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Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T. An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.19.24301519. [PMID: 38293032 PMCID: PMC10827254 DOI: 10.1101/2024.01.19.24301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
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Affiliation(s)
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Wonderful Choga
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - San E. James
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Stephanie van Wyk
- Collaborating Centre for Optimizing Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, South Africa
| | - Jennifer Giandhari
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
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Albshri M, Manikandan P, Allahyani M, Aljuaid A, Almehmadi MM, Alzabeedi K, Babalgaith M, Alghamdi M, Alharbi F, Alhazmi M. The Prevalence of Transfusion-Transmitted Diseases Among Blood Donors in the Central Blood Bank in Makkah, Saudi Arabia. Cureus 2023; 15:e48881. [PMID: 38106789 PMCID: PMC10724763 DOI: 10.7759/cureus.48881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Background This study aimed to analyze the health and demographic characteristics of blood donors in Makkah, Saudi Arabia, and assess the prevalence and correlation of two markers related to hepatitis B infection: hepatitis B virus surface antigen (HBsAg) and anti-hepatitis B virus surface antibody (HBsAb). Materials and methods The study used a retrospective design and collected data from the Central Blood Bank in Makkah, Saudi Arabia, in 2022. The sample size was 7,875 blood donors. The study used various methods, such as serological testing, nucleic acid testing (NAT), and statistical analysis. The data were analyzed using Pearson correlation to examine the relationships between different variables. Results The predominant age group was 29-39 years, accounting for 46.9% of the total donors. In terms of blood types, O+ve was the most common, representing 40.3% of the donors. The investigation into infectious markers revealed overall low levels of reactivity among donors. For HBsAg, a marker of active hepatitis B infection, only 0.36% of the units were reactive. Conversely, the anti-HBsAb, which indicates immunity to hepatitis B, was reactive in 6.83% of the units. The correlation analysis illuminated some critical relationships. The total number of units tested had a statistically significant, albeit weak, positive relationship with HBsAg reactivity, shown by a Pearson correlation coefficient of 0.030 and a p-value of 0.008. Conversely, the total number of units tested and anti-HBsAb reactivity showed a moderate negative correlation, with a Pearson correlation coefficient of -0.437 and a p-value of less than 0.001. However, no significant correlation was identified between HBsAg and anti-HBsAb reactivity, indicating that active infection and immunity status might not be directly linked. Conclusion This extensive study provides in-depth insights into the sociodemographic characteristics of blood donors and the prevalence of key infectious markers within this population. It underlines the imperative of rigorous screening of blood units, particularly given the low immunity levels to hepatitis B identified. Also, the study showed the importance of screening blood units and vaccinating people against hepatitis B. It also suggested the need for more research on blood safety and infection-immunity relationships.
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Affiliation(s)
| | - Palanisamy Manikandan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, SAU
| | - Mamdouh Allahyani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, SAU
| | - Abdulelah Aljuaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, SAU
| | - Mazen M Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, SAU
| | - Kamal Alzabeedi
- Department of Clinical Biochemistry, The Regional Laboratory, Makkah, SAU
| | - Mohamed Babalgaith
- Central Blood Bank, General Directorate of Health Affairs, Makkah Region, Makkah, SAU
| | - Mosa Alghamdi
- Central Blood Bank, General Directorate of Health Affairs, Makkah Region, Makkah, SAU
| | - Faris Alharbi
- Central Blood Bank, General Directorate of Health Affairs, Makkah Region, Makkah, SAU
| | - Mohammed Alhazmi
- Central Blood Bank, General Directorate of Health Affairs, Makkah Region, Makkah, SAU
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Abu N, Mohd Bakhori N, Shueb RH. Lateral Flow Assay for Hepatitis B Detection: A Review of Current and New Assays. MICROMACHINES 2023; 14:1239. [PMID: 37374824 DOI: 10.3390/mi14061239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
From acute to chronic hepatitis, cirrhosis, and hepatocellular cancer, hepatitis B infection causes a broad spectrum of liver diseases. Molecular and serological tests have been used to diagnose hepatitis B-related illnesses. Due to technology limitations, it is challenging to identify hepatitis B infection cases at an early stage, particularly in a low- and middle-income country with constrained resources. Generally, the gold-standard methods to detect hepatitis B virus (HBV) infection requires dedicated personnel, bulky, expensive equipment and reagents, and long processing times which delay the diagnosis of HBV. Thus, lateral flow assay (LFA), which is inexpensive, straightforward, portable, and operates reliably, has dominated point-of-care diagnostics. LFA consists of four parts: a sample pad where samples are dropped; a conjugate pad where labeled tags and biomarker components are combined; a nitrocellulose membrane with test and control lines for target DNA-probe DNA hybridization or antigen-antibody interaction; and a wicking pad where waste is stored. By modifying the pre-treatment during the sample preparation process or enhancing the signal of the biomarker probes on the membrane pad, the accuracy of the LFA for qualitative and quantitative analysis can be improved. In this review, we assembled the most recent developments in LFA technologies for the progress of hepatitis B infection detection. Prospects for ongoing development in this area are also covered.
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Affiliation(s)
- Norhidayah Abu
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Advanced Materials Research Centre (AMREC), SIRIM Berhad, Lot 34, Jalan Hi-Tech 2/3, Kulim Hi-Tech Park, Kulim 09000, Kedah, Malaysia
| | - Noremylia Mohd Bakhori
- Advanced Materials Research Centre (AMREC), SIRIM Berhad, Lot 34, Jalan Hi-Tech 2/3, Kulim Hi-Tech Park, Kulim 09000, Kedah, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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