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Weaver S, Dávila-Conn V, Ji D, Verdonk H, Ávila-Ríos S, Leigh Brown AJ, Wertheim JO, Kosakovsky Pond SL. AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584522. [PMID: 38559140 PMCID: PMC10979987 DOI: 10.1101/2024.03.11.584522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic distance threshold used to connect sequences in the transmission network is a key parameter informing the properties of inferred networks. Using a distance threshold that is too high can result in a network with many spurious links, making it difficult to interpret. Conversely, a distance threshold that is too low can result in a network with too few links, which may not capture key insights into clusters of public health concern. Published research using the HIV-TRACE software package frequently uses the default threshold of 0.015 substitutions/site for HIV pol gene sequences, but in many cases, investigators heuristically select other threshold parameters to better capture the underlying dynamics of the epidemic they are studying. Here, we present a general heuristic scoring approach for tuning a distance threshold adaptively, which seeks to prevent the formation of giant clusters. We prioritize the ratio of the sizes of the largest and the second largest cluster, maximizing the number of clusters present in the network. We apply our scoring heuristic to outbreaks with different characteristics, such as regional or temporal variability, and demonstrate the utility of using the scoring mechanism's suggested distance threshold to identify clusters exhibiting risk factors that would have otherwise been more difficult to identify. For example, while we found that a 0.015 substitutions/site distance threshold is typical for US-like epidemics, recent outbreaks like the CRF07_BC subtype among men who have sex with men (MSM) in China have been found to have a lower optimal threshold of 0.005 to better capture the transition from injected drug use (IDU) to MSM as the primary risk factor. Alternatively, in communities surrounding Lake Victoria in Uganda, where there has been sustained hetero-sexual transmission for many years, we found that a larger distance threshold is necessary to capture a more risk factor-diverse population with sparse sampling over a longer period of time. Such identification may allow for more informed intervention action by respective public health officials.
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Affiliation(s)
- Steven Weaver
- Center for Viral Evolution, Temple University, Philadelphia, PA, USA
| | - Vanessa Dávila-Conn
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Daniel Ji
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA 92093, USA
| | - Hannah Verdonk
- Center for Viral Evolution, Temple University, Philadelphia, PA, USA
| | - Santiago Ávila-Ríos
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Andrew J Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Olmesdahl NP, Nel C, Mannell A, Fatman L. A Retrospective Analysis of the Clinicopathological Features of Patients with Tuberculous Mastitis: A Single Institution's Experience. Acta Cytol 2023; 67:573-582. [PMID: 37729886 DOI: 10.1159/000534193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Tuberculosis remains a global health burden, especially in low- and middle-income countries. Breast tuberculosis is a rare disease with minimal research available. This disease produces a diagnostic challenge as the clinical presentation is variable, and diagnosis often requires additional investigations. This study was undertaken to determine the efficacy of cytology and histology, together with ancillary studies, in diagnosing tuberculous mastitis. METHODS This retrospective study was conducted in a Johannesburg Hospital over 5 years. Thirty-two patients with confirmed tuberculous mastitis were included. The patients were considered positive for tuberculous mastitis if histological or cytological findings were confirmed with either a positive tuberculosis culture, Ziehl-Neelsen stain, or polymerase chain reaction examination/GeneXpert. RESULTS This case series comprises 3 males and 29 females with a mean age of 35.66. A breast mass was the most common presentation. Over these 5 years, more biopsies were performed on inflammatory breast lesions than fine needle aspirations. There was a higher confirmation rate for cytology diagnoses compared to histology diagnoses. CONCLUSION This study supports using fine needle aspiration combined with GeneXpert as the primary diagnostic modality in diagnosing tuberculous mastitis. This test combination is advantageous in resource- and financially constrained environments as it is relatively simple to perform, cost-effective, and has a rapid turnaround time.
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Affiliation(s)
- Nine-Paula Olmesdahl
- Registrar, Anatomical Pathology, Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand, and National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Carolina Nel
- Consultant Anatomical Pathologist, Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand, and National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Aylwyn Mannell
- Consultant Surgeon, Department of Surgery, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Luvo Fatman
- Medical Officer, Department of Cytology, National Health Laboratory Services (NHLS), Johannesburg, South Africa
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Labarile M, Loosli T, Zeeb M, Kusejko K, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux C, Günthard HF, Pasin C, Kouyos RD, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach. J Infect Dis 2023; 227:554-564. [PMID: 36433831 DOI: 10.1093/infdis/jiac457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers. METHODS We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission. RESULTS We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54). CONCLUSIONS These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
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Affiliation(s)
- Marco Labarile
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Oliveira RC, Gräf T, Rego FFDA, Silva GPSA, Giovanetti M, Monteiro Cunha JP. Dynamic Dispersion of HIV-1 Subtype C Toward Brazilian Northeastern Region. AIDS Res Hum Retroviruses 2021; 37:913-921. [PMID: 34036794 DOI: 10.1089/aid.2020.0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The subtype C accounts for >50% of HIV type 1 (HIV-1) infections worldwide and it is currently the predominant viral form in South Brazil. Subtype C has been reported in all Brazilian regions; however, the phylogenetic relationship among strains circulating in those regions still remains unclear. This study aimed to investigate the origin and dynamic dispersion of HIV-1 subtype C toward Northeast Brazil. Our phylogenetic analysis suggests that most subtype C strains circulating in Brazil (99%) are descendant from the main lineage whose entrance in the country was previously described in the 1970s. According to the literature, additional introductions of subtype C were reported in the country through the Southeast region and in this study we identified another entry event that occurred most likely through the North region. Furthermore, our analysis suggests that the spread of subtype C to Brazilian Northeastern states occurred through multiple independent introductions of the main lineage that originated in South Brazil between mid-1980s and late 1990s. Despite the observation of eventual new HIV-1 subtype C introductions, our results highlight the predominance of a single lineage of this subtype in Brazil and the importance of South region in its dissemination throughout the country.
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Affiliation(s)
- Rodrigo Cunha Oliveira
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz—FIOCRUZ, Salvador, Brazil
| | | | | | - Marta Giovanetti
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joana Paixão Monteiro Cunha
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
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Aljedani SS, Liban TJ, Tran K, Phad G, Singh S, Dubrovskaya V, Pushparaj P, Martinez-Murillo P, Rodarte J, Mileant A, Mangala Prasad V, Kinzelman R, O’Dell S, Mascola JR, Lee KK, Karlsson Hedestam GB, Wyatt RT, Pancera M. Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. PLoS Pathog 2021; 17:e1009543. [PMID: 34559844 PMCID: PMC8494329 DOI: 10.1371/journal.ppat.1009543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/06/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.
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Affiliation(s)
- Safia S. Aljedani
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Tyler J. Liban
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Karen Tran
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Ganesh Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Viktoriya Dubrovskaya
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Justas Rodarte
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
| | - Alex Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Rachel Kinzelman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Richard T. Wyatt
- The Scripps Research Institute, IAVI Neutralizing Antibody Center, La Jolla, California, United States of America
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, United States of America
- * E-mail:
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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: 4] [Impact Index Per Article: 1.3] [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.
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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
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Characteristics Associated With Human Immunodeficiency Virus Transmission Networks Involving Adolescent Girls and Young Women in Human Immunodeficiency Virus Prevention Trials Network 068 Study. Sex Transm Dis 2020; 46:e46-e49. [PMID: 30985638 DOI: 10.1097/olq.0000000000000954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We combined behavioral survey data from the human immunodeficiency virus (HIV) Prevention Trials Network 068 study with phylogenetic information to determine if cluster membership was associated with characteristics of young women and their partners. Clusters were more likely to involve young women from specific villages and schools, indicating some localized transmission.Supplemental digital content is available in the text.
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Abstract
PURPOSE OF REVIEW To provide a summary of the current data on the global HIV subtype diversity and distribution by region. HIV is one of the most genetically diverse pathogens due to its high-mutation and recombination rates, large population size and rapid replication rate. This rapid evolutionary process has resulted in several HIV subtypes that are heterogeneously globally distributed. RECENT FINDINGS Subtype A remains the most prevalent strain in parts of East Africa, Russia and former Soviet Union countries; subtype B in Europe, Americas and Oceania; subtype C in Southern Africa and India; CRF01_AE in Asia and CRF02_AG in Western Africa. Recent studies based on near full-length genome sequencing highlighted the growing importance of recombinant variants and subtype C viruses. SUMMARY The dynamic change in HIV subtype distribution presents future challenges for diagnosis, treatment and vaccine design and development. An increase in recombinant viruses suggests that coinfection and superinfection by divergent HIV strains has become more common necessitating continuous surveillance to keep track of the viral diversity. Cheaper near full-length genome sequencing approaches are critical in improving HIV subtype estimations. However, missing subtype data and low sequence sampling levels are still a challenge in some geographical regions. VIDEO ABSTRACT: http://links.lww.com/COHA/A14.
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Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D, Fraser C. PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa. Curr Opin HIV AIDS 2019; 14:173-180. [PMID: 30946141 PMCID: PMC6629166 DOI: 10.1097/coh.0000000000000542] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW The HIV epidemic in sub-Saharan Africa is far from being under control and the ambitious UNAIDS targets are unlikely to be met by 2020 as declines in per-capita incidence being largely offset by demographic trends. There is an increasing number of proven and specific HIV prevention tools, but little consensus on how best to deploy them. RECENT FINDINGS Traditionally, phylogenetics has been used in HIV research to reconstruct the history of the epidemic and date zoonotic infections, whereas more recent publications focus on HIV diversity and drug resistance. However, it is also the most powerful method of source attribution available for the study of HIV transmission. The PANGEA (Phylogenetics And Networks for Generalized Epidemics in Africa) consortium has generated over 18 000 NGS HIV sequences from five countries in sub-Saharan Africa. Using phylogenetic methods, we will identify characteristics of individuals or groups, which are most likely to be at risk of infection or at risk of infecting others. SUMMARY Combining phylogenetics, phylodynamics and epidemiology will allow PANGEA to highlight where prevention efforts should be focussed to reduce the HIV epidemic most effectively. To maximise the public health benefit of the data, PANGEA offers accreditation to external researchers, allowing them to access the data and join the consortium. We also welcome submissions of other HIV sequences from sub-Saharan Africa to the database.
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Affiliation(s)
- Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mary K. Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Sivay MV, Fogel JM, Wang J, Zhang Y, Piwowar-Manning E, Clarke W, Breaud A, Blankson J, Hamilton EL, Kahn K, Selin A, Gomez-Olive FX, MacPhail C, Hughes JP, Pettifor A, Eshleman SH. Natural control of HIV infection in young women in South Africa: HPTN 068. HIV CLINICAL TRIALS 2018; 19:202-208. [PMID: 30522410 DOI: 10.1080/15284336.2018.1531534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Some individuals control HIV replication without antiretroviral (ARV) therapy. OBJECTIVE To analyze viral suppression in young women in rural South Africa enrolled in a trial evaluating a behavioral intervention for HIV prevention. METHODS Plasma samples were obtained from women ages 13-24 (81 infected at enrollment, 164 seroconverters). ARV testing was performed using an assay that detects 20 ARV drugs. Women were classified as viremic controllers if they were virally suppressed for ≥12 months with no ARV drug use. RESULTS Samples from 216/245 (88.2%) women had no ARV drugs detected at their first HIV-positive visit. Thirty-four (15.7%) of the 216 women had a viral load <2,000 copies/mL. Fifteen of the 34 women were followed for ≥12 months; 12 were virally suppressed with no ARV drugs detected during follow-up. These women were classified as viremic controllers (overall: 12/216 = 5.6%). The median CD4 cell count at the first HIV-positive visit was higher among the 12 controllers than among the 204 women who were not using ARV drugs (759 vs. 549 cells/mm3, p = 0.02). Some women had a viral load <40 copies/mL at a single study visit, but none were classified as elite controllers (viral load <40 copies/mL for ≥12 months with no ARV drug use). CONCLUSIONS In this cohort, 5.6% of women who were not using ARV drugs had sustained viral suppression. This represents a minimum estimate of the frequency of viremic controllers in this cohort, since some women were not followed long enough to meet the criteria for classification.
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Affiliation(s)
- Mariya V Sivay
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Jessica M Fogel
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Jing Wang
- b Statistical Center for HIV/ AIDS Research & Prevention (SCHARP) , Seattle , Washington , USA
| | - Yinfeng Zhang
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Estelle Piwowar-Manning
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - William Clarke
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Autumn Breaud
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Joel Blankson
- c Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Erica L Hamilton
- d Science Facilitation Department , FHI 360 , Durham , North Carolina , USA
| | - Kathleen Kahn
- e MRC/Wits Rural Public Health and Health, Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa
| | - Amanda Selin
- f University of North Carolina at Chapel Hill, Carolina Population Center , Chapel Hill , North Carolina , USA
| | - F Xavier Gomez-Olive
- e MRC/Wits Rural Public Health and Health, Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa
| | - Catherine MacPhail
- e MRC/Wits Rural Public Health and Health, Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa.,g School of Health and Society , University of Wollongong , Wollongong , Australia
| | - James P Hughes
- h Department of Biostatistics , University of Washington , Seattle , Washington , USA
| | - Audrey Pettifor
- e MRC/Wits Rural Public Health and Health, Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa.,i Department of Epidemiology , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , USA
| | - Susan H Eshleman
- a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
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