of sachet water periodically in order to enhance public health safety.Item Isolation and Genomic Characterization of Echovirus 11 from faeces of a Non-Human Primate in Nigeria(Springer Nature, 2021-05-16) Faleye, T. O. C.; George, U. E.; Klapsa, D.; Majumdar, M.; Oragwa, A. O.; Adewumi, O. M.; Martin, J.; Adeniji, J. A.We recently investigated the presence of enteroviruses (EVs) in non-human primates (NHPs) in Northern Nigeria and documented the presence of EV-A76 of South-East Asian ancestry in an NHP. In this study, we go further to ask if we could also find EVs in NHPs indigenous to the forested South-south Nigeria. Fresh faecal samples were collected from the floor of 10 cages housing NHPs in Cross River Nigeria, resuspended in PBS and subjected to RNA extraction, cDNA synthesis, PanEnt 50-UTR and PanEnt VP1 PCR assays. None of the samples was positive for the PanEnt VP1 assay, but one sample was positive for PanEnt 50- UTR PCR. This sample was subsequently inoculated into RD cell line, produced CPE and the isolate analysed by PCR assays, next-generation whole genome sequencing and passage in four different cell lines showing replication in two of them. Analysis of the complete genome of the isolate identified it as an Echovirus 11 (E11) and revealed a recombinant genomic structure. Phylogenetic analysis showed that the E11 NHP strain was related to human clinical isolates suggesting a zoonotic behaviour. We describe the first isolation and complete genome characterization of an E11 obtained from an NHP in Nigeria having zoonotic potential.Item Fecal Antibiotic Resistome of Pigs from a Small-Scale Piggery in Ibadan, South-West Nigeria(ResearchersLinks (Nexus Academic Publishers, NAP), 2021-05-28) Olayinka, O. A.; Faleye, T. O. C.; Omotosho, O. O.; Odukaye, O. A.; Oluremi, B.; Ibitoye, I. H.; Ope-Ewe, O. O.; George, U. E.; Arowolo, O. A; Ifeorah, I. M.; Omoruyi, E. C.; Donbraye, E; Adeniji, O. P.; Adewumi, O. M.; Adeniji, J. A.This study was designed to sample the fecal Resistome of Pigs from a small-scale Piggery in Ibadan, South-West Nigeria. Three fecal pellets were randomly picked from the floor of unit pens containing a minimum of three pigs per unit in selected piggery in Ibadan, Nigeria. The samples were pooled and resuspended in phosphate buffered saline. The suspension was then subjected to nucleic acid extraction, Cdna synthesis and Illumina sequencing. Antibiotic Resistance Genes (ARGs) in the raw reads were determined and assembled using the Kmer Resistance tool v2.2. From the 2,974,257 reads generated, 21 ARGs with statistically significant reads were identified. Almost all targeted broad-spectrum antibiotics with over 50% targeting Tetracyclines. Five (ant(6)-Ia_3, tet(40)_1, tet(Q)_1, tet(W)_5 and tet(O/W)_4) of the ARGs were predicted to be plasmid-borne. Our findings show that the Swine industry in the region might be both a mixing pot and reservoir of ARGs. It is therefore crucial that effort is made to educate the stakeholders on the importance of good antibiotics stewardship.Item Faecal antibiotic resistome of Nigerian chimpanzees from a wildlife sanctuary in cross-river state, Nigeria(Nexus Academic Publishers (NAP), 2021) George, U. E.; Arowolo, O. A.; Olayinka, O. A.; Ifeorah, I. M.; Faleye, T. O. C.; Oluremi, B.; Oragwa, A.O.; Omoruyi, E. C.; Udoh, E. E.; Osasona, O. G.; Donbraye, E.; Adeniji, O. P.; Adewumi, O. M.; Adeniji, J. A."Out of prescription, indiscriminate use, misuse and abuse of antibiotic administration and/or usage in both humans and farm animals have led to a consistent interference and contamination of biomes and ecobiomes. These resultantly give platforms for positive selection of resistant pathogens and high levels of Antibiotic Resistance Genes (ARGs). We examined Nigerian Chimpanzees in Boki Afi Mountain Wildlife Sanctuary, Cross-River State, Nigeria, to detect ARGs. Faecal samples from 15 Chimpanzees in pristine enclosures of Non-Human Primates in the Wildlife Sanctuary were analyzed. All faecal samples were pooled, then resuspended in phosphate-buffered saline. Subsequently, nucleic acid was extracted from the suspension and Illumina sequencing performed. ARGs in the raw reads were determined and assembled using the KmerResistance tool v2.2. From the 2,763,954 reads generated, 14 ARGs with statistically significant reads were identified. Precisely, 90.5% (12/14) of the ARGs detected target drugs that inhibit translation, of which 66.6% (8/12) were tetracycline resistance (TC-r) genes, while remaining 9.5% (2/14) inhibit cell wall synthesis (cfxA3_1 and cfxA6_1). Eight (aph(3’)-III_1, cfxA3_1, cfxA6_1, erm(B)_10, tet(Q)_1, tet(Q)_2, tet(Q)_4, tet(W)_5) of the ARGs detected were predicted to be plasmid-borne. We report using a cultivation-independent approach the presence of ARGs in Nigerian Chimpanzees. Findings suggest Nigerian Chimpanzees may constitute a hitherto overlooked source of antibiotic resistance in the environment. These ARGs may have been exchanged with handlers and rural dwellers around the Sanctuary. Surveillance of sympatric human faecal and environmental microbiota and their resistomes at the Wildlife Sanctuary are merited to inform public health interventions and decrease ARGs dissemination."Item Expanding the frontiers of bacterial diagnosis through bacteriophage biotechnology(AIMS Press, 2020) Majumdar, M.; Klapsa, D.; Wilton, T.; Bujaki, E.; Fernandez‐Garcia, E. M. D.; Faleye, T. O. C.; Oyero , A. O.; Adewumi, M. O.; Ndiaye, K.; Adeniji, J. A.; Martin, J.In a bid to achieve microbial diagnostic precision and reduce diagnostic turn-around time, the development of technologically advanced,novel techniques has been on the rise. There is a gradual phasing out of traditional diagnostic methods by more specific and highly sensitive molecular techniques. Asides from being technically demanding and cost-ineffective, these molecular methods have themselves not fulfilled perhaps the most essential diagnostic criterion of distinguishing between viable and dead bacterial cells. The use of bacteriophages as biorecognition elements for bacterial detectors offers numerous advantages in terms of cost, ease of accessibility, and high specificity binding of bacteriophages to their bacterial host. Biotechnological advancements further give bacteriophage use the leading edge as genetic modification of bacteriophage genome through the fluorescent gene insertion produces reporter bacteriophages. These recombinants can produce detectable fluorescent signals through intracellular lytic action, strictly in metabolically active bacteria cells. Fluorescent labelled enzyme-active and cell wall binding domains of bacteriophages also offer better alternatives to the use of antibodies as diagnostic markers because they are resistant to pH and temperature sensitivities. Overall, bacteriophage-based detection systems are less prone to detection errors and significantly reduce diagnostic time while also attaining high test sensitivity.Item A possible risk of environmental exposure to HEV in Ibadan, Oyo State, Nigeria(Taylor & Francis, 2020-08-13) Olayinka, A.; Ifeorah, I. M.; Omotosho, O.; Faleye, T. O. C.; Odukaye, O.; Bolaji, O.; Ibitoye, I.; Ope-Ewe, O.; Adewumi, M. O.; Adeniji, J. A."Hepatitis E virus (HEV) infection is both a major public health concern and emerging global health concern, with a documented incidence of 20 million, 3.4 million clinical cases, 70,000 deaths, and 3,000 stillbirths. The aetiologic agent, HEV is a primarily enterally transmitted hepatotropic virus. Fecal samples were collected from three selected pig farms across Ibadan, South-west Nigeria. Randomly picked samples were pooled per unit pen and fecal suspensions prepared were subjected to HEV Antigen (Ag) enzyme-linked immunosorbent assay. Molecular probing was done by Reverse Transcription and nested polymerase reaction (RT-nPCR) and deep sequencing. Sequencing was done paired-end for 300 cycles using the HiSeq system. Overall farm prevalence of 66.7% (2/3) and prevalence at individual level of 13.2% (9/68) were recorded. All nine samples positive for the ELISA screen were negative when subjected to RT-nPCR assays. Further, on deep sequencing, no HEV genomic fragment was found in the sample using de-novo assembly. Findings suggest possibly inapparent HEV in the pigs studied or a yet to be identified protein with HEV-Ag cross-reactivity ability on ELISA, thus constituting a possible risk of exposure to HEV infection in the population. Consequently, we recommend prompt intervention to unravel the mystery and break the chain of transmission.Item Non-polio enterovirus species c infection in AFP cases and its implication for the emergence of recombinant circulating vaccine- derived polioviruses(ResearchersLinks Ltd., 2020) Adewumi, O. M.; Faleye, T. O. C.; Ope-Ewe, O. O.; Ibitoye, I. H.; Arowosaye, A. O.; Adelowo, O. D.; Adeniji, J. A.Using 40 faecal samples from acute flaccid paralysis (AFP) cases collected in 2019, we examined how coupling Enterovirus (EV) isolation in RD and MCF-7 cell culture with direct detection from clinical sample might impact our ability to detect non-polio EV Species C (NPESC) members in stool samples. In all, 20% (8/40) of all the samples screened had NPESCs and 50% (8/16) of the EVs detected were NPESCs. However, the RD cell line missed all NPESCs. Hence, RD cell line alone should not be used for EV isolation if the desire is to also isolate NPESC.Item Near-complete genome sequence of an enterovirus species fisolate recovered from sewage in Nigeria(American Society for Microbiology (ASM), 2021) Faleye, T. O. C.; Ifeorah, M. I.; Olayinka, O. A.; Oluremi, B.; George, U. E.; Arowolo, O. A.; Omoruyi, E. C.; Donbraye, E.; Oyero, A. O.; Adewumi, O. M.; Adeniji, J.A.Here, we describe the near-complete genome of an enterovirus F (EV-F) isolate from Nigeria. The obtained sequence was 7,378 nucleotides (nt) long and encodes 2 open reading frames (ORFs), an upstream ORF (uORF; 56 amino acids [aa])and a polyprotein ORF (ppORF; 2,167 aa). Both ORFs overlap but are in different reading frames, with the uORF in a _1 reading frame relative to the ppORF.Item Genome sequences of novel members of previously described DNA and RNA virus families, isolated from feces of a drill monkey in Nigeria(American Society for Microbiology (ASM), 2020) George,U.; Simsek, C.; Faleye, T. O. C.; Arowolo,O. A.; Oragwa, A.; Adewumi,O. M.; Matthijnssens, J.; Adeniji, J. A; Adeniji, J. AThe genomes of seven novel members of previously described DNA and RNA virus families are described here. These viruses were recovered using a viral metagenomic approach from the stool of a drill monkey (Mandrillus leucophaeus) housed in a sanctuary in Cross River State, Nigeria.