1
|
Martin F, Marcelino JM, Palladino C, Bártolo I, Tracana S, Moranguinho I, Gonçalves P, Mateus R, Calado R, Borrego P, Leitner T, Clemente S, Taveira N. Long-Term and Low-Level Envelope C2V3 Stimulation by Highly Diverse Virus Isolates Leads to Frequent Development of Broad and Elite Antibody Neutralization in HIV-1-Infected Individuals. Microbiol Spectr 2022; 10:e0163422. [PMID: 36445130 PMCID: PMC9769935 DOI: 10.1128/spectrum.01634-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/29/2022] [Indexed: 12/03/2022] Open
Abstract
A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemics in the world. Three hundred twenty-two HIV-1-infected adults from Angola were included in this retrospective study. Phylogenetic analysis of C2V3C3 env gene sequences was used for virus subtyping. Env-binding antibody reactivity was tested against polypeptides comprising the C2, V3, and C3 regions. Neutralizing-antibody responses were determined against a reference panel of tier 2 Env pseudoviruses in TZM-bl cells; neutralizing epitope specificities were predicted using ClustVis. All subtypes were found, along with untypeable strains and recombinant forms. Notably, 56% of the patients developed cross neutralizing, broadly neutralizing, or elite neutralizing responses. Broad and elite neutralization was associated with longer infection time, subtype C, lower CD4+ T cell counts, higher age, and higher titer of C2V3C3-specific antibodies relative to failure to develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients. V3 and C3 regions were significantly less variable in elite neutralizers than in weak neutralizers and nonneutralizers, suggesting an active role of V3C3-directed bNAbs in controlling HIV-1 replication and diversification. In conclusion, prolonged and low-level envelope V3C3 stimulation by highly diverse and ancestral HIV-1 isolates promotes the frequent elicitation of bNAbs. These results provide important clues for the development of an effective HIV-1 vaccine. IMPORTANCE Studies on neutralization by antibodies and their determinants in HIV-1-infected individuals have mostly been conducted in relatively recent epidemics caused by subtype B and C viruses. Results have suggested that elicitation of broadly neutralizing antibodies (bNAbs) is uncommon. The mechanisms underlying the elicitation of bNAbs are still largely unknown. We performed the first characterization of the plasma neutralizing response in a cohort of HIV-1-infected patients from Angola. Angola is characterized by an old and dynamic epidemic caused by highly diverse HIV-1 variants. Remarkably, more than half of the patients produced bNAbs, mostly targeting the V3-glycan supersite in HIV-1. This was associated with higher age, longer infection time, lower CD4+ T cell counts, subtype C infection, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. These results may help develop the next generation of vaccine candidates for HIV-1.
Collapse
Affiliation(s)
- Francisco Martin
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - José Maria Marcelino
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
| | - Claudia Palladino
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Inês Bártolo
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Tracana
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Inês Moranguinho
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Paloma Gonçalves
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Mateus
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Calado
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Borrego
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Nuno Taveira
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
| |
Collapse
|
2
|
Abidi SH, Siddiqui D, Mahmood SF, Siddiqui R, Nathwani AA, Hotwani A, Shah SA, Khan P, Ferrand RA, Mir F. Unassigned Complex Unique Recombinant Forms Related to CRF36_cpx in Children Identified in an HIV-1 Outbreak in Pakistan. AIDS Res Hum Retroviruses 2022; 38:806-811. [PMID: 35778855 PMCID: PMC7614887 DOI: 10.1089/aid.2021.0168] [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] [Indexed: 01/25/2023] Open
Abstract
In 2019, an outbreak of HIV infection predominantly affecting children occurred in Larkana district, Pakistan. This is the largest outbreak ever reported in this age group in Pakistan. In this study, we report two HIV-1 unique recombinant forms identified during the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. The pol gene was sequenced and used to detect HIV subtype/recombinant forms using subtype, recombination, and phylogenetic analyses. Drug resistance mutation (DRM) analysis was performed to characterize the DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals of the 344 samples collected. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned unique recombinant forms in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.
Collapse
Affiliation(s)
- Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - Dilsha Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Rehana Siddiqui
- Department of Community Health Sciences, Aga Khan University, Karachi, Pakistan
| | - Apsara Ali Nathwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Palwasha Khan
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Rashida Abbas Ferrand
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| |
Collapse
|
3
|
Nduva GM, Nazziwa J, Hassan AS, Sanders EJ, Esbjörnsson J. The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review. Viruses 2021; 13:1174. [PMID: 34205246 PMCID: PMC8235305 DOI: 10.3390/v13061174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.
Collapse
Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Eduard J. Sanders
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| |
Collapse
|
4
|
Calado R, Duarte J, Borrego P, Marcelino JM, Bártolo I, Martin F, Figueiredo I, Almeida S, Graça L, Vítor J, Aires da Silva F, Dias I, Carrapiço B, Taveira N. A Prime-Boost Immunization Strategy with Vaccinia Virus Expressing Novel gp120 Envelope Glycoprotein from a CRF02_AG Isolate Elicits Cross-Clade Tier 2 HIV-1 Neutralizing Antibodies. Vaccines (Basel) 2020; 8:E171. [PMID: 32272637 PMCID: PMC7349027 DOI: 10.3390/vaccines8020171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Development of new immunogens eliciting broadly neutralizing antibodies (bNAbs) is a main priority for the HIV-1 vaccine field. Envelope glycoproteins from non-B-non-C HIV-1clades have not been fully explored as components of a vaccine. We produced Vaccinia viruses expressing a truncated version of gp120 (gp120t) from HIV-1 clades CRF02_AG, H, J, B, and C and examined their immunogenicity in mice and rabbits. Mice primed with the recombinant Vaccinia viruses and boosted with the homologous gp120t or C2V3C3 polypeptides developed antibodies that bind potently to homologous and heterologous envelope glycoproteins. Notably, a subset of mice immunized with the CRF02_AG-based envelope immunogens developed a cross-reactive neutralizing response against tier 2 HIV-1 Env-pseudoviruses and primary isolates. Rabbits vaccinated with the CRF02_AG-based envelope immunogens also generated potent binding antibodies, and one animal elicited antibodies that neutralized almost all (13 of 16, 81.3%) tier 2 HIV-1 isolates tested. Overall, the results suggest that the novel CRF02_AG-based envelope immunogens and prime-boost immunization strategy elicit the type of immune responses required for a preventive HIV-1 vaccine.
Collapse
Affiliation(s)
- Rita Calado
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - Joana Duarte
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - Pedro Borrego
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - José Maria Marcelino
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, 2829-511 Monte de Caparica, Portugal
| | - Inês Bártolo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - Francisco Martin
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - Inês Figueiredo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
| | - Silvia Almeida
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, 1649-02 Lisboa, Portugal; (S.A.); (L.G.)
- Post-Graduate Program in Infectious Diseases, and Department of Social Medicine, Center of Health Sciences, Federal University of Espirito Santo, Vitória 29075-910, Brazil
| | - Luís Graça
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, 1649-02 Lisboa, Portugal; (S.A.); (L.G.)
| | - Jorge Vítor
- Biochemistry and Human Biology Dept, Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal;
| | - Frederico Aires da Silva
- Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal; (F.A.d.S.); (I.D.); (B.C.)
| | - Inês Dias
- Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal; (F.A.d.S.); (I.D.); (B.C.)
| | - Belmira Carrapiço
- Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal; (F.A.d.S.); (I.D.); (B.C.)
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.C.); (J.D.); (P.B.); (J.M.M.); (I.B.); (F.M.); (I.F.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, 2829-511 Monte de Caparica, Portugal
| |
Collapse
|
5
|
Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 2019; 15:e1007976. [PMID: 31809523 PMCID: PMC6897401 DOI: 10.1371/journal.ppat.1007976] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.
Collapse
|
6
|
Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
Collapse
Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
| |
Collapse
|
7
|
Early infant diagnosis of HIV-1 infection in Luanda, Angola, using a new DNA PCR assay and dried blood spots. PLoS One 2017; 12:e0181352. [PMID: 28715460 PMCID: PMC5513534 DOI: 10.1371/journal.pone.0181352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/29/2017] [Indexed: 11/30/2022] Open
Abstract
Background Early diagnosis and treatment reduces HIV-1-related mortality, morbidity and size of viral reservoirs in infants infected perinatally. Commercial molecular tests enable the early diagnosis of infection in infants but the high cost and low sensitivity with dried blood spots (DBS) limit their use in sub-Saharan Africa. Objectives To develop and validate a sensitive and cheap qualitative proviral DNA PCR-based assay for early infant diagnosis (EID) in HIV-1-exposed infants using DBS samples. Study design Chelex-based method was used to extract DNA from DBS samples followed by a nested PCR assay using primers for the HIV-1 integrase gene. Limit of detection (LoD) was determined by Probit regression using limiting dilutions of newly produced recombinant plasmids with the integrase gene of all HIV-1 subtypes and ACH-2 cells. Clinical sensitivity and specificity were evaluated on 100 HIV-1 infected adults; 5 infected infants; 50 healthy volunteers; 139 HIV-1-exposed infants of the Angolan Pediatric HIV Cohort (APEHC) with serology at 18 months of life. Results All subtypes and CRF02_AG were amplified with a LoD of 14 copies. HIV-1 infection in infants was detected at month 1 of life. Sensitivity rate in adults varied with viral load, while diagnostic specificity was 100%. The percentage of HIV-1 MTCT cases between January 2012 and October 2014 was 2.2%. The cost per test was 8-10 USD which is 2- to 4-fold lower in comparison to commercial assays. Conclusions The new PCR assay enables early and accurate EID. The simplicity and low-cost of the assay make it suitable for generalized implementation in Angola and other resource-constrained countries.
Collapse
|
8
|
Bagaya BS, Tian M, Nickel GC, Vega JF, Li Y, He P, Klein K, Mann JFS, Jiang W, Arts EJ, Gao Y. An in vitro Model to Mimic Selection of Replication-Competent HIV-1 Intersubtype Recombination in Dual or Superinfected Patients. J Mol Biol 2017; 429:2246-2264. [PMID: 28472629 PMCID: PMC6202033 DOI: 10.1016/j.jmb.2017.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/23/2022]
Abstract
The low frequency of HIV-1 recombinants within entire viral populations in both individual patients and culture-based infection models impedes investigation of the underlying factors contributing to either the occurrence of recombinants or the survival of recombinants once they are formed. So far, most of the related studies have no consideration of recombinants' functionality. Here, we established a functional recombinant production (FRP) system to produce pure and functional HIV-1 intersubtype Env recombinants and utilized 454 pyrosequencing to investigate the distribution of over 4000 functional and non-functional recombination breakpoints from either the FRP system or dual infection cultures. The results revealed that most of the breakpoints converged in gp41 (62%) and C1 (25.3%) domains of gp120, which has strong correlation with the similarity between the two recombining sequences. Yet, the breakpoints also appeared in C2 (5.2%) and C5 (4.6%) domains not correlated with the recombining sequence similarity. Interestingly, none of the intersubtype gp120 recombinants recombined between C1 and gp41 regions either from the FRP system or from the dual infection culture, and very few from the HIV epidemic were functional. The present study suggests that the selection of functional Env recombinants is one of the reasons for the predominance of C1 and gp41 Env recombinants in the HIV epidemic, and it provides an in vitro model to mimic the selection of replication-competent HIV-1 intersubtype recombination in dual or superinfected patients.
Collapse
Affiliation(s)
- Bernard S Bagaya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, N6A 3K7, Uganda
| | - Meijuan Tian
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Gabrielle C Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - José F Vega
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Yuejin Li
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ping He
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Katja Klein
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Eric J Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Yong Gao
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada.
| |
Collapse
|
9
|
Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo. J Virol 2017; 91:JVI.01841-16. [PMID: 28077647 PMCID: PMC5331799 DOI: 10.1128/jvi.01841-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/07/2016] [Indexed: 01/17/2023] Open
Abstract
As the epidemiological epicenter of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43.02%), but 7 other subtypes (33.14%), 20 circulating recombinant forms (CRFs; 11.63%), and 20 unclassified (11.63%) sequences were also found. Of the rare and unclassified subtypes, 18 specimens were selected for next-generation sequencing (NGS) by a modified HIV-switching mechanism at the 5' end of the RNA template (SMART) method to obtain full-genome sequences. NGS produced 14 new complete genomes, which included pure subtype C (n = 2), D (n = 1), F1 (n = 1), H (n = 3), and J (n = 1) genomes. The two subtype C genomes and one of the subtype H genomes branched basal to their respective subtype branches but had no evidence of recombination. The remaining 6 genomes were complex recombinants of 2 or more subtypes, including subtypes A1, F, G, H, J, and K and unclassified fragments, including one subtype CRF25 isolate, which branched basal to all CRF25 references. Notably, all recombinant subtype H fragments branched basal to the H clade. Spatial-geographical analysis indicated that the diverse sequences identified here did not expand globally. The full-genome and subgenomic sequences identified in our study population significantly increase the documented diversity of the strains involved in the continually evolving HIV-1 pandemic.IMPORTANCE Very little is known about the ancestral HIV-1 strains that founded the global pandemic, and very few complete genome sequences are available from patients in the Congo Basin, where HIV-1 expanded early in the global pandemic. By sequencing a subgenomic fragment of the HIV-1 envelope from study participants in the DRC, we identified rare variants for complete genome sequencing. The basal branching of some of the complete genome sequences that we recovered suggests that these strains are more closely related to ancestral HIV-1 strains than to previously reported strains and is evidence that the local diversification of HIV in the DRC continues to outpace the diversity of global strains decades after the emergence of the pandemic.
Collapse
|
10
|
Pineda-Peña AC, Varanda J, Sousa JD, Theys K, Bártolo I, Leitner T, Taveira N, Vandamme AM, Abecasis AB. On the contribution of Angola to the initial spread of HIV-1. INFECTION GENETICS AND EVOLUTION 2016; 46:219-222. [PMID: 27521160 DOI: 10.1016/j.meegid.2016.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022]
Abstract
Angola borders and has long-term links with Democratic Republic of Congo (DRC) as well as high levels of Human Immunodeficiency Virus (HIV) genetic diversity, indicating a potential role in the initial spread of the HIV-1 pandemic. Herein, we analyze 564 C2V3 and 354 pol publicly available sequences from DRC, Republic of Congo (RC) and Angola to better understand the initial spread of the virus in this region. Phylogeographic analyses were performed with the BEAST software. While our results pinpoint the origin of the pandemic to Kinshasa (DRC) around 1906, the introduction of HIV-1 to Angola could have occurred early between the 1910s and 1940s. Furthermore, most of the HIV-1 migrations out of Kinshasa were directed not only to Lubumbashi and Mbuji-Mayi (DRC), but also to Luanda and Brazzaville. Kinshasa census records corroborate these findings, indicating that the early exportation of the virus to Angola might be related to the high number of Angolans in Kinshasa at that time, originated mostly from the North of Angola. In summary, our results place Angola at the epicenter of the early HIV dissemination, together with DRC and RC.
Collapse
Affiliation(s)
- Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal; Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Jorge Varanda
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal; Department of Life Sciences, University of Coimbra, Coimbra, Portugal; CRIA-UC, Centre for Research in Anthropology, University of Coimbra, Coimbra, Portugal
| | - João Dinis Sousa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal; KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Kristof Theys
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Inês Bártolo
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal; KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Ana B Abecasis
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal; KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000 Leuven, Belgium.
| |
Collapse
|