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Coldbeck-Shackley RC, Adamson PJ, Whybrow D, Selway CA, Papanicolas LE, Turra M, Leong LEX. Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance. J Clin Virol 2024; 174:105709. [PMID: 38924832 DOI: 10.1016/j.jcv.2024.105709] [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: 03/11/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis. METHODS We implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis. RESULTS Optimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone. CONCLUSIONS These findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.
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Affiliation(s)
| | - Penelope J Adamson
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Daryn Whybrow
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Caitlin A Selway
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lito E Papanicolas
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Mark Turra
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lex E X Leong
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000 Australia
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2
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Ramirez-Mata AS, Ostrov D, Salemi M, Marini S, Magalis BR. Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology. Microbiol Spectr 2023; 11:e0308622. [PMID: 36847516 PMCID: PMC10100676 DOI: 10.1128/spectrum.03086-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
In human immunodeficiency virus (HIV) infection, virus replication in and adaptation to the central nervous system (CNS) can result in neurocognitive deficits in approximately 25% of patients with unsuppressed viremia. While no single viral mutation can be agreed upon as distinguishing the neuroadapted population, earlier studies have demonstrated that a machine learning (ML) approach could be applied to identify a collection of mutational signatures within the virus envelope glycoprotein (Gp120) predictive of disease. The S[imian]IV-infected macaque is a widely used animal model of HIV neuropathology, allowing in-depth tissue sampling infeasible for human patients. Yet, translational impact of the ML approach within the context of the macaque model has not been tested, much less the capacity for early prediction in other, noninvasive tissues. We applied the previously described ML approach to prediction of SIV-mediated encephalitis (SIVE) using gp120 sequences obtained from the CNS of animals with and without SIVE with 97% accuracy. The presence of SIVE signatures at earlier time points of infection in non-CNS tissues indicated these signatures cannot be used in a clinical setting; however, combined with protein structural mapping and statistical phylogenetic inference, results revealed common denominators associated with these signatures, including 2-acetamido-2-deoxy-beta-d-glucopyranose structural interactions and high rate of alveolar macrophage (AM) infection. AMs were also determined to be the phyloanatomic source of cranial virus in SIVE animals, but not in animals that did not develop SIVE, implicating a role for these cells in the evolution of the signatures identified as predictive of both HIV and SIV neuropathology. IMPORTANCE HIV-associated neurocognitive disorders remain prevalent among persons living with HIV (PLWH) owing to our limited understanding of the contributing viral mechanisms and ability to predict disease onset. We have expanded on a machine learning method previously used on HIV genetic sequence data to predict neurocognitive impairment in PLWH to the more extensively sampled SIV-infected macaque model in order to (i) determine the translatability of the animal model and (ii) more accurately characterize the predictive capacity of the method. We identified eight amino acid and/or biochemical signatures in the SIV envelope glycoprotein, the most predominant of which demonstrated the potential for aminoglycan interaction characteristic of previously identified HIV signatures. These signatures were not isolated to specific points in time or to the central nervous system, limiting their use as an accurate clinical predictor of neuropathogenesis; however, statistical phylogenetic and signature pattern analyses implicate the lungs as a key player in the emergence of neuroadapted viruses.
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Affiliation(s)
- Andrea S. Ramirez-Mata
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - David Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Simone Marini
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Brittany Rife Magalis
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [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: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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4
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Guang A, Howison M, Ledingham L, D’Antuono M, Chan PA, Lawrence C, Dunn CW, Kantor R. Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses. Front Microbiol 2022; 12:803190. [PMID: 35250908 PMCID: PMC8891961 DOI: 10.3389/fmicb.2021.803190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022] Open
Abstract
Background Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown. Methods We introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island. Results Profile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions. Discussion Profile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.
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Affiliation(s)
- August Guang
- Center for Computational Biology of Human Disease, Brown University, Providence, RI, United States
- Center for Computation and Visualization, Brown University, Providence, RI, United States
- *Correspondence: August Guang,
| | - Mark Howison
- Research Improving People’s Lives, Providence, RI, United States
| | - Lauren Ledingham
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, United States
| | - Matthew D’Antuono
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, United States
| | - Philip A. Chan
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, United States
| | - Charles Lawrence
- Division of Applied Mathematics, Brown University, Providence, RI, United States
| | - Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Rami Kantor
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, United States
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5
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Aisyah DN, Story A, Kremyda-Vlachou M, Kozlakidis Z, Shalcross L, Hayward A. Assessing hepatitis C virus distribution among vulnerable populations in London using whole genome sequencing: results from the TB-REACH study. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16907.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Injecting drugs substantially increases the risk of hepatitis C virus (HCV) infection and is common in vulnerable population groups, such as the homeless and prisoners. Capturing accurate data on relative genotype distribution within these groups is essential to inform strategies to reduce HCV transmission. The aim of this study was to utilise a next-generation whole-genome sequencing method recently validated by Public Health England, in order to produce near complete HCV genomes. Methods: In total, 98 HCV positive patients were recruited from homeless hostels and drug treatment services through the National Health Services (NHS) Find and Treat (F&T) Service between May 2011 and June 2013 in London, UK. Samples were sequenced by Next-generation sequencing, with 88 complete HCV genomes constructed by a de novo assembly pipeline. They were analysed phylogenetically for an estimate of their genetic distance. Results: Of the 88 complete HCV genomes, 50/88 (56.8%) were genotype 1; 32/88 (36.4%) genotype 3; 4/88 (4.5%) genotype 2; and 1/88 (1.1%) for genotypes 4 and 6 each. Subtype 1a had the highest number of samples (51.1%), followed by subtype 3a (35.2%), 1b (5.7%), and 2b (3.4%). Samples collected from drug treatment services had the highest number of genotype 1 (69%); genotypes 4 and 6 were only found from samples collected in homeless shelters. Small clusters of highly related genomic sequences were observed both across and within the vulnerable groups sampled. Conclusions: Subsequent phylogenetic analysis provides a first indication that there are related HCV sequences amongst the three vulnerable population groups, reflecting their overlapping social behaviours. This study is the first presentation of whole genome HCV sequences from such vulnerable groups in London and paves the way for similar research in the future.
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Novitsky V, Steingrimsson J, Howison M, Dunn C, Gillani FS, Manne A, Li Y, Spence M, Parillo Z, Fulton J, Marak T, Chan P, Bertrand T, Bandy U, Alexander-Scott N, Hogan J, Kantor R. Longitudinal typing of molecular HIV clusters in a statewide epidemic. AIDS 2021; 35:1711-1722. [PMID: 34033589 PMCID: PMC8373695 DOI: 10.1097/qad.0000000000002953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND HIV molecular epidemiology is increasingly integrated into public health prevention. We conducted cluster typing to enhance characterization of a densely sampled statewide epidemic towards informing public health. METHODS We identified HIV clusters, categorized them into types, and evaluated their dynamics between 2004 and 2019 in Rhode Island. We grouped sequences by diagnosis year, assessed cluster changes between paired phylogenies, t0 and t1, representing adjacent years and categorized clusters as stable (cluster in t0 phylogeny = cluster in t1 phylogeny) or unstable (cluster in t0 ≠ cluster in t1). Unstable clusters were further categorized as emerging (t1 phylogeny only) or growing (larger in t1 phylogeny). We determined proportions of each cluster type, of individuals in each cluster type, and of newly diagnosed individuals in each cluster type, and assessed trends over time. RESULTS A total of 1727 individuals with available HIV-1 subtype B pol sequences were diagnosed in Rhode Island by 2019. Over time, stable clusters and individuals in them dominated the epidemic, increasing over time, with reciprocally decreasing unstable clusters and individuals in them. Conversely, proportions of newly diagnosed individuals in unstable clusters significantly increased. Within unstable clusters, proportions of emerging clusters and of individuals in them declined; whereas proportions of newly diagnosed individuals in growing clusters significantly increased over time. CONCLUSION Distinct molecular cluster types were identified in the Rhode Island epidemic. Cluster dynamics demonstrated increasing stable and decreasing unstable clusters driven by growing, rather than emerging clusters, suggesting consistent in-state transmission networks. Cluster typing could inform public health beyond conventional approaches and direct interventions.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People’s Life, Providence, RI, USA
| | | | | | | | | | | | | | | | | | - Philip Chan
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
| | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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7
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Parczewski M, Sulkowska E, Urbańska A, Scheibe K, Serwin K, Grabarczyk P. Transmitted HIV drug resistance and subtype patterns among blood donors in Poland. Sci Rep 2021; 11:12734. [PMID: 34140600 PMCID: PMC8211697 DOI: 10.1038/s41598-021-92210-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
Surveillance on the HIV molecular variability, risk of drug resistance transmission and evolution of novel viral variants among blood donors remains an understudied aspect of hemovigilance. This nationwide study analyses patterns of HIV diversity and transmitted resistance mutations. Study included 185 samples from the first time and repeat blood donors with HIV infection identified by molecular assay. HIV protease, reverse transcriptase and integrase were sequenced using population methods. Drug resistance mutation (DRM) patterns were analyzed based on the Stanford Interpretation Algorithm and standardized lists of transmitted mutations. Phylogeny was used to investigate subtyping, clustering and recombination patterns. HIV-1 subtype B (89.2%) followed by subtype A6 (7.6%) were predominant, while in three (1.6%) cases, novel recombinant B/A6 variants were identified. Non-B variants were more common among repeat donors (14.5%) compared to the first time ones (1.8%), p = 0.011, with higher frequency (9.9%) of A6 variant in the repeat donor group, p = 0.04. Major NRTI DRMs were observed in 3.8%, NNRTI and PI in 0.6% and INSTI 1.1% of cases. Additionally, E157Q polymorphism was observed in 9.8% and L74I in 11.5% of integrase sequences. Transmission of drug resistance among blood donors remains infrequent. Subtype patters increase in complexity with emergence of novel intersubtype A6B recombinants.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University, Arkońska 4, 71-455, Szczecin, Poland.
| | - Ewa Sulkowska
- Institute of Haematology and Transfusion Medicine in Warsaw, Warsaw, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University, Arkońska 4, 71-455, Szczecin, Poland
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University, Arkońska 4, 71-455, Szczecin, Poland
| | - Karol Serwin
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University, Arkońska 4, 71-455, Szczecin, Poland
| | - Piotr Grabarczyk
- Institute of Haematology and Transfusion Medicine in Warsaw, Warsaw, Poland
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8
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Novitsky V, Steingrimsson JA, Howison M, Gillani FS, Li Y, Manne A, Fulton J, Spence M, Parillo Z, Marak T, Chan PA, Bertrand T, Bandy U, Alexander-Scott N, Dunn CW, Hogan J, Kantor R. Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters. Sci Rep 2020; 10:18547. [PMID: 33122765 PMCID: PMC7596705 DOI: 10.1038/s41598-020-75560-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023] Open
Abstract
Public health interventions guided by clustering of HIV-1 molecular sequences may be impacted by choices of analytical approaches. We identified commonly-used clustering analytical approaches, applied them to 1886 HIV-1 Rhode Island sequences from 2004-2018, and compared concordance in identifying molecular HIV-1 clusters within and between approaches. We used strict (topological support ≥ 0.95; distance 0.015 substitutions/site) and relaxed (topological support 0.80-0.95; distance 0.030-0.045 substitutions/site) thresholds to reflect different epidemiological scenarios. We found that clustering differed by method and threshold and depended more on distance than topological support thresholds. Clustering concordance analyses demonstrated some differences across analytical approaches, with RAxML having the highest (91%) mean summary percent concordance when strict thresholds were applied, and three (RAxML-, FastTree regular bootstrap- and IQ-Tree regular bootstrap-based) analytical approaches having the highest (86%) mean summary percent concordance when relaxed thresholds were applied. We conclude that different analytical approaches can yield diverse HIV-1 clustering outcomes and may need to be differentially used in diverse public health scenarios. Recognizing the variability and limitations of commonly-used methods in cluster identification is important for guiding clustering-triggered interventions to disrupt new transmissions and end the HIV epidemic.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People's Life, Providence, RI, USA
| | | | | | | | | | | | | | | | - Philip A Chan
- Brown University, Providence, RI, USA
- Rhode Island Department of Health, Providence, RI, USA
| | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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9
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Abstract
PURPOSE OF REVIEW A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size. RECENT FINDINGS Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction. SUMMARY The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.
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10
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Molecular network-based intervention brings us closer to ending the HIV pandemic. Front Med 2020; 14:136-148. [PMID: 32206964 DOI: 10.1007/s11684-020-0756-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/13/2020] [Indexed: 01/08/2023]
Abstract
Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.
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11
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Kafando A, Serhir B, Doualla-Bell F, Fournier E, Sangaré MN, Martineau C, Sylla M, Chamberland A, El-Far M, Charest H, Tremblay CL. A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses. AIDS Res Hum Retroviruses 2019; 35:906-919. [PMID: 31407606 PMCID: PMC6806616 DOI: 10.1089/aid.2019.0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.
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Affiliation(s)
- Alexis Kafando
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Bouchra Serhir
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Ndongo Sangaré
- Département de Médecine Sociale et Préventive, École de Santé Publique, Université de Montréal, Montréal, Canada
| | - Christine Martineau
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Sylla
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Annie Chamberland
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Mohamed El-Far
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Hugues Charest
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Cécile L. Tremblay
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
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12
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Kostaki EG, Frampton D, Paraskevis D, Pantavou K, Ferns B, Raffle J, Grant P, Kozlakidis Z, Hadjikou A, Pavlitina E, Williams LD, Hatzakis A, Friedman SR, Nastouli E, Nikolopoulos GK. Near Full-length Genomic Sequencing and Molecular Analysis of HIV-Infected Individuals in a Network-based Intervention (TRIP) in Athens, Greece: Evidence that Transmissions Occur More Frequently from those with High HIV-RNA. Curr HIV Res 2019; 16:345-353. [PMID: 30706819 PMCID: PMC6446520 DOI: 10.2174/1570162x17666190130120757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/21/2019] [Accepted: 01/27/2019] [Indexed: 11/25/2022]
Abstract
Background: TRIP (Transmission Reduction Intervention Project) was a network-based, contact tracing approach to locate and link to care, mostly people who inject drugs (PWID) with recent HIV infection. Objective: We investigated whether sequences from HIV-infected participants with high viral load cluster together more frequently than what is expected by chance. Methods: Paired end reads were generated for 104 samples using Illumina MiSeq next-generation se-quencing. Results: 63 sequences belonged to previously identified local transmission networks of PWID (LTNs) of an HIV outbreak in Athens, Greece. For two HIV-RNA cut-offs (105 and 106 IU/mL), HIV transmissions were more likely between PWID with similar levels of HIV-RNA (p<0.001). 10 of the 14 sequences (71.4%) from PWID with HIV-RNA >106 IU/mL were clustered in 5 pairs. For 4 of these clusters (80%), there was in each one of them at least one sequence from a recently HIV-infected PWID. Conclusion: We showed that transmissions are more likely among PWID with high viremia.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Daniel Frampton
- Department of Infection and Immunity, UCL, London, United Kingdom
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Bridget Ferns
- NIHR Biomedical Research Centre, UCLH/UCL, London, United Kingdom
| | - Jade Raffle
- Department of Infection and Immunity, UCL, London, United Kingdom
| | - Paul Grant
- Department of Clinical Virology, UCLH, London, United Kingdom
| | - Zisis Kozlakidis
- Division of Infection and Immunity, Faculty of Medical Sciences, UCL and Farr Institute of Health Informatics Research, London, United Kingdom
| | - Andria Hadjikou
- Medical School, University of Cyprus, Nicosia, Cyprus.,European University Cyprus, Nicosia, Cyprus
| | - Eirini Pavlitina
- Transmission Reduction Intervention Project, Athens site, Athens, Greece
| | - Leslie D Williams
- National Development and Research Institutes, New York, United States
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Samuel R Friedman
- National Development and Research Institutes, New York, United States
| | - Eleni Nastouli
- NIHR Biomedical Research Centre, UCLH/UCL, London, United Kingdom.,Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
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13
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Abstract
PURPOSE OF REVIEW This review summarizes the use of genetic similarity clusters to understand HIV transmission and inform prevention efforts. RECENT FINDINGS Recent emphases include the development of real-time cluster identification in order to interrupt transmission chains, the use of clusters to estimate rates of transmission along the HIV care cascade, and the extension of cluster analyses to understand transmission in the generalized epidemics of sub-Saharan Africa. Importantly, this recent empirical work has been accompanied by theoretical work that elucidates the processes that underlie HIV genetic similarity clusters; multiple studies suggest that clusters are not necessarily enriched with individuals with high transmission rates, but rather can reflect variation in sampling times within a population, with individuals sampled early in infection more likely to cluster. Analyses of genetic similarity clusters have great promise to inform HIV epidemiology and prevention. Future emphases should include the collection of additional sequence data from underrepresented populations, such as those in sub-Saharan Africa, and further development and evaluation of clustering methods.
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Affiliation(s)
- Mary Kate Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, MD, USA
| | - Joshua T Herbeck
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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14
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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15
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Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Nat Commun 2019; 10:1411. [PMID: 30926780 PMCID: PMC6441045 DOI: 10.1038/s41467-019-09139-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022] Open
Abstract
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
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Affiliation(s)
- Oliver Ratmann
- Department of Mathematics, Imperial College London, London, SW72AZ, UK.
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK.
| | - M Kate Grabowski
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Matthew Hall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Tanya Golubchik
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris Wymant
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Lucie Abeler-Dörner
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - David Bonsall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Andrew Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Tulio de Oliveira
- College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Paul Kellam
- Department of Medicine, Imperial College London, London, W12 0HS, UK
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
- Africa Health Research Institute, Private Bag X7, Durban, 4013, South Africa
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Godfrey Kigozi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Thomas C Quinn
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - Maria J Wawer
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Makerere University School of Public Health, Kampala, 8HQG+3V, Uganda
| | - Ronald H Gray
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
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16
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Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations. Sci Rep 2019; 9:1051. [PMID: 30705307 PMCID: PMC6355892 DOI: 10.1038/s41598-018-37458-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Although fishing communities (FCs) in Uganda are disproportionately affected by HIV-1 relative to the general population (GP), the transmission dynamics are not completely understood. We earlier found most HIV-1 transmissions to occur within FCs of Lake Victoria. Here, we test the hypothesis that HIV-1 transmission in FCs is isolated from networks in the GP. We used phylogeography to reconstruct the geospatial viral migration patterns in 8 FCs and 2 GP cohorts and a Bayesian phylogenetic inference in BEAST v1.8.4 to analyse the temporal dynamics of HIV-1 transmission. Subtype A1 (pol region) was most prevalent in the FCs (115, 45.1%) and GP (177, 50.4%). More recent HIV transmission pairs from FCs were found at a genetic distance (GD) <1.5% than in the GP (Fisher’s exact test, p = 0.001). The mean time depth for pairs was shorter in FCs (5 months) than in the GP (4 years). Phylogeographic analysis showed strong support for viral migration from the GP to FCs without evidence of substantial viral dissemination to the GP. This suggests that FCs are a sink for, not a source of, virus strains from the GP. Targeted interventions in FCs should be extended to include the neighbouring GP for effective epidemic control.
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17
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Kayondo HW, Mwalili S, Mango JM. Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/cmb.2019.94009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Hoshino K, Sugiyama M, Date T, Maruwaka S, Arakaki S, Shibata D, Maeshiro T, Hokama A, Sakugawa H, Kanto T, Fujita J, Mizokami M. Phylogenetic and phylodynamic analyses of hepatitis C virus subtype 1a in Okinawa, Japan. J Viral Hepat 2018; 25:976-985. [PMID: 29577516 DOI: 10.1111/jvh.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 02/02/2018] [Indexed: 12/28/2022]
Abstract
Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequences were obtained from 29 patients during 2011-2016. Phylogenetic trees were reconstructed to identify the origin and characteristics of HCV-1a in Okinawa with epidemiological information. A phylogenetic tree based on whole-genome sequencing revealed that all of the samples were located below the US branches. Additionally, we identified one cluster comprised of 17 strains (Okinawa, n = 16; United States, n = 1). The majority of the patients in this cluster were people who inject drugs (PWID), indicating the presence of a people who inject drugs (PWID) cluster. Subsequently, Bayesian analyses were employed to reveal viral population dynamics. Intriguingly, a phylodynamic analysis uncovered a substantial increase in effective population size of HCV-1a from 1965 to 1980 and a slight increase in mid-2000, which were associated with an increase in illicit drug use in Okinawa. The estimated divergence time of the PWID cluster was 1967.6 (1964.2-1971.1). These findings suggest that HCV-1a was introduced into Okinawa from the United States in the late 1960s, coincident with the Vietnam War. Subsequently, HCV-1a might have spread among the Japanese population with the spread of injecting drug use. Our study provides an understanding of HCV transmission dynamics in Okinawa, as well as the key role of PWID in HCV transmission.
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Affiliation(s)
- K Hoshino
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan.,Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - T Date
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - S Maruwaka
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - S Arakaki
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - D Shibata
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Maeshiro
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - A Hokama
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - H Sakugawa
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Kanto
- Department of Liver Diseases, National Center for Global Health and Medicine, Chiba, Japan
| | - J Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
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19
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Zhukova A, Cutino-Moguel T, Gascuel O, Pillay D. The Role of Phylogenetics as a Tool to Predict the Spread of Resistance. J Infect Dis 2017; 216:S820-S823. [PMID: 29029155 DOI: 10.1093/infdis/jix411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug resistance mutations emerge in genetic sequences of HIV through drug-selective pressure. Drug resistance can be transmitted. In this review we discuss phylogenetic methods used to study the emergence of drug resistance and the spread of resistant viruses.
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Affiliation(s)
- Anna Zhukova
- Unité Bioinformatique Evolutive, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, C3BI USR 3756 Institut Pasteur et CNRS, France
| | | | - Olivier Gascuel
- Unité Bioinformatique Evolutive, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, C3BI USR 3756 Institut Pasteur et CNRS, France
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, United Kingdom.,Africa Health Research Institute, KwaZulu-Natal, South Africa
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20
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Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost S, Gall A, Gaseitsiwe S, Grabowski MK, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Brown AL, de Oliveira T, Kellam P, Pillay D, Fraser C, on behalf of the PANGEA-HIV Consort. HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS Res Hum Retroviruses 2017; 33:1083-1098. [PMID: 28540766 PMCID: PMC5597042 DOI: 10.1089/aid.2017.0061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the “Phylogenetics and Networks for Generalised HIV Epidemics in Africa” consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n = 2,833; MRC/UVRI Uganda, n = 701; Mochudi Prevention Project, n = 359; Africa Health Research Institute Resistance Cohort, n = 92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3′ end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences (NGS) has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phylogeny reconstruction is expected.
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Affiliation(s)
- Oliver Ratmann
- MRC Centre for Outbreak Analyses and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Chris Wymant
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Siva Danaviah
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Max Essex
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Simon Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Astrid Gall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Mary K. Grabowski
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Ronald Gray
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Stephane Guindon
- Department of Statistics, University of Auckland, Auckland, New Zealand
- Laboratoire d'Informatique, de Robotique et de Microelectronique de Montpellier–UMR 5506, CNRS & UM, Montpellier, France
| | - Arndt von Haeseler
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | - Michelle Kendall
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Alexey Kozlov
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Justen Manasa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Bui Quang Minh
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Entebbe, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
- Department of Medicine Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jana Trifinopoulos
- Centre for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Maria Wawer
- Department of Epidemiology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Andy Leigh Brown
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Paul Kellam
- Department of Infectious Diseases and Immunity, Imperial College London, United Kingdom
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection & Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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21
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Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017; 12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. METHODS Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. RESULTS Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]). CONCLUSIONS A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.
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Affiliation(s)
- Sylvia Kiwuwa-Muyingo
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Jamirah Nazziwa
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Pauliina Ilmonen
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Harr Njai
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Chris Parry
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Asiki Gershim
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Neilsen
- International AIDS Vaccine Initiative, New York, United States of America
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Heikki Seppälä
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Fred Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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22
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Ahn MY, Wertheim JO, Kim WJ, Kim SW, Lee JS, Ann HW, Jeon Y, Ahn JY, Song JE, Oh DH, Kim YC, Kim EJ, Jung IY, Kim MH, Jeong W, Jeong SJ, Ku NS, Kim JM, Smith DM, Choi JY. Short Communication: HIV-1 Transmission Networks Across South Korea. AIDS Res Hum Retroviruses 2017; 33:827-831. [PMID: 28346838 DOI: 10.1089/aid.2016.0212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular epidemiology can help clarify the properties and dynamics of HIV-1 transmission networks in both global and regional scales. We studied 143 HIV-1-infected individuals recruited from four medical centers of three cities in South Korea between April 2013 and May 2014. HIV-1 env V3 sequence data were generated (337-793 bp) and analyzed using a pairwise distance-based clustering approach to infer putative transmission networks. Participants whose viruses were ≤2.0% divergent according to Tamura-Nei 93 genetic distance were defined as clustering. We collected demographic, risk, and clinical data and analyzed these data in relation to clustering. Among 143 participants, we identified nine putative transmission clusters of different sizes (range 2-4 participants). The reported risk factor of participants were concordant in only one network involving two participants, that is, both individuals reported homosexual sex as their risk factor. The participants in the other eight networks did not report concordant risk factors, although they were phylogenetically linked. About half of the participants refused to report their risk factor. Overall, molecular epidemiology provides more information to understand local transmission networks and the risks associated with these networks.
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Affiliation(s)
- Mi Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Joel O. Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Woo Joo Kim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, South Korea
| | - Shin-Woo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jin Soo Lee
- Department of Internal Medicine, Inha University School of Medicine, Incheon, South Korea
| | - Hea Won Ann
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yongduk Jeon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jin Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Je Eun Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Dong Hyun Oh
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong Chan Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Jin Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Moo Hyun Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Wooyoung Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
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