Simulating the entire natural course of HIV infection by extending the basic viral dynamics equations to include declining viral clearance

The basic model of viral dynamics is a relatively simple set of equations describing the most essential features of the host-pathogen interactions. Coupled with data, it has been used extensively and successfully to reproduce and explain the features of the early acute phase of HIV infection and the effects of antiretroviral treatment, as well as to estimate the lifespan of infected cells, viral growth and clearance rates and predict early outcomes under different circumstances. However, it cannot reproduce the entire natural course of untreated HIV infection consistently with constant parameters. Here we show that it is possible to qualitatively reproduce the whole course of untreated HIV infection within the general framework of the basic model by assuming progressively declining viral clearance coupled with viral load. We discuss the interpretation of this model as proof-of-concept that may inspire further research into the role of viral clearance in HIV infection.

How should HIV resources be allocated? Lessons learnt from applying Optima HIV in 23 countries

Introduction

With limited funds available, meeting global health targets requires countries to both mobilize and prioritize their health spending. Within this context, countries have recognized the importance of allocating funds for HIV as efficiently as possible to maximize impact. Over the past six years, the governments of 23 countries in Africa, Asia, Eastern Europe and Latin America have used the Optima HIV tool to estimate the optimal allocation of HIV resources.

Methods

Each study commenced with a request by the national government for technical assistance in conducting an HIV allocative efficiency study using Optima HIV. Each study team validated the required data, calibrated the Optima HIV epidemic model to produce HIV epidemic projections, agreed on cost functions for interventions, and used the model to calculate the optimal allocation of available funds to best address national strategic plan targets. From a review and analysis of these 23 country studies, we extract common themes around the optimal allocation of HIV funding in different epidemiological contexts.

Results and discussion

The optimal distribution of HIV resources depends on the amount of funding available and the characteristics of each country's epidemic, response and targets. Universally, the modelling results indicated that scaling up treatment coverage is an efficient use of resources. There is scope for efficiency gains by targeting the HIV response towards the populations and geographical regions where HIV incidence is highest. Across a range of countries, the model results indicate that a more efficient allocation of HIV resources could reduce cumulative new HIV infections by an average of 18% over the years to 2020 and 25% over the years to 2030, along with an approximately 25% reduction in deaths for both timelines. However, in most countries this would still not be sufficient to meet the targets of the national strategic plan, with modelling results indicating that budget increases of up to 185% would be required.

Conclusions

Greater epidemiological impact would be possible through better targeting of existing resources, but additional resources would still be required to meet targets. Allocative efficiency models have proven valuable in improving the HIV planning and budgeting process.

Optima Nutrition: an allocative efficiency tool to reduce childhood stunting by better targeting of nutrition-related interventions

Background

Child stunting due to chronic malnutrition is a major problem in low- and middle-income countries due, in part, to inadequate nutrition-related practices and insufficient access to services. Limited budgets for nutritional interventions mean that available resources must be targeted in the most cost-effective manner to have the greatest impact. Quantitative tools can help guide budget allocation decisions.

Methods

The Optima approach is an established framework to conduct resource allocation optimization analyses. We applied this approach to develop a new tool, ‘Optima Nutrition’, for conducting allocative efficiency analyses that address childhood stunting. At the core of the Optima approach is an epidemiological model for assessing the burden of disease; we use an adapted version of the Lives Saved Tool (LiST). Six nutritional interventions have been included in the first release of the tool: antenatal micronutrient supplementation, balanced energy-protein supplementation, exclusive breastfeeding promotion, promotion of improved infant and young child feeding (IYCF) practices, public provision of complementary foods, and vitamin A supplementation. To demonstrate the use of this tool, we applied it to evaluate the optimal allocation of resources in 7 districts in Bangladesh, using both publicly available data (such as through DHS) and data from a complementary costing study.

Results

Optima Nutrition can be used to estimate how to target resources to improve nutrition outcomes. Specifically, for the Bangladesh example, despite only limited nutrition-related funding available (an estimated $0.75 per person in need per year), even without any extra resources, better targeting of investments in nutrition programming could increase the cumulative number of children living without stunting by 1.3 million (an extra 5%) by 2030 compared to the current resource allocation. To minimize stunting, priority interventions should include promotion of improved IYCF practices as well as vitamin A supplementation. Once these programs are adequately funded, the public provision of complementary foods should be funded as the next priority. Programmatic efforts should give greatest emphasis to the regions of Dhaka and Chittagong, which have the greatest number of stunted children.

Conclusions

A resource optimization tool can provide important guidance for targeting nutrition investments to achieve greater impact.

The global Optima HIV allocative efficiency model: targeting resources in efforts to end AIDS

BACKGROUND

To move towards ending AIDS by 2030, HIV resources should be allocated cost-effectively. We used the Optima HIV model to estimate how global HIV resources could be retargeted for greatest epidemiological effect and how many additional new infections could be averted by 2030.

METHODS

We collated standard data used in country modelling exercises (including demographic, epidemiological, behavioural, programmatic, and expenditure data) from Jan 1, 2000, to Dec 31, 2015 for 44 countries, capturing 80% of people living with HIV worldwide. These data were used to parameterise separate subnational and national models within the Optima HIV framework. To estimate optimal resource allocation at subnational, national, regional, and global levels, we used an adaptive stochastic descent optimisation algorithm in combination with the epidemic models and cost functions for each programme in each country. Optimal allocation analyses were done with international HIV funds remaining the same to each country and by redistributing these funds between countries.

FINDINGS

Without additional funding, if countries were to optimally allocate their HIV resources from 2016 to 2030, we estimate that an additional 7·4 million (uncertainty range 3·9 million-14·0 million) new infections could be averted, representing a 26% (uncertainty range 13-50%) incidence reduction. Redistribution of international funds between countries could avert a further 1·9 million infections, which represents a 33% (uncertainty range 20-58%) incidence reduction overall. To reduce HIV incidence by 90% relative to 2010, we estimate that more than a three-fold increase of current annual funds will be necessary until 2030. The most common priorities for optimal resource reallocation are to scale up treatment and prevention programmes targeting key populations at greatest risk in each setting. Prioritisation of other HIV programmes depends on the epidemiology and cost-effectiveness of service delivery in each setting as well as resource availability.

INTERPRETATION

Further reductions in global HIV incidence are possible through improved targeting of international and national HIV resources.

FUNDING

World Bank and Australian NHMRC.

Acute systemic DNA damage in youth does not impair immune defense with aging

Aging‐related decline in immunity is believed to be the main driver behind decreased vaccine efficacy and reduced resistance to infections in older adults. Unrepaired DNA damage is known to precipitate cellular senescence, which was hypothesized to be the underlying cause of certain age‐related phenotypes. Consistent with this, some hallmarks of immune aging were more prevalent in individuals exposed to whole‐body irradiation (WBI), which leaves no anatomical repository of undamaged hematopoietic cells. To decisively test whether and to what extent WBI in youth will leave a mark on the immune system as it ages, we exposed young male C57BL/6 mice to sublethal WBI (0.5–4 Gy), mimicking human survivor exposure during nuclear catastrophe. We followed lymphocyte homeostasis thorough the lifespan, response to vaccination, and ability to resist lethal viral challenge in the old age. None of the irradiated groups showed significant differences compared with mock‐irradiated (0 Gy) animals for the parameters measured. Even the mice that received the highest dose of sublethal WBI in youth (4 Gy) exhibited equilibrated lymphocyte homeostasis, robust T‐ and B‐cell responses to live attenuated West Nile virus (WNV) vaccine and full survival following vaccination upon lethal WNV challenge. Therefore, a single dose of nonlethal WBI in youth, resulting in widespread DNA damage and repopulation stress in hematopoietic cells, leaves no significant trace of increased immune aging in a lethal vaccine challenge model.

Epitope-specific CD8+ T cell kinetics rather than viral variability determine the timing of immune escape in simian immunodeficiency virus infection

CD8(+) T cells are important for the control of chronic HIV infection. However, the virus rapidly acquires "escape mutations" that reduce CD8(+) T cell recognition and viral control. The timing of when immune escape occurs at a given epitope varies widely among patients and also among different epitopes within a patient. The strength of the CD8(+) T cell response, as well as mutation rates, patterns of particular amino acids undergoing escape, and growth rates of escape mutants, may affect when escape occurs. In this study, we analyze the epitope-specific CD8(+) T cells in 25 SIV-infected pigtail macaques responding to three SIV epitopes. Two epitopes showed a variable escape pattern and one had a highly monomorphic escape pattern. Despite very different patterns, immune escape occurs with a similar delay of on average 18 d after the epitope-specific CD8(+) T cells reach 0.5% of total CD8(+) T cells. We find that the most delayed escape occurs in one of the highly variable epitopes, and that this is associated with a delay in the epitope-specific CD8(+) T cells responding to this epitope. When we analyzed the kinetics of immune escape, we found that multiple escape mutants emerge simultaneously during the escape, implying that a diverse population of potential escape mutants is present during immune selection. Our results suggest that the conservation or variability of an epitope does not appear to affect the timing of immune escape in SIV. Instead, timing of escape is largely determined by the kinetics of epitope-specific CD8(+) T cells.

Understanding the relationship between Plasmodium falciparum growth rate and multiplicity of infection

Natural infections with Plasmodium falciparum are often composed of multiple concurrent genetically distinct parasite clones. Such multiclonal infections are more common in areas of high transmission, and the frequency of multiclonal infection also varies with age. A number of studies have suggested that multiclonal infection predicts the risk of subsequent clinical malaria. The multiplicity of infection is determined by the rate of new infections, the number of clones inoculated at each mosquito bite, and the duration of infections. Here, we used a mathematical modeling approach to understand how variation in the growth rate of blood-stage parasites affects the observed multiplicity of infection (MOI), as well as the relationship between the MOI and the risk of subsequent malaria. We then analyzed data from a study of multiclonal infection and malaria in an malaria-endemic area in Tanzania and show that the proportion of multiclonal infections varies with age and that the observed relationship between multiclonal infection and subsequent clinical events can be explained by a reduction in blood-stage parasite growth with age in this population.

Measuring turnover of SIV DNA in resting CD4+ T cells using pyrosequencing: implications for the timing of HIV eradication therapies

Resting CD4+ T cells are a reservoir of latent HIV-1. Understanding the turnover of HIV DNA in these cells has implications for the development of eradication strategies. Most studies of viral latency focus on viral persistence under antiretroviral therapy (ART). We studied the turnover of SIV DNA resting CD4+ T cells during active infection in a cohort of 20 SIV-infected pigtail macaques. We compared SIV sequences at two Mane-A1*084:01-restricted CTL epitopes using serial plasma RNA and resting CD4+ T cell DNA samples by pyrosequencing, and used a mathematical modeling approach to estimate SIV DNA turnover. We found SIV DNA turnover in resting CD4+ T cells was slow in animals with low chronic viral loads, consistent with the long persistence of latency seen under ART. However, in animals with high levels of chronic viral replication, turnover was high. SIV DNA half-life within resting CD4 cells correleated with viral load (p = 0.0052) at the Gag KP9 CTL epitope. At a second CTL epitope in Tat (KVA10) there was a trend towards an association of SIV DNA half-life in resting CD4 cells and viral load (p = 0.0971). Further, we found that the turnover of resting CD4+ T cell SIV DNA was higher for escape during early infection than for escape later in infection (p = 0.0084). Our results suggest viral DNA within resting CD4 T cells is more labile and may be more susceptible to reactivation/eradication treatments when there are higher levels of virus replication and during early/acute infection.

Decreased growth rate of P. falciparum blood stage parasitemia with age in a holoendemic population

In malaria holoendemic settings, decreased parasitemia and clinical disease is associated with age and cumulative exposure. The relative contribution of acquired immunity against various stages of the parasite life cycle is not well understood. In particular, it is not known whether changes in infection dynamics can be best explained by decreasing rates of infection, or by decreased growth rates of parasites in blood. Here, we analyze the dynamics of Plasmodium falciparum infection after treatment in a cohort of 197 healthy study participants of different ages. We use both polymerase chain reaction (PCR) and microscopy detection of parasitemia in order to understand parasite growth rates and infection rates over time. The more sensitive PCR assay detects parasites earlier than microscopy, and demonstrates a higher overall prevalence of infection than microscopy alone. The delay between PCR and microscopy detection is significantly longer in adults compared with children, consistent with slower parasite growth with age. We estimated the parasite multiplication rate from delay to PCR and microscopy detections of parasitemia. We find that both the delay between PCR and microscopy infection as well as the differing reinfection dynamics in different age groups are best explained by a slowing of parasite growth with age.

Density-dependent blood stage Plasmodium falciparum suppresses malaria super-infection in a malaria holoendemic population

Recent studies of Plasmodium berghei malaria in mice show that high blood-stage parasitemia levels inhibit the development of subsequent liver-stage infections. Whether a similar inhibitory effect on liver-stage Plasmodium falciparum by blood-stage infection occurs in humans is unknown. We have analyzed data from a treatment-time-to-infection cohort of children < 10 years of age residing in a malaria holoendemic area of Kenya where people experience a new blood-stage infection approximately every 2 weeks. We hypothesized that if high parasitemia blocked the liver stage, then high levels of parasitemia should be followed by a "skipped" peak of parasitemia. Statistical analysis of "natural infection" field data and stochastic simulation of infection dynamics show that the data are consistent with high P. falciparum parasitemia inhibiting liver-stage parasite development in humans.

The search for an HIV cure: tackling latent infection

Strategies to eliminate infectious HIV that persists despite present treatments and with the potential to cure HIV infection are of great interest. One patient seems to have been cured of HIV infection after receiving a bone marrow transplant with cells resistant to the virus, although this strategy is not viable for large numbers of infected people. Several clinical trials are underway in which drugs are being used to activate cells that harbour latent HIV. In a recent study, investigators showed that activation of latent HIV infection in patients on antiretroviral therapy could be achieved with a single dose of vorinostat, a licensed anticancer drug that inhibits histone deacetylase. Although far from a cure, such studies provide some guidance towards the logical next steps for research. Clinical studies that use a longer duration of drug dosing, alternative agents, combination approaches, gene therapy, and immune-modulation approaches are all underway.

The dynamics of naturally acquired immunity to Plasmodium falciparum infection

Severe malaria occurs predominantly in young children and immunity to clinical disease is associated with cumulative exposure in holoendemic settings. The relative contribution of immunity against various stages of the parasite life cycle that results in controlling infection and limiting disease is not well understood. Here we analyse the dynamics of Plasmodium falciparum malaria infection after treatment in a cohort of 197 healthy study participants of different ages in order to model naturally acquired immunity. We find that both delayed time-to-infection and reductions in asymptomatic parasitaemias in older age groups can be explained by immunity that reduces the growth of blood stage as opposed to liver stage parasites. We found that this mechanism would require at least two components – a rapidly acting strain-specific component, as well as a slowly acquired cross-reactive or general immunity to all strains. Analysis and modelling of malaria infection dynamics and naturally acquired immunity with age provides important insights into what mechanisms of immune control may be harnessed by malaria vaccine strategists.

Human malaria infections resulting in serious complications and death occur predominantly in young children, and resistance is gradually acquired with repeated exposure. Malaria parasites have two major stages within the human host during its life cycle: an initial liver stage, and the subsequent blood stage, where parasites replicate in and destroy red blood cells. The mechanisms of acquired resistance to severe malaria may involve immunity to both the liver and blood stage parasites. However the relative contribution of each type of immunity is not yet understood. To gain novel insight, we have analysed data from a malaria exposed cohort from western Kenya. We used mathematical modeling to understand what form of immunity is consistent with the observed rates of reinfection in adults and children seen in the field study data. We found that the reinfection pattern can be completely explained by blood stage immunity. Moreover, the blood stage immunity must consist of rapidly-induced strain-specific immunity that clears individual infections, and general immunity that accumulates slowly and decreases the average parasite growth rate with age. Understanding the dynamics of naturally acquired immunity and infection provides important insights for effective vaccine development.

Simian-human immunodeficiency infection--is the course set in the acute phase?

Identifying early predictors of infection outcome is important for the clinical management of HIV infection, and both viral load and CD4+ T cell level have been found to be useful predictors of subsequent disease progression. Very high viral load or extensively depleted CD4+ T cells in the acute phase often result in failure of immune control, and a fast progression to AIDS. It is usually assumed that extensive loss of CD4+ T cells in the acute phase of HIV infection prevents the establishment of robust T cell help required for virus control in the chronic phase. We tested this hypothesis using viral load and CD4+ T cell number of SHIV-infected rhesus macaques. In acute infection, the lowest level of CD4+ T cells was a good predictor of later survival; animals having less than 3.3% of baseline CD4+ T cells progressed to severe disease, while animals with more than 3.3% of baseline CD4+ T cells experienced CD4+ T cell recovery. However, it is unclear if the disease progression was caused by early depletion, or was simply a result of a higher susceptibility of an animal to infection. We derived a simple relationship between the expected number of CD4+ T cells in the acute and chronic phases for a constant level of host susceptibility or resistance. We found that in most cases, the depletion of CD4+ T cells in chronic infection was consistent with the prediction from the acute CD4+ T cell loss. However, the animals with less than 3.3% of baseline CD4 T cells in the acute phase were approximately 20% more depleted late in the infection than expected based on constant level of virus control. This suggests that severe acute CD4 depletion indeed impairs the immune response.

Vaccination-induced noncytolytic effects in the acute phase of SHIV infection

Many studies have shown that vaccines inducing CD8+ T cell responses can reduce viral loads and preserve CD4+ T cell numbers in monkey models of HIV infection. The mechanism of viral control by the vaccine-induced CD8+ T cells is usually assumed to be cytolysis of infected cells. However, in addition to cytolysis of infected cells, CD8+ T cells secrete a range of soluble factors that suppress viral replication. We have studied the dynamics of virus and CD4+ T cells in a successful vaccination-challenge model of SHIV infection. We find that better viral control in the acute phase of infection is associated with slower decay of peak viral load. Comparing viral and CD4+ T cell dynamics in acute infection, we find that a cytolytic mode of viral control with direct killing of infected cells is inconsistent with the observed trends. On the other hand, comparison of the predicted effects of noncytolytic CD8+ effector function with the experimental data shows that non-cytolytic control provides a better explanation of the experimental results. Our analysis suggests that vaccine-induced CD8+ T cells control SHIV infection by non-cytolytic means.

Does cytolysis by CD8+ T cells drive immune escape in HIV infection?

CD8(+) "cytotoxic" T cells are important for the immune control of HIV and the closely related simian models SIV and chimeric simian-human immunodeficiency virus (SHIV), although the mechanisms of this control are unclear. One effect of CD8(+) T cell-mediated recognition of virus-infected cells is the rapid selection of escape mutant (EM) virus that is not recognized. To investigate the mechanisms of virus-specific CD8(+) T cell control during immune escape in vivo, we used a real-time PCR assay to study the dynamics of immune escape in early SHIV infection of pigtail macaques. For immune escape mediated by cytolysis, we would expect that the death rate of wild type (WT) infected cells should be faster than that of EM-infected cells. In addition, escape should be fastest during periods when the total viral load is declining. However, we find that there is no significant difference in the rate of decay of WT virus compared with EM virus. Further, immune escape is often fastest during periods of viral growth, rather than viral decline. These dynamics are consistent with an epitope-specific, MHC class I-restricted, noncytolytic mechanism of CD8(+) T cell control of SHIV that specifically inhibits the growth of WT virus in vivo.

Timing of immune escape linked to success or failure of vaccination

Successful vaccination against HIV should limit viral replication sufficiently to prevent the emergence of viral immune escape mutations. Broadly directed immunity is likely to be required to limit opportunities for immune escape variants to flourish. We studied the emergence of an SIV Gag cytotoxic T cell immune escape variant in pigtail macaques expressing the Mane-A*10 MHC I allele using a quantitative RT-PCR to measure viral loads of escape and wild type variants. Animals receiving whole Gag expressing vaccines completely controlled an SIV_mac251 challenge, had broader CTL responses and exhibited minimal CTL escape. In contrast, animals vaccinated with only a single CTL epitope and challenged with the same SIV_mac251 stock had high levels of viral replication and rapid CTL escape. Unvaccinated naïve animals exhibited a slower emergence of immune escape variants. Thus narrowly directed vaccination against a single epitope resulted in rapid immune escape and viral levels equivalent to that of naïve unvaccinated animals. These results emphasize the importance of inducing broadly directed HIV-specific immunity that effectively quashes early viral replication and limits the generation of immune escape variants. This has important implications for the selection of HIV vaccines for expanded human trials.

Cell-autonomous and environmental contributions to the interstitial migration of T cells

A key to understanding the functioning of the immune system is to define the mechanisms that facilitate directed lymphocyte migration to and within tissues. The recent development of improved imaging technologies, most prominently multi-photon microscopy, has enabled the dynamic visualization of immune cells in real-time directly within intact tissues. Intravital imaging approaches have revealed high spontaneous migratory activity of T cells in secondary lymphoid organs and inflamed tissues. Experimental evidence points towards both environmental and cell-intrinsic cues involved in the regulation of lymphocyte motility in the interstitial space. Based on these data, several conceptually distinct models have been proposed in order to explain the coordination of lymphocyte migration both at the single cell and population level. These range from “stochastic” models, where chance is the major driving force, to “deterministic” models, where the architecture of the microenvironment dictates the migratory trajectory of cells. In this review, we focus on recent advances in understanding naïve and effector T cell migration in vivo. In addition, we discuss some of the contradictory experimental findings in the context of theoretical models of migrating leukocytes.

Limited CD4+ T cell proliferation leads to preservation of CD4+ T cell counts in SIV-infected sooty mangabeys

Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections result in chronic virus replication and progressive depletion of CD4+ T cells, leading to immunodeficiency and death. In contrast, 'natural hosts' of SIV experience persistent infection with high virus replication but no severe CD4+ T cell depletion, and remain AIDS-free. One important difference between pathogenic and non-pathogenic infections is the level of activation and proliferation of CD4+ T cells. We analysed the relationship between CD4+ T cell number and proliferation in HIV, pathogenic SIV in macaques, and non-pathogenic SIV in sooty mangabeys (SMs) and mandrills. We found that CD4+ T cell proliferation was negatively correlated with CD4+ T cell number, suggesting that animals respond to the loss of CD4+ T cells by increasing the proliferation of remaining cells. However, the level of proliferation seen in pathogenic infections (SIV in rhesus macaques and HIV) was much greater than in non-pathogenic infections (SMs and mandrills). We then used a modelling approach to understand how the host proliferative response to CD4+ T cell depletion may impact the outcome of infection. This modelling demonstrates that the rapid proliferation of CD4+ T cells in humans and macaques associated with low CD4+ T cell levels can act to 'fuel the fire' of infection by providing more proliferating cells for infection. Natural host species, on the other hand, have limited proliferation of CD4+ T cells at low CD4+ T cell levels, which allows them to restrict the number of proliferating cells susceptible to infection.

Spatial dependence of viscosity and thermal conductivity through a planar interface

We present a general algorithm for calculating the spatial variation of the shear viscosity and thermal conductivity through an equilibrium solid-liquid interface using the zero-flux version of the boundary fluctuation theory. In the case of an equilibrium interface between a high melting point Lennard-Jones solid and a low melting point Lennard-Jones liquid, we find that the transport coefficients deviate from the bulk values only in a narrow layer close to the interface. We observe a sliding friction of the liquid against the surface of the solid that increases with increased wetting of the solid by the liquid. The thermal conductivity, in contrast, is suppressed in the interfacial region, irrespective of how the liquid wets the solid.

Complexity of the inoculum determines the rate of reversion of SIV Gag CD8 T cell mutant virus and outcome of infection

Escape mutant (EM) virus that evades CD8+ T cell recognition is frequently observed following infection with HIV-1 or SIV. This EM virus is often less replicatively “fit” compared to wild-type (WT) virus, as demonstrated by reversion to WT upon transmission of HIV to a naïve host and the association of EM virus with lower viral load in vivo in HIV-1 infection. The rate and timing of reversion is, however, highly variable. We quantified reversion to WT of a series of SIV and SHIV viruses containing minor amounts of WT virus in pigtail macaques using a sensitive PCR assay. Infection with mixes of EM and WT virus containing ≥10% WT virus results in immediate and rapid outgrowth of WT virus at SIV Gag CD8 T cell epitopes within 7 days of infection of pigtail macaques with SHIV or SIV. In contrast, infection with biologically passaged SHIV_mn229 viruses with much smaller proportions of WT sequence, or a molecular clone of pure EM SIV_mac239, demonstrated a delayed or slow pattern of reversion. WT virus was not detectable until ≥8 days after inoculation and took ≥8 weeks to become the dominant quasispecies. A delayed pattern of reversion was associated with significantly lower viral loads. The diversity of the infecting inoculum determines the timing of reversion to WT virus, which in turn predicts the outcome of infection. The delay in reversion of fitness-reducing CD8 T cell escape mutations in some scenarios suggests opportunities to reduce the pathogenicity of HIV during very early infection.

Understanding how to contain HIV replication by the immune system is a key goal of vaccine strategies. HIV frequently mutates to avoid immune recognition, but this may come at a “fitness cost”, weakening the virus. When HIV is transmitted to a new host, the mutations often revert back to wild-type, allowing the virus to regain a fitter state. We found that when multiple HIV-like viruses are transmitted to monkeys, containing both mutant and wild-type, reversion to wild-type is very rapid and the fitter virus results in higher viral levels. In contrast, when only escape mutant virus initiates the infection, reversion to wild-type is delayed to later during early infection, and lower levels of virus result. Our results suggest that the composition of the infecting virus plays a role in determining the outcome of HIV infections. Strategies to maintain weakened virus strains during the early HIV infection may help the host control virus replication.

Simulation of two- and three-dimensional dense-fluid shear flows via nonequilibrium molecular dynamics: comparison of time-and-space-averaged stresses from homogeneous Doll's and Sllod shear algorithms with those from boundary-driven shear

Homogeneous shear flows (with constant strainrate dv(x)/dy) are generated with the Doll's and Sllod algorithms and compared to corresponding inhomogeneous boundary-driven flows. We use one-, two-, and three-dimensional smooth-particle weight functions for computing instantaneous spatial averages. The nonlinear normal-stress differences are small, but significant, in both two and three space dimensions. In homogeneous systems the sign and magnitude of the shearplane stress difference, Pxx-Pyy, depend on both the thermostat type and the chosen shearflow algorithm. The Doll's and Sllod algorithms predict opposite signs for this normal-stress difference, with the Sllod approach definitely wrong, but somewhat closer to the (boundary-driven) truth. Neither of the homogeneous shear algorithms predicts the correct ordering of the kinetic temperatures: Txx > Tzz > Tyy.

Equilibrium calculation of the friction coefficient for a massive particle moving in finite liquid volume

It is well established that the Green-Kubo type of expression of the friction coefficient for a massive colloidal particle, i.e., the force autocorrelation integral, vanishes at long times if the liquid volume is finite. Here I show that the nonzero friction coefficient, defined as the ratio of force on the particle and the average liquid velocity, can be found in the framework of the linear response theory as the ratio of the force autocorrelation integral and the correlation integral of liquid velocity and force on the particle. The finite inverse friction coefficient can be alternatively expressed as the autocorrelation integral of the liquid velocity.

Vaccination and timing influence SIV immune escape viral dynamics in vivo

CD8+ cytotoxic T lymphocytes (CTL) can be effective at controlling HIV-1 in humans and SIV in macaques, but their utility is partly offset by mutational escape. The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC-mismatched hosts can help us understand CTL-mediated viral control and the fitness cost extracted by immune escape mutation. Traditional methods for following CTL escape and reversion are, however, insensitive to minor viral quasispecies. We developed sensitive quantitative real-time PCR assays to track the viral load of SIV Gag_164–172 KP9 wild-type (WT) and escape mutant (EM) variants in pigtail macaques. Rapid outgrowth of EM virus occurs during the first few weeks of infection. However, the rate of escape plateaued soon after, revealing a prolonged persistence of WT viremia not detectable by standard cloning and sequencing methods. The rate of escape of KP9 correlated with levels of vaccine-primed KP9-specific CD8+ T cells present at that time. Similarly, when non-KP9 responder (lacking the restricting Mane-A*10 allele) macaques were infected with SHIV_mn229 stock containing a mixture of EM and WT virus, rapid reversion to WT was observed over the first 2 weeks following infection. However, the rate of reversion to WT slowed dramatically over the first month of infection. The serial quantitation of escape mutant viruses evolving during SIV infection shows that rapid dynamics of immune escape and reversion can be observed in early infection, particularly when CD8 T cells are primed by vaccination. However, these early rapid rates of escape and reversion are transient and followed by a significant slowing in these rates later during infection, highlighting that the rate of escape is significantly influenced by the timing of its occurrence.

Immune escape from AIDS virus–specific cellular immunity is common. The driving forces behind how quickly cellular immunity forces escape are poorly understood. We developed a novel assay for a common immune escape variant of SIV in macaques. This allowed us to sensitively track the rates of immune escape even when levels of escape mutant or wild-type virus were low. We found that prior immunization of macaques resulted in very rapid immune escape during acute infection. However, when escape starts to occur later, during chronic infection, the rate of immune escape is much more gradual. Thus, both prior vaccination and timing influence the rates of immune escape and provide a fuller picture of the effectiveness of T cell immunity to HIV.

In vivo fitness costs of different Gag CD8 T-cell escape mutant simian-human immunodeficiency viruses for macaques

The kinetics of immune escape and reversion depend upon the efficiency of CD8 cytotoxic T lymphocytes (CTL) and the fitness cost of escape mutations. Escape kinetics of three simian immunodeficiency virus Gag CTL epitopes in pigtail macaques were variable; those of KP9 and AF9 were faster than those of KW9. Kinetics of reversion of escape mutant virus to wild type upon passage to naïve major histocompatibility complex-mismatched macaques also varied. Rapid reversion occurred at KP9, gradual biphasic reversion occurred at AF9, and escape mutant KW9 virus failed to revert. The fitness impact of these mutations is KP9 > AF9 > KW9. These data provide insights into the differential utility of CTL in controlling viremia.

Crystal-melt coexistence under shear: Interpreting the nonlinear rheology

We propose a phenomenological model for shear-induced melting aimed at assisting the design of experimental studies of this phenomenon. For increasing strain rates, the model predicts the changes in liquid fraction and shear stress as a function of interfacial supercooling. We discuss the experimental conditions under which shear-induced melting could be observed in a range of materials.

An equilibrium calculation of the thermal transport coefficients between two planes of arbitrary separation in a condensed phase

We present a method for the direct calculation at equilibrium of the shear viscosity and thermal conductivity over distances as short as one molecular diameter. The method is directly applicable to the calculation of viscosity and thermal conductivity in inhomogeneities such as the interface between coexisting phases. The method makes use of a novel extension of our recently developed boundary fluctuation theory.

The boundary fluctuation theory of transport coefficients in the linear-response limit

In this paper we present, for the first time, a linear-response theory of transport coefficients-shear viscosity and thermal conductivity-involving thermal, as opposed to mechanical, fields. The theory involves the explicit treatment of the boundaries and the constraints that are applied to them. Expressions for the shear viscosity and thermal conductivity are obtained in terms of the fluctuations at the boundaries of the variable conjugate to that which is constrained. We explain how the choice of ensemble, as defined by the boundary constraints, determines the form in which the transport coefficients are evaluated.

Thermal conductivity of ethanol

We present a factorization of the Ewald sum permitting efficient computation of the reciprocal space part of the molecular representation for the heat flux vector. We use the derived expression to evaluate thermal conductivity of a model of ethanol at several near-ambient state points.

Conductivity of molten sodium chloride in an arbitrarily weak dc electric field

We use nonequilibrium molecular-dynamics (NEMD) simulations to characterize the response of a fluid subjected to an electric field. We focus on the response for very weak fields. Fields accessible by conventional NEMD methods are typically of the order of 10(9) V m(-1), i.e., several orders of magnitude larger than those typically used in experiments. Using the transient time-correlation function, we show how NEMD simulations can be extended to study systems subjected to a realistic dc electric field. We then apply this approach to study the response of molten sodium chloride for a wide range of dc electric fields.

Shear thickening in a model colloidal suspension

We study the rheology of model colloidal suspensions using molecular-dynamics simulations. We relate the onset of shear thickening to the transition from a low-viscosity regime, in which the solvent facilitates the flow of colloids, to a high-viscosity regime associated with jamming of the colloids and the formation of chains of colloids. In the low-viscosity regime, the colloidal particles are, on average, surrounded by two layers of solvent particles. On the contrary, in the high-viscosity regime, the solvent is expelled from the interstice between the jammed colloids. The thickening in suspensions is shown to obey the same criterion as in simple fluids. This demonstrates that jamming, even without the divergence of lubrication interactions, is sufficient to observe shear thickening.

Hydrogen bonding in ethanol under shear

We study the dependence of viscosity of ethanol on shear rate using constant volume and constant pressure nonequilibrium molecular dynamics simulations, with the emphasis of the interrelationship between breaking, stability, and alignment of hydrogen bonds and shear thinning at high shear rates. We find that although the majority of hydrogen bond breakings occur at low shear rates, we do not observe shear thinning until there is some shear-induced alignment of the hydrogen bonds with the direction of shear.

Linear response theory for thermal conductivity and viscosity in terms of boundary fluctuations

Boundary driven shear flows and wall thermostats are being used in computer simulations of materials with increasing frequency. One attraction is that such boundary constraints offer a more realistic representation of the physical constraints imposed experimentally than the widely employed homogeneous constraints. In this paper we derive the linear response expressions for shear viscosity and thermal conductivity based on the fluctuations associated with boundary constraints. We demonstrate that our approach provides an effective method of describing the rheology in interfaces as well as bulk samples.

Time dependence of phase variables in a steady shear flow algorithm

We study the periodic time dependence of shear stress that occurs in a low- and a high-density fluid in a molecular dynamics algorithm for simulation of constant shear flow. We present a generalization of the linear response theory for a case when the equilibrium relaxation function and the equilibrium shear stress depend on strain. The predictions of this generalization reveal that the time dependence at low densities is a completely nonlinear effect. At high densities the amplitude of equilibrium oscillations of shear stress with strain is modified by strain-dependent viscosity, causing a decrease in amplitude proportional to shear rate in the linear response regime.

Shear stress relaxation in liquids

We show that at high densities, as the system size decreases, liquid becomes able to permanently sustain increasing internal shear stress after a constant deformation, although the other characteristic liquid properties, such as the pair distribution function and diffusion coefficient do not change under strain. The system size necessary for observation of this effect increases with the decrease in temperature, and it is stronger in pair potentials with steeper repulsive part. We relate this result to the size of the "cooperatively rearranging regions" of the Adam-Gibbs theory of glass transition.

Influence of strain on transport in dense Lennard-Jones systems

We study the shear stress relaxation and temperature dependence of the diffusion coefficient, viscosity, and thermal conductivity along a high-density Lennard-Jones isochore of the reduced density of 1.0, as it crosses the freezing and melting lines, in equilibrium and under constant strain.

Non-Newtonian behavior in simple fluids

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheology of a microscopic sample of simple fluid. The calculations were performed using a configurational thermostat which unlike previous nonequilibrium molecular dynamics or nonequilibrium Brownian dynamics methods does not exert any additional constraint on the flow profile. Our findings are in agreement with experimental results on concentrated "hard sphere"-like colloidal suspensions. We observe: (i) a shear thickening regime under steady shear; (ii) a strain thickening regime under oscillatory shear at low frequencies; and (iii) shear-induced ordering under oscillatory shear at higher frequencies. These results significantly differ from previous simulation results which showed systematically a strong ordering for all frequencies. They also indicate that shear thickening can occur even in the absence of a solvent.

Cooperative effects, transport and entropy in simple liquids

We systematically investigate the cooperative effects in shear stress relaxation using equilibrium molecular-dynamics simulations in periodic boundary conditions containing a variable degree of strain. We show that, even in simple liquids, shear stress relaxation is a cooperative effect associated with a correlation length that increases with isobaric decrease in temperature. If the system size is less than the correlation length, shear stress in the system is determined by the boundary strain. Transport, however, does not depend on the boundary conditions. We relate these two effects to the number and properties of the configurations accessible to the system.

Reexamination of string phase and shear thickening in simple fluids

In 1984, Erpenbeck observed a shear-induced alignment of particles into strings in nonequilibrium molecular dynamics simulations of hard spheres. Since then, it has remained unclear if this effect was genuine or if it arose from the use of a thermostat which assumed an incorrect form for the velocity profile. All studies performed up to now have focused on improving the accuracy with which the velocity profile is determined. We propose here a radically different approach: we apply a recently developed configurational expression for the temperature. This expression does not require any knowledge of the streaming velocity profile. Using a configurational thermostat, we show that the string phase is an artifact and we observe a shear-thickening regime, as seen in experiments on concentrated "hard-sphere"-like colloidal dispersions.

Properties of isolated systems in external fields

We investigate evolution of an isolated system in an external field, and compare the ensemble averages of the response on successive constant internal energy surfaces to the ensemble averages of steady-state responses constrained to the same energy. We find that the two ensemble averages converge for sufficiently high energies, irrespective of the field strength and the initial energy from which the adiabatic evolution starts. This rule is satisfied for any phase-space distribution on the initial energy surface that can relax to equilibrium. At sufficiently high energies transport coefficients converge to their equilibrium values, because the effect of a constant field on the behavior of a system decreases with its temperature.

Homogeneous shear flow of a hard-sphere fluid: analytic solutions

Recently, a solution for collision-free trajectories in an N particle thermostatted hard-sphere system undergoing homogeneous shear (the so-called "Sllod" equations of motion) led to a kinetic theory of dilute hard-sphere gases under shear. However, a solution for collisions, necessary for a complete theory at higher densities, has been missing. We present an analytic solution to this problem, which provides surprising insights into the mechanical aspects of thermostatting a system in an external field. The equivalence of constant temperature and constant energy ensembles in the thermodynamic limit in equilibrium, the conditions for the nature of heat exchange with the environment (entropy creation and reduction) in the system, and the condition for appearance of the artificial string phase follow from our solution.