scholarly journals A quantitative analysis of the similarities and differences of the HIV/FIV gag genome

2022 ◽  
Author(s):  
Charlotte Siu ◽  
Xiao Wen Cheng
Keyword(s):  
Human Immunodeficiency Virus ◽  
Dna Sequences ◽  
Hiv Treatment ◽  
Behavioral Differences ◽  
Genome Sequences ◽  
Percent Identity ◽  
Immunodeficiency Virus ◽  
Bioinformatics Software ◽  
Similarities And Differences

Among viruses, human immunodeficiency virus (HIV) presents the greatest challenge to humans. Here, we retrieved genome sequences from NCBI and were then run through LALIGN bioinformatics software to compute the E value, bit score, Waterman eggert score, and percent identity, which are four important indicators of how similar the sequences are. The E value was 3.1 x 10^-9, the percent identity was 54.4 percent, and the bit score was 51.9. It was also sensed that bases 1600 to 1990 in HIV and bases 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genomes are rather similar, it is unlikely that this similarity is due to random chance; therefore, there are a noticeable number of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term, it will provide new insights into the differences observed in previous studies or even facilitate the development of an effective HIV treatment.

scholarly journals A quantitative analysis of the FIV and HIV genome using bioinformatics software

2022 ◽  
Author(s):  
Charlotte Siu ◽  
Xiao Wen Cheng ◽  
Meredith Horn
Keyword(s):  
Human Immunodeficiency Virus ◽  
Dna Sequences ◽  
Illumina Miseq ◽  
Hiv Treatment ◽  
Behavioral Differences ◽  
Percent Identity ◽  
Immunodeficiency Virus ◽  
Bioinformatics Software ◽  
Human Kinds

Among viruses, the human immunodeficiency virus (HIV) presented the greatest challenge to human kinds. the HIV and FIV gag genome was sequenced using the Illumina MiSeq Benchtop next-generation sequencer.The DNA sequences obtained were then run through the LALIGN bioinformatics software to compute the E value, bit score, waterman eggert score, percent identity,which are four important indicators of how similar the sequences are. The E value was 3.1 x 10 ^-9, the percent identity was 54.4 percent and the bit score was 51.9. It was also sensed that base 1600 to 1990 in HIV and base 800 to 910 in FIV have a higher than normal similarity. This reflects that while the DNA sequences of the gag region of both the HIV and FIV genome are rather similar and it is unlikely that this similarity is due to random chance, there are a noticeable amount of differences. A better understanding of the level of similarity and differences in the gag region of the genome sequence would facilitate our understanding of structural and cellular behavioral differences between FIV and HIV, and in the long term it prevides new explanations to differences observed in previous studies, or even facilitate the development of an effective HIV treatment.

scholarly journals Long-term survivor of human immunodeficiency virus-associated plasmablastic lymphoma

2013 ◽  
Vol 34 (2) ◽  
pp. 96 ◽  
Author(s):  
Atul Sharma ◽  
T. V. S. V. G. K. Tilak ◽  
Rakesh Lodha ◽  
MC Sharma ◽  
Deepak Dabkara
Keyword(s):  
Human Immunodeficiency Virus ◽  
Plasmablastic Lymphoma ◽  
Immunodeficiency Virus ◽  
Term Survivor

Combined Genotypes of CCR5, CCR2, SDF1, and HLA Genes Can Predict the Long-Term Nonprogressor Status in Human Immunodeficiency Virus-1–Infected Individuals

Blood ◽  
1999 ◽  
Vol 93 (3) ◽  
pp. 936-941 ◽  
Author(s):  
Magdalena Magierowska ◽  
Ioannis Theodorou ◽  
Patrice Debré ◽  
Françoise Sanson ◽  
Brigitte Autran ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Chemokine Receptor ◽  
Multivariate Logistic Regression Model ◽  
Hla B27 ◽  
Hla Alleles ◽  
Immunodeficiency Virus ◽  
Combined Genotypes ◽  
Hiv 1

Abstract Human immunodeficiency virus (HIV)-1–infected long-term nonprogressors (LT-NP) represent less than 5% of HIV-1–infected patients. In this work, we tried to understand whether combined genotypes of CCR5-▵32, CCR2-64I, SDF1-3′A and HLA alleles can predict the LT-NP status. Among the chemokine receptor genotypes, only the frequency of the CCR5-▵32 allele was significantly higher in LT-NP compared with the group of standard progressors. The predominant HLA alleles in LT-NP were HLA-A3, HLA-B14, HLA-B17, HLA-B27, HLA-DR6, and HLA-DR7. A combination of both HLA and chemokine receptor genotypes integrated in a multivariate logistic regression model showed that if a subject is heterozygous for CCR5-▵32 and homozygous for SDF1 wild type, his odds of being LT-NP are increased by 16-fold, by 47-fold when a HLA-B27 allele is present with HLA-DR6 absent, and by 47-fold also if at least three of the following alleles are present: HLA-A3, HLA-B14, HLA-B17, HLA-DR7. This model allowed a correct classification of 70% of LT-NPs and 81% of progressors, suggesting that the host’s genetic background plays an important role in the evolution of HIV-1. The chemokine receptor and chemokine genes along with the HLA genotype can serve as predictors of HIV-1 outcome for classification of HIV-1–infected subjects as LT-NPs or progressors.

scholarly journals Protein S deficiency in men with long-term human immunodeficiency virus infection [see comments]

Blood ◽  
1993 ◽  
Vol 81 (7) ◽  
pp. 1801-1807 ◽  
Author(s):  
CP Stahl ◽  
CS Wideman ◽  
TJ Spira ◽  
EC Haff ◽  
GJ Hixon ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Pneumocystis Carinii ◽  
Anticardiolipin Antibody ◽  
Protein S ◽  
Protein S Deficiency ◽  
Free Protein ◽  
Long Term Study ◽  
S Deficiency ◽  
Immunodeficiency Virus

Abstract Decreases in protein S levels have recently been reported in some human immunodeficiency virus (HIV)-infected patients. To examine predisposing factors, 25 men randomly selected from a long-term study of HIV- infected patients were studied. The minimum mean duration of HIV seropositivity in this group was 106.6 months (range 15 to 143 months). No patients were anticoagulated at the time of the study. Three of the 25 randomly selected patients gave a history of thrombosis, in each instance occurring after the onset of HIV positivity. Two of the 3 patients with thrombosis had more than one episode. Coagulation studies showed that 3 of 3 (100%) of the patients with thrombosis and 16 of 22 (72.7%) of those without previous thrombosis had decreased free protein S. Mean-free and total protein S levels were statistically lower for HIV-infected patients with and without previous thrombosis compared with healthy male controls. C4b-binding protein was not increased in study patients with decreased protein S levels. Decreases in protein S levels did not correlate with CD4+ cell levels, CDC class, p24 antigen positivity, zidovudine (AZT) use, or Pneumocystis carinii prophylaxis. The duration of disease statistically correlated with decreases in protein S levels (r = .37, P < .05). A linear correlation existed between increasing IgG anticardiolipin antibody levels and decreasing free protein S antigen (r = .67, P < .005). This study shows that protein S deficiency is common in long-term HIV-infected patients and is caused by a decrease in the free protein, rather than by changes in the bound complex. The data suggest that protein S deficiency is not correlated with HIV disease severity but may predispose patients to thromboembolic complications.

scholarly journals Immunization of mice with the nef gene from Human Immunodeficiency Virus type 1: Study of immunological memory and long-term toxicology

2007 ◽  
Vol 2 (1) ◽  
Author(s):  
Andreas Bråve ◽  
Lindvi Gudmundsdotter ◽  
Georg Gasteiger ◽  
Kristian Hallermalm ◽  
Wolfgang Kastenmuller ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Immunological Memory ◽  
Immunodeficiency Virus

Association of Primary Pleural Effusion Lymphoma of T-Cell Origin and Human Herpesvirus 8 in a Human Immunodeficiency Virus–Seronegative Man

2001 ◽  
Vol 125 (9) ◽  
pp. 1246-1248 ◽  
Author(s):  
Emmanuèle Lechapt-Zalcman ◽  
Dominique Challine ◽  
Marie-Hélène Delfau-Larue ◽  
Corinne Haioun ◽  
Dominique Desvaux ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cell ◽  
Dna Sequences ◽  
Primary Effusion Lymphoma ◽  
Polymerase Chain Reaction Amplification ◽  
Human Herpesvirus ◽  
Body Cavity ◽  
Human Herpesvirus 8 ◽  
Herpesvirus 8 ◽  
Immunodeficiency Virus

Abstract We describe a case of an 87-year-old human immunodeficiency virus (HIV)–negative man who developed a primary pleural lymphoma without any identifiable tumor mass associated with human herpesvirus 8 (HHV-8) infection. A large T-cell lymphoma was diagnosed based on morphologic, immunophenotypic, and molecular findings. The HHV-8 DNA sequences were detected using specific polymerase chain reaction amplification in the lymphomatous effusion. Study of the patient's serum confirmed the HHV-8 infection. This case report displays the characteristic features of HHV-8–related body cavity-based lymphoma/primary effusion lymphoma previously reported in HIV-seronegative patients, except that it is of T-cell origin. Whether this case may be included or not within the primary effusion lymphoma entity, the association of a pleural T-cell non-Hodgkin lymphoma with HHV-8 infection raises the question of the possible occurrence of T cells as the target of malignant transformation associated with HHV-8 infection.

scholarly journals Aviremia 10 Years Postdiscontinuation of Antiretroviral Therapy Initiated During Primary Human Immunodeficiency Virus-1 Infection and Association With Gag-Specific T-Cell Responses

2015 ◽  
Vol 2 (4) ◽  
Author(s):  
Sabine Kinloch-de Loes ◽  
Lucy Dorrell ◽  
Hongbing Yang ◽  
Gareth A. D. Hardy ◽  
Sabine Yerly ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cell ◽  
Antiretroviral Therapy ◽  
Viral Reservoir ◽  
Cell Responses ◽  
Immunodeficiency Virus ◽  
Cellular Immune ◽  
Drug Free ◽  
Human Immunodeficiency Virus 1

Abstract Combination antiretroviral therapy during primary human immunodeficiency virus-1 infection may enable long-term drug-free virological control in rare individuals. We describe a female who maintained aviremia and a normal CD4+/CD8+ T cell ratio for 10 years after stopping therapy, despite a persistent viral reservoir. Cellular immune responses may have contributed to this outcome.

scholarly journals Grossly Defective nef Gene Sequences in a Human Immunodeficiency Virus Type 1-Seropositive Long-Term Nonprogressor

1998 ◽  
Vol 72 (5) ◽  
pp. 3646-3657 ◽  
Author(s):  
Roberto Salvi ◽  
Anna Rosa Garbuglia ◽  
Antonino Di Caro ◽  
Simonetta Pulciani ◽  
Francesco Montella ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Length Polymorphism ◽  
Mononuclear Cells ◽  
Polymorphism Analysis ◽  
Immunodeficiency Virus ◽  
Peripheral Mononuclear Cells ◽  
Hiv 1

ABSTRACT We have been investigating a long-term nonprogressor who was found to be human immunodeficiency virus type 1 (HIV-1) seropositive in 1985 and has survived with stable CD4+ T-cell counts (>1,000 CD4 cells/μl) without any AIDS-related illness. We have previously reported that repeated attempts to measure HIV-1 RNA in the peripheral mononuclear cells obtained from this subject have invariably failed. In the present study, we have analyzed the molecular nature of the HIV-1 quasispecies infecting this patient by PCR amplification of two proviral regions, the 5′ long terminal repeat (5′LTR)/gagleader and the nef gene, directly from fresh uncultured peripheral mononuclear cells, followed by length polymorphism analysis (with 1994, 1995, and 1996 samples) and sequencing (with a 1996 sample). Only proviral forms with nef deletions were revealed by length polymorphism analysis in samples from all three time points. Sequence analysis of the nef gene from the 1996 sample confirmed the presence of similar proviral quasispecies characterized by the presence of several deletions located in thenef-alone and the nef/U3 overlapping regions. Length polymorphism analysis of the 5′LTR/gag leader region suggested the existence of two major quasispecies populations, one characterized by the presence of forms carrying deletions in the U3 region and the other showing a completely intact, full-length 5′LTR. Evidence of the role of nef gene defects in long-term survival of HIV-1-infected patients has been provided so far in two independent investigations involving patients infected with HIV through blood transfusion. Here we show the existence of a similar condition in a subject who acquired HIV-1 seropositivity through the sexual route.

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