ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.

MOTIVATION: The combined effect of a high replication rate and the low fidelity of the viral polymerase in most RNA viruses and some DNA viruses results in the formation of a viral quasispecies. Uncovering information about quasispecies populations significantly benefits the study of disease progression, antiviral drug design, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used. RESULTS: Benchmarking results showed that ViQuaS outperformed three other previously published methods named ShoRAH, QuRe and PredictHaplo, with improvements of at least 3.1-53.9% in recall, 0-12.1% in precision and 0-38.2% in F-score in terms of strain sequence assembly and improvements of at least 0.006-0.143 in KL-divergence and 0.001-0.035 in root mean-squared error in terms of strain frequency estimation, over the next-best algorithm under various simulation settings. We also applied ViQuaS on a real read set derived from an in vitro human immunodeficiency virus (HIV)-1 population, two independent datasets of foot-and-mouth-disease virus derived from the same biological sample and a real HIV-1 dataset and demonstrated better results than other methods available.

Oral lesions, HIV phenotypes, and management of HIV-related disease: Workshop 4A.

The workshop considered 5 questions related to oral lesions, HIV phenotypes, and the management of HIV-related disease, with a focus on evidence and challenges in resource-poor settings. First, are oral lesions unique with respect to geographic location or phenotype? Second, how useful would an oral lesion index be to predict HIV in resource-poor countries with no access to CD4 counts or viral load? Third, what are the latest methods and delivery modes for drugs used to treat oral lesions associated with HIV? Fourth, what is the role of the oral health care worker in rapid diagnostic testing for HIV? Fifth, what ethical and legal issues are to be considered when managing the HIV patient? The consensus of the workshop was the need for additional research in 4 key areas in developing countries: (1) additional investigation of comorbidities associated with HIV infection that may affect oral lesion presentation and distribution, especially in pediatric populations; (2) the development of region-specific algorithms involving HIV oral lesions, indicating cumulative risk of immune suppression and the presence of HIV disease; (3) well-designed clinical trials to test new therapies for oral lesions, new treatments for resistant oral fungal and viral diseases, effectiveness of therapies in children, and new drug delivery systems; and (4) the role of the oral health care worker in rapid diagnostic testing for HIV in various regions of the world.

A styrene-alt-maleic acid copolymer is an effective inhibitor of R5 and X4 human immunodeficiency virus type 1 infection.

An alternating copolymer of styrene and maleic acid (alt-PSMA) differs from other polyanionic antiviral agents in that the negative charges of alt-PSMA are provided by carboxylic acid groups instead of sulfate or sulfonate moieties. We hypothesized that alt-PSMA would have activity against human immunodeficiency virus type 1 (HIV-1) comparable to other polyanions, such as the related compound, poly(sodium 4-styrene sulfonate) (PSS). In assays using cell lines and primary immune cells, alt-PSMA was characterized by low cytotoxicity and effective inhibition of infection by HIV-1 BaL and IIIB as well as clinical isolates of subtypes A, B, and C. In mechanism of action assays, in which each compound was added to cells and subsequently removed prior to HIV-1 infection ("washout" assay), alt-PSMA caused no enhancement of infection, while PSS washout increased infection 70% above control levels. These studies demonstrate that alt-PSMA is an effective HIV-1 inhibitor with properties that warrant further investigation.

Minority report: hidden memory genomes in HIV-1 quasispecies and possible clinical implications.

The RNA viruses replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving quasispecies and its response to selective pressures such as antiviral treatment is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations in the mutant spectra of viral quasispecies. Biologically relevant mutants have long been known to be present as minority components of replicating viral populations. However, experiments designed with specific mutants of the animal pathogen foot-and-mouth disease virus in cell culture explained the presence of a class of minority genomes termed memory genomes. They descend from those variants that were dominant at an earlier phase of quasispecies evolution, and arise as a consequence of quasispecies dynamics, when viral populations are subjected to discontinuous selective pressures. The presence of memory genomes has also been documented during intrahost evolution of HIV-1 in vivo. The analysis of sequential viral samples of different HIV-1-infected patients showed that two distinct types of memory can operate in retroviruses: a replicative memory analogous to that observed in foot-and-mouth disease virus, as well as a reservoir memory derived from the integrative phase of the retroviral lifecycle. Despite being hidden as minority components of the HIV-1 viral population (ranging from about 0.1 to 20% of the total number of genomes in the quasispecies analyzed), memory genomes can drive the evolution of the virus during HIV-1 infections under antiviral therapy. The limited availability of current experimental data on minority HIV-1 subpopulations in vivo implies that further studies are required in order to define the cutoffs of clinically relevant minority genomes. Nevertheless, it is already evident that such low-abundance genomes remain undetectable by traditional genotyping methods such as consensus sequencing or conventional hybridization techniques. Several experimental systems are currently available for the detection and characterization of minority components of the mutant spectra of viral quasispecies including HIV, hepatitis C virus and hepatitis B virus. Some of these biotechnological approaches could, in the near future, be taken over and exploited in the clinical setting as useful biosensors with which to improve the management of HIV-infected patients.

Analysis of Variability in HIV-1 Subtype A Strains in Russia Suggests a Combination of Deep Sequencing and Multitarget RNA Interference for Silencing of the Virus.

Any method for silencing the activity of the HIV-1 retrovirus should tackle the extremely high variability of HIV-1 sequences and mutational escape. We studied sequence variability in the vicinity of selected RNA interference (RNAi) targets from isolates of HIV-1 subtype A in Russia, and we propose that using artificial RNAi is a potential alternative to traditional antiretroviral therapy. We prove that using multiple RNAi targets overcomes the variability in HIV-1 isolates. The optimal number of targets critically depends on the conservation of the target sequences. The total number of targets that are conserved with a probability of 0.7-0.8 should exceed at least 2. Combining deep sequencing and multitarget RNAi may provide an efficient approach to cure HIV/AIDS.

The role of crude human saliva and purified salivary MUC5B and MUC7 mucins in the inhibition of Human Immunodeficiency Virus type 1 in an inhibition assay.

BACKGROUND: Despite the continuous shedding of HIV infected blood into the oral cavity and the detectable presence of the AIDS virus at a high frequency, human saliva is reported to inhibit oral transmission of HIV through kissing, dental treatment, biting, and aerosolization. The purpose of this study was to purify salivary MUC5B and MUC7 mucins from crude saliva and determine their anti-HIV-1 activities. METHODS: Following Sepharose CL-4B column chromatography and caesium chloride isopycnic density-gradient ultra-centrifugation, the purity and identity of the mucins was determined by SDS-PAGE and Western blotting analysis respectively. Subsequently an HIV-1 inhibition assay was carried out to determine the anti-HIV-1 activity of the crude saliva and purified salivary mucins by incubating them with subtype D HIV-1 prior to infection of the CD4+ CEM SS cells. RESULTS: Western blotting analysis confirmed that the mucin in the void volume is MUC5B and the mucin in the included volume is MUC7. The HIV inhibition assay revealed that both the crude saliva and salivary MUC5B and MUC7 mucins inhibited HIV-1 activity by 100%. CONCLUSION: Although the mechanism of action is not clear the carbohydrate moieties of the salivary mucins may trap or aggregate the virus and prevent host cell entry.

Varying effects of temperature, Ca(2+) and cytochalasin on fusion activity mediated by human immunodeficiency virus type 1 and type 2 glycoproteins.

We examined fusion mediated by the human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) envelope glycoproteins under various experimental conditions. Incubation of HeLa cells expressing HIV-2(ROD) and HIV-2(SBL/ISY) envelope glycoproteins with HeLa-CD4 target cells resulted in fusion at temperatures >/=25 degrees C whereas fusion with cells expressing HIV-1(Lai) occurred only at >/=31 degrees C. HIV-2 envelope glycoprotein-mediated fusion proceeded in the absence of Ca(2+) in the culture medium, whereas HIV-1 fusion required Ca(2+) ions for fusion. In contrast to HIV-2 envelope glycoprotein fusion, incubations in the presence of the 0.5 microM cytochalasin B completely inhibited HIV-1 envelope glycoprotein-mediated fusion. Our results suggest that in contrast to HIV-2, HIV-1 fusion is dependent on dynamic processes in the target membrane.

Signature pattern analysis: a method for assessing viral sequence relatedness.

Signature pattern analysis identifies particular sites in amino acid or nucleic acid alignments of variable sequences that are distinctly representative of a query set of sequences relative to a background set. We explore the merits of using signature patterns for analysis of HIV-1 (human immunodeficiency virus type 1) sequences in cases of epidemiological linkage and potential superinfection. For these purposes, query sets are viral sequences that are all derived from one HIV-1 infected individual, hence the signature pattern is the array of sites that are characteristic of the range of viral variants obtained from that person. Once a signature pattern has been objectively defined, it can be used to examine other viral sequences from other individuals for evidence of genetic relatedness. A computer program to facilitate this analysis, VESPA, is described and applied to sequence data gathered during the investigation of HIV-1 transmission in a dental practice. The implications of signature polymorphisms seen within an infected individual, and shared polymorphisms between linked individuals, are also considered. VESPA may also be applied to the molecular analysis of biological phenotypes.

Rapid molecular epidemiology of human immunodeficiency virus transmission.

Close sequence homology between strains of HIV-1 have been used to corroborate cases of epidemiologically identified transmission. As an alternative to extensive DNA sequence analysis, genetic relateness between pairs of HIV quasispecies was estimated using the reduced electrophoretic mobilities of HIV-1 envelope DNA heteroduplexes through polyacrylamide gels. All six infections acquired in a dental practice in the late 1980s and four of six infections acquired through blood product transfusions and sexual contact in 1984-1985 could be rapidly identified. A rising level of genetic diversity within HIV-1 subtype B facilitated the detection of later transmission events. Transmission linkages could be detected up to 4 years following infection. The simple and rapid technique of DNA heteroduplex tracking can therefore assist epidemiological investigations of HIV transmission and potentially of other genetically variable infectious agents.

Surgeons with HIV infection: the risk to patients.

The risk of human immunodeficiency virus (HIV) transmission from an infected surgeon to a patient is probably very low. In separate studies, the patients of four surgeons with acquired immunodeficiency syndrome (AIDS) have been followed up; no evidence of transmission was found. However, a recent report suggests that a dentist with AIDS may have transmitted HIV infection to a patient during the extraction of two molar teeth. Whether HIV-infected health care workers who perform invasive procedures ought to be obliged to discontinue or modify their practice continues to be debated.

The case of the undetectable viral load.

AIDS: A case study is presented of an African-American gay man who tested positive for HIV in 1996 after going to a clinic for treatment of fever, mouth ulcers, and a dermatomal vesicular rash. He began treatment, was judged to be adherent to his regimen, and remained well clinically. However, despite a significant virologic response, his CD4 cell count never rose. Since these clinical findings were inconsistent and puzzling, the clinician suspected the man had a variant HIV-1 subtype that was not being measured by the viral load test, the Roche RT-PCR. The viral load testing process is described. This case demonstrates the difficulty in measuring viral load reductions in patients with variant subtypes of HIV-1. Viral load testing remains an important component of treatment management, but clinicians need to be reminded that it is not always accurate.^ieng

Deactivation of human immunodeficiency virus type 1 in medium by copper oxide-containing filters.

Human immunodeficiency virus type 1 (HIV-1) can be transmitted through breast-feeding and through contaminated blood donations. Copper has potent biocidal properties and has been found to inactivate HIV-1 infectivity. The objective of this study was to determine the capacity of copper-based filters to inactivate HIV-1 in culture media. Medium spiked with high titers of HIV-1 was exposed to copper oxide powder or copper oxide-impregnated fibers or passed through copper-based filters, and the infectious viral titers before and after treatment were determined. Cell-free and cell-associated HIV-1 infectivity was inhibited when exposed to copper oxide in a dose-dependent manner, without cytotoxicity at the active antiviral copper concentrations. Similar dose-dependent inhibition occurred when HIV-1 was exposed to copper-impregnated fibers. Filtration of HIV-1 through filters containing the copper powder or copper-impregnated fibers resulted in viral deactivation of all 12 wild-type or drug-resistant laboratory or clinical, macrophage-tropic and T-cell-tropic, clade A, B, or C, HIV-1 isolates tested. Viral inactivation was not strain specific. Thus, a novel means to inactivate HIV-1 in medium has been developed. This inexpensive methodology may significantly reduce HIV-1 transmission from "mother to child" and/or through blood donations if proven to be effective in breast milk or plasma and safe for use. The successful application of this technology may impact HIV-1 transmission, especially in developing countries where HIV-1 is rampant.

The origins of the human immunodeficiency viruses: an update.

In 1981 a new acquired immunodeficiency syndrome was first described. The disease has a 100% mortality rate and over 359,000 cases have been reported to the WHO from 162 countries. The WHO estimates that the cumulative global total of AIDS cases as of early 1991 is more than 1.5 million. The dental profession, in line with other health care professions, is involved with guiding rational efforts to stop transmission and with developing effective means of treatment and prevention. This paper reviews the nature of the virus, its possible origins, and the implications of such origins for treatment and prevention of the disease.

Characterization of human immunodeficiency virus type 1 in saliva and blood plasma by V3-specific heteroduplex tracking assay and genotype analyses.

The gp120 V3-encoding region of human immunodeficiency virus type 1 (HIV-1) RNA derived from the saliva and blood plasma of 11 individuals was characterized by heteroduplex tracking assay and sequence analyses. R5-like viral variants were identified in both fluids of all subjects. X4-like variants were detected in the plasma and/or saliva of three subjects, indicating that X4-like variants are not excluded from the saliva compartment. Viral subpopulations were similar in both fluids of most subjects, suggesting that HIV-1 in oral fluids and blood may stem from a common source. These findings raise the possibility of using saliva as a noninvasive fluid for evaluating and monitoring viral evolution in infected persons.

The use of tat and env sequences from human immunodeficiency virus 1 in phylogenetic epidemiological studies.

Using nucleotide sequences from the first exon of the tat gene of the human immunodeficiency virus 1 (HIV-1), we tested the hypothesis that a Florida dentist (a common source) infected five of his patients in the course of dental procedures against the null hypothesis that the dentist and each individual of the dental group independently acquired the virus within the local community. This novel approach of analyzing the tat gene region was used because it may, in some circumstances, be more informative for phylogenetic epidemiology than the more commonly used C2-V3 envelope gene region. The first exon of the tat gene was polymerase chain reaction (PCR)-amplified and directly sequenced from uncultured peripheral blood mononuclear cells. Patient's sequences were compared with sequences from six HIV-1 infected heterosexual couples unrelated to the dentist or the five patients, but from the same general geographic area. In addition, a sixth infected dental patient, previously inferred to have acquired HIV-1 from a source other than the dentist, was included. Multiple phylogenetic analyses demonstrated that the sequences of the five patients were significantly more closely related to each other than to sequences of the controls. Our results using tat sequences, combined with envelope sequence data, strongly support a common phylogenetic epidemiological relationship among these five patients, and the HIV-1 infected dentist who treated them. Correct recovery of known epidemiological relationships among couples included in the analysis further strengthens this conclusion.

Intraspecific phylogenetics: support for dental transmission of human immunodeficiency virus.

A new method to estimate within-species gene genealogies was used to establish linkages among individuals associated with the Florida dental human immunodeficiency virus transmission case. Phylogenetic relationships were estimated from 103 nucleotide sequences from the V3 region of the env gene representing the Florida dentist, eight of his seropositive patients, and many local controls. The cladogram estimation procedure supports linkages among individuals within the previously described dental clade, whereas local controls and other patients form independent networks or are outliers in the main network, indicating more distant evolutionary relationships. A nested statistical analysis also indicates significant cohesion of the dental clade group.

Cross-clade HIV-1-specific neutralizing IgA in mucosal and systemic compartments of HIV-1-exposed, persistently seronegative subjects.

There is an urgent need for a universally effective HIV-1 vaccine, but whether a vaccine will be able to protect against HIV-1 of different clades is a significant concern. IgA from HIV-1-exposed, persistently seronegative (HEPS) subjects has been shown to neutralize HIV-1 and to block epithelial HIV-1 transcytosis, and it may target novel HIV-1 epitopes. We have tested the ability of plasma and mucosal IgA purified from HEPS subjects to neutralize HIV-1 primary isolates of different viral clades and phenotypes. IgA from two groups of HEPS subjects was tested: sex workers from Nairobi, Kenya, where clades A and D predominate, and the heterosexual partners of individuals infected by clade B virus. HIV-1-infected and low-risk uninfected individuals were included as controls. IgA purified from the blood, genital tract, and saliva of most HEPS sex workers demonstrated significant cross-clade HIV-1 neutralization, whereas a more clade-restricted pattern of neutralization was found in partners of clade B-infected individuals. IgA purified from HIV-1-infected individuals also mediated cross-clade neutralization, whereas IgA from uninfected controls lacked neutralizing activity. In conclusion, mucosal and plasma IgA from HEPS subjects neutralizes HIV-1 of different clades. This ability to induce HIV-1-specific systemic and mucosal IgA may be an important feature of an effective prophylactic HIV-1 vaccine.

Polyanionic (i.e., polysulfonate) dendrimers can inhibit the replication of human immunodeficiency virus by interfering with both virus adsorption and later steps (reverse transcriptase/integrase) in the virus replicative cycle.

Polyanionic dendrimers were synthesized and evaluated for their antiviral effects. Phenyldicarboxylic acid (BRI6195) and naphthyldisulfonic acid (BRI2923) dendrimers were found to inhibit the replication of human immunodeficiency virus type 1 (HIV-1; strain III(B)) in MT-4 cells at a EC(50) of 0.1 and 0.3 microg/ml, respectively. The dendrimers were not toxic to MT-4 cells up to the highest concentrations tested (250 microg/ml). These compounds were also effective against various other HIV-1 strains, including clinical isolates, HIV-2 strains, simian immunodeficiency virus (SIV, strain MAC(251)), and HIV-1 strains that were resistant to reverse transcriptase inhibitors. HIV strains containing mutations in the envelope glycoprotein gp120 (engendering resistance to known adsorption inhibitors) displayed reduced sensitivity to the dendrimers. The compounds inhibited the binding of wild-type virus and recombinant virus (containing wild-type gp120) to MT-4 cells at concentrations comparable to those that inhibited the replication of HIV-1(III(B)) in these cells. Cellular uptake studies indicated that BRI2923, but not BRI6195, permeates into MT-4 and CEM cells. Accordingly, the naphtyldisulfonic acid dendrimer (BRI2923) proved able to inhibit later steps of the replication cycle of HIV, i.e., reverse transcriptase and integrase. NL4.3 strains resistant to BRI2923 were selected after passage of the virus in the presence of increasing concentrations of BRI2923. The virus mutants showed 15-fold reduced sensitivity to BRI2923 and cross-resistance to known adsorption inhibitors. However, these virus mutants were not cross-resistant to reverse transcriptase inhibitors or protease inhibitors. We identified several mutations in the envelope glycoprotein gp120 gene (i.e., V2, V3, and C3, V4, and C4 regions) of the BRI2923-resistant NL4.3 strains that were not present in the wild-type NL4.3 strain, whereas no mutations were found in the reverse transcriptase or integrase genes.