The neurotoxin-like sequence of human immunodeficiency virus GP120: A comparison of sequence data from patients with and without neurological symptoms

Virus Genes ◽  
1993 ◽  
Vol 7 (1) ◽  
pp. 23-31 ◽  
Author(s):  
Anders Sönnerborg ◽  
Bo Johansson
Keyword(s):  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Neurological Symptoms ◽  
Immunodeficiency Virus

scholarly journals Distinct Patterns of Gene Expression Associated with Development of Fluconazole Resistance in Serial Candida albicansIsolates from Human Immunodeficiency Virus-Infected Patients with Oropharyngeal Candidiasis

1998 ◽  
Vol 42 (11) ◽  
pp. 2932-2937 ◽  
Author(s):  
Jose L. Lopez-Ribot ◽  
Robert K. McAtee ◽  
Linda N. Lee ◽  
William R. Kirkpatrick ◽  
Theodore C. White ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Point Mutations ◽  
Oropharyngeal Candidiasis ◽  
Fluconazole Resistance ◽  
Expression Of Genes ◽  
Immunodeficiency Virus ◽  
Major Facilitator ◽  
Abc Transporter Genes

ABSTRACT Resistance to fluconazole is becoming an increasing problem in the management of oropharyngeal candidiasis in human immunodeficiency virus-infected patients. Strains obtained from five patients developed decreased fluconazole susceptibility over time. DNA strain typing confirmed the high degree of relatedness among isolates from one patient and the variability among isolates from different patients. Expression of genes involved in development of fluconazole resistance was monitored in each isolate using probes specific for ERG11 (lanosterol 14α-demethylase), MDR1 (a major facilitator), andCDR (ATP-binding cassette or ABC transporter) genes. Increased expression of CDR genes was detected in the series of isolates from two patients. Isolates from one of the two patients also demonstrated increased ERG11 expression, whereas isolates from the other patient did not. Increased levels ofMDR1 mRNA correlated with increased resistance in sequential isolates from another patient. Initial overexpression ofMDR1 with subsequent overexpression of CDRgenes and a final isolate again overexpressing MDR1 were detected in serial isolates from another patient. In another patient, overexpression of these genes was not detected despite an eightfold increase in fluconazole MIC. In this patient, sequence data of theERG11 gene revealed no point mutations associated with decreased susceptibility. Five different patterns of gene expression were observed in isolates recovered from five patients who developed resistance. Therefore, these experiments demonstrate that a variety of mechanisms or combinations of mechanisms are associated with the development of fluconazole drug resistance. Additional studies are needed to estimate the frequency and clinical impact of these mechanisms of resistance.

scholarly journals Human Immunodeficiency Virus (HIV) Outbreak Investigation Among Persons Who Inject Drugs in Massachusetts Enhanced by HIV Sequence Data

2020 ◽  
Vol 222 (Supplement_5) ◽  
pp. S259-S267
Author(s):  
Matthew Tumpney ◽  
Betsey John ◽  
Nivedha Panneer ◽  
R Paul McClung ◽  
Ellsworth M Campbell ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Hiv Infections ◽  
Persons Who Inject Drugs ◽  
Virus Surveillance ◽  
Case Count ◽  
Immunodeficiency Virus ◽  
Control And Prevention ◽  
Virus Sequence ◽  
Diagnosis Date

Abstract Background The Massachusetts Department of Public Health and the Centers for Disease Control and Prevention collaborated to characterize a human immunodeficiency virus (HIV) outbreak in northeastern Massachusetts and prevent further transmission. We determined the contributions of HIV sequence data to defining the outbreak. Methods Human immunodeficiency virus surveillance and partner services data were analyzed to understand social and molecular links within the outbreak. Cases were defined as HIV infections diagnosed during 2015–2018 among people who inject drugs with connections to northeastern Massachusetts or HIV infections among other persons named as partners of a case or whose HIV polymerase sequence linked to another case, regardless of diagnosis date or geography. Results Of 184 cases, 65 (35%) were first identified as part of the outbreak through molecular analysis. Twenty-nine cases outside of northeastern Massachusetts were molecularly linked to the outbreak. Large molecular clusters (75, 28, and 11 persons) were identified. Among 161 named partners, 106 had HIV; of those, 40 (38%) diagnoses occurred through partner services. Conclusions Human immunodeficiency virus sequence data increased the case count by 55% and expanded the geographic scope of the outbreak. Human immunodeficiency virus sequence and partner services data each identified cases that the other method would not have, maximizing prevention and care opportunities for HIV-infected persons and their partners.

scholarly journals Dynamics and Dispersal of Local Human Immunodeficiency Virus Epidemics Within San Diego and Across the San Diego–Tijuana Border

2020 ◽  
Author(s):  
Bram Vrancken ◽  
Sanjay R Mehta ◽  
Santiago Ávila-Ríos ◽  
Claudia García-Morales ◽  
Daniela Tapia-Trejo ◽  
...  
Keyword(s):  
Public Health ◽  
Human Immunodeficiency Virus ◽  
San Diego ◽  
Sequence Data ◽  
Border Region ◽  
San Diego County ◽  
Major Barrier ◽  
Subtype B ◽  
Immunodeficiency Virus ◽  
Mexico Border

Abstract Background Evolutionary analyses of well-annotated human immunodeficiency virus (HIV) sequence data can provide insights into viral transmission patterns and associated factors. Here, we explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) and Tijuana (Mexico) border region to identify factors that could help guide public health policy. Methods HIV pol sequences were collected from people with HIV in San Diego County and Tijuana between 1996–2018. A multistep phylogenetic approach was used to characterize the dynamics of spread. The contributions of geospatial factors and HIV risk group to the local dynamics were evaluated. Results Phylogeographic analyses of the 2034 sequences revealed an important contribution of local transmission in sustaining the epidemic, as well as a complex viral migration network across the region. Geospatial viral dispersal between San Diego communities occurred predominantly among men who have sex with men, with central San Diego being the main source (34.9%) and recipient (39.5%) of migration events. HIV migration was more frequent from San Diego county towards Tijuana than vice versa. Migrations were best explained by the driving time between locations. Conclusions The US-Mexico border may not be a major barrier to the spread of HIV, which may stimulate coordinated transnational intervention approaches. Whereas a focus on central San Diego has the potential to avert most spread, the substantial viral migration independent of central San Diego shows that county-wide efforts will be more effective. Combined, this work shows that epidemiological information gleaned from pathogen genomes can uncover mechanisms that underlie sustained spread and, in turn, can be a building block of public health decision-making.

scholarly journals Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3

2004 ◽  
Vol 78 (22) ◽  
pp. 12438-12445 ◽  
Author(s):  
Seema Thakore Meloni ◽  
Bohye Kim ◽  
Jean-Louis Sankalé ◽  
Donald J. Hamel ◽  
Sodsai Tovanabutra ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Sex Workers ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Immunodeficiency Virus ◽  
Subtype A ◽  
Hiv 1

ABSTRACT Phylogenetic analyses demonstrate significant diversity in worldwide circulating strains of human immunodeficiency virus type 1 (HIV-1). Detailed studies have revealed a complex pattern of intersubtype recombinations, as well as evidence of sub-subtypes circulating in various populations. In this study, we characterized an HIV-1 strain that had previously been identified as a distinct subcluster within the subtype A radiation based on partial sequence data. These viruses were of particular interest given that we recently found that their prevalence was significantly higher in dually infected individuals compared to women who were singly infected with HIV-1. Five viruses isolated from commercial sex workers in Dakar, Senegal, were full-length PCR amplified and sequenced. Phylogenetic analyses indicated that, whereas three of these viruses were closely related and clustered overall within the HIV-1 subtype A radiation, they were distinct from previously characterized sub-subtype A1 and A2 viruses. The clustering pattern was maintained in the individual gag, pol, and env regions of the genome. Distance calculations between these viruses, which we termed A3, and other reference sub-subtype A1 and A2 viruses fell in the range of distances between previously characterized sub-subtype groups. In addition, we found evidence of two A3-containing recombinants in our cohort. These recombinants are mosaics composed of sequence from both sub-subtype A3 and CRF02_AG, the major circulating recombinant form in this West African population. Based on phylogenetic analyses, we propose that the group of viruses found in the Dakar sex worker cohort, previously referred to as HIV-1 A subcluster 2, be referred to as HIV-1 sub-subtype A3.

scholarly journals Random Amplification of Polymorphic DNA and Microsatellite Genotyping of Pre- and Posttreatment Isolates ofCandida spp. from Human Immunodeficiency Virus-Infected Patients on Different Fluconazole Regimens

1998 ◽  
Vol 36 (8) ◽  
pp. 2308-2313 ◽  
Author(s):  
David Metzgar ◽  
Alex van Belkum ◽  
Dawn Field ◽  
Richard Haubrich ◽  
Christopher Wills
Keyword(s):  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Nucleotide Sequencing ◽  
Cell Counts ◽  
Cd4 Cell Counts ◽  
Random Amplification ◽  
Immunodeficiency Virus ◽  
Allele Composition ◽  
Different Strains ◽  
Cd4 Cell

Twelve patients infected with the human immunodeficiency virus (HIV) and with CD4 cell counts below 100 cells/μl received fluconazole daily (200 mg; five patients) or weekly (400 mg; seven patients) for fungal prophylaxis during a 6-month period. Oropharyngeal swabs were taken at regular intervals in order to detect colonization with Candida spp. All yeast isolates were examined with respect to the development over time of fluconazole resistance. Genetic diversity among the strains was assessed in order to discriminate between selection of a resistant subclone and patient recolonization. Genotyping was performed through random amplification of polymorphic DNA (RAPD) analysis. Specific site polymorphisms were assayed by tracking length variability in several microsatellite loci. Finally, to maximize resolution, one of these loci (ERK1) was analyzed by nucleotide sequencing. Although the number of strains analyzed was too small to allow statistical verification, it appeared that when fluconazole was given weekly, a smaller fraction of the strains showed diminished sensitivity than when it was given daily. Genetic analyses allowed three different scenarios to be discerned. Resistance development in an otherwise apparently unchanged strain was seen for 1 of the 12 patients. Clear strain replacement was observed for 3 of the remaining 11 patients. For all other patients minor differences were seen in either the RAPD genotype or the microsatellite allele composition during the course of treatment. In general, microsatellite sequence data is in agreement with data obtained by other methods, but occasionally within-patient heterogeneity is indicated. The present results show that during fluconazole treatment colonizing strains can remain identical, be replaced by clearly different strains, or undergo small changes. Within a patient there may be different levels of intrastrain variation.

scholarly journals Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Elena E. Giorgi ◽  
Hui Li ◽  
Tanmoy Bhattacharya ◽  
George M. Shaw ◽  
Bette Korber
Keyword(s):  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Poisson Model ◽  
Viral Population ◽  
Virus Infections ◽  
Hiv Prevention Strategies ◽  
Immunodeficiency Virus ◽  
Time Of Infection ◽  
Study Participants ◽  
Editing Enzyme

ABSTRACT Many HIV prevention strategies are currently under consideration where it is highly informative to know the study participants’ times of infection. These can be estimated using viral sequence data sampled early in infection. However, there are several scenarios that, if not addressed, can skew timing estimates. These include multiple transmitted/founder (TF) viruses, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like)-mediated mutational enrichment, and recombination. Here, we suggest a pipeline to identify these problems and resolve the biases that they introduce. We then compare two modeling strategies to obtain timing estimates from sequence data. The first, Poisson Fitter (PF), is based on a Poisson model of random accumulation of mutations relative to the TF virus (or viruses) that established the infection. The second uses a coalescence-based phylogenetic strategy as implemented in BEAST. The comparison is based on timing predictions using plasma viral RNA (cDNA) sequence data from 28 simian-human immunodeficiency virus (SHIV)-infected animals for which the exact day of infection is known. In this particular setting, based on nucleotide sequences from samples obtained in early infection, the Poisson method yielded more accurate, more precise, and unbiased estimates for the time of infection than did the explored implementations of BEAST. IMPORTANCE The inference of the time of infection is a critical parameter in testing the efficacy of clinical interventions in protecting against HIV-1 infection. For example, in clinical trials evaluating the efficacy of passively delivered antibodies (Abs) for preventing infections, accurate time of infection data are essential for discerning levels of the Abs required to confer protection, given the natural Ab decay rate in the human body. In such trials, genetic sequences from early in the infection are regularly sampled from study participants, generally prior to immune selection, when the viral population is still expanding and genetic diversity is low. In this particular setting of early viral growth, the Poisson method is superior to the alternative approach based on coalescent methods. This approach can also be applied in human vaccine trials, where accurate estimates of infection times help ascertain if vaccine-elicited immune protection wanes over time.

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