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Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
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Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
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2
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Begovac J, Romih Pintar V, Vrsaljko N, Močibob L, Bogdanić N, Zekan Š, Đaković Rode O. Incidence, risk factors, and clinical findings of syphilis among men living with HIV in Croatia during the COVID-19 pandemic. Sci Rep 2023; 13:11784. [PMID: 37479770 PMCID: PMC10361976 DOI: 10.1038/s41598-023-38807-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023] Open
Abstract
We conducted a nationwide longitudinal observational study to estimate the incidence of syphilis in a cohort of male persons living with HIV (MLWH) in Croatia in the pre-COVID-19 and COVID-19 years. Data were reviewed and extracted from the clinical database. We analyzed 1187 MLWH (≥ 18 years) in care in Croatia from 2018 to 2021 and used Poisson regression to calculate rates. We observed a 91.4% increase in incidence between 2019 and 2020; the overall rate was 6.0/100 person-years, and the annual rate ranged from 3.3/100 person-years in 2018 to 9.3/100 person-years in 2021. We found higher rates in men who have sex with men, MLWH with a baseline history of syphilis, MLWH with a more recent HIV diagnosis, and a lower rate in those who had clinical AIDS. The rate of syphilis serological testing was 3.5% lower in 2020 compared to 2019. Recurrent syphilis was more likely asymptomatic compared to the first episodes. In conclusion, during the COVID-19 epidemic years, there was a huge increase in syphilis. Results highlight the need for enhanced and novel prevention interventions.
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Affiliation(s)
- Josip Begovac
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia.
- School of Medicine, University of Zagreb, Zagreb, Croatia.
| | - Vanja Romih Pintar
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Nina Vrsaljko
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Loris Močibob
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Nikolina Bogdanić
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
| | - Šime Zekan
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Oktavija Đaković Rode
- University Hospital for Infectious Diseases "Dr. Fran Mihaljević", Zagreb, Croatia
- School of Dental Medicine, University of Zagreb, Zagreb, Croatia
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Alexiev I, Shankar A, Pan Y, Grigorova L, Partsuneva A, Dimitrova R, Gancheva A, Kostadinova A, Elenkov I, Yancheva N, Grozdeva R, Strashimirov D, Stoycheva M, Baltadzhiev I, Doichinova T, Pekova L, Kosmidis M, Emilova R, Nikolova M, Switzer WM. Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012-2020). Viruses 2023; 15:v15040941. [PMID: 37112921 PMCID: PMC10146724 DOI: 10.3390/v15040941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988-2011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012-2020 using polymerase sequences from 1053 of 2010 (52.4%) antiretroviral therapy (ART)-naive individuals. Sequences were analyzed for DRM using the WHO HIV SDRM list implemented in the calculated population resistance tool at Stanford University. Genetic diversity was inferred using automated subtyping tools and phylogenetics. Cluster detection and characterization was performed using MicrobeTrace. The overall rate of SDRMs was 5.7% (60/1053), with 2.2% having resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 1.8% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 2.1% to protease inhibitors (PIs), and 0.4% with dual-class SDRMs. We found high HIV-1 diversity, with the majority being subtype B (60.4%), followed by F1 (6.9%), CRF02_AG (5.2%), A1 (3.7%), CRF12_BF (0.8%), and other subtypes and recombinant forms (23%). Most (34/60, 56.7%) of the SDRMs were present in transmission clusters of different subtypes composed mostly of male-to-male sexual contact (MMSC), including a 14-member cluster of subtype B sequences from 12 MMSC and two males reporting heterosexual contact; 13 had the L90M PI mutation and one had the T215S NRTI SDRM. We found a low SDRM prevalence amid high HIV-1 diversity among ART-naive patients in Bulgaria during 2012-2020. The majority of SDRMs were found in transmission clusters containing MMSC, indicative of onward spread of SDRM in drug-naive individuals. Our study provides valuable information on the transmission dynamics of HIV drug resistance in the context of high genetic diversity in Bulgaria, for the development of enhanced prevention strategies to end the epidemic.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anupama Shankar
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Alexandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Rusina Grozdeva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Mariana Stoycheva
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Ivan Baltadzhiev
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Tsetsa Doichinova
- Department of Infectious Diseases, Medical University, 5800 Pleven, Bulgaria
| | - Lilia Pekova
- Clinic of Infectious Diseases, Medical University, 6000 Stara Zagora, Bulgaria
| | - Minas Kosmidis
- Clinic of Infectious Diseases, Medical University, 9002 Varna, Bulgaria
| | - Radoslava Emilova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Maria Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - William M Switzer
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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HIV-1 subtype B spread through cross-border clusters in the Balkans: a molecular analysis in view of incidence trends. AIDS 2023; 37:125-135. [PMID: 36129113 DOI: 10.1097/qad.0000000000003394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To analyze phylogenetic relations and assess the role of cross-border clusters in the spread of HIV-1 subtype B across the Balkans, given the general trends of new HIV diagnoses in seven Balkan countries. DESIGN Retrospective phylogenetic and trend analysis. METHODS In-depth phylogenetic, phylodynamic and phylogeographic analysis performed on 2415 HIV-1 subtype B sequences from 1999 to 2019 using maximal likelihood and Bayesian methods. The joinpoint regression analysis of new HIV diagnoses by country and modes of transmission using 2004-2019 ECDC data. RESULTS Ninety-three HIV-1 Subtype B transmission clusters (68% of studied sequences) were detected of which four cross-border clusters (11% of studied sequences). Phylodynamic analysis showed activity of cross-border clusters up until the mid-2000s, with a subsequent stationary growth phase. Phylogeography analyses revealed reciprocal spread patterns between Serbia, Slovenia and Montenegro and several introductions to Romania from these countries and Croatia. The joinpoint analysis revealed a reduction in new HIV diagnoses in Romania, Greece and Slovenia, whereas an increase in Serbia, Bulgaria, Croatia and Montenegro, predominantly among MSM. CONCLUSION Differing trends of new HIV diagnoses in the Balkans mirror differences in preventive policies implemented in participating countries. Regional spread of HIV within the countries of former Yugoslavia has continued to play an important role even after country break-up, whereas the spread of subtype B through multiple introductions to Romania suggested the changing pattern of travel and migration linked to European integration of Balkan countries in the early 2000s.
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Tunc H, Dogan B, Darendeli Kiraz BN, Sari M, Durdagi S, Kotil S. Prediction of HIV-1 protease resistance using genotypic, phenotypic, and molecular information with artificial neural networks. PeerJ 2023; 11:e14987. [PMID: 36967989 PMCID: PMC10038082 DOI: 10.7717/peerj.14987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/12/2023] [Indexed: 03/29/2023] Open
Abstract
Drug resistance is a primary barrier to effective treatments of HIV/AIDS. Calculating quantitative relations between genotype and phenotype observations for each inhibitor with cell-based assays requires time and money-consuming experiments. Machine learning models are good options for tackling these problems by generalizing the available data with suitable linear or nonlinear mappings. The main aim of this study is to construct drug isolate fold (DIF) change-based artificial neural network (ANN) models for estimating the resistance potential of molecules inhibiting the HIV-1 protease (PR) enzyme. Throughout the study, seven of eight protease inhibitors (PIs) have been included in the training set and the remaining ones in the test set. We have obtained 11,803 genotype-phenotype data points for eight PIs from Stanford HIV drug resistance database. Using the leave-one-out (LVO) procedure, eight ANN models have been produced to measure the learning capacity of models from the descriptors of the inhibitors. Mean R2 value of eight ANN models for unseen inhibitors is 0.716, and the 95% confidence interval (CI) is [0.592-0.840]. Predicting the fold change resistance for hundreds of isolates allowed a robust comparison of drug pairs. These eight models have predicted the drug resistance tendencies of each inhibitor pair with the mean 2D correlation coefficient of 0.933 and 95% CI [0.930-0.938]. A classification problem has been created to predict the ordered relationship of the PIs, and the mean accuracy, sensitivity, specificity, and Matthews correlation coefficient (MCC) values are calculated as 0.954, 0.791, 0.791, and 0.688, respectively. Furthermore, we have created an external test dataset consisting of 51 unique known HIV-1 PR inhibitors and 87 genotype-phenotype relations. Our developed ANN model has accuracy and area under the curve (AUC) values of 0.749 and 0.818 to predict the ordered relationships of molecules on the same strain for the external dataset. The currently derived ANN models can accurately predict the drug resistance tendencies of PI pairs. This observation could help test new inhibitors with various isolates.
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Affiliation(s)
- Huseyin Tunc
- Department of Biostatistics and Medical Informatics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Berna Dogan
- Department of Medicinal Biochemistry, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Büşra Nur Darendeli Kiraz
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Murat Sari
- Department of Mathematics Engineering, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- Department of Pharmaceutical Chemistry, School of Pharmacy, Bahcesehir University, Istanbul, Turkey
| | - Seyfullah Kotil
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
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6
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Mortier V, Debaisieux L, Dessilly G, Stoffels K, Vaira D, Vancutsem E, Van Laethem K, Vanroye F, Verhofstede C. Prevalence and evolution of transmitted HIV drug resistance in Belgium between 2013 and 2019. Open Forum Infect Dis 2022; 9:ofac195. [PMID: 35794938 PMCID: PMC9251670 DOI: 10.1093/ofid/ofac195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/08/2022] [Indexed: 11/27/2022] Open
Abstract
Background To assess the prevalence and evolution of transmitted drug resistance (TDR) in Belgium, a total of 3708 baseline human immunodeficiency virus (HIV)-1 polymerase sequences from patients diagnosed between 2013 and 2019 were analyzed. Methods Protease and reverse-transcriptase HIV-1 sequences were collected from the 7 national Aids Reference Laboratories. Subtype determination and drug resistance scoring were performed using the Stanford HIV Drug Resistance Database. Trends over time were assessed using linear regression, and the maximum likelihood approach was used for phylogenetic analysis. Results A total of 17.9% of the patients showed evidence of TDR resulting in at least low-level resistance to 1 drug (Stanford score ≥15). If only the high-level mutations (Stanford score ≥60) were considered, TDR prevalence dropped to 6.3%. The majority of observed resistance mutations impacted the sensitivity for nonnucleoside reverse-transcriptase inhibitors (NNRTIs) (11.4%), followed by nucleoside reverse-transcriptase inhibitors (6.2%) and protease inhibitors (2.4%). Multiclass resistance was observed in 2.4%. Clustered onward transmission was evidenced for 257 of 635 patients (40.5%), spread over 25 phylogenetic clusters. Conclusions The TDR prevalence remained stable between 2013 and 2019 and is comparable to the prevalence in other Western European countries. The high frequency of NNRTI mutations requires special attention and follow-up. Phylogenetic analysis provided evidence for local clustered onward transmission of some frequently detected mutations.
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Affiliation(s)
- Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurent Debaisieux
- Aids Reference Laboratory, Université Libre de Bruxelles, CUB Hôpital Erasme, 1070 Brussels, Belgium
| | - Géraldine Dessilly
- Aids Reference Laboratory, Medical Microbiology Unit, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Karolien Stoffels
- Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium
| | - Dolores Vaira
- Aids Reference Laboratory, Centre Hospitalier Universitaire de Liège, 4000 Liège, Belgium
| | - Ellen Vancutsem
- Aids Reference Laboratory, Vrije Universiteit Brussel VUB, 1090 Brussels, Belgium
| | - Kristel Van Laethem
- Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, 3000 Leuven, Belgium Aids Reference Laboratory, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Fien Vanroye
- Aids Reference Laboratory, Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
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Abstract
HIV-1 is genetically heterogeneous, having different subtypes and circulating recombinant forms (CRFs). HIV-1 genotyping is used to determine drug resistance profiles and is based on the use of a mixture of consensus and degenerate primers targeting the pol gene. However, the use of this type of primers is associated with either PCR bias or PCR failure. Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) can detect and identify unknown and distantly related gene sequences by PCR. CODEHOPs designed using different HIV-1 subtypes and CRFs were evaluated for HIV-1 genotyping by Sanger and MinION sequencing. A total of 321 plasma samples were used for the validation of CODEHOP-mediated HIV-1 genotyping. CODEHOP-mediated PCR showed 100% sensitivity and specificity, with limits of detection and genotyping below 200 copies/ml. The head-to-head evaluation of CODEHOP-mediated PCR and standard PCR showed 97 to 98% and 82 to 84% PCR success rates, respectively. There was 100% agreement between the CODEHOP and the reference method in the drug resistance profiles determined by Sanger-based sequencing. Using MinION sequencing, the CODEHOP-mediated PCR scheme resulted in better depth of genome coverage and detection of more drug resistance variants in the protease and reverse transcriptase genes than the standard amplification scheme. The overall prevalences of drug resistance mutations were 17.1% in treatment-experienced patients and 1.2% in treatment-naive patients. They were mainly associated with resistance to reverse transcriptase inhibitors and were linked to virological failure and the patient’s treatment history. Findings from this study suggest that the performance of HIV-1 genotyping is improved by using CODEHOP-mediated PCR. IMPORTANCE HIV-1 drug resistance is the main cause of treatment failure. Regular surveillance of resistance-associated mutations in HIV-1 genomes is essential for the optimal management of HIV-1 infections. Due to HIV-1’s genetic diversity, different HIV-1 genotypes are circulating worldwide. Standard primers used in the amplification of HIV-1 RNA have not been designed to cover all HIV-1 genotypes and are the main cause of amplification and drug resistance test failure. In this study, new sets of PCR primers targeting the protease, reverse transcriptase, and integrase genes were designed using the CODEHOP approach. They were compared to primers recommended in part by WHO for drug resistance testing using in-house PCR. Unsuccessful HIV-1 RNA amplification was less likely to occur with CODEHOP primers, leading to fewer test failures and lower cost. Furthermore, CODEHOP primers were more effective than standard primers for the detection of minority resistant variants by MinION sequencing.
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8
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Zhang F, Liang B, Liang X, Lin Z, Yang Y, Liang N, Yang Y, Liang H, Jiang J, Huang J, Huang R, Zhong S, Qin C, Jiang J, Ye L, Liang H. Using Molecular Transmission Networks to Reveal the Epidemic of Pretreatment HIV-1 Drug Resistance in Guangxi, China. Front Genet 2021; 12:688292. [PMID: 34567064 PMCID: PMC8460771 DOI: 10.3389/fgene.2021.688292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction Pretreatment drug resistance (PDR) is becoming an obstacle to the success of ART. This study investigated the prevalence of PDR and the transmission clusters (TCs) of drug resistance mutations (DRMs) in two cities where drug abuse used to be high to describe the local HIV-1 transmission dynamics. Methods Plasma samples were obtained from 1,027 ART-naïve patients in Guangxi. Viral subtypes and DRMs were identified. Transmission network and related factors were also determined. Results A total of 1,025 eligible sequences were obtained from Qinzhou (65.8%) and Baise (34.2%) cities. The predominant HIV-1 genotype was CRF08_BC (45.0%), followed by CRF01_AE (40.9%). The overall prevalence of PDR was 8.3%, and resistance to NNRTI was the most common. Putative links with at least one other sequence were found in 543/1,025 (53.0%) sequences, forming 111 clusters (2–143 individuals). The most prevalent shared DRMs included V106I (45.35%), V179D (15.1%), and V179E (15.1%). Clusters related to shared DRMs were more frequent and larger in CRF08_BC. The prevalence of shared DRMs increased with time, while the proportion of PDR gradually decreased. Age > 50 years was associated with clustering. Subtype CRF08_BC was more likely to have DRMs, PDR propagation, and DRM sharing. Conclusion PDR prevalence is moderate in this region. The association between PDR and subtype CRF08_BC suggested that DRMs spreading from injection drug users (IDUs) to heterosexuals (HETs) might be the major source of PDR in this region. Our findings highlight the significance of continuous surveillance of PDR.
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Affiliation(s)
- Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Xu Liang
- Baise Center for Disease Control and Prevention, Baise, China
| | - Zhaosen Lin
- Qinzhou Center for Disease Control and Prevention, Qinzhou, China
| | - Yuan Yang
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Na Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yao Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Huayue Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiaxiao Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Rongye Huang
- Qinzhou Center for Disease Control and Prevention, Qinzhou, China
| | - Shanmei Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Cai Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China.,Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
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9
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Sno R, Labadie-Bracho MY, Grünberg MG, Adhin MR. First Assessment of Acquired HIV-1 Drug Resistance and Mutation Patterns in Suriname. AIDS Res Hum Retroviruses 2021; 37:557-565. [PMID: 33287618 DOI: 10.1089/aid.2020.0194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
HIV drug resistance testing is fundamental in clinical patient management, but data on HIV-1 drug-resistant mutations (DRMs) is scarce in the Caribbean and in Suriname limited to one survey on transmitted resistance. The aim of this study was to address this gap, to gain insight in acquired HIV drug resistance (ADR) prevalence and mutation patterns, and to improve HIV-1 treatment outcome of people living with HIV (PLHIV) in Suriname. A prospective cross-sectional study was conducted from July 2018 through January 2019 among treatment-experienced PLHIV (n = 72), with either treatment failure or antiretroviral therapy restart. Genotypic drug resistance testing was performed and DRM impact on drug effectiveness was examined. Genotypic drug resistance testing revealed 97.2% HIV-1 subtype B, 2.8% B/D recombinants and a ADR prevalence of 63.2% in treatment failure patients, with a predominance of nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations. The most common DRMs were M184V (23.6%) and K103N (18.8%). A high level of non-DRM polymorphisms was observed in both the reverse transcriptase (RT) and protease (PR) gene. Interesting deviations from the existing mutation datasets were noted at position E248 and R83 of the RT gene and L63 and V77 in the PR gene. Full susceptibility to all examined drugs was 54.2%, while high-level drug resistance was estimated at 37.5%, which seems promising for treatment outcomes for PLHIV in Suriname, although cross-resistance to next-generation NNRTIs was already estimated for nearly a quarter of the patients. The meager 2.9% of PR DRMs rendered protease inhibitors as an effective rescue HIV-1 treatment.
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Affiliation(s)
- Rachel Sno
- “Prof. Dr. Paul C. Flu” Institute for Biomedical Sciences, Paramaribo, Suriname
| | | | - Meritha G. Grünberg
- “Prof. Dr. Paul C. Flu” Institute for Biomedical Sciences, Paramaribo, Suriname
| | - Malti R. Adhin
- Department of Biochemistry, Faculty of Medical Sciences, Anton de Kom Universiteit van Suriname, Paramaribo, Suriname
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10
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Áy É, Pocskay Á, Lakatos B, Szlávik J, Mezei M, Minárovits J. Prevalence of resistance mutations associated with integrase inhibitors in therapy-naive HIV-positive patients in Hungary. Acta Microbiol Immunol Hung 2021; 68:87-91. [PMID: 34125695 DOI: 10.1556/030.2021.01433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 11/19/2022]
Abstract
Widespread introduction of HIV integrase inhibitors into clinical care may result in appearance of drug resistance mutations affecting treatment outcome. The aim of our study was to monitor the resistance patterns of integrase inhibitors beside protease and reverse transcriptase inhibitors in newly diagnosed therapy-naive HIV-positive patients in Hungary between 2017 and 2019.Genotype-based resistance testing of HIV integrase, protease and reverse transcriptase was performed by amplification and Sanger population sequencing from plasma samples. Drug resistance mutations were identified by the algorithm of Stanford HIV Drug Resistance Database.Potentially transmitted, non-polymorphic integrase major mutation was detected in 1 out of 249 samples, while accessory mutations were observed in further 31 patients (12.4%). The overall prevalence of transmitted drug resistance (TDR) mutations related to protease and reverse transcriptase inhibitors was 5.8% (10/173) between the end of 2017 and 2019. Nucleoside reverse transcriptase inhibitor associated resistance mutations were the most frequent indicators of TDR (6/173; 3.5%), followed by resistance mutations associated with protease (3/173; 1.7%) and non-nucleoside reverse transcriptase inhibitors (2/173, 1.2%).The first detection of integrase major mutation and the changing patterns of other resistance mutations in Hungarian untreated HIV-positive population indicate the necessity of continuous molecular surveillance of Hungarian HIV epidemic.
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Affiliation(s)
- Éva Áy
- 1National Reference Laboratory for Retroviruses, Department of Virology, National Public Health Center, Budapest, Hungary
| | - Ágnes Pocskay
- 1National Reference Laboratory for Retroviruses, Department of Virology, National Public Health Center, Budapest, Hungary
| | - Botond Lakatos
- 2Department of Infectious Diseases, Center of HIV, National Institute of Hematology and Infectious Diseases, South-Pest Central Hospital, Budapest, Hungary
| | - János Szlávik
- 2Department of Infectious Diseases, Center of HIV, National Institute of Hematology and Infectious Diseases, South-Pest Central Hospital, Budapest, Hungary
| | - Mária Mezei
- 1National Reference Laboratory for Retroviruses, Department of Virology, National Public Health Center, Budapest, Hungary
| | - János Minárovits
- 3Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
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Bogdanić N, Bendig L, Lukas D, Zekan Š, Begovac J. Timeliness of antiretroviral therapy initiation in the era before universal treatment. Sci Rep 2021; 11:10508. [PMID: 34006927 PMCID: PMC8131373 DOI: 10.1038/s41598-021-90043-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
We assessed the prevalence and factors related to the time to antiretroviral (ART) initiation among persons who entered HIV care and subsequently started ART in Croatia from 2005 to 2014. Included were patients ≥ 18 years, the follow-up ended on Dec/31/2017. 628 patients were included into the study 91.9% were men; median age was 36.1 (Q1-Q3: 29.6-43.8) years. Rapid (within 7 days of diagnosis) ART initiation was observed in 21.8% patients, 49.8% initiated ART within 30 days, 21.7% and 28.5% had intermediate (31 days-1 year) and late initiation (> 1 year), respectively. Of 608 patients that achieved an undetectable viral load, 94% had a plasma HIV-1 RNA < 50 copies/ml at last measurement after a median follow-up of 5.2 years. On quantile regression analysis, calendar year of entry into care, and markers of more advanced HIV disease (higher viral load, lower CD4 cell count and clinical AIDS) were significantly associated with earlier ART initiation. Early ART was not related to a gap in care afterwards at all quantiles. In conclusion, a significant proportion of patients started ART early in Croatia in 2005-2014. Early ART initiation led to durable viral load suppression and was not associated with a subsequent gap in care.
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Affiliation(s)
- Nikolina Bogdanić
- University Hospital for Infectious Diseases, Mirogojska 8, Zagreb, Croatia
| | - Liam Bendig
- Medical Scholars Program, AU/UGA Medical Partnership, Athens, GA, USA
| | - Davorka Lukas
- University Hospital for Infectious Diseases, Mirogojska 8, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Šime Zekan
- University Hospital for Infectious Diseases, Mirogojska 8, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Josip Begovac
- University Hospital for Infectious Diseases, Mirogojska 8, Zagreb, Croatia.
- University of Zagreb School of Medicine, Zagreb, Croatia.
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12
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Kantzanou M, Karalexi MA, Papachristou H, Vasilakis A, Rokka C, Katsoulidou A. Transmitted drug resistance among HIV-1 drug-naïve patients in Greece. Int J Infect Dis 2021; 105:42-48. [PMID: 33592343 DOI: 10.1016/j.ijid.2021.02.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES Despite the success of antiretroviral treatment (ART), the persisting transmitted drug resistance (TDR) and HIV genetic heterogeneity affect the efficacy of treatment. This study explored the prevalence of TDR among ART-naïve HIV patients in Greece during the period 2016-2019. METHODS Genotypic resistance testing was available for 438 ART-naïve HIV patients. Multivariable Poisson regression models were fitted. RESULTS The majority of patients were male, and there was a slight predominance of Hellenic (26.5%) over non-Hellenic (21.9%) nationality. The prevalence of TDR was 7.8%. There was a predominance of mutations for non-nucleoside reverse-transcriptase inhibitors (5.7%) over nucleoside reverse-transcriptase inhibitors (0.2%). No mutations to protease inhibitors were detected. The prevalence of resistance was 22.1% based on all mutations identified through the HIVdb interpretation system. The most frequent resistance sites were E138A (9.6%), K103N (6.4%), and K101E (2.1%). The majority of detected mutations were confined to subtype A (52.6%), followed by B (19.6%). Non-Hellenic nationality was significantly associated with an increased risk of TDR (relative risk 1.32, 95% confidence interval 1.04-1.69). CONCLUSIONS Non-B HIV infections predominate in Greece, with an increasing trend in recent years. The prevalence of TDR remains stable. Ongoing surveillance of resistance testing is needed to secure the long-term success of ART.
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Affiliation(s)
- Maria Kantzanou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece; National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Maria A Karalexi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece.
| | - Helen Papachristou
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Alexis Vasilakis
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Chrysoula Rokka
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Antigoni Katsoulidou
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
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