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Seto N, Fukuchi T, Kawakami M, Nagashima M, Sadamasu K, Hatakeyama S. Seronegative HIV-1 infection in a Japanese man presenting with Pneumocystis pneumonia: Analysis of long-term antibody response and literature review. J Infect Chemother 2024; 30:917-921. [PMID: 38331251 DOI: 10.1016/j.jiac.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024]
Abstract
Seronegative human immunodeficiency virus (HIV) infection, where an HIV-specific antibody response is lacking even in chronic or late-stage HIV infections, is extremely rare. Here, we report the case of a 50-year-old Japanese man presenting with Pneumocystis pneumonia who did not produce antibodies against HIV-1 until the initiation of antiretroviral therapy (ART). Fourth-generation antigen-antibody testing temporarily reverted from weakly positive to negative soon after initiating ART, likely due to a reduction in viral load (assessed by p24 antigen levels). His HIV-1 antibody titers remained low or indeterminate even after four years of ART. A literature review suggested that the absence of HIV-1-specific antibody production may be associated with unimpeded HIV replication and rapid CD4+ T cell decline. Seronegative HIV infection can lead to deferred diagnosis and treatment, thereby increasing the risk of transmitting the virus to others or developing opportunistic illnesses. It is important to combine multiple tests for diagnosis, depending on the medical condition. Further studies are required to investigate the host factors involved in the production of HIV-1-specific antibodies.
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Affiliation(s)
- Nayuta Seto
- Division of General Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Takahiko Fukuchi
- Division of General Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Mamiyo Kawakami
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Mami Nagashima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Shuji Hatakeyama
- Division of Infectious Diseases, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan; Division of General Medicine, Center for Community Medicine, Jichi Medical University, Tochigi, Japan.
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2
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Rampini S, Li P, Gandhi D, Mutas M, Ran YF, Carr M, Lee GU. Design of micromagnetic arrays for on-chip separation of superparamagnetic bead aggregates and detection of a model protein and double-stranded DNA analytes. Sci Rep 2021; 11:5302. [PMID: 33674645 PMCID: PMC7935980 DOI: 10.1038/s41598-021-84395-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/10/2021] [Indexed: 01/17/2023] Open
Abstract
Magnetically actuated lab-on-a-chip (LOC) technologies have enabled rapid, highly efficient separation of specific biomarkers and cells from complex biological samples. Nonlinear magnetophoresis (NLM) is a technique that uses a microfabricated magnet array (MMA) and a time varying external magnetic field to precisely control the transport of superparamagnetic (SPM) beads on the surface of a chip based on their size and magnetization. We analyze the transport and separation behavior of SPM monomers and dimers on four MMA geometries, i.e., circular, triangular, square and rectangular shaped micromagnets, across a range of external magnetic field rotation frequencies. The measured critical frequency of the SPM beads on an MMA, i.e., the velocity for which the hydrodynamic drag on a bead exceeds the magnetic force, is closely related to the local magnetic flux density landscape on a micromagnet in the presence of an external magnetic field. A set of design criteria has been established for the optimization of MMAs for NLM separation, with particular focus on the shape of the micromagnets forming the array. The square MMA was used to detect a model protein biomarker and gene fragment based on a magnetic bead assembly (MBA) assay. This assay uses ligand functionalized SPM beads to capture and directly detect an analyte through the formation of SPM bead aggregates. These beads aggregates were detected through NLM separation and microscopic analysis resulting in a highly sensitive assay that did not use carrier fluid.
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Affiliation(s)
- Stefano Rampini
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Peng Li
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Dhruv Gandhi
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Marina Mutas
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Ying Fen Ran
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-ku, Sapporo, Japan
| | - Gil U Lee
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland. .,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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3
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Li P, Gandhi D, Mutas M, Ran YF, Carr M, Rampini S, Hall W, Lee GU. Direct identification of the herpes simplex virus UL27 gene through single particle manipulation and optical detection using a micromagnetic array. NANOSCALE 2020; 12:3482-3490. [PMID: 31971211 DOI: 10.1039/c9nr10362g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Magnetophoretic lab on a chip technologies are rapidly evolving into integrated systems for the identification of biomarkers and cells with ultra-high sensitivity. We demonstrate the highly efficient detection of the Human herpes simplex virus type 1 (HSV) UL27 gene through the programmed assembly of superparamagnetic (SPM) nanoparticles based on oligonucleotide hybridization. The state of assembly of the SPM nanoparticles was determined by optical signature of the synchronized motion on the beads on a micromagnetic array (MMA). This technique has been used to identify <200 copies of the HSV UL27 gene without amplification in less than 20 minutes. The MAA can also be used to separate gene-SPM bead aggregates from millions of unreacted SPM beads based on nonlinear magnetophoresis (NLM). The MMA-optical detection system promises to enable highly sensitive, nucleic acid analysis to be performed without amplification and with the consumption of minimal amounts of reagent.
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Affiliation(s)
- Peng Li
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Dhruv Gandhi
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Marina Mutas
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Yin-Fen Ran
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Michael Carr
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland and Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan
| | - Stefano Rampini
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - William Hall
- UCD National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gil U Lee
- School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
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4
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López P, De Jesús O, Yamamura Y, Rodríguez N, Arias A, Sánchez R, Rodríguez Y, Tamayo-Agrait V, Cuevas W, Rivera-Amill V. Molecular Epidemiology of HIV-1 Virus in Puerto Rico: Novel Cases of HIV-1 Subtype C, D, and CRF-24BG. AIDS Res Hum Retroviruses 2018; 34:507-516. [PMID: 29658302 DOI: 10.1089/aid.2017.0305] [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: 11/12/2022] Open
Abstract
HIV-1 subtype B virus is the most prevalent subtype in Puerto Rico (PR), accounting for about 90% of infection in the island. Recently, other subtypes and circulating recombinant forms (CRFs), including F(12_BF), A (01_BF), and CRF-39 BF-like, have been identified. The purpose of this study is to assess the distribution of drug resistance mutations and subtypes in PR. A total of 846 nucleotide sequences from the period comprising 2013 through 2017 were obtained from our "HIV Genotyping" test file. Phylogenetic and molecular epidemiology analyses were performed to evaluate the evolutionary dynamics and prevalence of drug resistance mutations. According to our results, we detected a decrease in the prevalence of protease inhibitor, nucleoside reverse transcriptase inhibitor (NRTI), and non-NRTI (NNRTI) resistance mutations over time. In addition, we also detected recombinant forms and, for the first time, identified subtypes C, D, and CRF-24BG in PR. Recent studies suggest that non-subtypes B are associated with a high risk of treatment failure and disease progression. The constant monitoring of viral evolution and drug resistance mutation dynamics is important to establish appropriate efforts for controlling viral expansion.
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Affiliation(s)
- Pablo López
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Omayra De Jesús
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Yasuhiro Yamamura
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Nayra Rodríguez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Andrea Arias
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Raphael Sánchez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Yadira Rodríguez
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
| | - Vivian Tamayo-Agrait
- Puerto Rico Community Network for Clinical Research on AIDS, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Wilfredo Cuevas
- HIV Clinic Outpatient Department, Ryder Memorial Hospital, Humacao, Puerto Rico
| | - Vanessa Rivera-Amill
- AIDS Research Program, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico
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5
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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6
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SAKUDO AKIKAZU, IKUTA KAZUYOSHI. A technique for capturing broad subtypes and circulating recombinant forms of HIV-1 based on anionic polymer-coated magnetic beads. Int J Mol Med 2012; 30:437-42. [DOI: 10.3892/ijmm.2012.1009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/23/2012] [Indexed: 11/06/2022] Open
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7
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Most HIV type 1 non-B infections in the Spanish cohort of antiretroviral treatment-naïve HIV-infected patients (CoRIS) are due to recombinant viruses. J Clin Microbiol 2011; 50:407-13. [PMID: 22162552 DOI: 10.1128/jcm.05798-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
HIV-1 group M is classified into 9 subtypes, as well as recombinants favored by coinfection and superinfection events with different variants. Although HIV-1 subtype B is predominant in Europe, intersubtype recombinants are increasing in prevalence and complexity. In this study, phylogenetic analyses of pol sequences were performed to detect the HIV-1 circulating and unique recombinant forms (CRFs and URFs, respectively) in a Spanish cohort of antiretroviral treatment-naïve HIV-infected patients included in the Research Network on HIV/AIDS (CoRIS). Bootscanning and other methods were used to define complex recombinants not assigned to any subtype or CRF. A total of 670 available HIV-1 pol sequences from different patients were collected, of which 588 (87.8%) were assigned to HIV-1 subtype B and 82 (12.2%) to HIV-1 non-B variants. Recombinants caused the majority (71.9%) of HIV-1 non-B infections and were found in 8.8% of CoRIS patients. Eleven URFs (accounting for 13.4% of HIV-1 non-B infections), presenting complex mosaic patterns, were detected. Among them, 10 harbored subtype B fragments. Four of the 11 URFs were found in Spanish natives. A cluster of three B/CRF02_AG recombinants was detected. We conclude that complex variants, including unique recombinant forms, are being introduced into Spain through both immigrants and natives. An increase in the frequency of mosaic viruses, reflecting the increasing heterogeneity of the HIV epidemic in our country, is expected.
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Sensitivity of seven HIV subtyping tools differs among subtypes/recombinants in the Spanish cohort of naïve HIV-infected patients (CoRIS). Antiviral Res 2011; 89:19-25. [DOI: 10.1016/j.antiviral.2010.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 10/13/2010] [Accepted: 10/29/2010] [Indexed: 11/22/2022]
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9
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Abstract
HIV-1-specific antibodies can be detected in HIV-1-positive patients within weeks of primary infection. Rare cases have been reported of patients who are persistently seronegative despite evidence of HIV-1 infection. We present a retrospective review of the clinical, virologic and immunologic characteristics of 25 persistently seronegative patients whose cases have been published to date and postulate a biologic mechanism for this phenomenon.
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10
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Rapid clinical progression to AIDS and death in a persistently seronegative HIV-1 infected heterosexual young man. AIDS 2009; 23:2359-62. [PMID: 19809269 DOI: 10.1097/qad.0b013e328332d5e1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Seronegative HIV-1 infection has important implications for diagnosis and prevention. We describe a case of HIV-1 infection without seroconversion and fast progression to AIDS and death.Genetic and phylogenetic analysis indicated that the patient was infected with a CRF14_BG-like strain selectively transmitted by his seropositive sexual partner. The results suggest a massive infection with a highly aggressive CRF14_BG-like strain and/or the presence of an unidentified immunological deficiency that has prevented the formation of HIV-1-specific antibodies.
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11
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Holguín A, Lospitao E, López M, de Arellano ER, Pena MJ, del Romero J, Martín C, Soriano V. Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools. J Med Virol 2008; 80:383-91. [DOI: 10.1002/jmv.21105] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Novitsky V, Gaolathe T, Woldegabriel E, Makhema J, Essex M. A Seronegative Case of HIV-1 Subtype C Infection in Botswana. Clin Infect Dis 2007; 45:e68-71. [PMID: 17682982 DOI: 10.1086/520683] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 05/08/2007] [Indexed: 11/03/2022] Open
Abstract
We report the first case, to our knowledge, of antibody-negative human immunodeficiency virus type 1 (HIV-1) subtype C infection, which was identified during screening for acute HIV-1 infection in Botswana. Results of tests for HIV-1 antibodies were consistently negative, including rapid and regular enzyme-linked immunosorbent assay and Western blot. The nonrecombinant HIV-1 subtype C infection was confirmed by viral genotyping within the gag, pol, and env genes. The period between referral of the patient in a clinically stable condition and AIDS-related death was approximately 3 months. The reported case indicates the importance of studying the prevalence of seronegative HIV-1 infection in southern Africa, where subtype C predominates.
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Affiliation(s)
- Vladimir Novitsky
- Botswana-Harvard School of Public Health AIDS Initiative Partnership for HIV Research and Education, Princess Marina Hospital, Gaborone, Botswana
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13
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Sakudo A, Suganuma Y, Kobayashi T, Onodera T, Ikuta K. Near-infrared spectroscopy: promising diagnostic tool for viral infections. Biochem Biophys Res Commun 2006; 341:279-84. [PMID: 16414011 PMCID: PMC7092872 DOI: 10.1016/j.bbrc.2005.12.153] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 12/23/2005] [Indexed: 11/29/2022]
Abstract
Although several methods, including enzyme-linked immunosorbent assay, polymerase chain reaction, immunofluorescent assay, and Western blotting, have been used for the diagnosis of viral infections, none of them is ideal in terms of cost-effectiveness, speed, and accuracy. Currently, the rate of outbreak of emerging viruses is increasing and therefore the development and establishment of analytical methods for such viral infections are becoming more important. Near-infrared (NIR) spectroscopy is a fast, multicomponent assay that enables non-invasive, non-destructive analysis. Recently, the diagnosis of viral infections using NIR spectroscopy has been attempted. In this review, the potential of the NIR method in the medical and virological fields is discussed.
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Affiliation(s)
- Akikazu Sakudo
- Department of Virology, Center for Infectious Disease Control, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
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14
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Abstract
The genetic variability within PT/SAP, LYP and LXXLF HIV-1 P6gag motifs, required for the binding to Tsg101 and AIP1 cellular host proteins during viral budding, was examined in 122 HIV-infected subjects. PT/SAP duplications were statistically more frequent in B versus non-B subtypes. Substitutions at LYP were fourfold less frequent in antiretroviral-experienced only in clade B. P6gag variability across HIV-1 subtypes and after antiretroviral exposure may influence interactions with host cells involved in viral budding.
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Affiliation(s)
- Africa Holguín
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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15
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Sakudo A, Tsenkova R, Onozuka T, Morita K, Li S, Warachit J, Iwabu Y, Li G, Onodera T, Ikuta K. A novel diagnostic method for human immunodeficiency virus type-1 in plasma by near-infrared spectroscopy. Microbiol Immunol 2005; 49:695-701. [PMID: 16034213 DOI: 10.1111/j.1348-0421.2005.tb03648.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Presently, the diagnosis of virus infections is based mainly on serological assays. Although polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) have been increasingly used for the diagnosis of such viral infections, the risk of transfusion-transmitted blood-borne viruses remains. Furthermore, PCR and ELISA are expensive and time-consuming, and sometimes cause falsepositive or false-negative results. Therefore, a rapid, accurate and cost-effective diagnostic procedure is needed. We subjected plasma from individuals infected with human immunodeficiency virus type-1 (HIV-1), the causative agent of acquired immune deficiency syndrome (AIDS), as well as plasma from uninfected individuals as a control to near-infrared (NIR) spectroscopy, which may provide a rapid diagnostic method for HIV-1 infection without using any reagent. NIR spectra in the 600-1,000 nm region for plasma from pre-serologically HIV-1-infected individuals and healthy donors were subjected to partial least squares (PLS) regression analysis and leave-out cross-validation to develop a multivariate model to estimate the concentration of HIV-1. Simultaneously, the same plasma samples were examined for HIV-1 p24 by ELISA. The results obtained by the NIR spectroscopy model for HIV-1 yielded a good correlation with those obtained by the reference method (HIV-1 p24 ELISA). These results suggest that NIR spectroscopy using plasma could provide a rapid, accurate, cost-effective tool for large-scale diagnosis of HIV-1 infection.
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Affiliation(s)
- Akikazu Sakudo
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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16
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Cho YK, Sung H, Bae IG, Oh HB, Kim NJ, Woo JH, Kim YB. Full sequence of HIV type 1 Korean subtype B in an AIDS case with atypical seroconversion: TAAAA at TATA box. AIDS Res Hum Retroviruses 2005; 21:961-4. [PMID: 16386114 DOI: 10.1089/aid.2005.21.961] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A patient who presented with late stage HIV-associated diseases could not be diagnosed by commercial ELISA tests and a Western blot. However, we could amplify proviral DNA of HIV-1. We found a novel GPGGMI motif in the V3 loop, a novel insertion of a proline in the C3 region, and persistent deletion of two amino acids in the vif gene. The patient had been treated with HAART after diagnosis. Forty months after the first amplification of HIV-1 DNA, anti-HIV-1 antibody was confirmed by ELISA and Western blot and, thus, we amplified and sequenced HIV-1 full sequences. Interestingly, the sequence at the TATAA box was TAAAA, although full sequences were not CRF01_AE. The major differences in the level of the HIV-1 gene between the seronegative and seropositive states were changes at the glycosylation site (NXT) next to the inserted proline and many resistance mutations including M184V to antiretroviral drugs occurred. This is the first report on HIV-1 full sequences isolated from seronegative AIDS patients infected with subtype B in Korea.
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Affiliation(s)
- Young K Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 138-040, South Korea.
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17
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Dineva MA, Candotti D, Fletcher-Brown F, Allain JP, Lee H. Simultaneous visual detection of multiple viral amplicons by dipstick assay. J Clin Microbiol 2005; 43:4015-21. [PMID: 16081944 PMCID: PMC1233981 DOI: 10.1128/jcm.43.8.4015-4021.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A sensitive, simple, and instrument-independent method for the visual detection and identification of multiple nucleic acid amplicons by dipstick has been developed. This method is based on nucleic acid hybridization on the dipstick membrane and a signal amplification system to allow visual detection. With hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus type 1 (HIV-1) as model analytes, it is demonstrated that the visual dipstick test combined with multiplex reverse transcription (RT)-PCR for the amplification of viral nucleic acid provides a specific and sensitive detection method. The RT-PCR products were detected by the dipstick with an efficiency similar to that of a complex, expensive, and instrument-dependent method based on fluorogenic oligonucleotide probes. The detection limits of the dipstick combined with multiplex RT-PCR were 50, 125, and 500 IU/ml for HBV DNA, HCV RNA, and HIV-1 RNA, respectively. The dipstick assay detected with similar efficiencies amplicons derived from strains of HBV genotypes A through F, HCV genotypes 1 to 6, and HIV-1 subtypes A through H as well as CRF02 circulating recombinant forms of HIV-1. Analysis of 295 clinical samples and 19 pools of 10 plasma specimens from blood donors revealed that multiplex dipstick detection was reproducible, sensitive, and specific. The visual dipstick detection of multiple amplicons thus provides an attractive alternative to complex, instrument-dependent detection methods currently in use for nucleic acid testing. This new and sensitive method for nucleic acid detection should increase the availability of genomic screening in resource-limited settings and its applicability to near-patient testing.
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Affiliation(s)
- Magda Anastassova Dineva
- Department of Haematology, University of Cambridge, Cambridge CB2 2PT, United Kingdom, National Blood Service Cambridge, Cambridge CB2 2PT, United Kingdom
| | - Daniel Candotti
- Department of Haematology, University of Cambridge, Cambridge CB2 2PT, United Kingdom, National Blood Service Cambridge, Cambridge CB2 2PT, United Kingdom
| | - Fiona Fletcher-Brown
- Department of Haematology, University of Cambridge, Cambridge CB2 2PT, United Kingdom, National Blood Service Cambridge, Cambridge CB2 2PT, United Kingdom
| | - Jean-Pierre Allain
- Department of Haematology, University of Cambridge, Cambridge CB2 2PT, United Kingdom, National Blood Service Cambridge, Cambridge CB2 2PT, United Kingdom
| | - Helen Lee
- Department of Haematology, University of Cambridge, Cambridge CB2 2PT, United Kingdom, National Blood Service Cambridge, Cambridge CB2 2PT, United Kingdom
- Corresponding author. Mailing address: Department of Haematology, University of Cambridge, National Blood Service, Long Road, Cambridge CB2 2PT, United Kingdom. Phone: 44 1223 548080. Fax: 44 1223 242044. E-mail:
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18
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Holguín A, Alvarez A, Soriano V. Heterogeneous nature of HIV-1 recombinants spreading in Spain. J Med Virol 2005; 75:374-80. [PMID: 15648070 DOI: 10.1002/jmv.20280] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
HIV-1 infections due to non-B subtypes are increasing rapidly in number and spreading across Europe. The genetic nature of HIV-1 non-B variants containing subtype G sequences at the protease (PR)-coding region are described from 48 unrelated subjects living in Spain. Phylogenetic analyses of the HIV-1 reverse transcriptase (RT) and envelope (env) genes (including the V3 loop) were performed. Up to 32 (66.6%) of samples carried inter-subtype recombinant viruses. Although double recombinants were found most frequently (G/A in 20; G/B in 8; G/K in 2), two individuals harbored triple recombinant viruses (GPR/BRT/Aenv and GPR/KRT/Aenv, respectively). Only 33 (68.7%) and 9 (18.7%) sequences clustered with clade G when examining the RT and env genes, respectively. Nearly 70% of samples with pol sequences (PR/RT) belonging to subtype G harbored env sequences ascribed to other clades: A (55.6%), B (11.1%), or K (3.7%). Of note, most recombinant viruses clustered with CRF02_AG, although CRF14_BG recombinants were also found. This study demonstrates that most viruses circulating in Spain with clade G sequences at the pol-coding region are in fact inter-subtype recombinants, with CRF02_AG being the most prevalent virus.
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Affiliation(s)
- Africa Holguín
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
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Holguín A, Paxinos E, Hertogs K, Womac C, Soriano V. Impact of frequent natural polymorphisms at the protease gene on the in vitro susceptibility to protease inhibitors in HIV-1 non-B subtypes. J Clin Virol 2004; 31:215-20. [PMID: 15465415 DOI: 10.1016/j.jcv.2004.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/27/2004] [Accepted: 03/15/2004] [Indexed: 10/26/2022]
Abstract
BACKGROUND Naturally-occurring polymorphisms at the human immunodeficiency virus type 1 (HIV-1) protease which have been associated to resistance to protease inhibitors (PIs) in clade B viruses are frequently found in non-B subtypes, with unknown clinical significance. OBJECTIVE To assess the susceptibility of non-B viruses to different PIs. STUDY DESIGN Plasma samples from 58 drug-naive individuals infected with HIV-1 non-B subtypes (2A, 22C, 2D, 1F, 29G and 2J) defined by phylogenetic analyses of the protease gene were tested using a phenotypic assay (PhenoSense, ViroLogic, South San Francisco, CA, USA). Twenty of them were further analyzed with another assay (Antivirogram, Virco, Mechelen, Belgium). All 58 non-B viruses harbored amino acid substitutions associated with reduced PI susceptibility in clade B (positions 10, 20, 36, 63, 70, 77 and 82). RESULTS Using PhenoSense-HIV assay, all but two individuals harbored viruses completely susceptible to all six PIs tested (indinavir (IDV), ritonavir (RTV), saquinavir (SQV), nelfinavir (NFV), amprenavir (APV), lopinavir (LPV)). The two viruses with reduced susceptibility belonged to clade G. The first virus, which had K20I, M36I and V82I, showed 2.9-fold decreased susceptibility to APV, while the second virus showed 3.9-fold decreased susceptibility to both NFV and RTV, with amino acid substitutions K20I, M36I, L63P and V82I. Of note, several other viruses displayed the same constellation of mutations but without showing any reduced susceptibility, suggesting that these polymorphisms per se do not affect PI susceptibility. CONCLUSION PI susceptibility in HIV-1 non-B viruses seems to be preserved despite the presence of polymorphic changes which have been associated to PI resistance in clade B viruses.
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Affiliation(s)
- Africa Holguín
- Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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Candotti D, Temple J, Owusu-Ofori S, Allain JP. Multiplex real-time quantitative RT-PCR assay for hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1. J Virol Methods 2004; 118:39-47. [PMID: 15158067 DOI: 10.1016/j.jviromet.2004.01.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Revised: 12/22/2003] [Accepted: 01/06/2004] [Indexed: 01/12/2023]
Abstract
A multiplex real-time quantitative reverse transcription (RT)-PCR assay was developed for simultaneous detection, identification and quantification of hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) in plasma or serum samples. Genomic amplification of one virus was unaffected by the simultaneous amplification of the other two. Competition between HCV and HIV-1 amplifications slightly affected the yield of HIV-1 amplification. However, quantitation was possible when a single virus was present. The 95% detection limits were 30, 167 and 680IU/ml for HBV DNA, HCV RNA and HIV-1 RNA, respectively. The multiplex assay detected with similar efficiency strains of HBV genotypes A-F, HCV genotypes 1-6, and HIV-1 subtypes A-G. Applied to 267 pools of 10 plasmas from blood donors, multiplex screening indicated that the assay was reproducible, sensitive, and specific. This assay has the potential to be used for large-scale nucleic acid testing (NAT) of blood donations.
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Affiliation(s)
- Daniel Candotti
- National Blood Service Cambridge, Long Road, Cambridge CB2 2PT, UK.
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Cardoso AR, Gonçalves C, Pascoalinho D, Gil C, Ferreira AF, Bártolo I, Taveira N. Seronegative infection and AIDS caused by an A2 subsubtype HIV-1. AIDS 2004; 18:1071-4. [PMID: 15096813 DOI: 10.1097/00002030-200404300-00018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The study of true seronegative HIV-1 infections may have important implications for the diagnosis and prevention of HIV-1 infection. The case of an AIDS patient with persistently negative HIV serology is described. Genetic and phylogenetic analysis indicated that she was infected with A2 subsubtype HIV-1 transmitted by her seropositive and asymptomatic sexual partner. The clinical and serological discordant results suggest the presence of an immunological deficiency that prevents the formation of HIV-1-specific antibodies.
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Candotti D, Richetin A, Cant B, Temple J, Sims C, Reeves I, Barbara JAJ, Allain JP. Evaluation of a transcription-mediated amplification-based HCV and HIV-1 RNA duplex assay for screening individual blood donations: a comparison with a minipool testing system. Transfusion 2003; 43:215-25. [PMID: 12559017 DOI: 10.1046/j.1537-2995.2003.00308.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND NAT was introduced for HCV RNA in 1999 to screen blood donations and improve the safety of the blood supply. STUDY DESIGN AND METHODS The performance of a NAT multiplex for HCV and HIV-1 RNA based on transcription-mediated amplification (TMA) was assessed with various sensitivity panels and by screening 50,000 serologically unscreened, first-time donor plasma samples. Results were compared with a routine NAT screening for HCV RNA by RT-PCR in pools of 96 plasma samples. RESULTS The TMA multiplex 95 percent sensitivity ranged between 22 and 54 IU per mL for HIV-1 and 15 and 20 IU per mL for HCV RNA. The rate of test failure was 8.6 percent but decreased to 4.7 percent when results of two critical periods of equipment malfunction were excluded. Test failure was related to human error, minute control contamination, and insufficient mixing of reagents at the extraction stage. All 31 repeatedly reactive samples (0.06%) were seropositive for HCV (29) or HIV-1 (2) and contained RNA detectable by discriminatory TMA and confirmatory RT-PCR, indicating 100 percent specificity. A direct comparison of TMA in individual samples and RT-PCR in plasma pools was possible on 27 HCV RNA-containing samples. Twenty-six samples were detected in plasma pools; the lack of detection of 1 sample was due to an identification error at the pooling stage. CONCLUSION The HCV and HIV-1 multiplex NAT had high specificity and sensitivity.
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Baldrich-Rubio E, Anagonou S, Stirrups K, Lafia E, Candotti D, Lee H, Allain JP. A complex human immunodeficiency virus type 1 A/G/J recombinant virus isolated from a seronegative patient with AIDS from Benin, West Africa. J Gen Virol 2001; 82:1095-1106. [PMID: 11297684 DOI: 10.1099/0022-1317-82-5-1095] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A human immunodeficiency virus type 1 (HIV-1(B76)) originating from Benin (West Africa) was isolated and characterized. The patient had severe clinical AIDS and presented an unusual serological profile. Only one out of five different detection assays was able to demonstrate the presence of antibodies to HIV, whereas confirmatory assays remained indeterminate. In contrast, both plasma viral load and p24 antigen level were unusually high. HIV-1 infection was proved by viral RNA and proviral DNA amplification. HIV-1(B76) partially purified lysate reacted strongly with all anti-HIV-1-positive sera from the region but B76 plasma did not react with subtype A control viral antigen. This patient is likely to have had severe acquired immune dysfunction explaining her lack of immunological reactivity. Phylogenetic analysis of the genome identified a complex HIV-1 A/G/J recombinant. The gag and pol genes, and the majority of nef,are characteristic of subtype A; the gag/pol junction, the 3' end of pol, vpu and env genes were characteristic of subtype G; vif, vpr and the 5' end of nef were subtype J. In addition, part of the HIV-1(B76) genome had considerable sequence similarity with the previously described CRF06 cpx (BFP90) isolate. HIV-1(B76) did not exhibit any remarkable replication properties or cell tropism in vitro.
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Affiliation(s)
- E Baldrich-Rubio
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - S Anagonou
- Department of Microbiology, Centre National Hôpitalier Universitaire and Programme National de Lutte contre le SIDA, Cotonou, Benin2
| | - K Stirrups
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - E Lafia
- Department of Microbiology, Centre National Hôpitalier Universitaire and Programme National de Lutte contre le SIDA, Cotonou, Benin2
| | | | - H Lee
- Department of Haematology, University of Cambridge, East Anglia Blood Centre, Long Road, Cambridge CB2 2PT, UK1
| | - J P Allain
- Division of Transfusion Medicine, Department of Haematology, University of Cambridge, UK4
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