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Obeng BM, Kelleher AD, Di Giallonardo F. Molecular epidemiology to aid virtual elimination of HIV transmission in Australia. Virus Res 2024; 341:199310. [PMID: 38185332 PMCID: PMC10825322 DOI: 10.1016/j.virusres.2024.199310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
The Global UNAIDS 95/95/95 targets aim to increase the percentage of persons who know their HIV status, receive antiretroviral therapy, and have achieved viral suppression. Achieving these targets requires efforts to improve the public health response to increase access to care for those living with HIV, identify those yet undiagnosed with HIV early, and increase access to prevention for those most at risk of HIV acquisition. HIV infections in Australia are among the lowest globally having recorded significant declines in new diagnoses in the last decade. However, the HIV epidemic has changed with an increasing proportion of newly diagnosed infections among those born outside Australia observed in the last five years. Thus, the current prevention efforts are not enough to achieve the UNAIDS targets and virtual elimination across all population groups. We believe both are possible by including molecular epidemiology in the public health response. Molecular epidemiology methods have been crucial in the field of HIV prevention, particularly in demonstrating the efficacy of treatment as prevention. Cluster detection using molecular epidemiology can provide opportunities for the real-time detection of new outbreaks before they grow, and cluster detection programs are now part of the public health response in the USA and Canada. Here, we review what molecular epidemiology has taught us about HIV evolution and spread. We summarize how we can use this knowledge to improve public health measures by presenting case studies from the USA and Canada. We discuss the successes and challenges of current public health programs in Australia, and how we could use cluster detection as an add-on to identify gaps in current prevention measures easier and respond quicker to growing clusters. Lastly, we raise important ethical and legal challenges that need to be addressed when HIV genotypic data is used in combination with personal data.
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Affiliation(s)
- Billal M Obeng
- The Kirby Institute, University of New South Wales, Sydney, Australia
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2
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Bowden-Reid E, Ledger S, Zhang Y, Di Giallonardo F, Aggarwal A, Stella AO, Akerman A, Milogiannakis V, Walker G, Rawlinson W, Turville S, Kelleher AD, Ahlenstiel C. Novel siRNA therapeutics demonstrate multi-variant efficacy against SARS-CoV-2. Antiviral Res 2023; 217:105677. [PMID: 37478918 DOI: 10.1016/j.antiviral.2023.105677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a respiratory virus that causes COVID-19 disease, with an estimated global mortality of approximately 2%. While global response strategies, which are predominantly reliant on regular vaccinations, have shifted from zero COVID to living with COVID, there is a distinct lack of broad-spectrum direct acting antiviral therapies that maintain efficacy across evolving SARS-CoV-2 variants of concern. This is of most concern for immunocompromised and immunosuppressed individuals who lack robust immune responses following vaccination, and others at risk for severe COVID and long-COVID. RNA interference (RNAi) therapeutics induced by short interfering RNAs (siRNAs) offer a promising antiviral treatment option, with broad-spectrum antiviral capabilities unparalleled by current antiviral therapeutics and a high genetic barrier to antiviral escape. Here we describe novel siRNAs, targeting highly conserved regions of the SARS-CoV-1 and 2 genome of both human and animal species, with multi-variant antiviral potency against eight SARS-CoV-2 lineages - Ancestral VIC01, Alpha, Beta, Gamma, Delta, Zeta, Kappa and Omicron. Treatment with our siRNA resulted in significant protection against virus-mediated cell death in vitro, with >97% cell survival (P < 0.0001), and corresponding reductions of viral nucleocapsid RNA of up to 99.9% (P < 0.0001). When compared to antivirals; Sotrovimab and Remdesivir, the siRNAs demonstrated a more potent antiviral effect and similarly, when multiplexing siRNAs to target different viral regions simultaneously, an increased antiviral effect was observed compared to individual siRNA treatments (P < 0.0001). These results demonstrate the potential for a highly effective broad-spectrum direct acting antiviral against multiple SARS-CoV-2 variants, including variants resistant to antivirals and vaccine generated neutralizing antibodies.
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Affiliation(s)
| | - Scott Ledger
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Yuan Zhang
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | | | | | - Gregory Walker
- New South Wales Health Pathology, Sydney, NSW, Australia
| | - William Rawlinson
- New South Wales Health Pathology, Sydney, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), Prince of Wales Hospital, Sydney, NSW, Australia
| | - Stuart Turville
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Anthony D Kelleher
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Chantelle Ahlenstiel
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia.
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3
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Sghaier S, Sailleau C, Marcacci M, Thabet S, Curini V, Ben Hassine T, Teodori L, Portanti O, Hammami S, Jurisic L, Spedicato M, Postic L, Gazani I, Ben Osman R, Zientara S, Bréard E, Calistri P, Richt JA, Holmes EC, Savini G, Di Giallonardo F, Lorusso A. Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 2022; 15:16. [PMID: 36680057 PMCID: PMC9866946 DOI: 10.3390/v15010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Epizootic haemorrhagic disease (EHD) is a Culicoides-borne viral disease caused by the epizootic haemorrhagic disease virus (EHDV) associated with clinical manifestations in domestic and wild ruminants, primarily white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus). In late September 2021, EHDV was reported in cattle farms in central/western Tunisia. It rapidly spread throughout the country with more than 200 confirmed outbreaks. We applied a combination of classical and molecular techniques to characterize the causative virus as a member of the serotype EHDV-8. This is the first evidence of EHDV- 8 circulation since 1982 when the prototype EHDV-8 strain was isolated in Australia. This work highlights the urgent need for vaccines for a range of EHDV serotypes.
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Affiliation(s)
- Soufien Sghaier
- Institut de la Recherche Vétérinaire de Tunisie, Tunis 1006, Tunisia
| | - Corinne Sailleau
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Sarah Thabet
- Institut de la Recherche Vétérinaire de Tunisie, Tunis 1006, Tunisia
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Thameur Ben Hassine
- Direction Générale des Services Vétérinaires, Commissariat Régional au Développement Agricole de Nabeul, Nabeul 1082, Tunisia
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Salah Hammami
- Service de Microbiologie, Immunologie et Pathologie Générale, École Nationale de Médecine Vétérinaire de Sidi Thabet, IRESA, Universitè de la Manouba, Winnipeg 2010, Tunisia
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
- Facoltà di Medicina Veterinaria, Università degli Studi di Teramo, 64100 Piano D’Accio-Teramo, Italy
| | - Massimo Spedicato
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Lydie Postic
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Ines Gazani
- CRDA Ministère d’Agriculture, Avenue Habib Bourguiba, Kasserine 1200, Tunisia
| | - Raja Ben Osman
- National Drug Control Laboratory, Vaccine Control Unit, Tunis 1002, Tunisia
| | - Stephan Zientara
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Emmanuel Bréard
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Jürgen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | | | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
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Molini U, Curini V, Jacobs E, Tongo E, Berjaoui S, Hemberger MY, Puglia I, Jago M, Khaiseb S, Cattoli G, Dundon WG, Lorusso A, Di Giallonardo F. First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa. Acta Trop 2022; 232:106482. [PMID: 35537488 DOI: 10.1016/j.actatropica.2022.106482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 01/04/2023]
Abstract
Influenza D virus (IDV) was first isolated in 2011 in the USA and has since been shown to circulate in cattle, pigs, sheep, wild boar, and camels. In Africa, there is limited data on the epidemiology of IDV and, so, we investigated the presence of IDV among domestic ruminants and wild animals in Namibia by screening nasal swabs using an IDV-specific molecular assay. IDV RNA was detected in bovines (n=2), giraffes (n=2) and wildebeest (n=1). The hemagglutinin-esterase-fusion (HEF) gene from one of the bovine and the wildebeest samples was successfully sequenced as well as the full genome for the second bovine sample. Phylogenetic analysis of the HEF gene positioned the African virus variants within the D/OK lineage but with a long branch. The African variant had an amino acid diversity of 2.41% and most likely represents a distinct genotype within the lineage. Notably, the polymerase acidic protein gene (PA) was more closely related to a different lineage (D/660), indicative of potential reassortment. This is the first genetic characterization of IDV in Africa and it adds important data to our understanding of the global IDV distribution.
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Spedicato M, Compagni ED, Caporale M, Teodori L, Leone A, Ancora M, Mangone I, Perletta F, Portanti O, Di Giallonardo F, Bonfini B, Savini G, Lorusso A. Reemergence of an atypical bluetongue virus strain in goats, Sardinia, Italy. Res Vet Sci 2022; 151:36-41. [PMID: 35853329 DOI: 10.1016/j.rvsc.2022.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/19/2022]
Abstract
Bluetongue virus (BTV) is the etiologic agent of bluetongue, a WOAH (founded as Office International des Épizooties, OIE)-notifiable economically important disease of ruminants. BTV is transmitted by Culicoides biting midges and 24 different "classical" serotypes have been reported to date. In recent years, several putative novel BTV serotypes, often referred to as "atypical" BTVs, have been documented. These are characterized by unusual biological characteristics, most notably avirulence and vector-independent transmission. Here, we describe the recurrence of such an atypical virus strain BTV-X ITL2021 detected in goats six years after its first discovery in Sardinia, Italy. Combined serological and genome analysis results clearly suggest that the two strains belong to the same BTV serotype. However, unlike the 2015 strain, BTV-X ITL2021 was successfully isolated in BSR cell-culture allowing further serological characterization. Lastly, seropositivity for BTV-X ITL2021 was detected by virus-neutralization in approximately 74% of animals tested, suggesting that this atypical BTV serotype has been circulating undetected in asymptomatic animals for years.
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Affiliation(s)
- Massimo Spedicato
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy.
| | | | - Marialuigia Caporale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Alessandra Leone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Fabrizia Perletta
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | | | - Barbara Bonfini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-Teramo), Teramo, Italy
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6
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Amato L, Jurisic L, Puglia I, Di Lollo V, Curini V, Torzi G, Di Girolamo A, Mangone I, Mancinelli A, Decaro N, Calistri P, Di Giallonardo F, Lorusso A, D’Alterio N. Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Emerg Microbes Infect 2021; 10:1148-1155. [PMID: 34019466 PMCID: PMC8205086 DOI: 10.1080/22221751.2021.1933609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 01/24/2023]
Abstract
Several lineages of SARS-CoV-2 are currently circulating worldwide. During SARS-CoV-2 diagnostic activities performed in Abruzzo region (central Italy) several strains belonging to the B.1.177.75 lineage tested negative for the N gene but positive for the ORF1ab and S genes (+/+/- pattern) by the TaqPath COVID-19 CE-IVD RT-PCR Kit manufactured by Thermofisher. By sequencing, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that N gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present, in turn, in all B.1.177.75 sequences available on public databases. Furthermore, epidemiological analysis was also performed. The majority of the N-negative B.1.177.75 cases belonged to two clusters apparently unrelated to each other and both clusters involved young people. However, the phylogeny for sequences containing the +/+/- pattern strongly supports a genetic connection and one common source for both clusters. Though, genetic comparison suggests a connection rather than indicating the independent emergence of the same mutation in two apparently unrelated clusters. This study highlights once more the importance of sharing genomic data to link apparently unrelated epidemiological clusters and to, remarkably, update molecular tests.
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Affiliation(s)
- Laura Amato
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Giuseppe Torzi
- Azienda Sanitaria Locale, Lanciano-Vasto-Chieti, Chieti, Italy
| | | | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | | | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | | | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
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7
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Geoghegan JL, Giallonardo FD, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. Erratum: Virome composition in marine fish revealed by meta-transcriptomics. Virus Evol 2021; 7:veab035. [PMID: 34158971 PMCID: PMC8210879 DOI: 10.1093/ve/veab035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Affiliation(s)
- Leo A. Featherstone
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
| | | | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and BiosecurityThe University of Sydney Sydney NSW Australia
- Charles Perkins Centre School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- School of Medical Sciences The University of Sydney Sydney NSW Australia
| | - Timothy G. Vaughan
- Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland
- Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland
| | - Sebastián Duchêne
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
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9
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Kok YL, Vongrad V, Chaudron SE, Shilaih M, Leemann C, Neumann K, Kusejko K, Di Giallonardo F, Kuster H, Braun DL, Kouyos RD, Günthard HF, Metzner KJ. HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection. JCI Insight 2021; 6:143940. [PMID: 33784259 PMCID: PMC8262285 DOI: 10.1172/jci.insight.143940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/25/2021] [Indexed: 12/29/2022] Open
Abstract
HIV-1 is capable of integrating its genome into that of its host cell. We examined the influence of the activation state of CD4+ T cells, the effect of antiretroviral therapy (ART), and the clinical stage of HIV-1 infection on HIV-1 integration site features and selection. HIV-1 integration sites were sequenced from longitudinally sampled resting and activated CD4+ T cells from 12 HIV-1–infected individuals. In total, 589 unique HIV-1 integration sites were analyzed: 147, 391, and 51 during primary, chronic, and late presentation of HIV-1 infection, respectively. As early as during primary HIV-1 infection and independent of the activation state of CD4+ T cells collected on and off ART, HIV-1 integration sites were preferentially detected in recurrent integration genes, genes associated with clonal expansion of latently HIV-1–infected CD4+ T cells, cancer-related genes, and highly expressed genes. The preference for cancer-related genes was more pronounced at late stages of HIV-1 infection. Host genomic features of HIV-1 integration site selection remained stable during HIV-1 infection in both resting and activated CD4+ T cells. In summary, characteristic HIV-1 integration site features are preestablished as early as during primary HIV-1 infection and are found in both resting and activated CD4+ T cells.
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Affiliation(s)
- Yik Lim Kok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Mohaned Shilaih
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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10
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Geoghegan JL, Di Giallonardo F, Wille M, Ortiz-Baez AS, Costa VA, Ghaly T, Mifsud JCO, Turnbull OMH, Bellwood DR, Williamson JE, Holmes EC. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evol 2021; 7:veab005. [PMID: 33623709 PMCID: PMC7887440 DOI: 10.1093/ve/veab005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, negative-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae, and Flaviviridae, and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition-viral richness, abundance, and diversity-can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi, and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.,Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.,Institute of Environmental Science and Research, Wellington 5018, New Zealand
| | | | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vincenzo A Costa
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Timothy Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonathon C O Mifsud
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Olivia M H Turnbull
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - David R Bellwood
- ARC Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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11
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Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Selvey C, Nigro SJ, Fraser N, Price K, Holden J, Lee FJ, Dwyer DE, Bavinton BR, Geoghegan JL, Grulich AE, Kelleher AD. Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia. J Int AIDS Soc 2021; 24:e25655. [PMID: 33474833 PMCID: PMC7817915 DOI: 10.1002/jia2.25655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/27/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses. METHODS We used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01_AE (CRF01_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics. RESULTS We identified 104 subtype B and 11 CRF01_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01_AE respectively. We observed a > 2-fold increase in the number of NSW-specific CRF01_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above-average growth rate (>1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01_AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals. CONCLUSIONS The large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01_AE.
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Affiliation(s)
| | - Angie N Pinto
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
- Royal Prince Alfred HospitalSydneyNSWAustralia
| | - Phillip Keen
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
| | - Ansari Shaik
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
| | | | - Hanan Salem
- New South Wales Health Pathology‐RPARoyal Prince Alfred HospitalCamperdownNSWAustralia
| | | | | | - Neil Fraser
- Positive Life New South WalesSydneyNSWAustralia
| | | | | | - Frederick J Lee
- New South Wales Health Pathology‐RPARoyal Prince Alfred HospitalCamperdownNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Dominic E Dwyer
- New South Wales Health Pathology‐ICPMRWestmead HospitalWestmeadNSWAustralia
| | | | - Jemma L Geoghegan
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Andrew E Grulich
- The Kirby InstituteThe University of New South WalesSydneyNSWAustralia
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12
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Di Giallonardo F, Duchene S, Puglia I, Curini V, Profeta F, Cammà C, Marcacci M, Calistri P, Holmes EC, Lorusso A. Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses 2020; 12:E1438. [PMID: 33327566 PMCID: PMC7765063 DOI: 10.3390/v12121438] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide "lockdown" (8 March-3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.
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Affiliation(s)
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne 3010, Australia;
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
| | - Francesca Profeta
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, 70010 Valenzano, Italy
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney 2006, Australia;
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, 64100 Teramo, Italy; (I.P.); (V.C.); (F.P.); (C.C.); (M.M.); (P.C.); (A.L.)
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13
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Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Selvey C, Nigro SJ, Fraser N, Price K, Holden J, Lee FJ, Dwyer DE, Bavinton BR, Grulich AE, Kelleher AD, On Behalf Of The Nsw Hiv Prevention Partnership Project. Increased HIV Subtype Diversity Reflecting Demographic Changes in the HIV Epidemic in New South Wales, Australia. Viruses 2020; 12:E1402. [PMID: 33291330 PMCID: PMC7762219 DOI: 10.3390/v12121402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/24/2022] Open
Abstract
Changes over time in HIV-1 subtype diversity within a population reflect changes in factors influencing the development of local epidemics. Here we report on the genetic diversity of 2364 reverse transcriptase sequences from people living with HIV-1 in New South Wales (NSW) notified between 2004 and 2018. These data represent >70% of all new HIV-1 notifications in the state over this period. Phylogenetic analysis was performed to identify subtype-specific transmission clusters. Subtype B and non-B infections differed across all demographics analysed (p < 0.001). We found a strong positive association for infections among females, individuals not born in Australia or reporting heterosexual transmission being of non-B origin. Further, we found an overall increase in non-B infections among men who have sex with men from 50 to 79% in the last 10 years. However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. However, we found seven non-B clusters (≥5 sequences) indicative of local ongoing transmission. In conclusion, we present how the HIV-1 epidemic has changed over time in NSW, becoming more heterogeneous with distinct subtype-specific demographic associations.
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Affiliation(s)
| | - Angie N Pinto
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
- Royal Prince Alfred Hospital, Sydney 2050, Australia
| | - Phillip Keen
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Ansari Shaik
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Alex Carrera
- HIV Reference Laboratory, Sydney 2010, Australia
| | - Hanan Salem
- New South Wales Health Pathology-RPA, Royal Prince Alfred Hospital, Camperdown 2050, Australia
| | | | | | - Neil Fraser
- Positive Life New South Wales, Sydney 2010, Australia
| | - Karen Price
- AIDS Council of NSW (ACON), Sydney 2010, Australia
| | | | - Frederick J Lee
- New South Wales Health Pathology-RPA, Royal Prince Alfred Hospital, Camperdown 2050, Australia
- Sydney Medical School, University of Sydney, Sydney 2050, Australia
| | - Dominic E Dwyer
- New South Wales Health Pathology-ICPMR, Westmead Hospital, Westmead 2145, Australia
| | - Benjamin R Bavinton
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Andrew E Grulich
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
| | - Anthony D Kelleher
- The Kirby Institute, The University of New South Wales, Sydney 2052, Australia
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14
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Campbell SJ, Ashley W, Gil-Fernandez M, Newsome TM, Di Giallonardo F, Ortiz-Baez AS, Mahar JE, Towerton AL, Gillings M, Holmes EC, Carthey AJR, Geoghegan JL. Red fox viromes in urban and rural landscapes. Virus Evol 2020; 6:veaa065. [PMID: 33365150 PMCID: PMC7744383 DOI: 10.1093/ve/veaa065] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans whilst remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live at higher densities, and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To investigate this possibility, we used a meta-transcriptomic approach to characterise the virome of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. We identified ten potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae, and Picornaviridae as well as rabbit haemorrhagic disease virus-2. This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human–wildlife interface.
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Affiliation(s)
- Sarah J Campbell
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Wilbur Ashley
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Margarita Gil-Fernandez
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Thomas M Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jackie E Mahar
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alison L Towerton
- Greater Sydney Local Land Services, Sydney, New South Wales 2750, Australia
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.,Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.,Institute of Environmental Science and Research, Wellington 5018, New Zealand
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15
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Koh C, Audsley MD, Di Giallonardo F, Kerton EJ, Young PR, Holmes EC, McGraw EA. Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture. Virus Evol 2019; 5:vez012. [PMID: 31191980 PMCID: PMC6555872 DOI: 10.1093/ve/vez012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Wolbachia is an intracellular endosymbiont of insects that inhibits the replication of a range of pathogens in its arthropod hosts. The release of Wolbachia into wild populations of mosquitoes is an innovative biocontrol effort to suppress the transmission of arthropod-borne viruses (arboviruses) to humans, most notably dengue virus. The success of the Wolbachia-based approach hinges upon the stable persistence of the ‘pathogen blocking’ effect, whose mechanistic basis is poorly understood. Evidence suggests that Wolbachia may affect viral replication via a combination of competition for host resources and activation of host immunity. The evolution of resistance against Wolbachia and pathogen blocking in the mosquito or the virus could reduce the public health impact of the symbiont releases. Here, we investigate if dengue 3 virus (DENV-3) is capable of accumulating adaptive mutations that improve its replicative capacity during serial passage in Wolbachia wMel-infected cells. During the passaging regime, viral isolates in Wolbachia-infected cells exhibited greater variation in viral loads compared to controls. The viral loads of these isolates declined rapidly during passaging due to the blocking effects of Wolbachia carriage, with several being lost all together and the remainder recovering to low but stable levels. We attempted to sequence the genomes of the surviving passaged isolates but, given their low abundance, were unable to obtain sufficient depth of coverage for evolutionary analysis. In contrast, viral loads in Wolbachia-free control cells were consistently high during passaging. The surviving isolates passaged in the presence of Wolbachia exhibited a reduced ability to replicate even in Wolbachia-free cells. These experiments demonstrate the challenge for dengue in evolving resistance to Wolbachia-mediated blocking.
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Affiliation(s)
- Cassandra Koh
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Michelle D Audsley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,The Kirby Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Emily J Kerton
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Paul R Young
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Elizabeth A McGraw
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Department of Entomology, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
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16
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Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Telfer B, Cooper C, Price K, Selvey C, Holden J, Bachmann N, Lee FJ, Dwyer DE, Duchêne S, Holmes EC, Grulich AE, Kelleher AD. Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia. Viruses 2019; 11:v11050482. [PMID: 31137836 PMCID: PMC6563510 DOI: 10.3390/v11050482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Australia’s response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world’s lowest HIV incidence rates—0.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE sampled in NSW, were combined with those sampled globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences; however, five large clades comprising ≥10 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016/2017. Seven such clades each comprised ≥10 sequences, and are representative of individual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, individual sub-epidemics are present and should be closely monitored.
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Affiliation(s)
- Francesca Di Giallonardo
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Angie N Pinto
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
- Department of Infectious Diseases & Microbiology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia.
| | - Phillip Keen
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Ansari Shaik
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Alex Carrera
- New South Wales State Reference Laboratory for HIV/AIDS, Darlinghurst, New South Wales 2010, Australia.
| | - Hanan Salem
- New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia.
| | - Barbara Telfer
- Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia.
| | - Craig Cooper
- Positive Life New South Wales, Surry Hills, New South Wales 2010, Australia.
| | - Karen Price
- ACON Health Ltd., Surry Hills, New South Wales 2010, Australia.
| | - Christine Selvey
- Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia.
| | - Joanne Holden
- Centre for Population Health, New South Wales Ministry of Health, North Sydney, New South Wales 2059, Australia.
| | - Nadine Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland.
| | - Frederick J Lee
- New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia.
- Department of Clinical Immunology & Allergy, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia.
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia.
| | - Dominic E Dwyer
- New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia.
| | - Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Edward C Holmes
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia.
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia.
| | - Andrew E Grulich
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Anthony D Kelleher
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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17
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Abstract
Aquaculture is the fastest growing industry worldwide. Aquatic diseases have had enormous economic and environmental impacts in the recent past and the emergence of new aquatic pathogens, particularly viruses, poses a continuous threat. Nevertheless, little is known about the diversity, abundance and evolution of fish viruses. We used a meta-transcriptomic approach to help determine the virome of seemingly healthy fish sold at a market in Sydney, Australia. Specifically, by identifying and quantifying virus transcripts we aimed to determine (i) the abundance of viruses in market fish, (ii) test a key component of epidemiological theory that large and dense host populations harbour a greater number of viruses compared to their more solitary counterparts and (iii) reveal the relative roles of virus–host co-divergence and cross-species transmission in the evolution of fish viruses. The species studied comprised both shoaling fish—eastern sea garfish (Hyporhamphus australis) and Australasian snapper (Chrysophrys auratus)—and more solitary fish—eastern red scorpionfish (Scorpaena jacksoniensis) and largetooth flounder (Pseudorhombus arsius). Our analysis identified twelve potentially novel viruses, eight of which were likely vertebrate-associated across four viral families and that exhibited frequent cross-species transmission. Notably, the most solitary of the fish species studied, the largetooth flounder, harboured the least number of viruses while eastern sea garfish, a densely shoaling fish, had the highest number of viruses. These results support the emerging view that fish harbour a large and largely uncharacterised virome.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.,The Kirby Institute, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Kate Cousins
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
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18
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Pinto AN, Hawke K, Castley A, Chibo D, Giallonardo FD, Cooper C, Sawleshwarkar S, Kelleher A, Dwyer DE. HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia. Future Virol 2018. [DOI: 10.2217/fvl-2018-0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Australia has maintained a low prevalence of HIV, with a mainly concentrated epidemic and successful public health response. With the widespread availability of HIV genotyping for resistance testing, and development of phylogenetic methodologies, the field of molecular epidemiology has evolved a deeper understanding of diversity and transmission dynamics of HIV. Studies combining HIV genotype with epidemiological data have allowed insights to be gained into the changing subtype diversity, rates of transmitted drug resistance and transmission networks of HIV in Australia. This review provides an overview of HIV molecular epidemiology studies in Australia.
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Affiliation(s)
- Angie N Pinto
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Karen Hawke
- South Australian Health & Medical Research Institute, Adelaide, South Australia
| | - Allison Castley
- PathWest, Clinical Immunology, Department of Health, Murdoch, Western Australia, Australia
| | - Doris Chibo
- HIV Characterization Laboratory, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, Victoria, Australia
| | | | - Craig Cooper
- Positive Life NSW, Sydney, New South Wales, Australia
| | - Shailendra Sawleshwarkar
- The University of Sydney, Faculty of Medicine & Health, Westmead Clinical School, Western Sydney Sexual Health Centre, Parramatta, New South Wales, Australia
| | - Anthony Kelleher
- The Kirby Institute, The University of New South Wales, UNSW Sydney, Australia
| | - Dominic E Dwyer
- NSWHP-ICPMR, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, University of Sydney, Westmead, Australia
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19
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Di Giallonardo F, Audsley MD, Shi M, Young PR, McGraw EA, Holmes EC. Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line. J Gen Virol 2018; 99:832-836. [PMID: 29741476 DOI: 10.1099/jgv.0.001079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel negative-sense RNA virus, Aedes aegypti anphevirus, was recently identified in wild Aedes aegypti mosquitoes. We show that this virus is also present in the Aag2 Aedes aegypti cell line and characterize its complete genome and evolutionary history. The Aedes aegypti anphevirus genome is estimated to be 12 916 nucleotides in length, contains four genes and has a genome structure similar to that of other anpheviruses. Phylogenetically, Aedes aegypti anphevirus falls within an unclassified group of insect-specific viruses in the order Mononegavirales that form a sister-group to the chuviruses. Notably, the Aag2 cell line used here was also experimentally infected with dengue virus and naturally contained a Phasi Charoen-like virus and cell-fusing agent virus. All four viruses were at relatively high abundance, with 0.5 % of sequence reads assigned to Aedes aegypti anphevirus. The Aag2 cell line is therefore permissive to efficient co-infection with dengue virus and multiple insect-specific viruses.
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Affiliation(s)
| | - Michelle D Audsley
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul R Young
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Elizabeth A McGraw
- Department of Entomology and The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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20
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Pinto A, Di Giallonardo F, Keen P, Cooper C, Telfer B, Cooper D, Grulich A, Kelleher A. A10 Using the molecular epidemiology of HIV transmission in New South Wales to inform public health response: Assessing the representativeness of linked phylogenetic data. Virus Evol 2018. [PMCID: PMC5905514 DOI: 10.1093/ve/vey010.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Angie Pinto
- The Kirby Institute, UNSW, Kensington, Australia
| | | | - Phillip Keen
- The Kirby Institute, UNSW, Kensington, Australia
| | | | | | - David Cooper
- The Kirby Institute, UNSW, Kensington, Australia
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21
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Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SYW, Holmes EC. Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evol Biol 2016; 16:115. [PMID: 27230264 PMCID: PMC4880944 DOI: 10.1186/s12862-016-0688-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/19/2016] [Indexed: 01/12/2023] Open
Abstract
Background Recent developments in Bayesian phylogenetic models have increased the range of inferences that can be drawn from molecular sequence data. Accordingly, model selection has become an important component of phylogenetic analysis. Methods of model selection generally consider the likelihood of the data under the model in question. In the context of Bayesian phylogenetics, the most common approach involves estimating the marginal likelihood, which is typically done by integrating the likelihood across model parameters, weighted by the prior. Although this method is accurate, it is sensitive to the presence of improper priors. We explored an alternative approach based on cross-validation that is widely used in evolutionary analysis. This involves comparing models according to their predictive performance. Results We analysed simulated data and a range of viral and bacterial data sets using a cross-validation approach to compare a variety of molecular clock and demographic models. Our results show that cross-validation can be effective in distinguishing between strict- and relaxed-clock models and in identifying demographic models that allow growth in population size over time. In most of our empirical data analyses, the model selected using cross-validation was able to match that selected using marginal-likelihood estimation. The accuracy of cross-validation appears to improve with longer sequence data, particularly when distinguishing between relaxed-clock models. Conclusions Cross-validation is a useful method for Bayesian phylogenetic model selection. This method can be readily implemented even when considering complex models where selecting an appropriate prior for all parameters may be difficult. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0688-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastián Duchêne
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia. .,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Edward C Holmes
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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22
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Kok YL, Vongrad V, Shilaih M, Di Giallonardo F, Kuster H, Kouyos R, Günthard HF, Metzner KJ. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells. Sci Rep 2016; 6:24157. [PMID: 27067385 PMCID: PMC4828718 DOI: 10.1038/srep24157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/21/2016] [Indexed: 11/09/2022] Open
Abstract
The host genetic landscape surrounding integrated HIV-1 has an impact on the fate of the provirus. Studies analysing HIV-1 integration sites in macrophages are scarce. We studied HIV-1 integration site patterns in monocyte-derived macrophages (MDMs) and activated CD4(+) T cells derived from seven antiretroviral therapy (ART)-treated HIV-1-infected individuals whose cells were infected ex vivo with autologous HIV-1 isolated during the acute phase of infection. A total of 1,484 unique HIV-1 integration sites were analysed. Their distribution in the human genome and genetic features, and the effects of HIV-1 integrase polymorphisms on the nucleotide selection specificity at these sites were indistinguishable between the two cell types, and among HIV-1 isolates. However, the repertoires of HIV-1-hosting gene clusters overlapped to a higher extent in MDMs than in CD4(+) T cells. The frequencies of HIV-1 integration events in genes encoding HIV-1-interacting proteins were also different between the two cell types. Lastly, HIV-1-hosting genes linked to clonal expansion of latently HIV-1-infected CD4(+) T cells were over-represented in gene hotspots identified in CD4(+) T cells but not in those identified in MDMs. Taken together, the repertoire of genes targeted by HIV-1 in MDMs is distinct from and more restricted than that of CD4(+) T cells.
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Affiliation(s)
- Yik Lim Kok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Mohaned Shilaih
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, 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
| | - Karin J Metzner
- 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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23
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St. John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP. A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PLoS One 2016; 11:e0146687. [PMID: 26756901 PMCID: PMC4710461 DOI: 10.1371/journal.pone.0146687] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. METHODS A multicenter study was conducted to validate an updated assay design for 454 Life Sciences' GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940-447,400 copies/mL, two dilution series (52,129-1,340 and 25,130-734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10-99, RT codons 1-251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. RESULTS The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592-3,488) and 2,410 for V3 (IQR 786-3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P<0.001). The triplicate samples of a plasmid mixture confirmed the high inter-laboratory consistency (mean% ± stdev: 4.6 ±0.5, 4.8 ±0.4, 4.9 ±0.3) and revealed good intra-laboratory consistency (mean% range ± stdev range: 4.2-5.2 ± 0.04-0.65). In the two dilutions series, no variants >20% were missed, variants 2-10% were detected at most sites (even at low VT), and variants 1-2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. CONCLUSIONS This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing.
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Affiliation(s)
| | - Birgitte B. Simen
- 454 Life Sciences, A Roche Company, Branford, CT, United States of America
| | | | | | - Isabella Abbate
- National Institute for Infectious Diseases “L. Spallanzani, Rome, Italy
| | - Jeroen Aerssens
- Janssen Infectious Diseases—Diagnostics bvba, Beerse, Belgium
| | - Olivier Bouchez
- Plateforme Génomique Toulouse/Laboratoire Génétique Cellulaire, Toulouse, France
| | | | | | | | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Roger Paredes
- Institut de Recerca de la SIDA–IrsiCaixa, Badalona, Spain
| | - James Sakwa
- Technology Innovation Agency-National Genomics Platform, Durban, South Africa
| | | | | | | | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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24
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Duchêne S, Di Giallonardo F, Holmes EC. Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales. Mol Biol Evol 2015; 33:255-67. [PMID: 26416981 DOI: 10.1093/molbev/msv207] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Determining the time scale of virus evolution is central to understanding their origins and emergence. The phylogenetic methods commonly used for this purpose can be misleading if the substitution model makes incorrect assumptions about the data. Empirical studies consider a pool of models and select that with the highest statistical fit. However, this does not allow the rejection of all models, even if they poorly describe the data. An alternative is to use model adequacy methods that evaluate the ability of a model to predict hypothetical future observations. This can be done by comparing the empirical data with data generated under the model in question. We conducted simulations to evaluate the sensitivity of such methods with nucleotide, amino acid, and codon data. These effectively detected underparameterized models, but failed to detect mutational saturation and some instances of nonstationary base composition, which can lead to biases in estimates of tree topology and length. To test the applicability of these methods with real data, we analyzed nucleotide and amino acid data sets from the genus Flavivirus of RNA viruses. In most cases these models were inadequate, with the exception of a data set of relatively closely related sequences of Dengue virus, for which the GTR+Γ nucleotide and LG+Γ amino acid substitution models were adequate. Our results partly explain the lack of consensus over estimates of the long-term evolutionary time scale of these viruses, and indicate that assessing the adequacy of substitution models should be routinely used to determine whether estimates are reliable.
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Affiliation(s)
- Sebastián Duchêne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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25
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Affiliation(s)
- Francesca Di Giallonardo
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Biological Sciences, The University of Sydney, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Biological Sciences, The University of Sydney, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
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26
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Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Paredes R, Metzner KJ. Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing. J Antimicrob Chemother 2014; 70:930-40. [PMID: 25336166 PMCID: PMC4319483 DOI: 10.1093/jac/dku426] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives It is still debated if pre-existing minority drug-resistant HIV-1 variants (MVs) affect the virological outcomes of first-line NNRTI-containing ART. Methods This Europe-wide case–control study included ART-naive subjects infected with drug-susceptible HIV-1 as revealed by population sequencing, who achieved virological suppression on first-line ART including one NNRTI. Cases experienced virological failure and controls were subjects from the same cohort whose viraemia remained suppressed at a matched time since initiation of ART. Blinded, centralized 454 pyrosequencing with parallel bioinformatic analysis in two laboratories was used to identify MVs in the 1%–25% frequency range. ORs of virological failure according to MV detection were estimated by logistic regression. Results Two hundred and sixty samples (76 cases and 184 controls), mostly subtype B (73.5%), were used for the analysis. Identical MVs were detected in the two laboratories. 31.6% of cases and 16.8% of controls harboured pre-existing MVs. Detection of at least one MV versus no MVs was associated with an increased risk of virological failure (OR = 2.75, 95% CI = 1.35–5.60, P = 0.005); similar associations were observed for at least one MV versus no NRTI MVs (OR = 2.27, 95% CI = 0.76–6.77, P = 0.140) and at least one MV versus no NNRTI MVs (OR = 2.41, 95% CI = 1.12–5.18, P = 0.024). A dose–effect relationship between virological failure and mutational load was found. Conclusions Pre-existing MVs more than double the risk of virological failure to first-line NNRTI-based ART.
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Affiliation(s)
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Rob Schuurman
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserslautern, Germany
| | - Sue Aitken
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | | | - Antonella D'Arminio Monforte
- Department of Health Sciences, Clinic of Infectious Diseases, 'San Paolo' Hospital, University of Milan, Milan, Italy
| | - Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Clare L Booth
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Claudia Michalik
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany Clinical Trial Centre (ZKS), University of Cologne, Cologne, Germany
| | - Klaus Jansen
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany
| | - Bernard Masquelier
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Erika Castro
- Addiction Medicine, Service of Community Psychiatry, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Roger Paredes
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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27
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Giallonardo FD, Töpfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Däumer M, Beisel C, Rusert P, Trkola A, Günthard HF, Roth V, Beerenwinkel N, Metzner KJ. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res 2014; 42:e115. [PMID: 24972832 PMCID: PMC4132706 DOI: 10.1093/nar/gku537] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.
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Affiliation(s)
- Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Armin Töpfer
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Melanie Rey
- Department of Mathematics and Computer Science, University of Basel, 4056 Basel, Switzerland
| | - Sandhya Prabhakaran
- Department of Mathematics and Computer Science, University of Basel, 4056 Basel, Switzerland
| | - Yannick Duport
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Stefan Schmutz
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Nottania K Campbell
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Beda Joos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Maria Rita Lecca
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, 8057 Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, 8057 Zurich, Switzerland
| | - Martin Däumer
- Institut für Immunologie und Genetik, 67655 Kaiserslautern, Germany
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, 4056 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
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28
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Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP. An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. J Virol Methods 2014; 204:31-7. [PMID: 24731928 DOI: 10.1016/j.jviromet.2014.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 10/25/2022]
Abstract
The detection of mutant spectra within the viral quasispecies is critical for therapeutic management of HIV-1 infections. Routine clinical application of ultrasensitive genotyping requires reproducibility and concordance within and between laboratories. The goal of the study was to evaluate a new protocol on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing (454-UDS) in an international multicenter study. Sixteen blinded HIV-1 subtype B samples were provided for 454-UDS as both RNA and cDNA with viral titers of 88,600-573,000 HIV-1 RNA copies/ml. Eight overlapping amplicons spanning protease (PR) codons 10-99 and reverse transcriptase (RT) codons 1-251 were generated using molecular barcoded primers. 454-UDS was performed using the 454 Life Sciences/Roche GS FLX platform. PR and RT sequences were analyzed using 454 Life Sciences Amplicon Variant Analyzer (AVA) software. Quantified variation data were analyzed for intra-laboratory reproducibility and inter-laboratory concordance. Routine population sequencing was performed using the ViroSeq HIV-1 genotyping system. Eleven laboratories and the reference laboratory 454 Life Sciences sequenced the HIV-1 sample set. Data presented are derived from seven laboratories and the reference laboratory since severe study protocol execution errors occurred in four laboratories leading to exclusion. The median sequencing depth across all sites was 1364 reads per position (IQR=809-2065). 100% of the ViroSeq-reported mutations were also detected by 454-UDS. Minority HIV-1 drug resistance mutations, defined as HIV-1 drug resistance mutations identified at frequencies of 1-25%, were only detected by 454-UDS. Analysis of 10 preselected majority and minority mutations were consistently found across sites. The analysis of drug-resistance mutations detected between 1 and 10% demonstrated high intra- and inter-laboratory consistency in frequency estimates for both RNA and prepared cDNA samples, indicating robustness of the method. HIV-1 drug resistance testing using 454 ultra-deep pyrosequencing results in an accurate and highly reproducible, albeit complex, approach to the analysis of HIV-1 mutant spectra, even at frequencies well below those detected by routine population sequencing.
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Affiliation(s)
| | | | - Isabella Abbate
- National Institute for Infectious Diseases "L. Spallanzani, Rome, Italy
| | - Jeroen Aerssens
- Janssen Infectious Diseases - Diagnostics bvba, Beerse, Belgium
| | - Yannick Bidet
- Centre Jean Perrin/Clermont University, Clermont-Ferrand, France
| | | | | | - Jacques Izopet
- INSERM U1043 and Virology Laboratory, CHU Toulouse, Toulouse, France
| | | | | | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | | | | | | | - James Sakwa
- TIA-National Genomics Platform, Durban, South Africa
| | | | | | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Martin P Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
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Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ. Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. PLoS One 2013; 8:e74249. [PMID: 24058534 PMCID: PMC3776835 DOI: 10.1371/journal.pone.0074249] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/31/2013] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04-0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9-2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification.
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Affiliation(s)
- Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Osvaldo Zagordi
- Department of Biosystems Sciences and Engineering, ETH Zurich, Basel, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Yannick Duport
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Beda Joos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Rémy Bruggmann
- Functional Genomics Center Zurich (FGCZ), University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Sciences and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- * E-mail:
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30
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Decker M, Adamska M, Cronin A, Di Giallonardo F, Burgener J, Marowsky A, Falck JR, Morisseau C, Hammock BD, Gruzdev A, Zeldin DC, Arand M. EH3 (ABHD9): the first member of a new epoxide hydrolase family with high activity for fatty acid epoxides. J Lipid Res 2012; 53:2038-2045. [PMID: 22798687 PMCID: PMC3435537 DOI: 10.1194/jlr.m024448] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 07/06/2012] [Indexed: 11/20/2022] Open
Abstract
Epoxide hydrolases are a small superfamily of enzymes important for the detoxification of chemically reactive xenobiotic epoxides and for the processing of endogenous epoxides that act as signaling molecules. Here, we report the identification of two human epoxide hydrolases: EH3 and EH4. They share 45% sequence identity, thus representing a new family of mammalian epoxide hydrolases. Quantitative RT-PCR from mouse tissue indicates strongest EH3 expression in lung, skin, and upper gastrointestinal tract. The recombinant enzyme shows a high turnover number with 8,9-, 11,12-, and 14,15-epoxyeicosatrienoic acid (EET), as well as 9,10-epoxyoctadec-11-enoic acid (leukotoxin). It is inhibited by a subclass of N,N'-disubstituted urea derivatives, including 12-(3-adamantan-1-yl-ureido)-dodecanoic acid, 1-cyclohexyl-3-dodecylurea, and 1-(1-acetylpiperidin-4-yl)-3-(4-(trifluoromethoxy)phenyl)urea, compounds so far believed to be selective inhibitors of mammalian soluble epoxide hydrolase (sEH). Its sensitivity to this subset of sEH inhibitors may have implications on the pharmacologic profile of these compounds. This is particularly relevant because sEH is a potential drug target, and clinical trials are under way exploring the value of sEH inhibitors in the treatment of hypertension and diabetes type II.
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Affiliation(s)
- Martina Decker
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Magdalena Adamska
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Annette Cronin
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | | | - Julia Burgener
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Anne Marowsky
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - John R Falck
- Southwestern Medical Center, University of Texas, Dallas, TX 75390
| | - Christophe Morisseau
- Entomology and Comprehensive Cancer Research Center, University of California, Davis, CA 95616; and
| | - Bruce D Hammock
- Entomology and Comprehensive Cancer Research Center, University of California, Davis, CA 95616; and
| | - Artiom Gruzdev
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Michael Arand
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland.
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31
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Althaus CF, Vongrad V, Niederöst B, Joos B, Di Giallonardo F, Rieder P, Pavlovic J, Trkola A, Günthard HF, Metzner KJ, Fischer M. Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells. Retrovirology 2012; 9:27. [PMID: 22458358 PMCID: PMC3341194 DOI: 10.1186/1742-4690-9-27] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/29/2012] [Indexed: 12/27/2022] Open
Abstract
Background The various classes of small noncoding RNAs (sncRNAs) are important regulators of gene expression across divergent types of organisms. While a rapidly increasing number of sncRNAs has been identified over recent years, the isolation of sncRNAs of low abundance remains challenging. Virally encoded sncRNAs, particularly those of RNA viruses, can be expressed at very low levels. This is best illustrated by HIV-1 where virus encoded sncRNAs represent approximately 0.1-1.0% of all sncRNAs in HIV-1 infected cells or were found to be undetected. Thus, we applied a novel, sequence targeted enrichment strategy to capture HIV-1 derived sncRNAs in HIV-1 infected primary CD4+ T-lymphocytes and macrophages that allows a greater than 100-fold enrichment of low abundant sncRNAs. Results Eight hundred and ninety-two individual HIV-1 sncRNAs were cloned and sequenced from nine different sncRNA libraries derived from five independent experiments. These clones represent up to 90% of all sncRNA clones in the generated libraries. Two hundred and sixteen HIV-1 sncRNAs were distinguishable as unique clones. They are spread throughout the HIV-1 genome, however, forming certain clusters, and almost 10% show an antisense orientation. The length of HIV-1 sncRNAs varies between 16 and 89 nucleotides with an unexpected peak at 31 to 50 nucleotides, thus, longer than cellular microRNAs or short-interfering RNAs (siRNAs). Exemplary HIV-1 sncRNAs were also generated in cells infected with different primary HIV-1 isolates and can inhibit HIV-1 replication. Conclusions HIV-1 infected cells generate virally encoded sncRNAs, which might play a role in the HIV-1 life cycle. Furthermore, the enormous capacity to enrich low abundance sncRNAs in a sequence specific manner highly recommends our selection strategy for any type of investigation where origin or target sequences of the sought-after sncRNAs are known.
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Affiliation(s)
- Claudia F Althaus
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland
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Metzner KJ, Leemann C, Di Giallonardo F, Grube C, Scherrer AU, Braun D, Kuster H, Weber R, Guenthard HF. Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection. PLoS One 2011; 6:e21734. [PMID: 21754996 PMCID: PMC3130779 DOI: 10.1371/journal.pone.0021734] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 06/06/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In the Zurich Primary HIV infection study (ZPHI), minority drug-resistant HIV-1 variants were detected in some acutely HIV-1-infected patients prior to initiation of early antiretroviral therapy (ART). Here, we investigated the reappearance of minority K103N and M184V HIV-1 variants in these patients who interrupted efficient early ART after 8-27 months according to the study protocol. These mutations are key mutations conferring drug resistance to reverse transcriptase inhibitors and they belong to the most commonly transmitted drug resistance mutations. METHODOLOGY/PRINCIPAL FINDINGS Early ART was offered to acutely HIV-1-infected patients enrolled in the longitudinal prospective ZPHI study. Six patients harboring and eleven patients not harboring drug-resistant viruses at low frequencies prior to ART were included in this substudy. Minority K103N and M184V HIV-1 variants were quantified in longitudinal plasma samples after treatment interruption by allele-specific real-time PCR. All 17 patients were infected with HIV-1 subtype B between 04/2003 and 09/2005 and received LPV/r+AZT+3TC during primary HIV-1 infection (PHI). Minority K103N HIV-1 variants reappeared after cessation of ART in two of four patients harboring this variant during PHI and even persisted in one of those patients at frequencies similar to the frequency observed prior to ART (<1%). The K103N mutation did not appear during treatment interruption in any other patient. Minority M184V HIV-1 variants were detected in two patients after ART interruption, one harboring and one not harboring these variants prior to ART. CONCLUSION Minority K103N HIV-1 variants, present in acutely HIV-1 infected patients prior to early ART, can reappear and persist after interruption of suppressive ART containing two nucleoside/nucleotide analogue reverse transcriptase inhibitors and a ritonavir-boosted protease inhibitor. TRIAL REGISTRATION Clinicaltrials.gov NCT00537966.
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Affiliation(s)
- Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Knoepfel SA, Di Giallonardo F, Däumer M, Thielen A, Metzner KJ. In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing. J Virol Methods 2011; 171:329-38. [PMID: 21111003 DOI: 10.1016/j.jviromet.2010.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 11/08/2010] [Accepted: 11/17/2010] [Indexed: 11/24/2022]
Abstract
Some APOBEC3 proteins cause G-to-A hypermutation in HIV-1 DNA when the accessory viral protein Vif is absent or non-functional. So far, cloning and sequencing has been performed to study G-to-A hypermutation. This is time-consuming and labour-intensive especially in the context of in vivo investigations where the number of hypermutated sequences can be very low. Thus, a massively parallel sequencing protocol has been developed for in-depth analysis of G-to-A hypermutation using the 454 pyrosequencing FLX system. Part of HIV-1 env was amplified and pyrosequenced after two rounds of infection in T cell lines and PBMCs using HIV-1 NL4-3Δvif. Specific criteria were applied to cope with major technical challenges: (1) the inclusion of hypermutated sequences, (2) the high genome diversity of HIV-1 env, and (3) the exclusion of sequences containing frameshift errors caused by pyrosequencing. In total, more than 140,000 sequences were obtained. 1.3-6.5% of guanines were mutated to adenine, most frequently in the GG dinucleotide context, the preferred deamination site of APOBEC3G. Non-G-to-A mutations occurred only in low frequencies (<0.6%). Single hypermutated sequences contained up to 24 G-to-A mutations. Overall, massively parallel sequencing is a very useful tool for in-depth analysis of G-to-A hypermutation in HIV-1 DNA induced by APOBEC3 proteins.
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Affiliation(s)
- Stefanie A Knoepfel
- Institute of Clinical and Molecular Virology, University of Erlangen-Nuremberg, Germany.
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Huelsmann PM, Hofmann AD, Knoepfel SA, Popp J, Rauch P, Di Giallonardo F, Danke C, Gueckel E, Schambach A, Wolff H, Metzner KJ, Berens C. A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication. BMC Biotechnol 2011; 11:4. [PMID: 21223573 PMCID: PMC3224247 DOI: 10.1186/1472-6750-11-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 01/11/2011] [Indexed: 12/15/2022] Open
Abstract
Background Regulated expression of suicide genes is a powerful tool to eliminate specific subsets of cells and will find widespread usage in both basic and applied science. A promising example is the specific elimination of human immunodeficiency virus type 1 (HIV-1) infected cells by LTR-driven suicide genes. The success of this approach, however, depends on a fast and effective suicide gene, which is expressed exclusively in HIV-1 infected cells. These preconditions have not yet been completely fulfilled and, thus, success of suicide approaches has been limited so far. We tested truncated Bid (tBid), a human pro-apoptotic protein that induces apoptosis very rapidly and efficiently, as suicide gene for gene therapy against HIV-1 infection. Results When tBid was introduced into the HIV-1 LTR-based, Tat- and Rev-dependent transgene expression vector pLRed(INS)2R, very efficient induction of apoptosis was observed within 24 hours, but only in the presence of both HIV-1 regulatory proteins Tat and Rev. Induction of apoptosis was not observed in their absence. Cells containing this vector rapidly died when transfected with plasmids containing full-length viral genomic DNA, completely eliminating the chance for HIV-1 replication. Viral replication was also strongly reduced when cells were infected with HIV-1 particles. Conclusions This suicide vector has the potential to establish a safe and effective gene therapy approach to exclusively eliminate HIV-1 infected cells before infectious virus particles are released.
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Affiliation(s)
- Peter M Huelsmann
- University of Erlangen-Nuremberg, Institute of Clinical and Molecular Virology, Erlangen, Germany
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