{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:08:06Z","timestamp":1772168886865,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.132498.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T00:00:00Z","timestamp":1755734400000}},{"DOI":"10.12688\/f1000research.132498.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T00:00:00Z","timestamp":1755734400000}},{"DOI":"10.12688\/f1000research.132498.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T00:00:00Z","timestamp":1755734400000}}],"reference-count":46,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T00:00:00Z","timestamp":1755734400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005274","name":"North-West University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005274","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001321","name":"National Research foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Organisation for Women in Science for the Developing Worlds"},{"name":"South African Centre for Epidemiological Modelling"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    Background Co-infection of hepatitis B virus (HBV) and human immunodeficiency virus (HIV) has an impact on high HBV replication and progression to liver cancer. These may lead to cross-resistance of drugs due to natural mutations or therapeutic pressure. These require continuous monitoring of HBV variants for better diagnosis and treatment strategies. Methods Convenience sampling was used to collect fifty archival sera from Inkosi Albert Luthuli Central Hospital. Sera were subjected to HBsAg screening using ELISA, DNA extraction, PCR amplification, Sanger sequencing, genotype prediction and mutation analysis. Results Of the 50 samples, 86% (43\/50) were HBsAg positive; 82% (41\/50) PCR positive with 92% (38\/41) sequenced and only 26 sequences were subjected to molecular characterization. The HBV sequences showed similarity to genotype A (73% [19\/26]), genotypes G (5% [3\/26]) and genotype C (15% [4\/26]). Prevalence of the mutations in the surface region was (47% [18\/38]); including diagnostic failure (K122R and T143S) and immune escape mutations (P127T, G145R, S207N, Y200T, E164D, Y206H and L209V). The mutations in the RT were at (36% [14\/38]) with drug resistance mutations (DRM) at (50% [7\/14]). Mutations showed resistance to lamivudine (LMV) at (35% [5\/14]), telbivudine (LdT) at (29% [4\/14]), (14% [2\/14]) for entecavir (ETV) and (21% [3\/14]) for adefovir (ADV). One sample had a combination of L180M, M204V, S202K, and M250I mutations. Conclusions Our findings highlight the prevalence of HBV genotype A in HIV-infected patients in South Africa. The study provides evidence of mutations linked to immune evasion and drug resistance; this infers that these mutations may have clinical implications for the diagnosis and treatment of HBV in HBV\/HIV co-infected individuals. Further\n                    <ns3:italic>in vitro<\/ns3:italic>\n                    studies must be conducted to explore the impact of the identified mutation on the surface protein expression during diagnosis; phenotype impact of the mutant virus towards the antiviral drugs.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.132498.4","type":"journal-article","created":{"date-parts":[[2025,8,21]],"date-time":"2025-08-21T14:10:06Z","timestamp":1755785406000},"page":"1232","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Investigation of mutations in the partial sequences of the surface and polymerase genes of hepatitis B virus associated with immune escape and drug resistance in HIV-infected patients"],"prefix":"10.12688","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7008-157X","authenticated-orcid":false,"given":"Lorato","family":"Modise","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nomathamsanqa","family":"Sithebe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1551-3314","authenticated-orcid":false,"given":"Hazel","family":"Mufhandu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2025,8,21]]},"reference":[{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.3390\/v13071273","article-title":"Detection of Q129H Immune Escape Mutation in Apparently Healthy Hepatitis B Virus Carriers in Southwestern Nigeria.","volume":"13","author":"O Adesina","year":"2021","journal-title":"Viruses."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1014-1023","DOI":"10.1002\/hep4.1118","article-title":"HBV reactivation in allogeneic stem cell transplant recipients: Risk factors, outcome, and role of hepatitis B virus mutations.","volume":"1","author":"O Anastasiou","year":"2017","journal-title":"Hepatol. 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We appreciate your reviews and recommendations, which have greatly enhanced the manuscript. We have carefully considered all your comments and revised them accordingly.&nbsp; \n<b>&nbsp;Specific reviewer comment<\/b> HBsAg assay \u2013 COV needs defining at first use. \uf0a7&nbsp;&nbsp; &nbsp;Response: Cut off value (COV) has been defined at first use. Reviewer comments Baseline demographic data \u2013 the median age is presented, and the range is, but I can\u2019t see the standard deviation, despite the authors stating it in the paragraph. Table 1 should be revised to be more informative (i.e. present proportions) \u2013 if all individuals were black Africans and HIV positive, this is not particularly useful information to present. I would encourage the authors to revise the data in table 1 to make it more informative, such as is there any data on their HIV treatment? Response:&nbsp; \uf0a7&nbsp;&nbsp; &nbsp;Since all the samples were from the same group, the information on the ethnicity of Black African has been deleted from the description in Table 1.  \uf0a7&nbsp;&nbsp; &nbsp;The description of the statistical analysis has been revised in the text and Table 1 to be specific to the standard deviation. The median age is presented with the interquartile range (IQR) the range and did not present the standard deviation because the data in not normally distributed and there is poor statistical power. Table 1 presents the demographic data collected from the participants which includes the age, sex and test done before. The data is already presented in proportions expressed by either a count by the total number and the proportion as a percentage. The age is already presented in proportions as indicated in the text (n=19\/50). \uf0a7&nbsp;&nbsp; &nbsp;The results are on demographic data which is the primary data on the participants HIV status. We can only report on the data that was collected and available for this study, The data on the treatment history of the participants specifically HIV treatment is not available hence, it is not included. This is highlighted in the limitations section.&nbsp; Reviewer comments Phylogenetic analysis \u2013 the authors state that sequences were obtained for 38\/41 samples that were PCR positive but only analysed n=26 sequences. Why were 12 sequences excluded from the analysis? The sequences analysed are relatively short, and as the authors state, this can affect the clustering, but the phylogenetic analysis presented remains very problematic for genotyping. The reference sequences do not cluster by genotype, making it difficult to use the tree to confidently genotype the sequences presented. Whilst the authors checked a few gtA the sequences with geno2pheno, I am puzzled by the interpretation of the other sequences (assumed not to be gtA). A few sequences do not clearly cluster with any of the reference sequences, and the authors describe these as \u201c24% (N=7\/26) as genotypes B, C, D, E, F and G\u201d, which is difficult to interpret. It is also a little unclear why sequences at the bottom of the tree \u2018Q6P7, Q17P7, and Q42P7\u2019 were decided to be closer to genotype H, D, B, and E than to genotype A without presenting bootstrapping data? This analysis needs revising, and perhaps the authors should consider a maximum-likelihood analysis as it may be more discriminatory for genotyping than the approach currently used. Alternatively, they may consider using geno2pheno to genotype their sequences, Response: \uf0a7&nbsp;&nbsp; &nbsp;The 12 sequences excluded from the analysis had poor sequence reads on the chromatogram, and they could not form the proper consensus sequences thus they were not considered for the analysis.&nbsp;  \uf0a7&nbsp;&nbsp; &nbsp;The genotyping of the sequences is revised with the use of geno2pheno software as advised and the data is presented in a table instead of a phylogenetic tree (Table 2). The sequences were uploaded onto the geno2pheno software and compared against standard (wildtype) genome with the highest nucleotide similarity to the study sequences.&nbsp;  \uf0a7&nbsp;&nbsp; &nbsp;The sequences that identify as genotype A have been clarified through revision. Additionally, the 24% (N=7\/26) that represent a combination of other genotypes (C and G) have been broken down to demonstrate the individual and specific genotypes C and G; 12% (N=3\/26) represent genotypes G, and 15% (N=4\/26) represent genotype C.  Association of the mutations \uf0a7&nbsp;&nbsp; &nbsp;Data on the association of mutations on the surface and polymerase regions has been removed due to the poor statistical power and statistical association. We focused on reporting the data on the mutations associated with drug resistance with a focus on their frequency as depicted in Table 3.  Reviewer comment The discussion is too long and should be more concise \u2013 the discussion of the wider literature on drug resistant mutations could be reduced. Some contexts may also be useful to discuss \u2013 these samples were taken from HIV-positive individuals, so were any of them on treatment for their HIV infections and were these treatments active against HBV also?  Response: \uf0a7&nbsp;&nbsp; &nbsp;The discussion has been summarised. The data on the treatment history of the participants specifically HIV treatment is not available hence, it is not included. Secondly, we don\u2019t know if HIV treatments is active against HBV because we do not have the information currently available to support that. However, we know the treatment history of HBV and that the participants are na&iuml;ve to HBV ARTs. We have also added information on the results interpretation of the mutations in HBV patients that are HBV treatment na&iuml;ve (last paragraph under the discussion section). \uf0a7&nbsp;&nbsp; &nbsp;Results \uf0a7&nbsp;&nbsp; &nbsp;Table 1: The median age was 33 years [IQR: 18-55] and there was no statistical difference on age between the genders with p=0.8. \uf0a7&nbsp;&nbsp; &nbsp;92% (N=38\/41) sequence products could be obtained by Sanger sequencing with only 26\/38 sequences used to perform genotyping, that is, 12 sequences were excluded due to the poor quality of their sequence reads. \uf0a7&nbsp;&nbsp; &nbsp;The genotype of the sequences was confirmed by depositing nucleotide sequences into the Genotype2pheno database, which showed that most of the nucleotide sequences had homology with genotype A at 73% (N=19\/26), genotype G at 12% (N=3\/26), and genotype C at 15% (N=4\/26) (Table 2). \uf0a7&nbsp;&nbsp; &nbsp;The study sequences with the highest similarity to Genotype A were: (Q4P7 and Q7P7 to KX520697.1|South Africa; Q9P7 to U87728.1|South Africa; Q27P7 to AY233274.1|South Africa. &nbsp;Reference sequence of AY233277.1|South Africa had between 97%-99% similarity to fifteen sequences (Q5P7, Q8P7, Q10P7, Q13P7, Q18P7, Q19P7, Q20P7, Q21P7, Q22P7, Q23P7, Q24P7, Q26P7, Q27P7, Q29P7 and Q39P7). &nbsp;The sequences Q6P7, Q17P7 and Q42P7 had similarity to genotype G (EU694179.1|South Africa; sequences Q11P7, Q43P7, Q44P7 and Q45P7 showed similarity to genotype C AB562444.1|Vietnam (Table 2). &nbsp;Sub-genotypes of the sequences were confirmed by depositing nucleotides sequences into the Genotype2pheno database. The results retrieved from the Geno2Pheno database had a 96.85%-99.0% percentage of similarity to sub-genotype A1 for the genotype A sequences only. Discussion Discussion on the interpretation of mutations in treatment-na&iuml;ve has been revised. This includes clarity on the impact of the mutations on the treatment\u2019s status of the participants. We also discuss how the study cannot answer on whether the treatment was active against HBV (see the last paragraph under the discussion section). However, we made recommendation that further in vitro studies must investigate the mechanism of action by DRMs on ARTs in vitro assays (last sentence under conclusion). Additional correction and response Reference removed from the list&nbsp; 1. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980; 16(2): 111\u2013120. PubMed Abstract|Publisher Full Text. 2. Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 2004; 5(2): 150\u2013163. PubMed Abstract|Publisher Full Text. 3. Malik A, Singhal DK, Albanyan A, et al.: Hepatitis B virus gene mutations in liver diseases: a report from New Delhi. PLoS One. 2012; 7(6): e39028. PubMed Abstract|Publisher Full Text|Free Full Text. 4. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987; 4(4): 406\u2013425. . Updated references and citation 1.&nbsp;&nbsp; &nbsp;Belyhun, Yeshambel, Melanie Maier, and Uwe Gerd Liebert. &quot;HIV therapy with unknown HBV status is responsible for higher rate of HBV genome variability in Ethiopia.&quot; Antiviral therapy 22.2 (2017): 97-111. 2.&nbsp;&nbsp; &nbsp;Geno2pheno. HBV genotyping 2023 [Available from: https:\/\/hbv.geno2pheno.org\/. 3.&nbsp;&nbsp; &nbsp;World Health Organization. Guidelines on Hepatitis B and C Testing 2017 update (available at https:\/\/apps.who.int\/iris\/bitstream\/handle\/10665\/254621\/9789241549981- eng.pdf.).","URL":"https:\/\/f1000research.com\/articles\/12-1232\/v4#referee-comment-13545","order":2,"name":"referee-comment-13545","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.179250.r386531, Anthony C. Ike, University of Nigeria, Nsukka, Enugu, 14 Jun 2025, version 3, 3 approved with reservations, 1 not approved","URL":"https:\/\/f1000research.com\/articles\/12-1232\/v3#referee-response-386531","order":3,"name":"referee-response-386531","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.186606.r407676, Tesfaye Gelanew, Armauer Hansen Research Institute, Addis Ababa, Addis Ababa, 11 Sep 2025, version 4, indexed","URL":"https:\/\/f1000research.com\/articles\/12-1232\/v4#referee-response-407676","order":4,"name":"referee-response-407676","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by funds from the North-West University, National Research foundation Innovation bursary (Grant No: SFH150727131319), Health and Welfare Sector Education and Training Authority, South African Centre for Epidemiological Modelling and Analysis and Organisation for Women in Science for the Developing Worlds (Grant No: 3240287283). These funding agencies were not involved and responsible in the study design and writing of the thesis and manuscript. The Authors in this study are solely responsible for the content and not the funding agencies involved. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}