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Lagatie O, Lauwers D, Singh H, Vanroye F, Stieh DJ, Vingerhoets J, Lavreys L, Oriol-Mathieu V, Colón W, Verhofstede C, Vercauteren K, Van den Bossche D, Pau MG. Towards Novel HIV-1 Serodiagnostic Tests without Vaccine-Induced Seroreactivity. Microbiol Spectr 2023; 11:e0071523. [PMID: 37222611 PMCID: PMC10269835 DOI: 10.1128/spectrum.00715-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023] Open
Abstract
Vaccine-induced seroreactivity/positivity (VISR/P) poses a significant and common challenge to HIV vaccine implementation, as up to 95% of vaccine recipients may be misclassified as having HIV infection by current HIV screening and confirmatory serological assays. We investigated whether internal HIV proteins could be used to overcome VISR and discovered a set of 4 antigens (gp41 endodomain, p31 integrase, p17 matrix protein, and Nef) that are recognized by antibodies produced in individuals with HIV infection but not in vaccinated individuals. When evaluated in a multiplex double-antigen bridging ELISA, this antigen combination had specificities of 98.1% prevaccination and 97.1% postvaccination, demonstrating the assay is minimally impacted by vaccine-induced antibodies. The sensitivity was 98.5%, further increasing to 99.7% when p24 antigen testing was included. Results were similar across HIV-1 clades. Although more technical advancements will be desired, this research provides the groundwork for the development of new fourth-generation HIV tests unaffected by VISR. IMPORTANCE While the detection of HIV infection is accomplished by several methods, the most common are serological tests that detect host antibodies produced in response to viral infection. However, the use of current serological tests may present a significant challenge to the adoption of an HIV vaccine in the future because the antibodies to HIV antigens detected in currently available tests also tend to be included as antigens in the HIV vaccines in development. The use of these serological tests may thus result in the misclassification of vaccinated HIV-negative individuals, which can have potential for significant harms for individuals and could prevent the widespread adoption and implementation of HIV vaccines. Our study aimed to identify and evaluate target antigens for inclusion in new serological tests that can be used to identify HIV infections without interference from vaccine-induced antibodies but also fit within existing platforms for HIV diagnostics.
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Affiliation(s)
- Ole Lagatie
- Johnson & Johnson Global Public Health Research & Development, Beerse, Belgium
| | - Dax Lauwers
- Johnson & Johnson Global Public Health Research & Development, Beerse, Belgium
| | - Harvinder Singh
- Johnson & Johnson Global Public Health Research & Development, Beerse, Belgium
| | - Fien Vanroye
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Daniel J. Stieh
- Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
| | | | - Ludo Lavreys
- Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
| | | | - Will Colón
- Johnson & Johnson Global Public Health Research & Development, Beerse, Belgium
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2
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Facente SN, Grebe E, Maher AD, Fox D, Scheer S, Mahy M, Dalal S, Lowrance D, Marsh K. Use of HIV Recency Assays for HIV Incidence Estimation and Other Surveillance Use Cases: Systematic Review. JMIR Public Health Surveill 2022; 8:e34410. [PMID: 35275085 PMCID: PMC8956992 DOI: 10.2196/34410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND HIV assays designed to detect recent infection, also known as "recency assays," are often used to estimate HIV incidence in a specific country, region, or subpopulation, alone or as part of recent infection testing algorithms (RITAs). Recently, many countries and organizations have become interested in using recency assays within case surveillance systems and routine HIV testing services to measure other indicators beyond incidence, generally referred to as "non-incidence surveillance use cases." OBJECTIVE This review aims to identify published evidence that can be used to validate methodological approaches to recency-based incidence estimation and non-incidence use cases. The evidence identified through this review will be used in the forthcoming technical guidance by the World Health Organization (WHO) and United Nations Programme on HIV/AIDS (UNAIDS) on the use of HIV recency assays for identification of epidemic trends, whether for HIV incidence estimation or non-incidence indicators of recency. METHODS To identify the best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for specific populations or geographic areas, we conducted a systematic review of the literature to (1) understand the use of recency testing for surveillance in programmatic and laboratory settings, (2) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases, and (3) assess the field performance characteristics of commercially available recency assays. RESULTS Among the 167 documents included in the final review, 91 (54.5%) focused on assay or algorithm performance or methodological descriptions, with high-quality evidence of accurate age- and sex-disaggregated HIV incidence estimation at national or regional levels in general population settings, but not at finer geographic levels for prevention prioritization. The remaining 76 (45.5%) described the field use of incidence assays including field-derived incidence (n=45), non-incidence (n=25), and both incidence and non-incidence use cases (n=6). The field use of incidence assays included integrating RITAs into routine surveillance and assisting with molecular genetic analyses, but evidence was generally weaker or only reported on what was done, without validation data or findings related to effectiveness of using non-incidence indicators calculated through the use of recency assays as a proxy for HIV incidence. CONCLUSIONS HIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and subnational regional levels; however, there is a lack of evidence validating the accuracy and effectiveness of using recency assays to identify epidemic trends in non-incidence surveillance use cases. More research is needed to validate the use of recency assays within HIV testing services, to ensure findings can be accurately interpreted to guide prioritization of public health programming.
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Affiliation(s)
- Shelley N Facente
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.,Facente Consulting, Richmond, CA, United States.,Vitalant Research Institute, San Francisco, CA, United States
| | - Eduard Grebe
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.,Vitalant Research Institute, San Francisco, CA, United States.,South African Centre for Epidemiological Modeling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Andrew D Maher
- South African Centre for Epidemiological Modeling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa.,Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Douglas Fox
- Facente Consulting, Richmond, CA, United States
| | | | - Mary Mahy
- Strategic Information Department, The Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
| | - Shona Dalal
- Global HIV, Hepatitis and Sexually Transmitted Infections Programmes, World Health Organisation, Geneva, Switzerland
| | - David Lowrance
- Global HIV, Hepatitis and Sexually Transmitted Infections Programmes, World Health Organisation, Geneva, Switzerland
| | - Kimberly Marsh
- Strategic Information Department, The Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
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3
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Chimungu B, Fu M, Wu J, Wu J, Huang L, Dai Y, Tang S, Zhang J, Wan C. Prevalence of sexually transmitted infections among foreigners living in Guangzhou, China: a cross-sectional study (2010-2017). BMC Infect Dis 2020; 20:345. [PMID: 32410628 PMCID: PMC7222532 DOI: 10.1186/s12879-020-04995-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The prevalence of HIV/HCV/HBV/ Treponema pallidum is an essential health issue in China. However, there are few studies focused on foreigners living in China. This study aimed to assess the prevalence and socio-demographic distribution of HIV, HBV, HCV, and T. pallidum among foreigners in Guangzhou in the period of 2010-2017. METHODS A cross-sectional study was conducted to screen serological samples of 40,935 foreigners from 2010 to 2017 at the Guangdong International Travel Health Care Center in Guangzhou. Samples were tested for hepatitis B surface antigen (HBsAg), anti-HCV, syphilis antibody (anti-TPPA) and anti-HIV 1 and 2. We collected secondary data from laboratory records and used multiple logistic regression analyses to verify the association between different factors and the seroprevalence of HIV/HBV/HCV/ T. pallidum. RESULTS The prevalence of HBV/HCV/HIV/ T. pallidum was 2.30, 0.42, 0.02, and 0.60%, respectively, and fluctuated slightly for 7 years. The results of multiple logistic regression showed that males were less susceptible to HBV than females (odds ratio [OR] = 0.77, 95% CI: 0.67-0.89). Participants under the age of 20 had a lower risk of HBV (OR = 0.25, 95% CI: 0.18-0.35), HCV (OR = 0.06, 95% CI: 0.02-0.18), and T. pallidum (OR = 0. 10, 95% CI: 0.05-0.20) than participants over the age of 50. Participants with an education level below high school were more likely to have HBV (OR = 2.98, 95% CI: 1.89-4.70) than others, and businessmen (OR = 3.02, 95% CI: 2.03-4.49), and designers (OR = 3.83, 95% CI: 2.49-5.90) had a higher risk of T. pallidum than others. Co-infection involved 58 (4.20%) total cases, and the highest co-infection rate was observed for HBV and T. pallidum (2.60%). CONCLUSION The prevalence of HBV/HCV/HIV/ T. pallidum was low among foreigners in Guangzhou. Region, gender, age, educational level, and occupation were risk factors for positive infection.
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Affiliation(s)
- Benard Chimungu
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Muqing Fu
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jian Wu
- Clinical laboratory, Guangdong International Travel Health Care Center, Guangzhou, 510635, China
| | - Jiali Wu
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Liping Huang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yingchun Dai
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jianming Zhang
- Clinical laboratory, Guangdong International Travel Health Care Center, Guangzhou, 510635, China.
| | - Chengsong Wan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China. .,Key Laboratory of Tropical Disease Research of Guangdong Province, Southern Medical University, Guangzhou, 510515, China.
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4
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Verhofstede C, Mortier V, Dauwe K, Callens S, Deblonde J, Dessilly G, Delforge ML, Fransen K, Sasse A, Stoffels K, Van Beckhoven D, Vanroye F, Vaira D, Vancutsem E, Van Laethem K. Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing. Viruses 2019; 11:v11121096. [PMID: 31779195 PMCID: PMC6950120 DOI: 10.3390/v11121096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.
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Affiliation(s)
- Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
- Correspondence:
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Steven Callens
- Aids Reference Center, Department of Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Jessika Deblonde
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Géraldine Dessilly
- Aids Reference Laboratory, Medical Microbiology Unit, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Marie-Luce Delforge
- Aids Reference Laboratory, Université Libre de Bruxelles, 1050 Brussels, Belgium;
| | - Katrien Fransen
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - André Sasse
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Karolien Stoffels
- Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium;
| | - Dominique Van Beckhoven
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Fien Vanroye
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - 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
- Aids Reference Laboratory, University Hospital Leuven, 3000 Leuven, Belgium;
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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5
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Demecheleer E, Hardy J, Mortier V, Verhofstede C. Single genome sequencing of near full-length HIV-1 RNA using a limiting dilution approach. J Virol Methods 2019; 274:113737. [PMID: 31562885 DOI: 10.1016/j.jviromet.2019.113737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 11/18/2022]
Abstract
Sequencing very long stretches of the HIV-1 genome can advance studies on virus evolution and in vivo recombination but remains technically challenging. We developed an efficient procedure to sequence near full-length HIV-1 RNA using a two-amplicon approach. The whole genome was successfully amplified for 107 (88%) of 121 plasma samples including samples from patients infected with HIV-1 subtype A1, B, C, D, F1, G, H, CRF01_AE and CRF02_AG. For the 17 samples with a viral load below 1000 c/ml and the 104 samples with a viral load above 1000 c/ml, the amplification efficiency was respectively 53% and 94%. The sensitivity of the method was further evaluated using limiting dilution of RNA extracted from a plasma pool containing an equimolar mixture of three HIV-1 subtypes (B, C and CRF02_AG) and diluted before and after cDNA generation. Both RNA and cDNA dilution showed comparable sensitivity and equal accuracy in reflecting the subtype distribution of the plasma pool. One single event of in vitro recombination was detected amongst the 41 sequences obtained after cDNA dilution but no indications for in vitro recombination were found after RNA dilution. In conclusion, a two-amplicon strategy and limiting dilution of viral RNA followed by reverse transcription, nested PCR and Sanger sequencing, allows near full genome sequencing of individual HIV-1 RNA molecules. This method will be a valuable tool in the study of virus evolution and recombination.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
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6
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Arendt V, Guillorit L, Origer A, Sauvageot N, Vaillant M, Fischer A, Goedertz H, François JH, Alexiev I, Staub T, Seguin-Devaux C. Injection of cocaine is associated with a recent HIV outbreak in people who inject drugs in Luxembourg. PLoS One 2019; 14:e0215570. [PMID: 31095576 PMCID: PMC6522034 DOI: 10.1371/journal.pone.0215570] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/04/2019] [Indexed: 02/05/2023] Open
Abstract
Background An outbreak of HIV infections among people who inject drugs (PWID) started in 2014 in Luxembourg. Objectives We conducted phylogenetic and epidemiological analyses among the PWID infected with HIV in Luxembourg or attending the supervised drug consumption facility (SDCF) to understand the main causes of the outbreak. Methods Between January 2013 and December 2017, analysis of medical files were performed from all PWID infected with HIV at the National Service of Infectious Diseases (NSID) providing clinical care nationwide. PWID were interviewed at NSID and SDCF using a standardized questionnaire focused on drug consumption and risk behaviours. The national drug monitoring system RELIS was consulted to determine the frequency of cocaine/heroin use. Transmission clusters were analysed by phylogenetic analyses using approximate maximum-likelihood. Univariate and multivariate logistic regression analyses were performed on epidemiological data collected at NSID and SDCF to determine risk factors associated with cocaine use. Results From January 2013 to December 2017, 68 new diagnosis of HIV infection reported injecting drug use as the main risk of transmission at NSID. The proportion of female cases enrolled between 2013–2017 was higher than the proportion among cases enrolled prior to 2013. (33% vs 21%, p < 0.05). Fifty six viral sequences were obtained from the 68 PWID newly diagnosed for HIV. Two main transmission clusters were revealed: one HIV-1 subtype B cluster and one CRF14_BG cluster including 37 and 9 patients diagnosed since 2013, respectively. Interviews from 32/68 (47%) newly diagnosed PWID revealed that 12/32 (37.5%) were homeless and 27/32 (84.4%) injected cocaine. Increased cocaine injection was indeed reported by the RELIS participants from 53 to 63% in drug users with services contacts between 2012 and 2015, and from 5 to 22% in SDCF users between 2012 and 2016. Compared with PWID who injected only heroin (n = 63), PWID injecting cocaine and heroin (n = 107) were younger (mean of 38 vs 44 years, p≤0.001), reported more frequent piercing (≤0.001), shared and injected drugs more often (p≤0.01), and were more frequently HIV positive (p<0.05) at SDCF using univariate logistic regression analysis. Finally, in the multivariate analysis, use of heroin and cocaine was independently associated with younger age, piercing, sharing of drugs, and regular consumption (p<0.05). Conclusions Injecting cocaine is a new trend of drug use in Luxembourg associated with HIV infection in this recent outbreak among PWID.
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Affiliation(s)
- Vic Arendt
- Service National des Maladies Infectieuses, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Laurence Guillorit
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch sur Alzette, Luxembourg
| | - Alain Origer
- National Drug Coordinator, Ministry of Health, Luxembourg, Luxembourg
| | - Nicolas Sauvageot
- Competence Center for Methodology and Statistics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Michel Vaillant
- Competence Center for Methodology and Statistics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Aurélie Fischer
- Clinical and Epidemiological Investigation Center, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | - Jean-Hugues François
- Molecular Biology Laboratory, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Thérèse Staub
- Service National des Maladies Infectieuses, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch sur Alzette, Luxembourg
- * E-mail:
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7
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Vinken L, Fransen K, Cuypers L, Alexiev I, Balotta C, Debaisieux L, Seguin-Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sönnerborg A, Vancutsem E, Vandamme AM, Van den Wijngaert S, Van Ranst M, Verhofstede C, Stadler T, Lemey P, Van Laethem K. Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium. Front Microbiol 2019; 10:613. [PMID: 30972053 PMCID: PMC6443750 DOI: 10.3389/fmicb.2019.00613] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59–74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23–12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0–75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000–2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.
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Affiliation(s)
- Lore Vinken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Katrien Fransen
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ivailo Alexiev
- National Reference Confirmatory Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Claudia Balotta
- Infectious Diseases and Immunopathology Section, 'L. Sacco' Department of Biomedical and Clinical Sciences, 'L. Sacco' Hospital, University of Milan, Milan, Italy
| | - Laurent Debaisieux
- AIDS Reference Laboratory, CUB-Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Sergio García Ribas
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Perpétua Gomes
- Serviço de Patologia Clínica, Laboratorio de Biologia Molecular, LMCBM, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jean Ruelle
- Unit of Medical Microbiology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Murat Sayan
- PCR Unit, Clinical Laboratory, Kocaeli University, İzmit, Turkey.,Research Center of Experimental Health Sciences, Near East University, Nicosia, Cyprus
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases 'Matei Bals', Bucharest, Romania
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Martine Peeters
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ellen Vancutsem
- AIDS Reference Laboratory, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Unidade de Microbiologia, Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sigi Van den Wijngaert
- AIDS Reference Laboratory, Department of Microbiology, Saint-Pierre University Hospital, Brussels, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Dauwe K, Mortier V, Verhofstede C. Frequency of occurrence of HIV-1 dual infection in a Belgian MSM population. PLoS One 2018; 13:e0195679. [PMID: 29624605 PMCID: PMC5889168 DOI: 10.1371/journal.pone.0195679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/27/2018] [Indexed: 12/20/2022] Open
Abstract
Introduction HIV-1 dual infection is a condition that results from infection with at least two HIV-1 variants from different sources. The scarceness of information on this condition is partly due to the fact that its detection is technically challenging. Using next-generation sequencing we defined the extent of HIV-1 dual infection in a cohort of men who have sex with men (MSM). Material & methods Eighty-six MSM, diagnosed with HIV-1 subtype B infection between 2008 and 2013 were selected for next-generation sequencing of the HIV-1 envelope V3. Sequencing was performed on 2 plasma samples collected with an interval of > 6 months before the initiation of antiretroviral therapy. Maximum likelihood phylogenetic trees were inspected for dual infection, defined as the presence of two or more monophyletic clusters with ≥ 90% bootstrap support and a mean between-cluster genetic distance of ≥ 10%. To confirm dual infection, deep V3 sequencing of intermediate samples was performed as well as clonal sequencing of the HIV-1 protease-reverse transcriptase gene. Results Five of the 74 patients (6.8%) for whom deep sequencing was successful, showed clear evidence of dual infection. In 4 of them, the second strain was absent in the first sample but occurred in subsequent samples. This was highly suggestive for superinfection. In 3 patients both virus variants were of subtype B, in 2 patients at least one of the variants was a subtype B/non-B recombinant virus. Conclusions Dual infection was confirmed in 6.8% of MSM diagnosed with HIV-1 in Belgium. This prevalence is probably an underestimation, because stringent criteria were used to classify viral variants as originating from a new infection event.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
- * E-mail:
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Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29522828 DOI: 10.1016/j.meegid.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.
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