The genetic diversity of human immunodeficiency virus (HIV) is a major concern thought to impact on immunologic escape and eventual vaccine efficacy. Here, simple and rapid methods are described for ...the detection and estimation of genetic divergence between HIV strains on the basis of the observation that DNA heteroduplexes formed between related sequences have a reduced mobility in polyacrylamide gels proportional to their degree of divergence. Reliable phylogenetic subtypes were assigned for HIV-1 strains from around the world. Relationships between viruses were closest when derived from the same or epidemiologically linked individuals. When derived from epidemiologically unlinked individuals, the relationships between viruses in a given geographic region correlated with the length of time HIV-1 had been detected in the population and the number of strains initiating widespread infection. Heteroduplex mobility analysis thus provides a tool to expedite epidemiological investigations by assisting in the classification of HIV and is readily applicable to the screening and characterization of other infectious agents and cellular genes.
We describe a mathematical model and Monte Carlo (MC) simulation of viral evolution during acute infection. We consider both synchronous and asynchronous processes of viral infection of new target ...cells. The model enables an assessment of the expected sequence diversity in new HIV-1 infections originating from a single transmitted viral strain, estimation of the most recent common ancestor (MRCA) of the transmitted viral lineage, and estimation of the time to coalesce back to the MRCA. We also calculate the probability of the MRCA being the transmitted virus or an evolved variant. Excluding insertions and deletions, we assume HIV-1 evolves by base substitution without selection pressure during the earliest phase of HIV-1 infection prior to the immune response. Unlike phylogenetic methods that follow a lineage backwards to coalescence, we compare the observed data to a model of the diversification of a viral population forward in time. To illustrate the application of these methods, we provide detailed comparisons of the model and simulations results to 306 envelope sequences obtained from eight newly infected subjects at a single time point. The data from
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patients were in good agreement with model predictions, and hence compatible with a single-strain infection evolving under no selection pressure. The diversity of the samples from the other two patients was too great to be explained by the model, suggesting multiple HIV-1-strains were transmitted. The model can also be applied to longitudinal patient data to estimate within-host viral evolutionary parameters.
1 Blood Systems Research Institute, San Francisco and the Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2 Departments of Medicine and Microbiology, University of ...Alabama at Birmingham, Birmingham, AL, USA
3 Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
4 Department of Ecology and Management of Plant and Animal Ressources, Faculty of Sciences, University of Kisangani, Democratic Republic of the Congo
5 UMR145, Institut de Recherche pour le Dévelopement and University of Montpellier 1, Montpellier, France
6 Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL 60614, USA
7 The Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL 60614, USA
8 Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
9 Jane Goodall Institute's Center for Primate Studies, Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
Correspondence Eric L. Delwart delwarte{at}medicine.ucsf.edu
Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem–loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller ( 1 kb) plant nanovirus circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.
Present address: Department of Anthropology, Washington University, St Louis, MO 63130, USA
The GenBank/EMBL/DDBJ accession numbers for the seven full ChiSCV genomes are GQ351272
GenBank
–GQ35127.
A supplementary figure showing recombination analyses is available with the online version of this paper.
Several domains of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein have been identified that are involved in HIV-1-mediated membrane fusion. One domain that is involved in ...membrane fusion is the hydrophobic amino terminus of the HIV-1 transmembrane glycoprotein gp41. Here we show that a polar substitution at gp41 amino acid 2 (the 41.2 mutation) results in an envelope glycoprotein that dominantly interferes with both syncytium formation and infection mediated by the wild-type HIV-1 envelope glycoprotein. The interference by the 41.2 mutant is not a result of aberrant envelope glycoprotein synthesis, processing, or transport. The 41.2 mutant elicits a dominant interfering effect even in the presence of excess wild-type glycoprotein, suggesting that a higher-order envelope glycoprotein complex is involved in membrane fusion. These results shed light on the process by which the HIV-1 envelope glycoproteins induce membrane fusion reactions and present a possible approach to anti-HIV therapy.
Background and Objectives Blood banks in the USA have recently introduced minipool nucleic acid amplification testing (MP‐NAT) of blood products to reduce the transmission of human immunodeficiency ...virus (HIV) and hepatitis C virus (HCV) by transfusions. However, MP‐NAT is limited in its ability to detect preseroconversion samples with very low viral RNA loads.
Materials and Methods To determine whether a red blood cell unit, from an MP‐NAT‐negative donation, transmitted HIV when transfused to a patient, we compared the viral sequences from the blood donor and recipient. The implicated donation was also tested by commercially available NAT assays at a range of dilution factors to determine whether the infectious unit could have been detected using individual‐donation NAT (ID‐NAT).
Results Phylogenetic linkage of HIV sequences in the blood donor and recipient confirmed the transmission of HIV by blood transfusion, the first such case identified since introduction of MP‐NAT screening in 1999. Viral RNA was reliably detected by ID‐NAT, but only inconsistently detected by MP‐NAT.
Conclusions Even following the introduction of MP‐NAT, a preseroconversion donation with a viral load of ≤ 150 copies of RNA/ml went undetected and resulted in an HIV transmission. Implementation of ID‐NAT will further reduce such rare transmissions, but at a considerable cost per infectious unit interdicted.
HAART can effectively reduce plasma HIV RNA levels to below the level of detection in most HIV-infected patients. The degree to which residual low-level viremia persists during HAART remains unclear.
...We identified 180 individuals (median duration of HIV infection 12 years) who had at least two consecutive plasma HIV-1 RNA levels below the level of detection (<50-75 copies/ml) while taking antiretroviral drugs; 36 of 180 had been virologically suppressed for more than 5 years. Longitudinal plasma samples that were taken from these individuals during periods of viral load suppression were selected and analyzed. The isothermal transcription-mediated amplification (TMA) (limit of detection <3.5 copies RNA/ml) assay was used to measure persistent viremia. A 'detuned' EIA assay was used to obtain quantitative HIV antibody levels.
A total of 1606 TMA assays were performed on 438 specimens in 180 HAART-suppressed individuals (median 3 replicates per specimen). In the first year of viral suppression, plasma RNA levels declined significantly (P = 0.001), but after month 12 there was no evidence for a continued decline (P = 0.383). In the first year of viral suppression, HIV antibody levels also declined (P = 0.054), but after month 12 there was no evidence for a continued decline (P = 0.988).
Viremia continued to decline during the first 12 months after viremia became undetectable using conventional methods, and then remained stable. HIV antibody levels also decreased in the first year of viral suppression and then remained stable. Viremia and the HIV-associated host response appear to achieve a steady-state 'set-point' during long-term combination therapy.
The frequency of hepatitis C virus (HCV) superinfection with a divergent viral strain was determined in a cohort of recently infected young injection drug users (IDUs) with an HCV incidence rate of ...25%. HCV was amplified, by use of polymerase chain reaction (PCR), from plasma samples collected from 25 HCV-infected individuals over an average period of 12 months, and their viral sequences were compared. Phylogenetic analysis identified 5 IDUs with superinfection (20%) occurring after seroconversion: 2 IDUs were superinfected with different HCV genotypes, and 3 were superinfected with divergent strains of the same genotype. The superinfecting strains were not detected as minority variants (<0.5%) in the initial plasma HCV quasi species. Extensive measures were taken to exclude PCR contamination and mix-up of samples, and superinfection results were concordant at 2 HCV genetic loci. HCV superinfection in IDUs, both intra- and intergenotype, is therefore a frequent event, with an incidence rate similar to that of de novo infections. These results suggest that no cross-protecting immunity develops during the first year of chronic infection with HCV.
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