Viral multiplicity of attachment and its implications for human immunodeficiency virus therapies

Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects

If viruses or other pathogens infect a single host, the outcome of infection may depend on the initial basic reproduction number R₀, the expected number of host cells infected by a single infected cell. This article shows that sometimes, phylogenetic models can estimate the initial R₀, using only sequences sampled from the pathogenic population during its exponential growth or shortly thereafter. When evaluated by simulations mimicking the bursting viral reproduction of HIV and simultaneous sampling of HIV gp120 sequences during early viremia, the estimated R₀ displayed useful accuracies in achievable experimental designs. Estimates of R₀ have several potential applications to investigators interested in the progress of infection in single hosts, including: (1) timing a pathogen’s movement through different microenvironments; (2) timing the change points in a pathogen’s mode of spread (e.g., timing the change from cell-free spread to cell-to-cell spread, or vice versa, in an HIV infection); (3) quantifying the impact different initial microenvironments have on pathogens (e.g., in mucosal challenge with HIV, quantifying the impact that the presence or absence of mucosal infection has on R₀); (4) quantifying subtle changes in infectability in therapeutic trials (either human or animal), even when therapies do not produce total sterilizing immunity; and (5) providing a variable predictive of the clinical efficacy of prophylactic therapies.

Phage therapy dosing: The problem(s) with multiplicity of infection (MOI)

The concept of bacteriophage multiplicity of infection (MOI) – ratios of phages to bacteria – historically has been less easily applied than many phage workers would prefer or, perhaps, may be aware. Here, toward clarification of the concept, I discuss multiplicity of infection in terms of semantics, history, mathematics, pharmacology, and actual practice. For phage therapy and other biocontrol purposes it is desirable, especially, not to solely employ MOI to describe what phage quantities have been applied during dosing. Why? Bacterial densities can change between bacterial challenge and phage application, may not be easily determined immediately prior to phage dosing, and/or target bacterial populations may not be homogeneous with regard to phage access and thereby inconsistent in terms of what MOI individual bacteria experience. Toward experiment reproducibility and as practiced generally for antibacterial application, phage dosing instead should be described in terms of concentrations of formulations (phage titers) as well as volumes applied and, in many cases, absolute numbers of phages delivered. Such an approach typically will be far more desirable from a pharmacological perspective than solely indicating ratios of agents to bacteria. This essay was adapted, with permission, from an appendix of the 2011 monograph, Bacteriophages and Biofilms, Nova Science Publishers.

Phage therapy: eco-physiological pharmacology

Bacterial virus use as antibacterial agents, in the guise of what is commonly known as phage therapy, is an inherently physiological, ecological, and also pharmacological process. Physiologically we can consider metabolic properties of phage infections of bacteria and variation in those properties as a function of preexisting bacterial states. In addition, there are patient responses to pathogenesis, patient responses to phage infections of pathogens, and also patient responses to phage virions alone. Ecologically, we can consider phage propagation, densities, distribution (within bodies), impact on body-associated microbiota (as ecological communities), and modification of the functioning of body "ecosystems" more generally. These ecological and physiological components in many ways represent different perspectives on otherwise equivalent phenomena. Comparable to drugs, one also can view phages during phage therapy in pharmacological terms. The relatively unique status of phages within the context of phage therapy as essentially replicating antimicrobials can therefore result in a confluence of perspectives, many of which can be useful towards gaining a better mechanistic appreciation of phage therapy, as I consider here. Pharmacology more generally may be viewed as a discipline that lies at an interface between organism-associated phenomena, as considered by physiology, and environmental interactions as considered by ecology.

An immunocytometric assay based on dengue infection via DC-SIGN permits rapid measurement of anti-dengue neutralizing antibodies

Dengue remains a global public health threat and development of a safe and effective vaccine is a principal public health goal. The primary correlate of immunity is thought to be neutralizing antibodies. Currently, the plaque reduction neutralization test (PRNT) is the gold standard measure of dengue neutralizing antibody responses, but this test is limited by time-consuming performance. In addition, some feel that use of viral strains adapted to grow in Vero or BHK cells may not accurately reflect protective responses. A human cell line transfected to express a putative natural dengue receptor, DC-SIGN (CD209), was used to measure antibody-mediated dengue neutralization. Using neutralizing monoclonal antibodies, immune sera, and laboratory adapted dengue viruses, serotype-specific neutralizing activity was demonstrated similar to that seen in the Vero PRNT. Importantly, serotype-specific neutralizing activity against recently isolated dengue strains with less heterotypic cross-neutralization than laboratory adapted viruses was also demonstrated.

Human immunodeficiency virus type 1 neutralization measured by flow cytometric quantitation of single-round infection of primary human T cells

There is currently intensive research on the design of novel human immunodeficiency virus type 1 (HIV-1) vaccine immunogens that can elicit potent neutralizing antibodies. A prerequisite for comparing and optimizing these strategies is the ability to precisely measure neutralizing antibody responses. To this end, we sought to develop an assay that directly quantifies single-round HIV-1 infection of peripheral blood mononuclear cells (PBMC). Initial experiments demonstrated that essentially all productively infected PBMC could be identified by flow cytometric detection of intracellular p24 antigen (p24-Ag). After infection of PBMC with HIV-1, p24(+) lymphocytes could be distinguished beginning 1 day postinfection, and the majority of CD8(-) T cells were p24-Ag positive by 3 to 4 days postinfection. To directly quantify first-round infection, we included a protease inhibitor in PBMC cultures. The resulting 2-day assay was highly sensitive and specific for the detection of HIV-1-infected PBMC. Serial dilutions of virus stocks demonstrated that the number of target cells infected was directly related to the amount of infectious virus input into the assay. In neutralization assays, the flow cytometric enumeration of first-round infection of PBMC provided quantitative data on the number of target cells infected and on the inactivation of infectious virus due to reaction with antibody. We also used this single-round assay to compare the percentage of cells expressing p24-Ag to the number of copies of HIV-1 gag per 100 PBMC. The precision and reproducibility of this assay will facilitate the measurement of HIV-1 neutralization, particularly incrementally improved neutralizing antibody responses generated by new candidate vaccines.

Neutralization profiles of sera from human immunodeficiency virus (HIV)-infected individuals: relationship to HIV viral load and CD4 cell count

The relationship of the neutralizing activity (NA) profile of sera from human immunodeficiency virus (HIV)-infected individuals to the HIV viral load and the absolute CD4 count was examined. The NA of 24 serum samples against autologous isolates (AI) and HIV type 1 strain MN was examined. Three NA patterns were recognized. Nine sera neutralized both AI and MN (+/+), six sera neutralized MN but not AI (-/+), and nine sera failed to neutralize both AI and MN (-/-). The identification of the three neutralization patterns (+/+, -/+, and -/-) indicated that resistance to neutralization was progressive. A reciprocal relationship between the viral burden of the patients and the NA profiles was observed. The nine subjects with a -/- NA profile had a plasma viral load of > or =5 x 10(4) copies/ml and a cellular viral burden of > or =1,122 infectious units per million viable cells, which were significantly different from those of the other groups (P < 0.02). These patterns were independent of the phenotypic characteristics of the virus. Longitudinally, subjects with a -/- profile at baseline gained their HIV-specific NA by 24 weeks of antiretroviral therapy when this was associated with a >/=1-log(10) decline in the plasma HIV viral load. The sera from week 24 from some patients were able to neutralize both the 24-week and the baseline dominant virus isolates. A change in CD4 cell count of 50 or more in either direction predicted a -/- or +/+ profile. The verification of the autologous NA profile might be important in selecting patients who may benefit from immune-based therapies involving neutralizing monoclonal antibodies.

Kinetics of stochastically gated diffusion-limited reactions and geometry of random walk trajectories

In this paper we study the kinetics of diffusion-limited, pseudo-first-order A+B-->B reactions in situations in which the particles' intrinsic reactivities are not constant but vary randomly in time. That is, we suppose that the particles are bearing "gates" which fluctuate in time, randomly and independently of each other, between two states-an active state, when the reaction may take place between A and B particles appearing in close contact; and a blocked state, when the reaction is completely inhibited. We focus here on two customary limiting cases of pseudo-first-order reactions-the so-called target annihilation and the Rosenstock trapping model-and consider four different particular models, such that the A particle can be either mobile or immobile or gated or ungated, and ungated or gated B particles can be fixed at random positions or move randomly. All models are formulated on a d-dimensional regular lattice, and we suppose that the mobile species perform independent, homogeneous, discrete-time lattice random walks. The model involving a single, immobile, ungated target A and a concentration of mobile, gated B particles is solved exactly. For the remaining three models we determine exactly, in the form of rigorous lower and upper bounds showing the same N dependence, the large-N asymptotical behavior of the probability that the A particle survives until the Nth step. We also realize that for all four models studied here the A particle survival probability can be interpreted as the moment generating function of some functionals of random walk trajectories, such as, e. g., the number of self-intersections, the number of sites visited exactly a given number of times, the "residence time" on a random array of lattice sites, etc. Our results thus apply to the asymptotic behavior of corresponding generating functions which are not known as yet.

A practical method for simultaneously determining the effective burst sizes and cycle times of viruses

We describe combined analytic and experimental methods for determining reproductive statistics from time-series data. Our computational methods derive four fundamental measures from laboratory experiments: (i) average number of viral daughters; (ii) mean viral cycle time; (iii) standard deviation of the viral cycling time; and (iv) viral doubling time. Taken together, these four reproductive statistics characterize "age-specific fertility," a quantity that provides complete information on the reproduction of the average viral particle. In this paper, we emphasize applications relating to HIV and experiments for assessing cellular tropism, viral phenotypes, antiviral drugs, humoral immunity, and cytotoxic cellular immunity. Nevertheless, our method is quite flexible and applicable to the evaluation of drugs against bacterial, fungal, and parasitic infections, antineoplastic agents against cancer cells, and perturbations involving pest and wildlife releases in ecosystems.

HIV-1 infection kinetics in tissue cultures

Despite intensive experimental work on HIV-1, very little theoretical work has focused on HIV-1 spread in tissue culture. This article uses two systems of ordinary differential equations to model two modes of viral spread, cell-free virus and cell-to-cell contact. The two models produce remarkably similar qualitative results. Simulations using realistic parameter regimes showed that starting with a small fraction of cells infected, both cell-free viral spread and direct cell-to-cell transmission give an initial exponential phase of viral growth, followed by either a crash or a gradual decline, extinguishing the culture. Under some conditions, an oscillatory phase may precede the extinction. Some previous models of in vivo HIV-1 infection oscillate, but only in unrealistic parameter regimes. Experimental tissue infections sometimes display several sequential cycles of oscillation, however, so our models can at least mimic them qualitatively. Significantly, the models show that infective oscillations can be explained by infection dynamics; biological heterogeneity is not required. The models also display proportionality between infected cells and cell-free virus, which is reassuringly consistent with assumptions about the equivalence of several measures of viral load, except that the proportionality requires a relatively constant total cell concentration. Tissue culture parameter values can be determined from accurate, controlled experiments. Therefore, if verified, our models should make interpreting experimental data and extrapolating it to in vivo conditions sharper and more reliable.

Quantitative model of antibody- and soluble CD4-mediated neutralization of primary isolates and T-cell line-adapted strains of human immunodeficiency virus type 1

Primary isolates (PI) of human immunodeficiency virus type 1 (HIV-1) are considerably less sensitive than T-cell line-adapted strains to neutralization by soluble CD4 and by most cross-reactive monoclonal antibodies to the viral envelope (Env) glycoprotein, as well as by postinfection and postvaccination sera (J. P. Moore and D. D. Ho, AIDS 9 [suppl. A]:5117-5136, 1995). We developed a quantitative model to explain the neutralization resistance of PI. The factors incorporated into the model are the dissociation constants for the binding of the neutralizing agent to native Env oligomers, the number of outer Env molecules on the viral surface (which decreases by shedding), and the minimum number of Env molecules required for attachment and fusion. We conclude that modest differences in all these factors can, when combined, explain a relative neutralization resistance of PI versus T-cell line-adapted strains that sometimes amounts to several orders of magnitude. The hypothesis that neutralization of HIV is due to the reduction below a minimum number of the Env molecules on a virion available for attachment and fusion is at odds with single- and few-hit neutralization theories. Our analysis of these ideas favors the hypothesis that neutralization of HIV is instead a competitive blocking of interactions with cellular factors, including adsorption receptors.

A cytopathic infectivity assay of human immunodeficiency virus type 1 in human primary macrophages

In addition to CD4+ T lymphocytes, cells of monocyte/macrophage lineage are a major target for human immunodeficiency virus type 1 (HIV-1) infection. In vitro studies of HIV-1 infection in human monocyte-derived macrophages can be undertaken by a reproducible cell-based assay. A macrophage-based infectivity assay was developed based on the semi-quantitative scoring of HIV-1 induced cytopathology in monolayer macrophage cultures. The assay exhibited dilution-dependent linearity with all three primary macrophage-tropic isolates tested. The end-point infectivity titers determined by this assay correlated with the results obtained by detecting viral p24 antigen in the culture supernatant. The applications of the assay in both neutralization and anti-viral protocols yielded identical results with the more time-consuming and costly p24 formats. Since the assay offers a simple and low-cost method of measuring HIV-1 infectivity in human primary macrophages, it can be used quite easily for large-scale screening or evaluation of candidate vaccines and anti-viral agents.

Murine leukemia virus envelope protein in transgenic-mouse serum blocks infection in vitro

Transgenic mice bearing a murine retroviral envelope transgene (Fv4) have Fv4 gp70env (SU) in their serum in amounts sufficient to block infection by ecotropic virus in vitro. Fv4 Env in serum is derived largely but not exclusively from hematopoietic cells. Tail cells from Fv4 mice and cell lines transduced with the Fv4 env transgene synthesize both components of the envelope protein (gp70 SU and p15E TM) but secrete the gp70 moiety, in the absence of retroviral particles. Blocking of the ecotropic viral receptor by secreted gp70 SU may contribute to resistance to retroviral infection in these mice.

Differential role of V3-specific antibodies in neutralization assays involving primary and laboratory-adapted isolates of HIV type 1

To identify epitopes important in neutralizing primary HIV-1 isolates, we have selectively depleted HIV-1 sera of antibodies specific for the third hypervariable region (V3) of the HIV-1 envelope glycoprotein gp120, and then assessed the functional consequences of such depletion in neutralization assays. The nucleotide sequence of the V3 loop region from HIV-1 PBMC DNA was determined for three HIV-1-infected patients, corresponding peptides were synthesized, and then subsequently used for V3 depletion of the patient sera. Depletion using a single clade B V3 peptide was capable of depleting > 98% of binding antibodies to multiple clade B V3 peptides, including those with changes within the GPGX tip of the loop. Depleted and undepleted sera were studied for their ability to neutralize both laboratory-adapted HIV-1MN and two primary HIV-1 isolates with known V3 sequences, using a viral infectivity reduction assay. While the majority of HIV-1MN neutralization was lost on V3 depletion, the loss in neutralization capacity against primary isolates by these same V3-depleted sera was substantially less pronounced. This suggests that V3 peptide-specific antibodies within HIV-1 serum play a fundamentally different role in mediating neutralization in assays involving laboratory-adapted and primary isolates and implicates antibodies with epitope specificities outside of V3 as major determinants in neutralization assays involving primary isolates.

Human plasma enhances the infectivity of primary human immunodeficiency virus type 1 isolates in peripheral blood mononuclear cells and monocyte-derived macrophages

Physiological microenvironments such as blood, seminal plasma, mucosal secretions, or lymphatic fluids may influence the biology of the virus-host cell and immune interactions for human immunodeficiency virus type 1 (HIV-1). Relative to media, physiological levels of human plasma were found to enhance the infectivity of HIV-1 primary isolates in both phytohemagglutinin-stimulated peripheral blood mononuclear cells and monocyte-derived macrophages. Enhancement was observed only when plasma was present during the virus-cell incubation and resulted in a 3- to 30-fold increase in virus titers in all of the four primary isolates tested. Both infectivity and virion binding experiments demonstrated a slow, time-dependent process generally requiring between 1 and 10 h. Human plasma collected in anticoagulants CPDA-1 and heparin, but not EDTA, exhibited this effect at concentrations from 90 to 40%. Furthermore, heat-inactivated plasma resulted in a loss of enhancement in peripheral blood mononuclear cells but not in monocyte-derived macrophages. Physiological concentrations of human plasma appear to recruit additional infectivity, thus increasing the infectious potential of the virus inoculum.

Virus receptors: implications for pathogenesis and the design of antiviral agents

A virus initiates infection by attaching to its specific receptor on the surface of a susceptible host cell. This prepares the way for the virus to enter the cell. Consequently, the expression of the receptor on specific cells and tissues of the host is a major determinant of the route of entry of the virus into the host and of the patterns of virus spread and pathogenesis in the host. This review emphasizes the virus-receptor interactions of human immunodeficiency virus, the rhinoviruses, the herpesviruses, and the coronaviruses. These interactions are often found to be complex and dynamic, involving multiple sites or factors on both the virus and the host cell. Also, the receptor may play an important role in virus entry per se in addition to its role in virus binding. In the cases of human immunodeficiency virus and the rhinoviruses, ingenious approaches to therapeutic strategies based on inhibiting virus attachment and entry are under development and in clinical trials.