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 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 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 Identification of previously untypable RD cell line isolates and detection of EV-A71 genotype C1 in a child with AFP in Nigeria(Taylor & Francis, 2018-11-26) Adewumi, O. M.; Faleye, T. O. C.; Okeowo, C. O.; Oladapo, A. M.; Oyathelemhi, J.; Olaniyi, O. A.; Isola, O. C.; Adeniji, J. A.We previously attempted to identify 96 nonpolio enteroviruses (EVs) recovered in RD cell culture from children <15years with acute flaccid paralysis in Nigeria. We succeeded in identifying 69 of the isolates. Here, we describe an attempt to identify the remaining 27 isolates. Twenty-six (the 27th isolate was exhausted) isolates/samples that could not be typed previously were further analyzed. All were subjected to RNA extraction, cDNA synthesis, enterovirus 5ʹ-UTR–VP2 PCR assay and a modified VP1 snPCR assay. Both the 5ʹ-UTR–VP2 and VP1 amplicons were sequenced, isolates identified and subjected to phylogenetic analysis. Twenty of the 26 samples analyzed were identified. Altogether, 23 (three samples had co-infection) EV strains were recovered. These belong to 11 EV (one EVA, nine EVB and one EVC) types which were EVA71 genotype C1 (1 strain), CVB3 (7 strains), CVB5 (1 strain), E5 (2 strain), E11 (3 strains), E13 (2 strain), E19 (1 strain), E20 (1 strain), E24 (2 strains), EVB75 (1strain) and EVC99 (2 strains). Of the 11 EV types, the 5ʹ-UTR-VP2 assay identified seven while the VP1 assay identified 10. Both assays simultaneously detected 7 of the 11 EV types identified in this study with 100% congruence. We successfully identified 20 of 26 samples that were previously untypable. We also provided evidence that suggests a clade of EVA71 genotype C1 might have been circulating in sub-Saharan Africa since 2008. Finally, we showed that the 5ʹ-UTR -VP2 assay might be as valuable as the VP1 assay in EV identification.Item Evaluation of performance testing of different rapid diagnostic kits in comparison with EIAs to validate detection of hepatitis B virus among high risk group in Nigeria(Taylor & Francis, 2018-05-15) Afolabi, A. Y.; Bakarey, A. S.; Adewumi, M.O.Background: Hepatitis B virus (HBV) causes chronic liver-associated diseases and its early detection is of high public health importance. Its diagnosis is mainly based on immunological assays among which Enzyme-Linked Immunosorbent Assay (ELISA) and rapid tests are the most common and widespread methods. However, a major challenge is the discordance of results of any two laboratory assays which cannot be easily resolved. Therefore, this study was designed to evaluate the validity and reliability of commercially available five rapid test kits in comparison with two Enzyme Immunoassays (EIAs) in Nigeria using hepatitis B surface antigen as a reference marker. Methods: A total of 100 sera of previously diagnosed consenting HBV-positive patients from private diagnostic laboratories in Ibadan between March and August, 2011 were tested using two EIA and five rapid commercially available HBV test kits in Nigeria. Data were analyzed by SPSS version 15, while bivariate and multivariate analyses were carried out to identify associations at P < 0.05 considered significant. Results: Overall, the sensitivity rates of the two EIA kits were 100% and 99.9% (95% confidence interval [CI] = 98.9–99.7) with specificity of 100% and 99.9% (95% CI = 98.9–99.7), respectively. The sensitivity of the five rapid test kits ranged from 97.5% (95% CI = 96.4–97.6) to 98.9% (95% CI = 97.9–99.9) with specificity of 80% (95% CI = 79.3–80.9) to 90% (95% CI = 89.2–91.0). Also, the positive predictive value ranged from 88% (95% CI = 88.2–89.9) to 89% (95% CI = 88.2–89.9), while the negative predictive value ranged from 80% (95% CI = 79.3–80.9) to 90% (95% CI = 89.2–91.0) for the five rapid kits. However, that of the two EIAs ranged from 99.9% (98.9– 99.7) to 100%. Further analysis showed significant (P = 0.033) variations in the sensitivity and specificity of the EIAs and rapid test kits. Conclusions: The results from this study have clearly revealed the challenges of diagnosis of HBV infections in Nigeria. This study has also demonstrated that the sensitivity of most of the rapid test kits may not be adequate when compared with EIA for early detection of HBV infections. The implications of possible misdiagnosis on the various intervention strategies that rely predominantly on correct HBV status of an individual are enormous. Therefore, there is the need to further compliment the use of rapid test kits with EIAs for HBV control in Nigeria.Item Extending the utility of the WHO recommended assay for direct detection of enteroviruses from clinical specimen for resolving poliovirus co‑infection(BMC Research Notes, 2018) Faleye, T. O. C; Adewumi, M. O.; Ozegbe, N. P.; Ogunsakin, O. E.; Ariyo, G.; Adeshina, F. W.; Ogunga, O. S.; Oluwadare, S. D.; Adeniji, J. A.Objectives: In a polio-free world there might be reduced funding for poliovirus surveillance. There is therefore the need to ensure that enterovirologist globally, especially those outside the global polio laboratory network, can participate in poliovirus surveillance without neglecting their enterovirus type of interest. To accomplish this, assays are needed that allow such active participation. Results: In this study we describes a sensitive and specific utility extension of the recently recommended WHO RT-snPCR assay that enables independent detection of the three poliovirus types especially in cases of co-infection. More importantly, it piggy-backs on the first round PCR product of the WHO recommended assay and consequently ensures that enterovirologists interested in nonpolio enteroviruses can continue their investigations, and contribute significantly and specifically to poliovirus surveillance, by using the excess of their first round PCR product.Item The fallacy of identification by neutralization in the light of non-cytopathic effect producing enterovirus strains(SCIENCEDOMAIN International, 2017) Adewumi, M. O.; Faleye, T. O. C.; Adeniji, J. A.We describe the characterization of an enterovirus isolate recovered from untreated raw sewage in Ibadan, southwest Nigeria in 2010. The isolate was neutralized by specific antisera and consequently identified as Echovirus 7 (E7). Subsequent molecular characterization showed the isolate to be a mixture of E7 and Coxsackievirus A24 (CV-A24) thereby suggesting the CV-A24 strain to be non-cytopathic effect producing. It is therefore crucial that identities of enterovirus strains determined by neutralization assay be verified by molecular characterization to ensure they do not have any non-cytopathic effect producing strain(s) lurking unnoticed.Item Isolation and Identification of Enteroviruses from Sewage and Sewage-Contaminated Water Samples from Ibadan, Nigeria, 2012-2013(SciTechnol, 2017) Adeniji, J. A.; Adewale, A. O.; Faleye, T. O. C.; Adewumi, M. O.In 2010, we described sewage contaminated water (SCW) bodies that consistently yielded enteroviruses (EVs) in enterovirus surveillance (ES) sites in Lagos, Nigeria. By 2012, we demonstrated the presence and circulation of Wild Poliovirus 3 (WPV3) in these ES sites. Here we describe ES sites that consistently yield EVs in Ibadan metropolis southwest Nigeria. Twenty-five ES samples were collected by grab method from nine sites between October, 2012 and March, 2013. Samples were concentrated and four (RD, HEp2C, MCF-7 and L20B) different cell lines used for virus isolation from the concentrates. Isolates were subjected to RNA extraction, cDNA synthesis, PanEnterovirus 5l-UTR and VP1 assays. Unidentifiable isolates were further subjected to species-specific RTPCR assays. Amplicons were sequenced, isolates identified and subjected to phylogenetic analysis. Twenty-five isolates were recovered from 8 (32%) of the samples collected. Twenty-three of the isolates were identified as EVs by the PanEntero5l-UTR assay. Thirteen (57%) of the 23 EVs were positive for the VP1 assay, and identified as Coxsackievirus B3 (CVB3) (1 isolate), CVB6 (1 isolate), E6 (2 isolates), E7 (5 isolates), E11 (1 isolate), E12 (1 isolate) and E13 (2 isolates). None and 2 (25%) of the remaining isolates were positive for the EV-B and EV-C assays, respectively. The 2 EV-C positive enteroviruses were isolated on MCF-7. This study describes three very productive ES sites, and documents the presence of CVB3, CVB6, E6, E7, E11, E12 and, E13 in Ibadan, Nigeria. Including other cell lines in EV isolation protocols can broaden the diversity of EV types recoverable.