ABSTRACT
Background@#The latent reservoir of Human Immunodificiency Virus-1 (HIV-1) has been a major barrier to the complete eradication of HIV-1 and the development of HIV therapy. Longterm non-progressors (LTNPs) are a rare group of patients with HIV-1 who can spontaneously control HIV-1 replication without antiretroviral therapy. Transcriptome analysis is necessary to predict the pathways involved in the natural control of HIV-1, elucidate the mechanisms involved in LTNPs, and find biomarkers for HIV-1 reservoir therapy. @*Materials and Methods@#In this study, we obtained peripheral blood mononuclear cells from two LTNP subjects at multiple time points and performed RNA-sequencing analyses. @*Results@#We found that LTNPs and normal subjects had different transcriptome profiles. Functional annotation analysis identified that differentially expressed genes in LTNPs were enriched in several biological pathways such as cell cycle-related pathways and the transforming growth factor-beta signaling pathway. However, genes that were downregulated in LTNPs were associated with immune responses such as the interferon response and IL2-STAT5 signaling. Protein-protein interaction network analysis showed that CD8A, KLRD1, ASGR1, and MLKL, whose gene expression was upregulated in LTNPs, directly interacted with HIV-1 proteins. The network analysis also found that viral proteins potentially regulated host genes that were associated with immune system processes, metabolic processes, and gene expression regulation. @*Conclusion@#Our longitudinal transcriptome analysis of the LTNPs identified multiple previously undescribed pathways and genes that may be useful in the discovery of novel therapeutic targets and biomarkers.
ABSTRACT
Background@#The latent reservoir of Human Immunodificiency Virus-1 (HIV-1) has been a major barrier to the complete eradication of HIV-1 and the development of HIV therapy. Longterm non-progressors (LTNPs) are a rare group of patients with HIV-1 who can spontaneously control HIV-1 replication without antiretroviral therapy. Transcriptome analysis is necessary to predict the pathways involved in the natural control of HIV-1, elucidate the mechanisms involved in LTNPs, and find biomarkers for HIV-1 reservoir therapy. @*Materials and Methods@#In this study, we obtained peripheral blood mononuclear cells from two LTNP subjects at multiple time points and performed RNA-sequencing analyses. @*Results@#We found that LTNPs and normal subjects had different transcriptome profiles. Functional annotation analysis identified that differentially expressed genes in LTNPs were enriched in several biological pathways such as cell cycle-related pathways and the transforming growth factor-beta signaling pathway. However, genes that were downregulated in LTNPs were associated with immune responses such as the interferon response and IL2-STAT5 signaling. Protein-protein interaction network analysis showed that CD8A, KLRD1, ASGR1, and MLKL, whose gene expression was upregulated in LTNPs, directly interacted with HIV-1 proteins. The network analysis also found that viral proteins potentially regulated host genes that were associated with immune system processes, metabolic processes, and gene expression regulation. @*Conclusion@#Our longitudinal transcriptome analysis of the LTNPs identified multiple previously undescribed pathways and genes that may be useful in the discovery of novel therapeutic targets and biomarkers.
ABSTRACT
BACKGROUND: The purpose of this study is to develop rapid and sensitive method to detect M. pneumoniae and C. pneumoniae. In addition, we prospectively investigate the prevalence of M. pneumoniae and C. pneumoniae infections in community-acquried pneumonia. METHODS: The nasopharyngeal aspirates were collected from July 1997 to April 2000. PCR or nested PCR techniques were used to detect causative agents. RFLP and nucleotide sequence analysis were performed to study molecular epidemiology. Furthermore, feasibility of one-step technique to detect two microorganisms was tested by use of multiplex PCR. RESULTS: Of 250 clinical specimens, 23 (9.2%) specimens were positive for M. pneumoniae and 33 (13.2%) for C. pneumoniae, including one dual-infected specimen. Most M. pneumoniae infection occurred during the colder months of the year. C. pneumoniae infection was predominently found between December to February. CONCLUSION: The result indicate that M. pneumoniae and C. pneumoniae infections are frequently found from patients with community-acquired pneumoniae.
Subject(s)
Adult , Humans , Base Sequence , Chlamydia , Chlamydophila pneumoniae , Korea , Molecular Epidemiology , Multiplex Polymerase Chain Reaction , Mycoplasma pneumoniae , Mycoplasma , Pneumonia , Pneumonia, Mycoplasma , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Prevalence , Prospective StudiesABSTRACT
No abstract available.
Subject(s)
Humans , Antiretroviral Therapy, Highly Active , RNA-Directed DNA PolymeraseABSTRACT
To investigate resistance to lamivudine (3TC), we examined the incidence of M184V in 20 HIV-1 patients treated with 3TC for 13.1 +/- 9 months. Fourteen of 20 patients had been exposed to zidovudine (ZDV) or didanosine (ddl) prior to 3TC therapy. Nested PCR targeting to reverse transcriptase (RT) and direct sequencing were performed for peripheral blood mononuclear cells sampled serially. There were resistance mutations to ZDV in at least 9 patients at baseline, although there was no resistance mutation to 3TC. We could detect M184V in 6 (30%) out of 20 patients. The incidence of M184V increased as the duration of therapy prolongs (13% in samples<12 months; 47% in samples gtoreq 12 months). The frequency of mutation M184V was higher in patients with previous mutation to ZDV than in patients with wild type. Resistance mutation was not detected in 7 patients. This study shows that resistance to 3TC tends to develop rapidly in patients with baseline mutations or two drugs combination therapy than in those treated simultaneously with triple drugs. This report is the first on resistance to 3TC in Korean AIDS patients.
Subject(s)
Humans , Didanosine , HIV-1 , Incidence , Lamivudine , Polymerase Chain Reaction , RNA-Directed DNA Polymerase , ZidovudineABSTRACT
The aim of this study was to investigate viral etiology in dilated cardiomyopathy (DCM) by polymerase chain reaction (PCR) or nested reverse tanscription PCR (RT-PCR), and characterize the enteroviral RNA presented in the clinical specimens. Twenty-eight paraffin-embedded heart tissue samples were assayed to detect cytomegalovirus, herpes simplex virus type 1, type 2, parvovirus, adenovirus, and enterovirus (EV) with each specific primer. Of these 28 patients (mean age: 27, M: 24, F: 4), 26 were histologically diagnosed as DCM and 2 as myocardial infarction (MI). Nested RT-PCR detected enteroviral RNA in 7 (26.9%) of 26 patients with DCM, and none of patients with MI. And none of DNA viruses tested were detected from the samples. Amplified products were also genotyped by single-variation of EV is present in the explanted heart tissues from patients with DCM. Although most of the sequences among the wild isolates have the greatest similarity to those of coxsackievirus B3, there are specific regions of variable sequences (no 490 - no 510). The data suggest that enterovirus may be a major viral pathogen for the DCM in Korea and nucleotide sequence data indicate that coxsackievirus B3 may be a leading etiologic agent of DCM.
Subject(s)
Humans , Adenoviridae , Base Sequence , Cardiomyopathy, Dilated , Cytomegalovirus , DNA Viruses , Enterovirus , Heart , Herpesvirus 1, Human , Korea , Myocardial Infarction , Parvovirus , Polymerase Chain Reaction , RNAABSTRACT
No abstract available.
Subject(s)
Humans , Genes, pol , HIV-1 , RNA-Directed DNA Polymerase , ZidovudineABSTRACT
BACKGROUND: We studied the epidemics of respiratory viral infections in Korea and examined various respiratory tract specimens for the presence of respiratory viruses, since the accuracy of rapid detection method depends, in part, on the source of the specimens. METHODS: Over a 24-month period, from March 1997 through February 1999, a total of 1,574 clinical specimens were submitted for the detection of respiratory viruses. A shell vial technique with commercially available monoclonal antibodies directed against respiratory viruses was used to detect respiratory syncytial virus, adenovirus, influenza virus, and parainfluenza virus in clinical specimens, which included throat swab, nasopharyngeal aspirate, tracheal aspirate, and bronchoalveolar lavage (BAL) fluid. RESULTS: Overall positive rate of respiratory viruses was 73/1574 (4.6%). Respiratory viruses were predominantly found between December and February. High incidences were observed among those younger than 2 years and those older than 50 years. The numbers of viral isolates were 3/69 (4.3%) for throat swab, 26/459 (5.7%) for nasopharyngeal aspirate, 11/315 (3.2%) for tracheal aspirate, and 30/528 (5.7%) for BAL fluid. CONCLUSIONS: Nasopharyngeal aspirate and BAL fluid appear to permit increased detection of the respiratory viruses compared with throat swab or tracheal aspirate. However, throat swab may be good specimen for the detection of influenza virus and parainfluenza virus.
Subject(s)
Adenoviridae , Antibodies, Monoclonal , Bronchoalveolar Lavage , Incidence , Korea , Orthomyxoviridae , Paramyxoviridae Infections , Pharynx , Respiratory Syncytial Viruses , Respiratory System , Respiratory Tract InfectionsABSTRACT
To characterize the molecular nature of human immunodeficiency virus (HIV)-1, we determined the full-length HIV-1 sequences from cultured peripheral blood mononuclear cells (PBMC) of a Korean long-term nonprogressor (LTNP). Without antiretroviral therapy, the individual has maintained CD4+ T counts over 500/microliter from 1989 to 1999. Plasma viral RNA copy was 992 U/ml in 1998. Culture supernatant showed positive from culture days 9.4 series of 9 overlapping PCR products were amplified from cultured PBMC and cloned. About 9.2 kb from R of 5' LTR to R of 3' LTR was determined by automated sequencing. The G-to-A hypermutations were shown throughout the entire region. As a result of G to A hypermutations, premature stop codon was found in integrase coding region. Though there was no recombination between subtypes over all genomes, TATA box in both LTRs was TAAAA which is detected in subtype E instead of TATAA in subtype B. And, there were nucleotide GC insertion between NF- kappaB I and Spl III, and duplication of TCF-lalpha in LTR. We could not find any deletion of amino acid in Nef, Gog, Pol and Euv gene. This study is the first report on molecular nature of full genomes of HIV-1 isolated in Korea.
Subject(s)
Clinical Coding , Clone Cells , Codon, Nonsense , Genome , HIV , HIV-1 , Integrases , Korea , Plasma , Polymerase Chain Reaction , Recombination, Genetic , RNA, Viral , TATA BoxABSTRACT
To characterize the molecular nature of human immunodeficiency virus (HIV)-1, we determined the full-length HIV-1 sequences from cultured peripheral blood mononuclear cells (PBMC) of a Korean long-term nonprogressor (LTNP). Without antiretroviral therapy, the individual has maintained CD4+ T counts over 500/microliter from 1989 to 1999. Plasma viral RNA copy was 992 U/ml in 1998. Culture supernatant showed positive from culture days 9.4 series of 9 overlapping PCR products were amplified from cultured PBMC and cloned. About 9.2 kb from R of 5' LTR to R of 3' LTR was determined by automated sequencing. The G-to-A hypermutations were shown throughout the entire region. As a result of G to A hypermutations, premature stop codon was found in integrase coding region. Though there was no recombination between subtypes over all genomes, TATA box in both LTRs was TAAAA which is detected in subtype E instead of TATAA in subtype B. And, there were nucleotide GC insertion between NF- kappaB I and Spl III, and duplication of TCF-lalpha in LTR. We could not find any deletion of amino acid in Nef, Gog, Pol and Euv gene. This study is the first report on molecular nature of full genomes of HIV-1 isolated in Korea.
Subject(s)
Clinical Coding , Clone Cells , Codon, Nonsense , Genome , HIV , HIV-1 , Integrases , Korea , Plasma , Polymerase Chain Reaction , Recombination, Genetic , RNA, Viral , TATA BoxABSTRACT
Cytomegalovirus is the most common cause of life-threatening viral infection in HIV-infected patients. This study was done prospectively to investigate the incidence of CMV infection according to the decrease of CD4+ T cell count (CD4+) in Korean AIDS patients. Thirty-nine HIV-infected patients diagnosed before 1994 were followed for regular immunological monitoring. We have used urine shell vial method for the CMV detection from 1994 and have also checked clinical findings. Positive urine culture rate definitely depended on the CD4+ as follows; 45%, 22%, 17%, 11% and 0%, CD4+ >50, 50-100, 100-200, 200-500 and <500, respectively. Except culture positive 2 patients with CD4+ of 200~300/ul, all eight culture positive patients with CD4+ less than 200/ul showed CMV related diseases on or before urine culture. But, we could not get a positive culture for a late AIDS patient with vision loss. With ganciclovir therapy, all culture results were at least negative just after or on late of first 14 days-ganciclovir infusion-course. These data suggest that the incidence of CMV disease in Korean AIDS patients is very high, and early diagnosis and treatment for CMV diseases is required for the prevention of life threatening results.
Subject(s)
Humans , Cell Count , Cytomegalovirus , Early Diagnosis , Ganciclovir , Incidence , Monitoring, Immunologic , Prospective StudiesABSTRACT
Human immunodeficiency virus type 1 (HIV-1) phenotype plays an important role in the pathogenesis of AIDS. The presence of syncytium-inducing (SI) HIV-1 isolates in infected persons is associated with a rapid decline of CD4+T cells (CD4+), rapid disease progression, and reduced survival time after AIDS diagnosis. We have reported the effects of Korean red ginseng (KRG) on HIV-1 infected patients. To investigate whether KRG affects HIV-1 at gene level and there is a correlation between genotype and decline of CD4+, the C2-V3 region of env gene from 65 HIV-1 isolates were cloned and sequenced. Distributions of subtype were subtype B 57 (88%), subtype A 4 (6%), subtype C 2 (3%), subtype G 1 (2%), and subtype H 1 (2%). The prevalences of SI according to the number of CD4+ are as follows; 40% (6/15) in CD4+ 200/ul. Seventy-five percent (6/8) of SI were detected in rapid progressor with the decline of CD4+ over 60/ul per year. The correlation between SI genotype and the detection of immune complex dissociated (ICD) p24 antigen was significant (p<0.001). In the 40 patients followed-up over 60 months by CD4+, there was significant correlation between annual decrease of CD4+ and duration of KRG intake (R=-0.380, p<0.01), whereas no correlation between CD4+ and zidovudine (ZDV) was observed. The intrapatient variation of amino acid level showed significant inverse correlation with the months of KRG intake (R=-0.47, p<0.01). These results suggest that the determination of genotype by C2- V3 sequencing may be used for the evaluation of prognosis of AIDS patient, and long-term intake of KRG may prevent or delay the progression from NSI to SI.
Subject(s)
Humans , Antigen-Antibody Complex , Clone Cells , Diagnosis , Disease Progression , Genes, env , Genotype , HIV , HIV-1 , Panax , Phenotype , Prevalence , Prognosis , Sequence Analysis , ZidovudineABSTRACT
In order to investigate psychological and behavioral characteristics homosexuals and to present evidence that homosexuals are in danger of HIV infection in Korea, this study was done by self-administered questionnaire and then direct interview with the 28(35%) HIV infected homosexual/bisexuals of 79 HIV infected persons reported in 1992. Homosexuals without heterosexual activity were 9 and the others were bisexuals. Sixty-five percent of respondents had a guilty conscience for their homosexual activity. Twenty(71%) were in twenties and 5(18%) in thirties. Twelve(43%) were detected via health card checking by health office, 21% by blood donation, 18% by hospital visit, and 7% by partner notification. Motivations for homosexual activity were curiosity(36%), temptation or recommendation(14%) and compulsion(11%). Eighteen(72%) never used condom on anal sex. Nine of 26 respondents had experience for anal sex with foreigners. Fourteen(54%) of 26 respondents had history for sexually transmitted diseases. Fightly percent did not have sexual contact after HIV infection and the others usually used condom. It was confirmed that over 57% of the respondents were infected within 1 year before HIV diagnosis and over 82% within 2 years. These data suggest that HIV infection among homosexual group is rapidly spreading.
Subject(s)
Humans , Bisexuality , Blood Donors , Condoms , Conscience , Contact Tracing , Surveys and Questionnaires , Diagnosis , Emigrants and Immigrants , Heterosexuality , HIV Infections , HIV , Homosexuality , Korea , Surveys and Questionnaires , Sexual Behavior , Sexually Transmitted DiseasesABSTRACT
No abstract available.