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Anejo-Okopi J, Okeke E, Davwar PM, Onwuamah C, Onywera H, Omaiye P, Duguru M, Okojokwu OJ, Ujah OI, Jonathan B, George CA, Crown RS, Yakubu FB, Sokei JO, Okoli LC, Audu O, Inzaule SC, Abah IO, Agaba P, Agbaji OO, Sagay AS, Hawkins C. Molecular detection of hepatitis B virus genotype E with immune escape mutations in chronic hepatitis B patients on long-term antiviral therapy in Jos, Nigeria. Afr J Lab Med 2022; 11:1677. [PMID: 36337771 PMCID: PMC9634812 DOI: 10.4102/ajlm.v11i1.1677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Background Previous studies in Nigeria have reported the presence of hepatitis B virus (HBV) genotype E and the availability of immune escape mutants. There is a paucity of data on chronic patients on long-term antiviral therapy for HBV infection. Objective This study assessed HBV genotypes and drug resistance variants among patients with chronic HBV infection receiving tenofovir in Jos, Nigeria. Methods This cross-sectional study consecutively enrolled 101 patients (51 with HIV/HBV co-infection and 50 with HBV infection only) on antiviral therapy from February 2018 to May 2019 at four hospitals in Jos, Nigeria. DNA quantification of HBV was performed on all samples; 30 samples with detectable viral load were selected for genotyping using Sanger sequencing by targeting the full-length sequences of reverse transcriptase gene of the HBV genome. Phylogenetic analysis was performed with reference sequences from GenBank. Escape mutant and drug resistance analysis were performed using HBV drug resistance interpretation and Geno2pheno. Results Only 30 (29.7%) of the 101 study participants had detectable HBV DNA. Of these, six (20.0%) isolates were successfully amplified and sequenced. The identified genotype was E, including escape mutations L127R (16.7%) and G145A (16.7%). Conclusion This study revealed exclusive dominance of genotype E in Nigeria. The S gene mutations G145A and L271R are known to be associated with modified antigenicity and impaired serologic assays, which may cause false negatives in the detection of anti-HBV surface antigen. The presence of mutants that are associated with vaccine immune escape may also have diagnostic and vaccine immune response implications.
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Affiliation(s)
- Joseph Anejo-Okopi
- Department of Microbiology, University of Jos, Jos, Nigeria
- AIDS Prevention Initiative in Nigeria, Jos University Teaching Hospital, Jos, Nigeria
| | - Edith Okeke
- Department of Internal Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Pantong M. Davwar
- Department of Internal Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Chika Onwuamah
- Center for Human Virology and Genomics Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Harris Onywera
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Research, Innovations, and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya
| | - Patience Omaiye
- Department of Internal Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Mary Duguru
- Department of Internal Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | | | - Otobo I. Ujah
- Department of Community and Family Health, College of Public Health, University of South Florida, Tampa, Florida, United States
| | - Bulus Jonathan
- Department of Family Medicine, Plateau State Specialist Hospital, Jos, Nigeria
| | - Chima A. George
- Department of Family Medicine, Bingham University Teaching Hospital, Jos, Nigeria
| | - Ramyil S. Crown
- Department of Medical Microbiology and Parasitology, Bingham University Teaching Hospital, Jos, Nigeria
| | - Fiyaktu B. Yakubu
- Department of Chemical Pathology, Jos University Teaching Hospital, Jos, Nigeria
| | - Judith O. Sokei
- Center for Human Virology and Genomics Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Leona C. Okoli
- Center for Human Virology and Genomics Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Onyemocho Audu
- Department of Epidemiology and Community Health, Benue State University, Makurdi, Nigeria
| | - Seth C. Inzaule
- Department of HIV and Global Hepatitis Program, World Health Organization, Geneva, Switzerland
| | - Isaac O. Abah
- Department of Pharmacology, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Patricia Agaba
- AIDS Prevention Initiative in Nigeria, Jos University Teaching Hospital, Jos, Nigeria
- Department of Family Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Oche O. Agbaji
- Department of Internal Medicine, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Atiene S. Sagay
- Department of Obstetrics and Gynaecology, University of Jos, Jos University Teaching Hospital, Jos, Nigeria
| | - Claudia Hawkins
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
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Onwuamah CK, Okwuraiwe AP, Ahmed RA, Sokei JO, Ponmak J, Okoli LC, Kagurusi BA, Anejo-Okopi J. Laboratory Optimization Tweaks for Sanger Sequencing in a Resource-Limited Setting. J Biomol Tech 2021; 31:157-164. [PMID: 33100921 DOI: 10.7171/jbt.20-3104-006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Despite various challenges that hinder the implementation of high-tech molecular methods in resource-limited settings, we have been able to implement and achieve International Organization for Standardization 15189:2012 accreditation for genotypic HIV drug resistance testing in our facility. At the Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Nigeria has recorded a high sequencing success rate and good quality sequence data. This was achieved by optimizing laboratory processes from 2008 to the current date. We have optimized sample preparation, RT-PCR, several post-PCR processes, and the cycle sequencing to improve the sensitivity of amplification even with limited plasma samples and low viral copy numbers. The optimized workflow maximizes output, minimizes reagent wastage, and achieves substantial cost savings without compromising the quality of the sequence data. Our performance at our last external quality assurance program is a testimonial to the efficiency of the workflow. For the 5-sample panel, each with 67-68 mutation points evaluated, we scored 100% for all 5 specimens. Our optimized laboratory workflow is thus documented to support laboratories and to help researchers achieve excellent results the first time and eliminate contamination while minimizing the wastage of costly sequencing reagents.
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Affiliation(s)
- Chika K Onwuamah
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Azuka P Okwuraiwe
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Rahaman A Ahmed
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Judith O Sokei
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Jamda Ponmak
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | - Leona C Okoli
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba 101212, Lagos, Nigeria
| | | | - Joseph Anejo-Okopi
- AIDS Prevention Initiative in Nigeria, Jos, University Teaching Hospital, Jos, Nigeria
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Okwuraiwe AP, Onwuamah CK, Shaibu JO, Amoo SO, Ige FA, James AB, Okoli LC, Ahmed AR, Ponmak J, Sokei JO, Akanmu S, Salako BL, Audu RA. Low level SARS-CoV-2 RNA detected in plasma samples from a cohort of Nigerians: Implications for blood transfusion. PLoS One 2021; 16:e0252611. [PMID: 34111179 PMCID: PMC8191972 DOI: 10.1371/journal.pone.0252611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/18/2021] [Indexed: 01/12/2023] Open
Abstract
The present global pandemic triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has lingered for over a year in its devastating effects. Diagnosis of coronavirus disease 2019 (COVID-19) is currently established with a polymerase chain reaction (PCR) test by means of oropharyngeal-, nasopharyngeal-, anal-swabs, sputum and blood plasma. However, oral and nasal swabs are more commonly used. This study, therefore, assessed sensitivity and specificity of plasma as a diagnostic in comparison with a combination of oral and nasal swab samples, and the implications for blood transfusion. Oropharyngeal (OP) and nasopharyngeal (NP) swab samples were obtained from 125 individuals suspected to have COVID-19 and stored in viral transport medium (VTM) tubes. Ten millilitres of blood samples in EDTA were also obtained by venepuncture and spun to obtain plasma. Viral RNA was obtained from both swabs and plasma by manual extraction with Qiagen QIAamp viral RNA Mini Kit. Detection was done using a real time fluorescent RT-qPCR BGI kit, on a QuantStudio 3 real-time PCR instrument. Average age of study participants was 41 years, with 74 (59.2%) being male. Out of the 125 individuals tested for COVID-19, 75 (60%) were positive by OP/NP swab. However, only 6 (4.8%) had a positive plasma result for COVID-19 with median Ct value of 32.4. Sensitivity and specificity of RT-PCR SARS-CoV-2 test using plasma was 8% and 100% respectively. There was no false positive recorded, but 69 (55.2%) false negatives were obtained by plasma. SARS-CoV-2 viral RNA was detected, albeit low (4.8%) in plasma. Plasma is likely not a suitable biological sample to diagnose acute SARS-CoV-2 infection. The implication of transfusing blood in this era of COVID-19 needs further investigations.
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Affiliation(s)
- Azuka Patrick Okwuraiwe
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- * E-mail: ,
| | - Chika Kingsley Onwuamah
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Joseph Ojonugwa Shaibu
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samuel Olufemi Amoo
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Fehintola Anthonia Ige
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Leona Chika Okoli
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Abul-Rahman Ahmed
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria
| | - Jamda Ponmak
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Federal College of Veterinary and Medical Laboratory Technology, Vom, Plateau State, Nigeria
| | - Judith O. Sokei
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Sulaimon Akanmu
- Department of Haematology, College of Medicine, University of Lagos, Idi-Araba, Lagos, Nigeria
| | - Babatunde Lawal Salako
- Clinical Sciences Division, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosemary Ajuma Audu
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
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Onwuamah CK, Okwuraiwe AP, Salu OB, Shaibu JO, Ndodo N, Amoo SO, Okoli LC, Ige FA, Ahmed RA, Bankole MA, Sokei JO, Mutiu BP, Ayorinde J, Saka BA, Obiekea C, Mba N, Adegbola RA, Omilabu S, Ihekweazu C, Salako BL, Audu R. Comparative performance of SARS-CoV-2 real-time PCR diagnostic assays on samples from Lagos, Nigeria. PLoS One 2021; 16:e0246637. [PMID: 33539485 PMCID: PMC7861429 DOI: 10.1371/journal.pone.0246637] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/23/2021] [Indexed: 11/19/2022] Open
Abstract
A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors. We now report the comparative performance of five real-time diagnostic assays. Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria. The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit. All five assays are one-step reverse transcriptase real-time PCR assays. Testing was done according to each assay’s manufacturer instructions for use using real-time PCR platforms. 63 samples were tested using the five qPCR assays, comprising of 15 negative samples, 15 positive samples (Ct = 16–30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36–41. All assays detected all high positive samples correctly. Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample. The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value. The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected. Comparative assays’ performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value.
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Affiliation(s)
- Chika Kingsley Onwuamah
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
- * E-mail:
| | - Azuka Patrick Okwuraiwe
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Olumuyiwa B. Salu
- Department of Medical Microbiology and Parasitology, Centre for Human & Zoonotic Virology, College of Medicine, University of Lagos, Idi-Araba, Lagos State, Nigeria
| | - Joseph O. Shaibu
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Nnaemeka Ndodo
- National Reference Laboratory, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Samuel O. Amoo
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Leona C. Okoli
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Fehintola A. Ige
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Rahaman A. Ahmed
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Munir Akinwale Bankole
- Lagos State Biosecurity and Biobank Laboratory, Mainland Hospital, Lagos State Ministry of Health, Lagos, Lagos State, Nigeria
| | - Judith O. Sokei
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Bamidele Paul Mutiu
- Lagos State Biosecurity and Biobank Laboratory, Mainland Hospital, Lagos State Ministry of Health, Lagos, Lagos State, Nigeria
| | - James Ayorinde
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Babatunde Akeem Saka
- Global Emerging Pathogens Treatment Consortium (GET), Yaba, Lagos State, Nigeria
| | - Celestina Obiekea
- National Reference Laboratory, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Nwando Mba
- National Reference Laboratory, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Richard A. Adegbola
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Sunday Omilabu
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
- Department of Medical Microbiology and Parasitology, Centre for Human & Zoonotic Virology, College of Medicine, University of Lagos, Idi-Araba, Lagos State, Nigeria
| | - Chikwe Ihekweazu
- Director-General’s Office, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Babatunde Lawal Salako
- Director-General’s Office, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Rosemary Audu
- Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
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