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Alburkat H, Smura T, Bouilloud M, Pradel J, Anfray G, Berthier K, Dutra L, Loiseau A, Niamsap T, Olander V, Sepulveda D, Venkat V, Charbonnel N, Castel G, Sironen T. Evolution and genetic characterization of Seoul virus in wild rats Rattus norvegicus from an urban park in Lyon, France 2020-2022. PLoS Negl Trop Dis 2024; 18:e0012142. [PMID: 38739651 PMCID: PMC11149884 DOI: 10.1371/journal.pntd.0012142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/04/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Seoul virus (SEOV) is an orthohantavirus primarily carried by rats. In humans, it may cause hemorrhagic fever with renal syndrome (HFRS). Its incidence is likely underestimated and given the expansion of urban areas, a better knowledge of SEOV circulation in rat populations is called for. Beyond the need to improve human case detection, we need to deepen our comprehension of the ecological, epidemiological, and evolutionary processes involved in the transmission of SEOV. METHODOLOGY / PRINCIPAL FINDINGS We performed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus in a popular urban park within a large city (Lyon, France) to provide essential information to design surveillance strategies regarding SEOV. We sampled rats within the urban park of 'La Tête d'Or' in Lyon city from 2020 to 2022. We combined rat population genetics, immunofluorescence assays, SEOV high-throughput sequencing (S, M, and L segments), and phylogenetic analyses. We found low structuring of wild rat populations within Lyon city. Only one sampling site within the park (building created in 2021) showed high genetic differentiation and deserves further attention. We confirmed the circulation of SEOV in rats from the park with high seroprevalence (17.2%) and high genetic similarity with the strain previously described in 2011 in Lyon city. CONCLUSION/SIGNIFICANCE This study confirms the continuous circulation of SEOV in a popular urban park where the risk for SEOV transmission to humans is present. Implementing a surveillance of this virus could provide an efficient early warning system and help prepare risk-based interventions. As we reveal high gene flow between rat populations from the park and the rest of the city, we advocate for SEOV surveillance to be conducted at the scale of the entire city.
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Affiliation(s)
- Hussein Alburkat
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Marie Bouilloud
- CBGP, IRD, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Pradel
- CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | | | - Karine Berthier
- CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Lara Dutra
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Thanakorn Niamsap
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Viktor Olander
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Vinaya Venkat
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, Institut Agro, IRD, Univ Montpellier, Montpellier, France
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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2
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Odegard EA, Meeds HL, Kleiboeker SB, Ziady A, Sabulski A, Jodele S, Seif AE, Davies SM, Laskin BL, Blackard JT. BK Polyomavirus Diversity After Hematopoietic Stem Cell Transplantation. J Infect Dis 2023; 228:1208-1218. [PMID: 37165301 PMCID: PMC10629712 DOI: 10.1093/infdis/jiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
BK polyomavirus (BKPyV) infection is common after hematopoietic stem cell transplantation (HSCT) and is associated with the development of hemorrhagic cystitis (HC). The role that BKPyV plays in the pathogenesis of HC is not well characterized. We investigated the impact of BKPyV diversity on the development of HC using a previously established cohort of pediatric HSCT patients. There were 147 urine samples with quantifiable BKPyV at month 1 after HSCT; 137 (93.2%) were amplified using our in-house polymerase chain reaction approach and sent for next-generation sequencing. Subtype Ia was most frequent (61.3%), followed by subtype Ib1 (31.4%). The median viral load of subtype Ia samples was higher than for subtype Ib1 at month 1. Across the protein coding regions, APOBEC-induced mutations and signature patterns associated with HC were identified. This is the largest sequencing study of a single cohort of HSCT patients, providing a vast resource of sequence data for future analyses.
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Affiliation(s)
- Elizabeth A Odegard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | - Heidi L Meeds
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | | | - Assem Ziady
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Anthony Sabulski
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Sonata Jodele
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Alix E Seif
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Oncology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Stella M Davies
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Benjamin L Laskin
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Nephrology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
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3
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Rose R, McGrath MS. HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105514. [PMID: 37832752 PMCID: PMC10842591 DOI: 10.1016/j.meegid.2023.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. METHODS 2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. RESULTS In validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. CONCLUSIONS Recent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.
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Affiliation(s)
| | | | - Enoch S Liu
- Natural Selection, San Diego, California, USA
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4
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Patel AR, Dulcey M, Abid N, Cash MN, Dailey J, Salemi M, Mavian C, Vittor AY. Infectivity of three Mayaro Virus geographic isolates in human cell lines. Acta Trop 2023; 242:106894. [PMID: 36965613 DOI: 10.1016/j.actatropica.2023.106894] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/27/2023]
Abstract
Mayaro virus (MAYV) is an emergent arthropod-borne virus that causes an acute febrile illness accompanied by arthralgia, similar to chikungunya virus. Increasing urbanization of MAYV outbreaks in the Americas has led to concerns for geographic expansion and spillover. Given the potential importance of this pathogen, we sought to fill critical gaps in knowledge regarding MAYV infectivity and geographic variation. This study describes the cytopathogenicity of MAYV in human dermal fibroblasts, human skeletal muscle satellite cells, human embryonic kidney cells (HEK), peripherally derived human macrophages, and Vero cells. We found that regional differences between these viruses do not affect replication kinetics, with high titers peaking at 37 h post infection. MAYV-U, did however, cause the most cytopathic effect in a time-dependent manner. Compared to the other two prototypic isolates, MAYV-U harbors unique mutations in the E2 protein, D60G and S205F, that are likely to interact with the host cell receptor and could affect infectivity. We further demonstrate that pre-treatment of cells with interferon-β inhibited viral replication in a dose-dependent manner. Together, these findings advance our understanding of MAYV infection of human target cells and provide initial data regarding variation according to geography.
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Affiliation(s)
- Aum R Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Melissa Dulcey
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, USA
| | - Nabil Abid
- High Institute of Biotechnology, University of Monastir, Tunisia; Faculty of Pharmacy of Monastir, Laboratory of Transmissible Diseases and Biological Active Substances, University of Monastir, Tunisia
| | - Melanie N Cash
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jordan Dailey
- College of Medicine, Virginia Commonwealth University, VA, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carla Mavian
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Amy Y Vittor
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Division of Infectious Disease and Global Medicine, University of Florida, Gainesville, FL, USA.
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Boswell MT, Nazziwa J, Kuroki K, Palm A, Karlson S, Månsson F, Biague A, da Silva ZJ, Onyango CO, de Silva TI, Jaye A, Norrgren H, Medstrand P, Jansson M, Maenaka K, Rowland-Jones SL, Esbjörnsson J. Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS. Virus Evol 2022; 8:veac075. [PMID: 36533148 PMCID: PMC9753047 DOI: 10.1093/ve/veac075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/24/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2023] Open
Abstract
HIV-2 infection will progress to AIDS in most patients without treatment, albeit at approximately half the rate of HIV-1 infection. HIV-2 capsid (p26) amino acid polymorphisms are associated with lower viral loads and enhanced processing of T cell epitopes, which may lead to protective Gag-specific T cell responses common in slower progressors. Lower virus evolutionary rates, and positive selection on conserved residues in HIV-2 env have been associated with slower progression to AIDS. In this study we analysed 369 heterochronous HIV-2 p26 sequences from 12 participants with a median age of 30 years at enrolment. CD4% change over time was used to stratify participants into relative faster and slower progressor groups. We analysed p26 sequence diversity evolution, measured site-specific selection pressures and evolutionary rates, and determined if these evolutionary parameters were associated with progression status. Faster progressors had lower CD4% and faster CD4% decline rates. Median pairwise sequence diversity was higher in faster progressors (5.7x10-3 versus 1.4x10-3 base substitutions per site, P<0.001). p26 evolved under negative selection in both groups (dN/dS=0.12). Median virus evolutionary rates were higher in faster than slower progressors - synonymous rates: 4.6x10-3 vs. 2.3x10-3; and nonsynonymous rates: 6.9x10-4 vs. 2.7x10-4 substitutions/site/year, respectively. Virus evolutionary rates correlated negatively with CD4% change rates (ρ = -0.8, P=0.02), but not CD4% level. The signature amino acid at p26 positions 6, 12 and 119 differed between faster (6A, 12I, 119A) and slower (6G, 12V, 119P) progressors. These amino acid positions clustered near to the TRIM5α/p26 hexamer interface surface. p26 evolutionary rates were associated with progression to AIDS and were mostly driven by synonymous substitutions. Nonsynonymous evolutionary rates were an order of magnitude lower than synonymous rates, with limited amino acid sequence evolution over time within hosts. These results indicate HIV-2 p26 may be an attractive therapeutic target.
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Affiliation(s)
- M T Boswell
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
| | - J Nazziwa
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - K Kuroki
- Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - A Palm
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - S Karlson
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - F Månsson
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - A Biague
- National Public Health Laboratory, V94M+HM4, Bissau, Guinea-Bissau
| | - Z J da Silva
- National Public Health Laboratory, V94M+HM4, Bissau, Guinea-Bissau
| | - C O Onyango
- US Centres for Disease Control, KEMRI Complex, Mbagathi Road off Mbagathi Way PO Box 606-00621, Kenya
| | - T I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Beech Hill Rd, S10 2RX, Sheffield, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - A Jaye
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - H Norrgren
- Department of Clinical Sciences Lund, Lund University, Sölvegatan 19, 221 84 Lund, Sweden
| | - P Medstrand
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - M Jansson
- Department of Laboratory Medicine, Lund University, Sölvegatan 19, Sweden
| | - K Maenaka
- Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - S L Rowland-Jones
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - J Esbjörnsson
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
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Frutos MC, Blanco S, Balangero M, Carrizo LH, Santos Rocha A, Figueiredo Barbosa-Stancioli E, Nates S, Gallego S. Seronegative human T-cell lymphotropic virus 1 carriers in blood banks: A potential viral source for silent transmission? Vox Sang 2022; 117:1090-1097. [PMID: 35768998 DOI: 10.1111/vox.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVES Transfusion-transmitted viruses count among the greatest threats to blood safety. In Argentina, current laws oblige testing all donated blood for the presence of antibodies against human T-cell lymphotropic viruses 1 and 2 (HTLV-1/2). In endemic zones of the country, a high rate of seronegative HTLV-1 individuals with clear evidence of infection because of symptoms and/or presence of tax sequences of HTLV-1 and/or IgG anti-Tax antibodies has been recently described. Migration from endemic to nonendemic zones of Argentina is very frequent. MATERIALS AND METHODS During a 1-year period, in the blood bank of Córdoba city, we performed molecular screening of all donors who were born in or arose from endemic zones for HTLV-1/2 in Argentina and neighbouring countries. RESULTS By screening 219 bp of HTLV-1/2 tax gene, 0.6% (2/317) of the blood donors proved to be positive for HTLV-1 tax sequence. One of the donors presented anti-Tax antibodies, demonstrating the transcriptional activity of the tax gene, and the other donor was also positive for LTR and pol gene sequences. The HTLV-1 genetic analysis of the LTR sequence determined that it belonged to the Cosmopolitan subtype HTLV-1aA. CONCLUSION These findings suggest potential limitations of some currently approved screening assays for HTLV-1 detection applied in some donor populations and the possibility of an HTLV-1 seronegative carrier state with the potential for silent transmission by blood.
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Affiliation(s)
- María C Frutos
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sebastián Blanco
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Fundación Banco Central de Sangre, Córdoba, Argentina
| | - Marcos Balangero
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Anderson Santos Rocha
- Laboratório de Virología Básica e Aplicada, Departamento de Microbiología, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil.,Interdisciplinary HTLV Research Group, Belo Horizonte, Minas Gerais, Brazil
| | - Edel Figueiredo Barbosa-Stancioli
- Laboratório de Virología Básica e Aplicada, Departamento de Microbiología, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil.,Interdisciplinary HTLV Research Group, Belo Horizonte, Minas Gerais, Brazil
| | - Silvia Nates
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sandra Gallego
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina.,Fundación Banco Central de Sangre, Córdoba, Argentina
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Ruhanya V, Jacobs GB, Paul RH, Joska JA, Seedat S, Nyandoro G, Glashoff RH, Engelbrecht S. HIV-1 subtype C Tat exon-1 amino acid residue 24K is a signature for neurocognitive impairment. J Neurovirol 2022; 28:392-403. [PMID: 35394614 DOI: 10.1007/s13365-022-01073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
Variation and differential selection pressures on Tat genes have been shown to alter the biological function of the protein, resulting in pathological consequences in a number of organs including the brain. We evaluated the impact of genetic variation and selection pressure on 147 HIV-1 subtype C Tat exon 1 sequences from monocyte-depleted peripheral lymphocytes on clinical diagnosis of neurocognitive impairment. Genetic analyses identified two signature amino acid residues, lysine at codon 24 (24K) with a frequency of 43.4% and arginine at codon 29 (29R) with a frequency of 34.0% in individuals with HIV-associated neurocognitive impairment. The analyses also revealed two signature residues, asparagine, 24 N (31.9%), and histidine, 29H (21.3%), in individuals without neurocognitive impairment. Both codons, 24 and 29, were associated with high entropy but only codon 29 was under positive selection. The presence of signature K24 increased by 2.08 times the risk of neurocognitive impairment, 3.15 times higher proviral load, and 69% lower absolute CD4 T-cell count compared to those without the signature. The results support a linkage between HIV-1 C Tat N24K polymorphism, proviral load, immunosuppression, and neurocognitive impairment. The signature may induce more neurotoxic effects, which contributes to establishment and severity of HIV-associated neurocognitive impairment.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa. .,Department of Medical Microbiology, Harare, Zimbabwe.
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa
| | - Robert H Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, University Boulevard, St Louis, USA
| | - John A Joska
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | | | - Richard H Glashoff
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
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8
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Abstract
Background HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. Methods For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. Results Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. Conclusion The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.
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9
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Cho YK, Kim JE, Foley BT. Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years. Viruses 2021; 13:v13050806. [PMID: 33946221 PMCID: PMC8145643 DOI: 10.3390/v13050806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 01/27/2023] Open
Abstract
We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Correspondence: ; Tel.: +82-2-3010-4283; Fax: +82-2-3010-4259
| | - Jung-Eun Kim
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Brian T. Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA;
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10
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Lopez Luis BA, Angulo-Medina L, Rodriguez-Diaz R, Soto-Ramírez LE. Baseline Hepatitis C Virus NS5A Resistance-Associated Polymorphisms in Patients With and Without Human Immunodeficiency Virus Coinfection in Mexico. Microb Drug Resist 2021; 27:1195-1202. [PMID: 33794105 DOI: 10.1089/mdr.2020.0436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective: We aimed to evaluate the frequency and associated factors of baseline NS5A resistance-associated substitutions (RASs) in patients coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) monoinfection with genotype 1b (GT1b) or genotype 1a (GT1a). Moreover, we performed a phylogenetic analysis to evaluate the pattern of clustering among samples of patients with RASs. Results: Fifty-five patients were infected with GT1a, of whom 44 (80%) were HIV-infected patients. RAS prevalence in GT1a was 14% (6/44) and distributed as follows: 5 (11%) harbored M28V and 1 (2%) A92T. Twenty-four patients were infected with HCV GT1b, of whom only 5 (21%) were HIV coinfected; RASs were found in 17/24 (71%) patients, as follows: Y93H+F37L+Q54H (1/24), Y93H+F37L (1/24), P58S (1/24), L31F+F37L (1/24), F37L+H/Q54H (3/24), and F37L (10/24). Only GT1b was significantly associated with RASs (adjusted odds ratio 16.37; 95% confidence interval 2.74-97.48; p = 0.002) in the multivariate analysis. A cluster of sequences from HIV/HCV GT1a patients was found; however, we did not find phylogenetic relationships among sequences with NS5A RASs. Conclusions: In our population of HCV-infected patients, the frequency of NS5A RASs at baseline was somewhat similar to the previously reported worldwide rate. HCV GT1b showed the most significant association with harboring of NS5A RASs. Of note, despite there being clusters among sequences of HIV-coinfected patients, NS5A RASs were not transmitted.
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Affiliation(s)
- Bruno Ali Lopez Luis
- Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Luis Angulo-Medina
- Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Roberto Rodriguez-Diaz
- Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Luis Enrique Soto-Ramírez
- Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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11
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, De Rochars VMB, Salemi M, Morris JG. Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33791709 PMCID: PMC8010738 DOI: 10.1101/2021.03.19.21253391] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae – Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus, – human infections reported to date have been limited to alpha- and betacoronaviruses3. We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect protein’s flexibility and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.
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12
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Intra-Clade C signature polymorphisms in HIV-1 LTR region: The Indian and African lookout. Virus Res 2021; 297:198370. [PMID: 33684417 DOI: 10.1016/j.virusres.2021.198370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 01/28/2023]
Abstract
Polymorphisms occurring in LTR (Long Terminal Repeat) region can profoundly impact pathogenicity, transmission and biology of Human Immunodeficiency Virus Type 1 (HIV-1). We investigated intra-clade polymorphisms, associated with HIV-1 clade-C infections that occur in India and Africa. Plasma samples were obtained from 24 HIV-infected ART-experienced individuals. Next Generation Sequencing was performed on Illumina Hi Seq X system. Sequence analysis was done using MEGA v7. Transcription factor binding sites (TFBS) were investigated to unveil signature sequences. Signature nucleotides in Indian sequences were observed at 19 positions, of which 7 nucleotide signatures occurred in transcription binding sites (TFBS), namely NF-AT-II, NF-AT-III, USF, TCF- 1alpha, Sp1-I and TAR. Intra-clade C variations in HIV-1 LTR that inscribe signature nucleotides in Indian sequences lead to formation monophyletic cluster of Indian sequences. Moreover, occurrence of intra-clade signature nucleotides was observed at the key positions in the transcription factor binding sites in Indian and African clade-C sequences.
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13
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McMullen K, Bateman K, Stanley A, Combrinck M, Engelbrecht S, Bryer A. Viral protein R polymorphisms in the pathogenesis of HIV-associated acute ischaemic stroke: a case-control study. J Neurovirol 2021; 27:137-144. [PMID: 33462790 DOI: 10.1007/s13365-020-00936-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022]
Abstract
HIV-1 viral proteins have been implicated in endothelial dysfunction, which is a major determinant of ischaemic stroke risk in HIV-infected individuals. Polymorphisms in HIV-1 viral protein R (Vpr) may alter its potential to promote endothelial dysfunction, by modifying its effects on viral replication, reactivation of latent cells, upregulation of pro-inflammatory cytokines and infection of macrophages. We analysed Vpr polymorphisms and their association with acute ischaemic stroke by comparing Vpr signature amino acids between 54 HIV-infected individuals with acute ischaemic stroke, and 80 age-matched HIV-infected non-stroke controls. Isoleucine at position 22 and serine at position 41 were associated with ischaemic stroke in HIV. Individuals with stroke had lower CD4 counts and CD4 nadirs than controls. These polymorphisms are unique to individuals with stroke compared to South African subtype C and the control group consensus sequences. Signature Vpr polymorphisms are associated with acute ischaemic stroke in HIV. These may increase stroke risk by promoting endothelial dysfunction and susceptibility to opportunistic infections. Therapeutic targeting of HIV-1 viral proteins may present an additional mechanism of decreasing stroke risk in HIV-infected individuals.
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Affiliation(s)
- Kate McMullen
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
| | - Kathleen Bateman
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Alan Stanley
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Marc Combrinck
- Division of Geriatric Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Services, Cape Town, South Africa
| | - Alan Bryer
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
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14
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Olusola BA, Olaleye DO, Odaibo GN. Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences. Front Microbiol 2021; 11:615721. [PMID: 33505382 PMCID: PMC7829476 DOI: 10.3389/fmicb.2020.615721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
In 2019, 38 million people lived with HIV-1 infection resulting in 690,000 deaths. Over 50% of this infection and its associated deaths occurred in Sub-Saharan Africa. The West African region is a known hotspot of the HIV-1 epidemic. There is a need to develop an HIV-1 vaccine if the HIV epidemic would be effectively controlled. Few protective cytotoxic T Lymphocytes (CTL) epitopes within the HIV-1 GAG (HIV_gagconsv) have been previously identified to be functionally conserved among the HIV-1 M group. These epitopes are currently the focus of universal HIV-1 T cell-based vaccine studies. However, these epitopes' phenotypic and genetic properties have not been observed in natural settings for HIV-1 strains circulating in the West African region. This information is critical as the usefulness of universal HIV-1 vaccines in the West African region depends on these epitopes' occurrence in strains circulating in the area. This study describes non-synonymous substitutions within and without HIV_gagconsv genes isolated from 10 infected Nigerians at the early stages of HIV-1 infection. Furthermore, we analyzed these substitutions longitudinally in five infected individuals from the early stages of infection till after seroconversion. We identified three non-synonymous substitutions within HIV_gagconsv genes isolated from early HIV infected individuals. Fourteen and nineteen mutations outside the HIV_gagconsv were observed before and after seroconversion, respectively, while we found four mutations within the HIV_gagconsv. These substitutions include previously mapped CTL epitope immune escape mutants. CTL immune pressure likely leaves different footprints on HIV-1 GAG epitopes within and outside the HIV_gagconsv. This information is crucial for universal HIV-1 vaccine designs for use in the West African region.
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Affiliation(s)
| | | | - Georgina N. Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
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15
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, Beau De Rochars VM, Salemi M, Morris JG. Independent infections of porcine deltacoronavirus among Haitian children. Nature 2021; 600:133-137. [PMID: 34789872 PMCID: PMC8636265 DOI: 10.1038/s41586-021-04111-z] [Citation(s) in RCA: 179] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/07/2021] [Indexed: 01/07/2023]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, the emergence of coronavirus in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae, human infections reported so far have been limited to alphacoronaviruses and betacoronaviruses3-5. Here we identify porcine deltacoronavirus strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the genes encoding Nsp15 and the spike glycoprotein. In particular, structural analysis predicts that one of the changes in the spike S1 subunit, which contains the receptor-binding domain, may affect the flexibility of the protein and its binding to the host cell receptor. Our findings highlight the potential for evolutionary change and adaptation leading to human infections by coronaviruses outside of the previously recognized human-associated coronavirus groups, particularly in settings where there may be close human-animal contact.
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Affiliation(s)
- John A. Lednicky
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Massimiliano S. Tagliamonte
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Sarah K. White
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Maha A. Elbadry
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Md. Mahbubul Alam
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Caroline J. Stephenson
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Tania S. Bonny
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Julia C. Loeb
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | | | | | - David A. Ostrov
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Carla Mavian
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Valery Madsen Beau De Rochars
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. .,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - J. Glenn Morris
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Medicine, College of Medicine, University of Florida, Gainesville, FL USA
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16
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Mosa AI. Implications of viral transmitted/founder (T/F) dynamics on vaccine development. Hum Vaccin Immunother 2020; 17:2293-2297. [PMID: 33377822 DOI: 10.1080/21645515.2020.1861878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Viral infection typically originates from a limited number of virions known as transmitted/founder (T/F) viruses. Studies of cross-species transmission, and intra-species transmission of antigenically variable viruses, indicates T/F variants may express distinct, transmissibility enhancing phenotypes. However, with evidence that transmissibility is associated with not only intrinsic virological features, such as virion composition, but also extrinsic factors, such as viral population structure, the challenge of resolving T/F signatures that can be targeted by rational vaccine or antiviral design is substantial. Nonetheless, failure to develop vaccines for antigenically variable viruses, such as HIV/HCV, and the ongoing risk of cross-species transmission with pandemic potential, recommends development of T/F targeting vaccines. In this commentary, the T/F phenomena is introduced, explored in both the classical (HIV) and non-canonical (coronaviruses) instances, and discussed in relation to rational and preemptive vaccine design.
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Affiliation(s)
- Alexander I Mosa
- Institute of Medical Sciences, University of Toronto, Toronto, Canada.,Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, Canada
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17
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Tagliamonte MS, Abid N, Borocci S, Sangiovanni E, Ostrov DA, Kosakovsky Pond SL, Salemi M, Chillemi G, Mavian C. Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements. Int J Mol Sci 2020; 22:E80. [PMID: 33374797 PMCID: PMC7794730 DOI: 10.3390/ijms22010080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/12/2023] Open
Abstract
Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the N-terminal domain and the C-terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in C-terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the N-terminal domain and C-terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.
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Affiliation(s)
- Massimiliano S. Tagliamonte
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia;
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute for Biological Systems, National Research Council, Via Salaria, Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Elisa Sangiovanni
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Marco Salemi
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
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18
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Chang L, Zhao J, Guo F, Ji H, Zhang L, Jiang X, Wang L. HIV-1 gp41 genetic diversity and enfuvirtide resistance-associated mutations among enfuvirtide-naïve patients in southern China. Virus Res 2020; 292:198215. [PMID: 33166562 DOI: 10.1016/j.virusres.2020.198215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) increasing molecular diversity and emergence of drug resistant mutants remain a major concern in China. Enfuvirtide (ENF/T-20) is the first entry inhibitor used in patients failing highly active antiretroviral therapy (HAART). However, data on HIV-1 gp41genetic diversity and primary ENF resistance-associated mutations among treatment-naïve patients in China is limited. The objective was to identify molecular diversity and ENF resistance patterns of HIV-1 in southern China, using envelope (env) gp41 sequences and bioinformatics tools, which may help optimize antiretroviral therapy. METHODS From November 2018 to January 2019, 439 blood plasma samples from ENF-naïve patients were collected from Shenzhen, Wuhan and Chongqing, of which 396 HIV env regions were sequenced and subtyped, and were performed the analysis of drug resistance-associated mutations (DRMs). RESULTS The main subtypes were circulating recombinant form (CRF) 01_AE (30.6 %) and CRF07_BC (48.7 %). CRF55_01B had been the fourth subtype in the study, and many rare CRFs were observed. Notably, CRF02_AG and CRF_BF strains typically found in Africa and US respectively were identified amongst Chinese patients. Known DRMs were detected in 27.5 % (109/396) of ENF treatment-naïve patients. One major DRM (L44 M), many secondary DRMs (including N126 K, E137 K, S138A), and lots of polymorphisms were found in the study, which have been proved to elevate resistance to ENF. CONCLUSIONS HIV-1 molecular diversity was observed in the study, which indicating that HIV-1 variability is becoming increasingly complex in southern China. A diverse set of primary DRMs discovered in this study described the serious threat to ART, which reminds us the urgent need of timely surveillance of HIV-1 viral diversity and drug resistance in China.
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Affiliation(s)
- Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Junpeng Zhao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Fei Guo
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Huimin Ji
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Lu Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Xinyi Jiang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China.
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19
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Menon M, Budhwar R, Shukla RN, Bankar K, Vasudevan M, Ranga U. The Signature Amino Acid Residue Serine 31 of HIV-1C Tat Potentiates an Activated Phenotype in Endothelial Cells. Front Immunol 2020; 11:529614. [PMID: 33101270 PMCID: PMC7546421 DOI: 10.3389/fimmu.2020.529614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
The natural cysteine to serine variation at position 31 of Tat in HIV-1C disrupts the dicysteine motif attenuating the chemokine function of Tat. We ask if there exists a trade-off in terms of a gain of function for HIV-1C Tat due to this natural variation. We constructed two Tat-expression vectors encoding Tat proteins discordant for the serine 31 residue (CS-Tat vs. CC-Tat), expressed the proteins in Jurkat cells under doxycycline control, and performed the whole transcriptome analysis to compare the early events of Tat-induced host gene expression. Our analysis delineated a significant enrichment of pathways and gene ontologies associated with the angiogenic signaling events in CS-Tat stable cells. Subsequently, we validated and compared angiogenic signaling events induced by CS- vs. CC-Tat using human umbilical vein endothelial cells (HUVEC) and the human cerebral microvascular endothelial cell line (hCMEC/D3). CS-Tat significantly enhanced the production of CCL2 from HUVEC and induced an activated phenotype in endothelial cells conferring on them enhanced migration, invasion, and in vitro morphogenesis potential. The ability of CS-Tat to induce the activated phenotype in endothelial cells could be of significance, especially in the context of HIV-associated cardiovascular and neuronal disorders. The findings from the present study are likely to help appreciate the functional significance of the SAR (signature amino acid residues) influencing the unique biological properties.
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Affiliation(s)
- Malini Menon
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | | | | | | | | | - Udaykumar Ranga
- Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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20
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Arantes I, Ribeiro-Alves M, S. D. de Azevedo S, Delatorre E, Bello G. Few amino acid signatures distinguish HIV-1 subtype B pandemic and non-pandemic strains. PLoS One 2020; 15:e0238995. [PMID: 32960906 PMCID: PMC7508567 DOI: 10.1371/journal.pone.0238995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/27/2020] [Indexed: 11/26/2022] Open
Abstract
The Human Immunodeficiency Virus Type I (HIV-1) subtype B comprises approximately 10% of all HIV infections in the world. The HIV-1 subtype B epidemic comprehends a pandemic variant (named BPANDEMIC) disseminated worldwide and non-pandemic variants (named BCAR) that are mostly restricted to the Caribbean. The goal of this work was the identification of amino acid signatures (AAs) characteristic to the BCAR and BPANDEMIC variants. To this end, we analyzed HIV-1 subtype B full-length (n = 486) and partial (n = 814) genomic sequences from the Americas classified within the BCAR and BPANDEMIC clades and reconstructed the sequences of their most recent common ancestors (MRCA). Analysis of contemporary HIV-1 sequences revealed 13 AAs between BCAR and BPANDEMIC variants (four on Gag, three on Pol, three on Rev, and one in Vif, Vpu, and Tat) of which only two (one on Gag and one on Pol) were traced to the MRCA. All AAs correspond to polymorphic sites located outside essential functional proteins domains, except the AAs in Tat. The absence of stringent AAs inherited from their ancestors between modern BCAR and BPANDEMIC variants support that ecological factors, rather than viral determinants, were the main driving force behind the successful spread of the BPANDEMIC strain.
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Affiliation(s)
- Ighor Arantes
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em DST-AIDS, Rio de Janeiro, Brazil
| | - Suwellen S. D. de Azevedo
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Universidade Federal do Espírito Santo, Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Alegre, Brazil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
- * E-mail: ,
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21
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Murri S, Madrières S, Tatard C, Piry S, Benoit L, Loiseau A, Pradel J, Artige E, Audiot P, Leménager N, Lacôte S, Vulin J, Charbonnel N, Marianneau P, Castel G. Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica. Pathogens 2020; 9:pathogens9090721. [PMID: 32882953 PMCID: PMC7559001 DOI: 10.3390/pathogens9090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/15/2020] [Accepted: 08/22/2020] [Indexed: 12/30/2022] Open
Abstract
Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.
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Affiliation(s)
- Séverine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Sarah Madrières
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sylvain Piry
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Laure Benoit
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Julien Pradel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Emmanuelle Artige
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Nicolas Leménager
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sandra Lacôte
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Johann Vulin
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Marianneau
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
- Correspondence:
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22
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Diversity of the hepatitis C virus NS5B gene during HIV co-infection. PLoS One 2020; 15:e0237162. [PMID: 32750098 PMCID: PMC7402467 DOI: 10.1371/journal.pone.0237162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/20/2020] [Indexed: 01/06/2023] Open
Abstract
Viral diversity is an important feature of hepatitis C virus (HCV) infection and an important predictor of disease progression and treatment response. HIV/HCV co-infection is associated with enhanced HCV replication, increased fibrosis, and the development of liver disease. HIV also increases quasispecies diversity of HCV structural genes, although limited data are available regarding the impact of HIV on non-structural genes of HCV, particularly in the absence of direct-acting therapies. The genetic diversity and presence of drug resistance mutations within the RNA-dependent RNA polymerase (NS5B) gene were examined in 3 groups of women with HCV genotype 1a infection, including those with HCV mono-infection, antiretroviral (ART)-naïve women with HIV/HCV co-infection and CD4 cell count <350 cells/mm3, and ART-naïve women with HIV/HCV co-infection and CD4 cell count ≥350 cells/mm3. None had ever been treated for HCV infection. There was evidence of significant diversity across the entire NS5B gene in all women. There were several nucleotides and amino acids with distinct distributions across the three study groups, although no obvious clustering of NS5B sequences was observed based on HIV co-infection or CD4 cell count. Polymorphisms at amino acid positions associated with resistance to dasabuvir and sofosbuvir were limited, although the Q309R variant associated with ribavirin resistance was present in 12 individuals with HCV mono-infection, 8 HIV/HCV co-infected individuals with CD4 <350 cells/mm3, and 12 HIV/HCV co-infected individuals with CD4 ≥350 cells/mm3. Previously reported fitness altering mutations were rare. CD8+ T cell responses against the human leukocyte antigen (HLA) B57-restricted epitopes NS5B2629-2637 and NS5B2936-2944 are critical for HCV control and were completely conserved in 44 (51.8%) and 70 (82.4%) study participants. These data demonstrate extensive variation across the NS5B gene. Genotypic variation may have a profound impact on HCV replication and pathogenesis and deserves careful evaluation.
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23
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Cerón Téllez F, González Méndez AS, Tórtora Pérez JL, Loza-Rubio E, Ramírez Álvarez H. Lack of association between amino acid sequences of the bovine leukemia virus envelope and varying stages of infection in dairy cattle. Virus Res 2020; 278:197866. [PMID: 31968223 DOI: 10.1016/j.virusres.2020.197866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 02/05/2023]
Abstract
We collected 724 blood samples from dairy cattle from six Mexican states, and tested them for the presence of antibodies against BLV using a commercial ELISA test. Our study groups consisted of 32 samples: 12 asymptomatic cows, 12 cows with lymphocytosis and 8 samples of tumor tissue of the abomasum and heart of cattle with lymphoma. We designed three pairs of primers to amplify the complete BLV env gene, and obtained a fragment of 1548 nucleotides in length with the sequenced products. According to the phylogenetic tree we constructed to identify the viral genotype, 96.87 % of the sequences grouped into genotype 1, while a single sample from a cow with lymphocytosis (3.13 %) was associated with genotype 3 sequences. The similarity between the Mexican BLV sequences ranged from 0.985-1.00. In addition, the proportion of non-synonymous and synonymous mutations indicated negative selection. We did not identify any conserved residues in the viral protein sequences that could be related to BLV infection stage in cattle. Proviral quantification was performed using quantitative polymerase chain reaction, and we used Mood´s median test as statistical analysis. We found no significant association between proviral load and phase of infection. The sequences showed high similarity without any association between BLV surface glycoprotein and the different infection stages, nor differences in the proviral load. BLV genotype 1 was identified as prevalent in the studied samples, and for the first time in Mexico, we identified BLV genotype 3 in cattle.
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Affiliation(s)
- Fernando Cerón Téllez
- Virology, Genetics and Molecular Biology Laboratory, Faculty of Higher Education, Cuautitlan, Veterinary Medicine, Campus 4, National Autonomous University of Mexico, Km. 2.5 Carretera Cuautitlán-Teoloyucan San Sebastián Xhala, Cuautitlán Izcalli Estado de México, C.P. 54714, Mexico.
| | - Ana Silvia González Méndez
- Virology, Genetics and Molecular Biology Laboratory, Faculty of Higher Education, Cuautitlan, Veterinary Medicine, Campus 4, National Autonomous University of Mexico, Km. 2.5 Carretera Cuautitlán-Teoloyucan San Sebastián Xhala, Cuautitlán Izcalli Estado de México, C.P. 54714, Mexico.
| | - Jorge Luis Tórtora Pérez
- Virology, Genetics and Molecular Biology Laboratory, Faculty of Higher Education, Cuautitlan, Veterinary Medicine, Campus 4, National Autonomous University of Mexico, Km. 2.5 Carretera Cuautitlán-Teoloyucan San Sebastián Xhala, Cuautitlán Izcalli Estado de México, C.P. 54714, Mexico.
| | - Elizabeth Loza-Rubio
- National Center of Research in Animal Microbiology and Innocuity, INIFAP, CP. 05110, Mexico City, Mexico.
| | - Hugo Ramírez Álvarez
- Virology, Genetics and Molecular Biology Laboratory, Faculty of Higher Education, Cuautitlan, Veterinary Medicine, Campus 4, National Autonomous University of Mexico, Km. 2.5 Carretera Cuautitlán-Teoloyucan San Sebastián Xhala, Cuautitlán Izcalli Estado de México, C.P. 54714, Mexico.
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Castells M, Giannitti F, Caffarena RD, Casaux ML, Schild C, Castells D, Riet-Correa F, Victoria M, Parreño V, Colina R. Bovine coronavirus in Uruguay: genetic diversity, risk factors and transboundary introductions from neighboring countries. Arch Virol 2019; 164:2715-2724. [PMID: 31456086 PMCID: PMC7087214 DOI: 10.1007/s00705-019-04384-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/30/2019] [Indexed: 11/15/2022]
Abstract
Bovine coronavirus (BCoV) is a recognized cause of severe neonatal calf diarrhea, with a negative impact on animal welfare, leading to economic losses to the livestock industry. Cattle production is one of the most important economic sectors in Uruguay. The aim of this study was to determine the frequency of BCoV infections and their genetic diversity in Uruguayan calves and to describe the evolutionary history of the virus in South America. The overall detection rate of BCoV in Uruguay was 7.8% (64/824): 7.7% (60/782) in dairy cattle and 9.5% (4/42) in beef cattle. The detection rate of BCoV in samples from deceased and live calves was 10.0% (6/60) and 7.6% (58/763), respectively. Interestingly, there was a lower frequency of BCoV detection in calves born to vaccinated dams (3.3%, 8/240) than in calves born to unvaccinated dams (12.2%, 32/263) (OR: 4.02, 95%CI: 1.81–8.90; p = 0.00026). The frequency of BCoV detection was higher in colder months (11.8%, 44/373) than in warmer months (1.5%, 3/206) (OR: 9.05, 95%CI: 2.77–29.53, p = 0.000013). Uruguayan strains grouped together in two different lineages: one with Argentinean strains and the other with Brazilian strains. Both BCoV lineages were estimated to have entered Uruguay in 2013: one of them from Brazil (95%HPD interval: 2011–2014) and the other from Argentina (95%HPD interval: 2010–2014). The lineages differed by four amino acid changes, and both were divergent from the Mebus reference strain. Surveillance should be maintained to detect possible emerging strains that can clearly diverge at the antigenic level from vaccine strains.
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Affiliation(s)
- Matías Castells
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay.,Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Rubén Darío Caffarena
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay.,Facultad de Veterinaria, Universidad de la República, Alberto Lasplaces 1620, Montevideo, Uruguay
| | - María Laura Casaux
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Carlos Schild
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Daniel Castells
- Centro de Investigación y Experimentación Dr. Alejandro Gallinal, Secretariado Uruguayo de la Lana, Ruta 7 km 140, Cerro Colorado, Florida, Uruguay
| | - Franklin Riet-Correa
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Ruta 50 km 11, La Estanzuela, 70000, Colonia, Uruguay
| | - Matías Victoria
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay
| | - Viviana Parreño
- Sección de Virus Gastroentéricos, Instituto de Virología, CICV y A, INTA Castelar, Buenos Aires, Argentina
| | - Rodney Colina
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Centro Universitario de Salto, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay.
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25
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Peres-da-Silva A, Antunes D, Quintanilha Torres AL, Caffarena ER, Lampe E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses 2019; 11:E691. [PMID: 31366046 PMCID: PMC6723822 DOI: 10.3390/v11080691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.
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Affiliation(s)
- Allan Peres-da-Silva
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Deborah Antunes
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - André Luiz Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
- Laboratório de Bioinformática, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro/UFRJ, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ernesto Raul Caffarena
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
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26
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Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission. J Virol 2019; 93:JVI.01769-18. [PMID: 30996101 DOI: 10.1128/jvi.01769-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/15/2019] [Indexed: 11/20/2022] Open
Abstract
To better understand the transmission of human immunodeficiency virus type 1 (HIV-1), the genetic characteristics of blood and genital viruses from males were compared to those of the imputed founding virus population in their female partners. Initially serodiscordant heterosexual African couples with sequence-confirmed male-to-female HIV-1 transmission and blood and genital specimens collected near the time of transmission were studied. Single viral templates from blood plasma and genital tract RNA and DNA were sequenced across HIV-1 env gp160. Eight of 29 couples examined yielded viral sequences from both tissues. Analysis of these couples' sequences demonstrated, with one exception, that the women's founding viral populations arose from a single viral variant and were CCR5 tropic, even though CXCR4 variants were detected within four males. The median genetic distance of the imputed most recent common ancestor of the women's founder viruses showed that they were closer to the semen viruses than to the blood viruses of their transmitting male partner, but this finding was biased by detection of a greater number of viral clades in the blood. Using multiple assays, the blood and genital viruses were consistently found to be compartmentalized in only two of eight men. No distinct amino acid signatures in the men's viruses were found to link to the women's founders, nor did the women's env sequences have shorter variable loops or fewer N-linked glycosylation sites. The lack of selective factors, except for coreceptor tropism, is consistent with others' findings in male-to-female and high-risk transmissions. The infrequent compartmentalization between the transmitters' blood and semen viruses suggests that cell-free blood virus likely includes HIV-1 sequences representative of those of viruses in semen.IMPORTANCE Mucosal transmissions account for the majority of HIV-1 infections. Identification of the viral characteristics associated with transmission would facilitate vaccine design. This study of HIV strains from transmitting males and their seroconverting female partners found that the males' genital tract viruses were rarely distinct from the blood variants. The imputed founder viruses in women were genetically similar to both the blood and genital tract variants of their male partners, indicating a lack of evidence for genital tract-specific lineages. These findings suggest that targeting vaccine responses to variants found in blood are likely to also protect from genital tract variants.
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27
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Cho YK, Kim JE, Foley BT. Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs. Viruses 2019; 11:v11060545. [PMID: 31212650 PMCID: PMC6631484 DOI: 10.3390/v11060545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 01/14/2023] Open
Abstract
We determined the earliest full-length HIV-1 gag gene sequences in 110 patients with HIV-1, including 20 hemophiliacs (HPs) and 90 local controls (LCs). The gag gene from stored sera was amplified using RT-PCR, and was subjected to direct sequencing. Phylogenetic analysis indicated that 94 and 16 sequences belonged to the Korean subclade of HIV-1 subtype B (KSB) and subtype B, respectively. A total of 12 signature pattern amino acids were found within the KSB, distinct from the worldwide consensus of subtype B. Within the KSB, the gag gene sequences from donors O and P and those from the 20 HPs comprised two subclusters. In particular, sequences from donor O strongly clustered with those of eight HPs. Moreover, signature pattern analysis indicated that 14 signature nucleotides were shared between the HPs and LCs within KSB (p < 0.01). Among the 14 nucleotides, positions 9 and 5 belonged to clusters O and P, respectively. In conclusion, signature pattern analysis for the gag gene revealed 12 signature pattern residues within the KSB and also confirmed the previous conclusion that the 20 HPs were infected with viruses due to incompletely inactivated clotting factor IX. This study is the first genetic analysis of the HIV-1 gag gene in Korea.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Brian T Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.
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28
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Di Lello FA, Ridruejo E, Martínez AP, Pérez PS, Campos RH, Flichman DM. Molecular epidemiology of hepatitis B virus mutants associated with vaccine escape, drug resistance and diagnosis failure. J Viral Hepat 2019; 26:552-560. [PMID: 30576055 DOI: 10.1111/jvh.13052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/21/2018] [Indexed: 12/27/2022]
Abstract
The massive implementation of the vaccine and antiviral agents against hepatitis B virus (HBV), targeting the envelope and viral polymerase genes, induces a selection pressure that might lead to the emergence of variants that impair the effectiveness of the vaccine, diagnostic methods and antiviral therapy. The aim of this study was to evaluate the prevalence of HBV vaccine escape mutants (VEMs), diagnostic failure mutants (DFMs) and treatment resistance mutants (ARMs) among individuals from Buenos Aires, Argentina. HBV surface antigen and polymerase sequences obtained from serum samples of 530 HBV-infected individuals were analysed. Samples belonged to genotypes A (28.1%), D (13.6%) and F (58.3%). VEMs, DMFs and ARMs were present in 40 (7.5%), 57 (10.7%) and 27 (5.1%) samples within the studied population. Additionally, eight nonpreviously reported VEMs and nine DFMs were identified. VEMs and DFMs were biased by genotype, being higher in genotype D (33.3% and 33.3%) compared to genotype A (6% and 17.4%) and genotype F (2.3% and 2.3%) (P > 0.001). On the contrary, there was no association between the presence of ARMs and HBV genotype (P = 0.324). VEMs, DFMs and ARMs create public health concerns. The current study provided valuable information about mutants in surface antigen and polymerase in HBV-infected patients from Argentina where HBV-F is the most prevalent genotype. Consequently, it constitutes an important reference for Latin American clinicians in order to optimize the management of HBV-infected patients.
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Affiliation(s)
- Federico A Di Lello
- Facultad de Farmacia y Bioquímica, Cátedra de Virología, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Hepatology Section, Department of Medicine, Centro de Educación Médica e Investigaciones Clínicas, Norberto Quirno "CEMIC", Buenos Aires, Argentina
| | - Alfredo P Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas, Norberto Quirno "CEMIC", Buenos Aires, Argentina
| | - Paula S Pérez
- Instituto de Investigaciones Biomédicas en Retrovirus y Síndrome de Inmunodeficiencia Adquirida (INBIRS)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rodolfo H Campos
- Facultad de Farmacia y Bioquímica, Cátedra de Virología, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego M Flichman
- Facultad de Farmacia y Bioquímica, Cátedra de Virología, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Ambike SS, Thakar MR, Patil AA, Gangakhedkar RR, Kurle SN. Partial pol Sequences from Drug Naive HIV-2 Infected Individuals from Maharashtra, India. AIDS Res Hum Retroviruses 2019; 35:505-508. [PMID: 30681008 DOI: 10.1089/aid.2018.0282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
HIV-2 is important due to its unique challenges in diagnosis, treatment, and drug resistance. The data on Indian HIV-2 pol gene as well as resistance to antiretroviral drugs are limited. Here we report sequence data of protease (PR) and reverse transcriptase (RT) genes from HIV-2 infected treatment naive individuals (N = 32) from Maharashtra, India. These sequences were found to be closely related to HIV-2 subtype A sequences from Guinea Bissau. We observed two unique residues at positions 14 and 70 in the PR region specific to Indian HIV-2. Mutations associated with resistance to RT and protease inhibitors were observed in 3 of 32 (9.37%) samples. To our knowledge, this is the first study from India to report drug resistance among treatment naive HIV-2 infected individuals. The results emphasize need for larger nationwide surveillance for HIV-2 drug resistance to better understand the primary drug resistance among HIV-2 infected individuals.
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Affiliation(s)
- Shubhankar S. Ambike
- HIV Drug Resistance Laboratory, ICMR-National AIDS Research Institute, Pune, India
| | - Madhuri R. Thakar
- Department of Immunology and Serology, National AIDS Research Institute, Pune, India
| | - Ajit A. Patil
- HIV Drug Resistance Laboratory, ICMR-National AIDS Research Institute, Pune, India
| | | | - Swarali N. Kurle
- HIV Drug Resistance Laboratory, ICMR-National AIDS Research Institute, Pune, India
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Gambato M, Gregori J, Quer J, Koutsoudakis G, González P, Caro-Pérez N, García-Cehic D, García-González N, González-Candelas F, Esteban JI, Crespo G, Navasa M, Forns X, Pérez-Del-Pulgar S. Hepatitis C virus intrinsic molecular determinants may contribute to the development of cholestatic hepatitis after liver transplantation. J Gen Virol 2018; 100:63-68. [PMID: 30451649 DOI: 10.1099/jgv.0.001175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cholestatic hepatitis C (CHC) is a severe form of hepatitis C virus (HCV) infection recurrence that leads to high graft loss rates early after liver transplantation (LT). To investigate the pathogenic mechanisms of CHC, we analysed HCV quasispecies in CHC patients compared to a control group (mild hepatitis C recurrence) by deep pyrosequencing. At the time of LT, NS5B quasispecies complexity was similar between the two groups but, after LT, it decreased more sharply in CHC patients than in the control group. Interestingly, the major variant before LT propagated efficiently and remained as the dominant sequence after LT in 62 % of CHC patients versus 11 % of controls (P=0.031). Sequence analysis of the complete non-structural region in a limited number of patients revealed a potential 12 aa signature specific to the CHC group. These data suggest that intrinsic molecular determinants in the circulating HCV quasispecies may provide a fitness advantage, contributing to the development of CHC.
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Affiliation(s)
- Martina Gambato
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain.,2Multivisceral Transplant Unit and Gastroenterology, Padova University Hospital, Padova, Italy.,†Present address: Multivisceral Transplant Unit and Gastroenterology, Padova University Hospital, Padova, Italy
| | - Josep Gregori
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.,4Roche Diagnostics SL. Sant Cugat del Vallès, Barcelona, Spain
| | - Josep Quer
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - George Koutsoudakis
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Patricia González
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Noelia Caro-Pérez
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain.,‡Present address: Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Damir García-Cehic
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - Neris García-González
- 5Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Fernando González-Candelas
- 5Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Juan Ignacio Esteban
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - Gonzalo Crespo
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Miquel Navasa
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Xavier Forns
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
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Choga WT, Anderson M, Zumbika E, Moyo S, Mbangiwa T, Phinius BB, Melamu P, Kayembe MK, Kasvosve I, Sebunya TK, Blackard JT, Essex M, Musonda RM, Gaseitsiwe S. Molecular characterization of hepatitis B virus in blood donors in Botswana. Virus Genes 2018; 55:33-42. [PMID: 30382563 DOI: 10.1007/s11262-018-1610-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) poses a significant threat to blood transfusion safety in sub-Saharan Africa (SSA) where allogeneic blood donations are screened serologically, and more sensitive nucleic acid tests (NATs) are utilized infrequently. HBV strains circulating among blood donors in Botswana are not yet characterized. We designed a cross-sectional study to determine the HBV sub-genotypes and prevalence of hepatitis B surface antigen (HBsAg) among blood donors between November 2014 and October 2015. A total of 12,575 blood donations were screened for HBsAg and 50 consecutive plasma samples were selected for genotyping from confirmed HBsAg+ donations. Overlapping Pol and complete S (Pol/S) open reading frames (ORFs) were sequenced from extracted HBV DNA. To identify any signature amino acids, mutations were compared to sequences from a cohort of chronic HBV patients co-infected with HIV and were treatment naïve. The prevalence of HBsAg+ blood donors was 1.02% (95% CI 0.9-1.2%), and the circulating sub-genotypes were A1 serotype adw2 (36.1%), D2 serotype ayw2 (2.9%), and D3 serotypes ayw 1/2 (58.3%). Prevalence of escape mutations was 14% from HBV isolates of blood donors and 15% from isolates of HBV/HIV co-infected patients (p = 0.6926). The escape mutations sP120L, sG130R, sY134H, and sD144A were identified predominantly among HBV isolates from blood donors. These escape mutations have been associated with accelerated HBV sequelae [e.g., liver cirrhosis (LC) and hepatocellular carcinoma (HCC)], failure to detect HBsAg, inability to respond to immunoglobulin (Ig) therapy, and HBV vaccine escape. Characterizing the HBV burden, circulating sub-genotypes, and clinically relevant mutations among blood donors in Botswana is important to elucidate the efficacy of currently available vaccines, predicting HBV-transmission patterns, understanding the cohort's risk to HBV-related complications, and to developing prevention strategies and effective genotype-based antiretroviral therapies.
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Affiliation(s)
- Wonderful T Choga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Motswedi Anderson
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Edward Zumbika
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Sikhulile Moyo
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tshepiso Mbangiwa
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Bonolo B Phinius
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Pinkie Melamu
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mukendi K Kayembe
- National Health Laboratory (NHL), Ministry of Health and Wellness, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Theresa K Sebunya
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Jason T Blackard
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Max Essex
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rosemary M Musonda
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Private Bag BO 320, Gaborone, Botswana.
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32
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Patiño-Galindo JÁ, Domínguez F, Cuevas MT, Delgado E, Sánchez M, Pérez-Álvarez L, Thomson MM, Sanjuán R, González-Candelas F, Cuevas JM. Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1. INFECTION GENETICS AND EVOLUTION 2018; 66:43-47. [PMID: 30219320 DOI: 10.1016/j.meegid.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
This work is aimed at assessing the presence of positive selection and/or shifts of the evolutionary rate in a fast-expanding HIV-1 subtype F1 transmission cluster affecting men who have sex with men in Spain. We applied Bayesian coalescent phylogenetics and selection analyses to 23 full-coding region sequences from patients belonging to that cluster, along with other 19 F1 epidemiologically-unrelated sequences. A shift in the overall evolutionary rate of the virus, explained by positively selected sites in the cluster, was detected. We also found one substitution in Nef (H89F) that was specific to the cluster and experienced positive selection. These results suggest that fast transmission could have been facilitated by some inherent genetic properties of this HIV-1 variant.
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Affiliation(s)
- Juan Á Patiño-Galindo
- Joint Research Unit "Infection and Public Health" FISABIO-Universitat de València, València, Spain; CIBER in Epidemiology and Public Health, Madrid, Spain
| | - Francisco Domínguez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María T Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain
| | - Fernando González-Candelas
- Joint Research Unit "Infection and Public Health" FISABIO-Universitat de València, València, Spain; CIBER in Epidemiology and Public Health, Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain.
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33
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Alessandri-Gradt E, Collin G, Tourneroche A, Bertine M, Leoz M, Charpentier C, Unal G, Descamps D, Plantier JC. HIV-1 non-group M phenotypic susceptibility to integrase strand transfer inhibitors. J Antimicrob Chemother 2018; 72:2431-2437. [PMID: 28859447 DOI: 10.1093/jac/dkx190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/23/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives To determine natural phenotypic susceptibility of non-group M HIV-1 to integrase strand transfer inhibitors (INSTIs) in a large panel of 39 clinical strains from groups O, N and P and to identify genotypic polymorphisms according to susceptibility levels. Methods Susceptibility to raltegravir, elvitegravir and dolutegravir was evaluated in 36 HIV-1/O, 2 HIV-1/N and 1 HIV-1/P strains plus an HIV-1/M reference strain. IC50 values were determined after 3 days, and fold changes (FCs) were calculated relative to the HIV-1/M strain. Genotypic polymorphism was determined by amplification of codons 19-263 of the integrase; the natural occurrence of resistance-associated mutations was analysed using the main resistance algorithms and the IAS-USA list. VESPA analysis of the strain sequences was used to determine a signature pattern associated with higher FC. Results Similar IC50 results were observed for the three drugs. Based on the value for the HIV-1/M reference strain, the data showed FC values <2.5 for raltegravir and dolutegravir, whereas the distribution for elvitegravir was heterogeneous, with FC > 10 for six strains (15%). Analysis of the non-M integrase sequences showed a high level of polymorphism without a major genotypic impact; it also revealed mutations that may be associated with the highest FC values obtained for elvitegravir. Conclusions Our phenotypic data showed that non-M strains are globally susceptible to the three currently used INSTIs, but the impact of the high FC values observed for some strains with elvitegravir needs to be explored. Clinical data are now needed to confirm these phenotypic results.
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Affiliation(s)
- E Alessandri-Gradt
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - G Collin
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - A Tourneroche
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - M Bertine
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - M Leoz
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - C Charpentier
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - G Unal
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
| | - D Descamps
- IAME, UMR 1137, Univ. Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France.,IAME, UMR 1137, INSERM, F-75018 Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, F-75018 Paris, France
| | - J C Plantier
- Normandie Univ., UNIROUEN, EA2656, GRAM, CHU de Rouen, Laboratoire de Virologie associé au CNR du VIH, F-76000 Rouen, France
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van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C, Cornelissen M. The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012. Virus Res 2018; 250:51-64. [PMID: 29654800 DOI: 10.1016/j.virusres.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/18/2022]
Abstract
For the production of viral genomic RNA, HIV-1 is dependent on an early viral protein, Tat, which is required for high-level transcription. The quantity of viral RNA detectable in blood of HIV-1 infected individuals varies dramatically, and a factor involved could be the efficiency of Tat protein variants to stimulate RNA transcription. HIV-1 virulence, measured by set-point viral load, has been observed to increase over time in the Netherlands and elsewhere. Investigation of tat gene evolution in clinical isolates could discover a role of Tat in this changing virulence. A dataset of 291 Dutch HIV-1 subtype B tat genes, derived from full-length HIV-1 genome sequences from samples obtained between 1985-2012, was used to analyse the evolution of Tat. Twenty-two patient-derived tat genes, and the control TatHXB2 were analysed for their capacity to stimulate expression of an LTR-luciferase reporter gene construct in diverse cell lines, as well as for their ability to complement a tat-defective HIV-1LAI clone. Analysis of 291 historical tat sequences from the Netherlands showed ample amino acid (aa) variation between isolates, although no specific mutations were selected for over time. Of note, however, the encoded protein varied its length over the years through the loss or gain of stop codons in the second exon. In transmission clusters, a selection against the shorter Tat86 ORF was apparent in favour of the more common Tat101 version, likely due to negative selection against Tat86 itself, although random drift, transmission bottlenecks, or linkage to other variants could also explain the observation. There was no correlation between Tat length and set-point viral load; however, the number of non-intermediate variants in our study was small. In addition, variation in the length of Tat did not significantly change its capacity to stimulate transcription. From 1985 till 2012, variation in the length of the HIV-1 subtype B tat gene is increasingly found in the Dutch epidemic. However, as Tat proteins did not differ significantly in their capacity to stimulate transcription elongation in vitro, the increased HIV-1 virulence seen in recent years could not be linked to an evolving viral Tat protein.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Monique Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Fokla Zorgdrager
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Chris Wymant
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - François Blanquart
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Christophe Fraser
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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Ramírez JC, Torres C, Curto MDLA, Schijman AG. New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis. PLoS Negl Trop Dis 2017; 11:e0006139. [PMID: 29253860 PMCID: PMC5749901 DOI: 10.1371/journal.pntd.0006139] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/02/2018] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi has been subdivided into seven Discrete Typing Units (DTUs), TcI-TcVI and Tcbat. Two major evolutionary models have been proposed to explain the origin of hybrid lineages, but while it is widely accepted that TcV and TcVI are the result of genetic exchange between TcII and TcIII strains, the origin of TcIII and TcIV is still a matter of debate. T. cruzi satellite DNA (SatDNA), comprised of 195 bp units organized in tandem repeats, from both TcV and TcVI stocks were found to have SatDNA copies type TcI and TcII; whereas contradictory results were observed for TcIII stocks and no TcIV sequence has been analyzed yet. Herein, we have gone deeper into this matter analyzing 335 distinct SatDNA sequences from 19 T. cruzi stocks representative of DTUs TcI-TcVI for phylogenetic inference. Bayesian phylogenetic tree showed that all sequences were grouped in three major clusters, which corresponded to sequences from DTUs TcI/III, TcII and TcIV; whereas TcV and TcVI stocks had two sets of sequences distributed into TcI/III and TcII clusters. As expected, the lowest genetic distances were found between TcI and TcIII, and between TcV and TcVI sequences; whereas the highest ones were observed between TcII and TcI/III, and among TcIV sequences and those from the remaining DTUs. In addition, signature patterns associated to specific T. cruzi lineages were identified and new primers that improved SatDNA-based qPCR sensitivity were designed. Our findings support the theory that TcIII is not the result of a hybridization event between TcI and TcII, and that TcIV had an independent origin from the other DTUs, contributing to clarifying the evolutionary history of T. cruzi lineages. Moreover, this work opens the possibility of typing samples from Chagas disease patients with low parasitic loads and improving molecular diagnostic methods of T. cruzi infection based on SatDNA sequence amplification.
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Affiliation(s)
- Juan C. Ramírez
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), CONICET, Buenos Aires, Argentina
- * E-mail: (JCR); (AGS)
| | - Carolina Torres
- Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - María de los A. Curto
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), CONICET, Buenos Aires, Argentina
| | - Alejandro G. Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), CONICET, Buenos Aires, Argentina
- * E-mail: (JCR); (AGS)
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36
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Probing the compartmentalization of HIV-1 in the central nervous system through its neutralization properties. PLoS One 2017; 12:e0181680. [PMID: 28841647 PMCID: PMC5571919 DOI: 10.1371/journal.pone.0181680] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022] Open
Abstract
Compartmentalization of HIV-1 has been observed in the cerebrospinal fluid (CSF) of patients at different clinical stages. Considering the low permeability of the blood-brain barrier, we wondered if a reduced selective pressure by neutralizing antibodies (NAb) in the central nervous system (CNS) could favor the evolution of NAb-sensitive viruses in this compartment. Single genome amplification (SGA) was used to sequence full-length HIV-1 envelope variants (453 sequences) from paired CSF and blood plasma samples in 9 subjects infected by HIV variants of various clades and suffering from diverse neurologic disorders. Dynamics of viral evolution were evaluated with a bayesian coalescent approach for individuals with longitudinal samples. Pseudotyped viruses expressing envelope glycoproteins variants representative of the quasi-species present in each compartment were generated, and their sensitivity to autologous neutralization, broadly neutralizing antibodies (bNAbs) and entry inhibitors was assessed. Significant compartmentalization of HIV populations between blood and CSF were detected in 5 out of 9 subjects. Some of the previously described genetic determinants for compartmentalization in the CNS were observed regardless of the HIV-1 clade. There was no difference of sensitivity to autologous neutralization between blood- and CSF-variants, even for subjects with compartmentalization, suggesting that selective pressure by autologous NAb is not the main driver of HIV evolution in the CNS. However, we observed major differences of sensitivity to sCD4 or to at least one bNAb targeting either the N160-V1V2 site, the N332-V3 site or the CD4bs, between blood- and CSF-variants in all cases. In particular, HIV-1 variants present in the CSF were more resistant to bNAbs than their blood counterpart in some cases. Considering the possible migration from CSF to blood, the CNS could be a reservoir of bNAb resistant viruses, an observation that should be considered for immunotherapeutic approaches.
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Cho YK, Kim JE, Jeong D, Foley BT. Signature pattern analysis for the full-length env gene of the earliest Korean subclade B of HIV-1: outbreak among Korean hemophiliacs. Virus Genes 2017. [PMID: 28639219 DOI: 10.1007/s11262-017-1477-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The epidemiological link in the hypervariable env gene between viruses infecting HIV-positive hemophiliacs (HPs) and plasma donors was not studied. We determined full-length env gene sequences in 20 HPs, 3 plasma donors whose plasma was used for domestic clotting factor (DCF) production, and 54 local controls (LCs). Env genes from viruses in frozen stored sera obtained 1-3 years after diagnosis and from samples collected several years after infection were amplified via RT-PCR and subjected to direct sequencing. Phylogenetic analysis indicated that all sequences were subtype B, including 133 sequences from 77 cases (20 HPs, 3 plasma donors, and 54 LCs) belonging to the Korean subclade B (KSB) and 6 sequences from 5 cases that did not belong to the KSB. Env gene sequences from donors O and P and those of the 20 HPs comprised 2 subclusters within the KSB, although phylogenetic analysis did not support significant bootstrap values. In contrast, signature pattern analysis indicated signature nucleotides at 43 positions between the HPs and LCs (P < 0.05). In particular, specific signature nucleotides at 4 positions were fully conserved in the HPs, but not in the LCs (P < 0.0001). Furthermore, there were 26 signature residues within the KSB and were distinct from the worldwide consensus for subtype B. In conclusion, signature pattern analysis for the hypervariable env gene revealed an epidemiological link that the 20 HPs in this study had been infected with viruses from the DCF used for treatment, consistent with our previous finding.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea.
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Daeun Jeong
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Brian T Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
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Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3. J Virol 2017; 91:JVI.00250-17. [PMID: 28331087 PMCID: PMC5432859 DOI: 10.1128/jvi.00250-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 02/28/2017] [Indexed: 11/20/2022] Open
Abstract
The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated antiviral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway. Although the Vif-APOBEC3 interaction and its evolutionary significance, particularly those of primate lentiviruses (including HIV) and primates (including humans), have been well investigated, those of nonprimate lentiviruses and nonprimates are poorly understood. Moreover, the factors that determine lentiviral pathogenicity remain unclear. Here, we focus on feline immunodeficiency virus (FIV), a pathogenic lentivirus in domestic cats, and the interaction between FIV Vif and feline APOBEC3 in terms of viral virulence and evolution. We reveal the significantly reduced diversity of FIV subtype B compared to that of other subtypes, which may associate with the low pathogenicity of this subtype. We also demonstrate that FIV subtype B Vif is less active with regard to feline APOBEC3 degradation. More intriguingly, we further reveal that FIV protease cleaves feline APOBEC3 in released virions. Taken together, our findings provide evidence that a lentivirus encodes two types of anti-APOBEC3 factors, Vif and viral protease.IMPORTANCE During the history of mammalian evolution, mammals coevolved with retroviruses, including lentiviruses. All pathogenic lentiviruses, excluding equine infectious anemia virus, have acquired the vif gene via evolution to combat APOBEC3 proteins, which are intrinsic restriction factors against exogenous lentiviruses. Here we demonstrate that FIV, a pathogenic lentivirus in domestic cats, antagonizes feline APOBEC3 proteins by both Vif and a viral protease. Furthermore, the Vif proteins of an FIV subtype (subtype B) have attenuated their anti-APOBEC3 activity through evolution. Our findings can be a clue to elucidate the complicated evolutionary processes by which lentiviruses adapt to mammals.
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Frutos MC, Gastaldello R, Balangero M, Remondegui C, Blanco S, Otsuki K, Paulo Vicente AC, Elías D, Mangeaud A, Nates S, Gallego S. Silent dissemination of HTLV-1 in an endemic area of Argentina. Epidemiological and molecular evidence of intrafamilial transmission. PLoS One 2017; 12:e0174920. [PMID: 28384180 PMCID: PMC5383099 DOI: 10.1371/journal.pone.0174920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/17/2017] [Indexed: 11/25/2022] Open
Abstract
Background Molecular and epidemiological studies of transmission routes and risk factors for infection by HTLV-1 are extremely important in order to implement control measures, especially because of the high prevalence of HTLV-1 in several regions of the world. San Salvador de Jujuy, Northwest Argentina, is a highly endemic area for HTLV-1 and foci of tropical spastic paraparesis/HTLV-1-associated myelopathy. Objective To gain further insight into the role of intrafamilial transmission of HTLV-1 in a highly endemic region in Argentina. Method Cross-sectional study in Northwest Argentina. Epidemiological data and blood samples were collected from 28 HTLV-1 infected subjects (index cases) and 92 close relatives/cohabitants. HTLV-1 infection was diagnosed by detection of antibodies and proviral DNA. The LTR region was sequenced and analyzed for genetic distances (VESPA software), in addition to determination and identification of polymorphisms to define HTLV-1 family signatures. Results Fifty seven of the 120 subjects enrolled had antibodies against HTLV-1 and were typified as HTLV-1 by PCR. The prevalence rate of HTLV-1 infection in family members of infected index cases was 31.52% (29/92). The infection was significantly associated with gender, age and prolonged lactation. Identity of LTR sequences and presence of polymorphisms revealed high prevalence of mother-to-child and interspousal transmission of HTLV-1 among these families. Conclusion There is an ongoing and silent transmission of HTLV-1 through vertical and sexual routes within family clusters in Northwest Argentina. This evidence highlights that HTLV-1 infection should be considered as a matter of public health in Argentina, in order to introduce preventive measures as prenatal screening and breastfeeding control.
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Affiliation(s)
- María C. Frutos
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
- * E-mail:
| | - Rene Gastaldello
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Marcos Balangero
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Carlos Remondegui
- Departamento de Enfermedades Infecciones, Hospital San Roque, San Salvador de Jujuy, Argentina
| | - Sebastián Blanco
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Koko Otsuki
- Laboratorio de Genética Molecular de Microorganismos, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - David Elías
- Departamento de Matemática. Facultad de Ciencias Exactas, Físicas y Naturales- Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Arnaldo Mangeaud
- Departamento de Matemática. Facultad de Ciencias Exactas, Físicas y Naturales- Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Silvia Nates
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sandra Gallego
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas–Universidad Nacional de Córdoba, Córdoba, Argentina
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Rossenkhan R, MacLeod IJ, Brumme ZL, Magaret CA, Sebunya TK, Musonda R, Gashe BA, Edlefsen PT, Novitsky V, Essex M. Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection. AIDS Res Hum Retroviruses 2016; 32:1031-1045. [PMID: 27349335 DOI: 10.1089/aid.2015.0330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission.
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Affiliation(s)
- Raabya Rossenkhan
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Iain J. MacLeod
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Craig A. Magaret
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Theresa K. Sebunya
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Rosemary Musonda
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Berhanu A. Gashe
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Paul T. Edlefsen
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
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Echeverría N, Betancour G, Gámbaro F, Hernández N, López P, Chiodi D, Sánchez A, Boschi S, Fajardo A, Sóñora M, Moratorio G, Cristina J, Moreno P. Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: Their relevance for developing countries. Virus Res 2016; 223:140-6. [PMID: 27449600 DOI: 10.1016/j.virusres.2016.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 01/20/2023]
Abstract
Hepatitis C virus (HCV) is a major cause of global morbidity and mortality, with an estimated 130-150 million infected individuals worldwide. HCV is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options in developing countries involve pegylated interferon-α and ribavirin as dual therapy or in combination with one or more direct-acting antiviral agents (DAA). The emergence of resistance-associated variants (RAVs) after treatment reveals the great variability of this virus leading to a great difficulty in developing effective antiviral strategies. Baseline RAVs detected in DAA treatment-naïve HCV-infected patients could be of great importance for clinical management and outcome prediction. Although the frequency of naturally occurring HCV NS3 protease inhibitor mutations has been addressed in many countries, there are only a few reports on their prevalence in South America. In this study, we investigated the presence of RAVs in the HCV NS3 serine protease region by analysing a cohort of Uruguayan patients with chronic hepatitis C who had not been treated with any DAAs and compare them with the results found for other South American countries. The results of these studies revealed that naturally occurring mutations conferring resistance to NS3 inhibitors exist in a substantial proportion of Uruguayan treatment-naïve patients infected with HCV genotype 1 enrolled in these studies. The identification of these baseline RAVs could be of great importance for patients' management and outcome prediction in developing countries.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Gabriela Betancour
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Fabiana Gámbaro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Nelia Hernández
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Pablo López
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Daniela Chiodi
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Adriana Sánchez
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Susana Boschi
- Laboratorio de Biología Molecular, Asociación Española, Palmar 1465, Montevideo, Uruguay, Uruguay
| | - Alvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Martín Sóñora
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
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Hraber PT, Leach RW, Reilly LP, Thurmond J, Yusim K, Kuiken C. Los Alamos Hepatitis C Virus Sequence and Human Immunology Databases: An Expanding Resource for Antiviral Research. ACTA ACUST UNITED AC 2016; 18:113-23. [PMID: 17626595 DOI: 10.1177/095632020701800301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The hepatitis C virus (HCV) resource at Los Alamos (hcv.lanl.gov) provides access to multiple databases: one containing annotated sequences and the other a repository of immunogenic epitopes. They are derived from databases originally developed for HIV research (hiv.lanl.gov). HCV and HIV are RNA viruses with relatively compact genomes (around 10 kb) that are extraordinarily variable, both within and between hosts. This diversity requires methods to track and exclude variants from an individual infection or from epidemiologically related infections, and tools to analyse the variation. The HCV immunology database contains a curated inventory of immunogenic epitopes and information about their interaction with the host immune system, with associated retrieval and analysis tools. This interactive resource provides flexible retrieval tools for sequences, epitopes, clinical information, and metadata, as well as utilities for scientific data analysis, to investigators with internet access and a web browser. This paper describes the types of data and the services that these databases offer, the tools they provide, and their configuration and use. Examples of applications to clonal analysis for drug-resistance mutations are shown.
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Affiliation(s)
- Peter T Hraber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA.
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Mojsiejczuk LN, Torres C, Sevic I, Badano I, Malan R, Flichman DM, Liotta DJ, Campos RH. Molecular epidemiology of hepatitis B virus in Misiones, Argentina. INFECTION GENETICS AND EVOLUTION 2016; 44:34-42. [PMID: 27321439 DOI: 10.1016/j.meegid.2016.06.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/18/2022]
Abstract
Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aims of this study were to describe the molecular epidemiology of HBV in the Province of Misiones, Argentina and estimate the phylodynamic of the main groups in a Bayesian coalescent framework. To this end, partial or complete genome sequences were obtained from 52 blood donor candidates. The phylogenetic analysis based on partial sequences of S/P region showed a predominance of genotype D (65.4%), followed by genotype F (30.8%) and genotype A as a minority (3.8%). At subgenotype level, the circulation of subgenotypes D3 (42.3%), D2 (13.5%), F1b (11.5%) and F4 (9.6%) was mainly identified. The Bayesian coalescent analysis of 29 complete genome sequences for the main groups revealed that the subgenotypes D2 and D3 had several introductions to the region, with ancestors dating back from 1921 to 1969 and diversification events until the late '70s. The genotype F in Misiones has a more recent history; subgenotype F4 isolates were intermixed with sequences from Argentina and neighboring countries and only one significant cluster dated back in 1994 was observed. Subgenotype F1b isolates exhibited low genetic distance and formed a closely related monophyletic cluster, suggesting a very recent introduction. In conclusion, the phylogenetic and coalescent analyses showed that the European genotype D has a higher circulation, a longer history of diversification and may be responsible for the largest proportion of chronic HBV infections in the Province of Misiones. Genotype F, especially subgenotype F1b, had a more recent introduction and its diversification in the last 20years might be related to its involvement in new transmission events.
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Affiliation(s)
- Laura Noelia Mojsiejczuk
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Carolina Torres
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ina Sevic
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Argentina
| | - Inés Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas Químicas y Naturales. Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Richard Malan
- Banco de Sangre Central de Misiones, Av. Cabred y Av. López Torres, Posadas, Misiones, Argentina
| | - Diego Martin Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Domingo Javier Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas Químicas y Naturales. Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas, Misiones, Argentina
| | - Rodolfo Hector Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4to Piso, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
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Aralaguppe SPG, Sharma S, Menon M, Prasad VR, Saravanan S, Murugavel KG, Solomon S, Ranga U. The Evolving Profile of the Signature Amino Acid Residues in HIV-1 Subtype C Tat. AIDS Res Hum Retroviruses 2016; 32:503-14. [PMID: 26678403 DOI: 10.1089/aid.2015.0208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Using several HIV-1 tat exon 1 amino acid sequences available from public databases and additional sequences derived from a southern Indian clinical cohort, we compared the profile of the signature amino acid residues (SAR) between two different time periods, 1986-2004 and 2005-2014. The analysis identified eight positions as signature residues in subtype C Tat and demonstrated a changing pattern at four of these positions between the two periods. At three locations (histidine 29, serine 57, and proline 60), there appears to be a nonuniform negative selection against the SAR. The negative selection appears to be severe, especially against histidine 29 (p < .0001) and moderate against proline 60 (p < .0001). The negative selection against serine 57 is statistically insignificant and appears to have begun recently. At position 63, the frequency of signature residue glutamic acid increased over the past decade, although the difference was not significant. Importantly, at the three locations where the negative selection is in progress, the substitute amino acids are the generic residues present in most of the other HIV-1 subtypes. Our data demonstrate that viral evolution can subject specific amino acid residues to subtle and progressive selection pressures without affecting the prevalence of other amino acid residues.
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Affiliation(s)
- Shambhu Prasad G. Aralaguppe
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Shilpee Sharma
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Malini Menon
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Vinayaka R. Prasad
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, New York
| | | | | | - Suniti Solomon
- YRG Centre for AIDS Research and Education, Chennai, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, López-Labrador FX. Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6. Antimicrob Agents Chemother 2016; 60:2402-16. [PMID: 26856832 PMCID: PMC4808155 DOI: 10.1128/aac.02776-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 01/06/2023] Open
Abstract
There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - Karina Salvatierra
- Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain
| | - Fernando González-Candelas
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - F Xavier López-Labrador
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
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46
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Shi Y, Wang J, Wang Y, Wang A, Guo H, Wei F, Mehta SR, Espitia S, Smith DM, Liu L, Zhang Y, Chen D. A novel mutant 10Ala/Arg together with mutant 144Ser/Arg of hepatitis B virus X protein involved in hepatitis B virus-related hepatocarcinogenesis in HepG2 cell lines. Cancer Lett 2015; 371:285-91. [PMID: 26706415 DOI: 10.1016/j.canlet.2015.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 12/26/2022]
Abstract
Hepatitis B virus (HBV) infection-related hepatocellular carcinoma (HCC) represents a major health problem worldwide. HBV X (HBx) protein is the most common open reading frame that may undergo mutations, resulting in the development of HCC. This study aimed to determine specific HBx mutations that differentiate the central- and para-tumor tissues, and identify their association with HCC development. HBx gene from HCC tumor and para-tumor tissues of 47 HCC patients was amplified, sequenced and statistically analyzed. A novel combination of 2 mutations at residues 10 and 144 was identified which might play a significant role in HCC development. Expression vectors carrying HBx with the specific mutations were constructed and transfected into HepG2 and p53-null HepG2 cells. Compared to wild type (WT) and single mutation of HBx at residue 10 or 144, the 10/144 double mutations strongly up-regulated p21 expression and prolonged G1/S transition in WT- and p53-null HepG2 cells. Apoptosis was also inhibited by HBx harboring 10/44 double-mutation. Binding of 10/144 double-mutant HBx to p53 was lower than WT HBx. Conclusively, the 10/144 double mutation of HBx might play a crucial role in HCC formation.
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Affiliation(s)
- Ying Shi
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China
| | - Junwei Wang
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China; Shandong Cancer Hospital and Institute, Jinan, China
| | - Yuhe Wang
- Department of General Surgery, Changping District Hospital, Beijing 102200, China
| | - Anna Wang
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China
| | - Hongliang Guo
- Shandong Cancer Hospital and Institute, Jinan, China
| | - Feili Wei
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China
| | - Sanjay R Mehta
- Department of General Surgery, Changping District Hospital, Beijing 102200, China
| | - Stephen Espitia
- San Diego Veterans Affairs Medical Center, La Jolla, CA, USA; Division of Infectious Diseases, University of California, San Diego, CA, USA
| | - Davey M Smith
- San Diego Veterans Affairs Medical Center, La Jolla, CA, USA; Division of Infectious Diseases, University of California, San Diego, CA, USA
| | - Longgen Liu
- Department of Infectious Diseases, The Third Hospital of Changzhou, Changzhou Institute of Hepatology, Changzhou City 213001, Jiangsu Province, China.
| | - Yulin Zhang
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China; Department of Infectious Diseases, The Third Hospital of Changzhou, Changzhou Institute of Hepatology, Changzhou City 213001, Jiangsu Province, China.
| | - Dexi Chen
- Capital Medical University Affiliated Beijing Youan Hospital, Beijing Institute of Hepatology, Beijing 100054, China.
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Lopez L, Flichman D, Mojsiejczuk L, Gonzalez MV, Uriarte R, Campos R, Cristina J, Garcia-Aguirre L. Genetic variability of hepatitis B virus in Uruguay: D/F, A/F genotype recombinants. Arch Virol 2015; 160:2209-17. [PMID: 26100402 DOI: 10.1007/s00705-015-2477-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 05/29/2015] [Indexed: 12/22/2022]
Abstract
Hepatitis B virus (HBV) infection is a serious global health problem. Approximately 2 billion people worldwide have been infected, and approximately 350 million individuals currently suffer from HBV-induced chronic liver infection, which causes 600,000 deaths annually from chronic hepatitis, cirrhosis and hepatocellular carcinoma. HBV is classified in eight genotypes (A-H), and two more have been proposed (I-J). In this paper, complete genome sequences of nine Uruguayan HBV are reported. Five samples belong to genotype F1b and one to genotype A2. Three HBV recombinants were detected: A1/F1b, A2/F1b and D3/F1b. The following mutations were detected: a G1896A substitution, a 33-nucleotide deletion from position 2896 to 2928 in the Pre-S1 region involving Pre-S1 residues 3-13, a 33-nt deletion in the Pre-S1 region involving nt 2913-2945 and Pre-S1 residues 9-19. More F genotypes strains than expected were detected in this study, supporting the hypothesis that there are more people of indigenous origin than declared in our population. Also, one third of the samples analyzed were recombinants. This cannot be explained by the low HBV prevalence in Uruguay, but a high HBV infection rate in drug addicts and dialysis patients could act in favor of multiple-genotype HBV infections that could lead to recombination.
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Affiliation(s)
- L Lopez
- Laboratorio de Virología Molecular, Facultad de Ciencias, Centro de Investigaciones Nucleares, Udelar, Montevideo, Uruguay
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48
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Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins. J Virol 2015; 89:8206-18. [PMID: 26018161 DOI: 10.1128/jvi.01302-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Human herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are large-genome DNA viruses that establish a persistent infection in sensory neurons and commonly manifest with recurring oral or genital erosions that transmit virus. HSV encodes 12 predicted glycoproteins that serve various functions, including cellular attachment, entry, and egress. Glycoprotein G is currently the target of an antibody test to differentiate HSV-1 from HSV-2; however, this test has shown reduced capacity to differentiate HSV strains in East Africa. Until the recent availability of 26 full-length HSV-1 and 36 full-length HSV-2 sequences, minimal comparative information was available for these viruses. In this study, we use a variety of sequence analysis methods to compare all available sequence data for HSV-1 and HSV-2 glycoproteins, using viruses isolated in Europe, Asia, North America, the Republic of South Africa, and East Africa. We found numerous differences in diversity, nonsynonymous/synonymous substitution rates, and recombination rates between HSV-1 glycoproteins and their HSV-2 counterparts. Phylogenetic analysis revealed that while most global HSV-2 glycoprotein G sequences did not form clusters within or between continents, one clade (supported at 60.5%) contained 37% of the African sequences analyzed. Accordingly, sequences from this African subset contained unique amino acid signatures, not only in glycoprotein G, but also in glycoproteins I and E, which may account for the failure of sensitive antibody tests to distinguish HSV-1 from HSV-2 in some African individuals. Consensus sequences generated in the study can be used to improve diagnostic assays that differentiate HSV-1 from HSV-2 in global populations. IMPORTANCE Human herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are large DNA viruses associated with recurring oral or genital erosions that transmit virus. Up to 12 HSV-1 and HSV-2 glycoproteins are involved in HSV cell entry or are required for viral spread in animals, albeit some are dispensable for replication in vitro. The recent availability of comparable numbers of full-length HSV-1 and HSV-2 sequences enabled comparative analysis of gene diversity of glycoproteins within and between HSV types. Overall, we found less glycoprotein sequence diversity within HSV-2 than within the HSV-1 strains studied, while at the same time, several HSV-2 glycoproteins were evolving under less selective pressure. Because HSV glycoproteins are the focus of antibody tests to detect and differentiate between infections with the two strains and are constituents of vaccines in clinical-stage development, these findings will aid in refining the targets for diagnostic tests and vaccines.
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49
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Hepatitis B virus genotype distribution and genotype-specific BCP/preCore substitutions in acute and chronic infections in Argentina. PLoS One 2015; 10:e0121436. [PMID: 25822666 PMCID: PMC4378996 DOI: 10.1371/journal.pone.0121436] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
AIM In order to assess Hepatitis B Virus genotype (g) and subgenotype (sg) implications in the course of infection, 234 HBsAg positive patients in different infection stages were characterized (66 acute infections, 63 HBeAg positive chronic infections and 105 anti-HBe positive chronic infections). RESULTS Overall, sgA2 (17.9%), gD (20.9%), sgF1b (34.2%) and sgF4 (19.7%) were the most prevalent. Subgenotype F1b was overrepresented in acute and chronic HBeAg infections (56.1%), whereas gD was the most frequent (40.0%) in anti-HBe positive chronic infections. Among chronic infections, HBeAg positivity rates were 50.0, 12.5, 62.8 and 35.3% for sgA2, gD, sgF1b and sgF4, respectively (p <0.05). A bias toward BCP/preCore mutations was observed among genotypes. In anti-HBe positive chronic infections, sgF1b was more prone to have A1762T/G1764A mutation than sgA2, sgF4 and gD (75.0, 40.0, 33.3 and 31.8%, p<0.005), whereas in the pC region, gD and sgF4 were more likely to have G1896A than sgA2 and sgF1b (81.0, 72.7, 0.0 and 31.3%, p <0.001). The unexpected low frequency of the G1896A mutation in the sgF1b (despite carrying 1858T) prompted us to perform a further analysis in order to identify genotype-specific features that could justify the pattern mutations observed. A region encompassing nucleotides 1720 to 1920 showed the higher dissimilarity between sgF1b and sgF4. Genotypes and subgenotypes carrying the 1727G, 1740C and 1773T polymorphisms were prevented to mutate position 1896. DISCUSSION HBeAg seroconversion is a critical event in the natural history of HBV infection. Differences in the HBeAg positivity rate might be relevant since different studies have observed that delayed HBeAg seroconversion is associated with a more severe clinical course of infection, highlighting the critical role that genotypes/subgenotypes might play in the progression of HBV infection. Polymorphisms in the regions 1720 to 1920 could be involved in the molecular mechanisms underlying seroconversion of each genotype/subgenotype.
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50
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Song J, Doggett N, Wren M, Burr T, Fenimore PW, Hatcher EL, Bruno WJ, Li PE, Stubben C, Wolinsky M. Development of forensic assay signatures for ebolaviruses. J Forensic Sci 2015; 60:315-25. [PMID: 25677086 DOI: 10.1111/1556-4029.12655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 11/29/2022]
Abstract
Ebolaviruses are a diverse group of RNA viruses comprising five different species, four of which cause fatal hemorrhagic fever in humans. Because of their high infectivity and lethality, ebolaviruses are considered major biothreat agents. Although detection assays exist, no forensic assays are currently available. Here, we report the development of forensic assays that differentiate ebolaviruses. We performed phylogenetic analyses and identified canonical SNPs for all species, major clades and isolates. TaqMan-MGB allelic discrimination assays based on these SNPs were designed, screened against synthetic RNA templates, and validated against ebolavirus genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the species and variants with additional resolution at the isolate level. These assays enabled accurate forensic analysis on 4 "unknown" ebolaviruses. Unknowns were correctly classified to species and variant. A goal of providing resolution below the isolate level was not successful. These high-resolution forensic assays allow rapid and accurate genotyping of ebolaviruses for forensic investigations.
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Affiliation(s)
- Jian Song
- Bioenergy and Biome Sciences (B-11), Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545
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