The coreceptor mutation CCR5Delta32 influences the dynamics of HIV epidemics and is selected for by HIV

Biodiversity in the cyclic competition system of three species according to the emergence of mutant species

Understanding mechanisms which promote or hinder existing ecosystems are important issues in ecological sciences. In addition to fundamental interactions such as competition and migration among native species, existing ecosystems can be easily disturbed by external factors, and the emergence of new species may be an example in such cases. The new species which does not exist in a current ecosystem can be regarded as either alien species entered from outside or mutant species born by mutation in existing normal species. Recently, as existing ecosystems are getting influenced by various physical/chemical external factors, mutation due to anthropogenic and environmental factors can occur more frequently and is thus attracting much attention for the maintenance of ecosystems. In this paper, we consider emergences of mutant species among self-competing three species in the cyclic dominance. By defining mutation as the birth of mutant species, we investigate how mutant species can affect biodiversity in the existing ecosystem. Through microscopic and macroscopic approaches, we have found that the society of existing normal species can be disturbed by mutant species either the society is maintained accompanying with the coexistence of all species or jeopardized by occupying of mutant species. Due to the birth of mutant species, the existing society may be more complex by constituting two different groups of normal and mutant species, and our results can be contributed to analyze complex ecosystems of many species. We hope our findings may propose a new insight on mutation in cyclic competition systems of many species.

Postvaccination C-Reactive Protein and C5/gp41732-744 Antibody Level Fold-Changes Over Baseline Are Independent Predictors of Therapeutic HIV Vaccine Effect in a Phase 2 Clinical Study of Vacc-4x

Therapeutic vaccination has the potential to contribute to functional HIV cure strategies. However, to show functional HIV cure, study participants must be taken off combination antiretroviral therapy (cART). The availability of suitable biomarkers that can predict viral load (VL) or CD4 count outcomes following therapeutic HIV vaccination would reduce the risks associated with cART interruption in such studies. This report sought to determine baseline and postvaccination biomarker predictors of vaccine effect (VE) on VL and CD4 counts following cART interruption in a double-blind, randomized phase 2 study of the peptide-based therapeutic HIV vaccine, Vacc-4x (n = 93), versus placebo (n = 43). Antibody responses to a novel envelope glycoprotein antigen, C5/gp41^732-744, and three safety marker measurements [C-reactive protein (CRP), white blood cell, and lactate dehydrogenase] were considered. Interaction tests in univariate and multivariate linear regression models were used to estimate the effect of biomarkers on VE, defined as the VL or CD4 count difference in Vacc-4x versus placebo groups. The reported q-values (considered significant for hypothesis-generating purposes if ≤0.2) accounted for multiple comparisons using the false discovery rate method. Data were analyzed from all available 58 Vacc-4x and 25 placebo recipients before cART resumption. Lower postvaccination fold-change over baseline of CRP concentration (interaction p- (q-) value = 0.005 (0.11) for VL) and higher fold-change of anti-C5/gp41^732-744 antibody levels (0.005 (0.11) for VL and 0.009 (0.20) for CD4) were associated with Vacc-4x benefit. These findings suggest potential roles for inflammation and immune activation markers in predicting therapeutic HIV VE.

Genetics of Sub-Saharan African Human Population: Implications for HIV/AIDS, Tuberculosis, and Malaria

Sub-Saharan Africa has continued leading in prevalence and incidence of major infectious disease killers such as HIV/AIDS, tuberculosis, and malaria. Epidemiological triad of infectious diseases includes susceptible host, pathogen, and environment. It is imperative that all aspects of vertices of the infectious disease triad are analysed to better understand why this is so. Studies done to address this intriguing reality though have mainly addressed pathogen and environmental components of the triad. Africa is the most genetically diverse region of the world as well as being the origin of modern humans. Malaria is relatively an ancient infection in this region as compared to TB and HIV/AIDS; from the evolutionary perspective, we would draw lessons that this ancestrally unique population now under three important infectious diseases both ancient and exotic will be skewed into increased genetic diversity; moreover, other evolutionary forces are also still at play. Host genetic diversity resulting from many years of malaria infection has been well documented in this population; we are yet to account for genetic diversity from the trio of these infections. Effect of host genetics on treatment outcome has been documented. Host genetics of sub-Saharan African population and its implication to infectious diseases are an important aspect that this review seeks to address.

Rapid adversarial co-evolution of viruses and cellular restriction factors

Since the discovery of viruses over a century ago, virologists have recognized that host genetics plays a major role in viral tropism and the distribution of viruses in nature. Traditionally, studies of tropism have centered on identification of cellular factors required for viral replication, such as cell-surface entry receptors. However, over the past 20 years, there has been a steady increase in the identification and characterization of restriction factors (RFs), here defined as dominant cellular factors that have evolved specifically to interfere with viral replication. Genetic studies suggest that restriction factors impose significant barriers to interspecies movement of viruses and are therefore critical determinants of viral tropism. Furthermore, the scope of the ever-expanding list of restriction factors, and the variety of antiviral mechanisms they represent, testifies to the extraordinary impact viruses have had on organismal evolution-an impact hitherto underappreciated by evolutionary biologists and virologists alike. Recent studies of RF-encoding genes that combine molecular evolutionary analysis with functional assays illustrate the potential for asking questions about virus-host interactions as they play out in natural populations and across evolutionary timescales. Most notably, it has become common to apply tests of positive selection to RF genes and couple these analyses with virological assays, to reveal evidence for antagonistic virus-host co-evolution. Herein, I summarize recent work on the evolutionary genetics of mammalian RFs, particularly those of humans, non-human primates, and model organisms, and how RFs can reveal the influence of virus-host interactions on organismal evolution. Because intensive investigation of RF evolution is fairly new (and because there is still much to learn), the discussion is organized around five broad, outstanding questions that will need to be answered before we can fully appreciate the evolutionary biology of restriction.

Distribution of the CCR5delta32 allele (gene variant CCR5) in Rondônia, Western Amazonian region, Brazil

Since around 1723, on the occasion of its initial colonization by Europeans, Rondonia has received successive waves of immigrants. This has been further swelled by individuals from northeastern Brazil, who began entering at the beginning of the twentieth century. The ethnic composition varies across the state according to the various sites of settlement of each wave of immigrants. We analyzed the frequency of the CCR5Δ32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in five sample sets from the population. Four were collected in Porto Velho, the state capital and the site of several waves of migration. Of these, two, from the Hospital de Base were comprised of HB Mothers and HB Newborns presenting allele frequencies of 3.5% and 3.1%, respectively, a third from the peri-urban neighborhoods of Candelária/Bate-Estaca (1.8%), whereas a fourth, from the Research Center on Tropical Medicine/CEPEM (0.6%), was composed of malaria patients under treament. The fifth sample (3.4%) came from the inland Quilombola village of Pedras Negras. Two homozygous individuals (CCR5Δ32/CCR5Δ32) were detected among the HB Mother samples. The frequency of this allele was heterogeneous and higher where the European inflow was more pronounced. The presence of the allele in Pedras Negras revealed European miscegenation in a community largely comprising Quilombolas.

Cord blood stem cell therapy for acquired immune deficiency syndrome

Cord blood stem cell transplantation is routinely used to treat hematopoietic diseases. Individuals who are homozygous for the 32 polymorphism of the CCR5 locus, encoding a co-receptor for HIV-1, are normal and are resistant to HIV infection. Here we suggest that public cord blood repositories are likely to contain CCR5 homozygous units that could be used as a therapy for HIV-infected individuals.

Has human evolution stopped?

It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.

Significantly reduced CCR5-tropic HIV-1 replication in vitro in cells from subjects previously immunized with Vaccinia Virus

Background

At present, the relatively sudden appearance and explosive spread of HIV throughout Africa and around the world beginning in the 1950s has never been adequately explained. Theorizing that this phenomenon may be somehow related to the eradication of smallpox followed by the cessation of vaccinia immunization, we undertook a comparison of HIV-1 susceptibility in the peripheral blood mononuclear cells from subjects immunized with the vaccinia virus to those from vaccinia naive donors.

Results

Vaccinia immunization in the preceding 3-6 months resulted in an up to 5-fold reduction in CCR5-tropic but not in CXCR4-tropic HIV-1 replication in the cells from vaccinated subjects. The addition of autologous serum to the cell cultures resulted in enhanced R5 HIV-1 replication in the cells from unvaccinated, but not vaccinated subjects. There were no significant differences in the concentrations of MIP-1α, MIP-1β and RANTES between the cell cultures derived from vaccinated and unvaccinated subjects when measured in culture medium on days 2 and 5 following R5 HIV-1 challenge.

Discussion

Since primary HIV-1 infections are caused almost exclusively by the CCR5-tropic HIV-1 strains, our results suggest that prior immunization with vaccinia virus might provide an individual with some degree of protection to subsequent HIV infection and/or progression. The duration of such protection remains to be determined. A differential elaboration of MIP-1α, MIP-1β and RANTES between vaccinated and unvaccinated subjects, following infection, does not appear to be a mechanism in the noted protection.

Impact of ERCC2 gene polymorphism on HIV-1 disease progression to AIDS among North Indian HIV patients

HIV/AIDS remains to be one of the killing diseases of mankind. Host genetic response is one of the factor which determine susceptibility to HIV and disease progression to AIDS. The aim of the present study was to evaluate the impact of ERCC2 Lyc ( 751 ) Gln (excision repair cross complementing rodent repair deficiency, complementation group 2) polymorphism on HIV-1 susceptibility and disease progression to AIDS, as this gene has been reported to intervene in degrading retroviral cDNA before it integrates with the host DNA. This case control study included 300 HIV seropositive cases and an equal number of HIV seronegative controls. DNA was isolated from the blood samples of study subjects and genotyping of ERCC2 was conducted by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method. The Gln/Gln genotype showed a significant variation between cases and controls (P = 0.047, OR 1.71, 95% CI 1.00-2.93), indicating a possible role of susceptibility in reference to controls and disease progression when compared within cases.

Mathematical and computational approaches can complement experimental studies of host-pathogen interactions

In addition to traditional and novel experimental approaches to study host-pathogen interactions, mathematical and computer modelling have recently been applied to address open questions in this area. These modelling tools not only offer an additional avenue for exploring disease dynamics at multiple biological scales, but also complement and extend knowledge gained via experimental tools. In this review, we outline four examples where modelling has complemented current experimental techniques in a way that can or has already pushed our knowledge of host-pathogen dynamics forward. Two of the modelling approaches presented go hand in hand with articles in this issue exploring fluorescence resonance energy transfer and two-photon intravital microscopy. Two others explore virtual or 'in silico' deletion and depletion as well as a new method to understand and guide studies in genetic epidemiology. In each of these examples, the complementary nature of modelling and experiment is discussed. We further note that multi-scale modelling may allow us to integrate information across length (molecular, cellular, tissue, organism, population) and time (e.g. seconds to lifetimes). In sum, when combined, these compatible approaches offer new opportunities for understanding host-pathogen interactions.

Distribution of CCR5 genotypes and HLA Class I B alleles in HIV-1 infected and uninfected injecting drug users from Rio de Janeiro, Brazil

Host genetic factors play an important role in the HIV epidemic dynamics, and have been considered in studies assessing susceptibility/resistance to HIV-1 infection as well as clinical evolution. Class I and Class II HLA alleles have been associated with the heterogeneity of HIV-1 infection susceptibility, as protective or risk factors for HIV-1 transmission. Moreover, a 32-base pair deletion in the HIV-1 CCR5 gene-coding region confers resistance to HIV-1 infection in homozygous individuals for the deleted allele. In this study, DNA samples from HIV-1 infected and uninfected injecting drug users (IDUs) from Rio de Janeiro were PCR amplified to determine CCR5 genotypes based on the presence of the CCR5Delta32 mutation and typed for the HLA-B locus, in an attempt to assess possible associations between these genetic factors and susceptibility/resistance to HIV-1 infection. The distribution of CCR5 genotypes between the two IDU groups did not differ. The homozygous mutant genotype Delta32/Delta32 was not found in this study. Except for HLA-B*45 (4.0% vs. 3.0%; p=0.04) and for B*51 (12.1% vs. 4.4%; p=0.002), no statistically significant differences were made evident when analyzing the frequencies of each HLA-B allele between Caucasian and non-Caucasian IDUs. The most frequent HLA-B alleles were B*15; B*35; B*44 and B*51. Although some differences in the allele frequencies could be observed between the two IDU groups, none of these was statistically significant. Therefore, no putative association between these genetic markers and susceptibility/resistance to HIV-1 infection could be made evident in the present study. So far, the assessment of genetic markers among the IDU population has been restricted to North American, European, and Asian studies and this report represents a pioneer descriptive study of the distribution of CCR5 genotypes and HLA-B alleles in Rio de Janeiro, Brazil.

Role of CCL3L1-CCR5 genotypes in the epidemic spread of HIV-1 and evaluation of vaccine efficacy

BACKGROUND

Polymorphisms in CCR5, the major coreceptor for HIV, and CCL3L1, a potent CCR5 ligand and HIV-suppressive chemokine, are determinants of HIV-AIDS susceptibility. Here, we mathematically modeled the potential impact of these genetic factors on the epidemic spread of HIV, as well as on its prevention.

METHODS AND RESULTS

Ro, the basic reproductive number, is a fundamental concept in explaining the emergence and persistence of epidemics. By modeling sexual transmission among HIV+/HIV- partner pairs, we find that Ro estimates, and concordantly, the temporal and spatial patterns of HIV outgrowth are highly dependent on the infecting partners' CCL3L1-CCR5 genotype. Ro was least and highest when the infected partner possessed protective and detrimental CCL3L1-CCR5 genotypes, respectively. The modeling data indicate that in populations such as Pygmies with a high CCL3L1 gene dose and protective CCR5 genotypes, the spread of HIV might be minimal. Additionally, Pc, the critical vaccination proportion, an estimate of the fraction of the population that must be vaccinated successfully to eradicate an epidemic was <1 only when the infected partner had a protective CCL3L1-CCR5 genotype. Since in practice Pc cannot be >1, to prevent epidemic spread, population groups defined by specific CCL3L1-CCR5 genotypes might require repeated vaccination, or as our models suggest, a vaccine with an efficacy of >70%. Further, failure to account for CCL3L1-CCR5-based genetic risk might confound estimates of vaccine efficacy. For example, in a modeled trial of 500 subjects, misallocation of CCL3L1-CCR5 genotype of only 25 (5%) subjects between placebo and vaccine arms results in a relative error of approximately 12% from the true vaccine efficacy.

CONCLUSIONS

CCL3L1-CCR5 genotypes may impact on the dynamics of the HIV epidemic and, consequently, the observed heterogeneous global distribution of HIV infection. As Ro is lowest when the infecting partner has beneficial CCL3L1-CCR5 genotypes, we infer that therapeutic vaccines directed towards reducing the infectivity of the host may play a role in halting epidemic spread. Further, CCL3L1-CCR5 genotype may provide critical guidance for optimizing the design and evaluation of HIV-1 vaccine trials and prevention programs.

Duffy antigen receptor for chemokines mediates trans-infection of HIV-1 from red blood cells to target cells and affects HIV-AIDS susceptibility

Duffy antigen receptor for chemokines (DARC) expressed on red blood cells (RBCs) influences plasma levels of HIV-1-suppressive and proinflammatory chemokines such as CCL5/RANTES. DARC is also the RBC receptor for Plasmodium vivax. Africans with DARC -46C/C genotype, which confers a DARC-negative phenotype, are resistant to vivax malaria. Here, we show that HIV-1 attaches to RBCs via DARC, effecting trans-infection of target cells. In African Americans, DARC -46C/C is associated with 40% increase in the odds of acquiring HIV-1. If extrapolated to Africans, approximately 11% of the HIV-1 burden in Africa may be linked to this genotype. After infection occurs, however, DARC-negative RBC status is associated with slower disease progression. Furthermore, the disease-accelerating effect of a previously described CCL5 polymorphism is evident only in DARC-expressing and not in DARC-negative HIV-infected individuals. Thus, DARC influences HIV/AIDS susceptibility by mediating trans-infection of HIV-1 and by affecting both chemokine-HIV interactions and chemokine-driven inflammation.

Immunogenicity of a DNA prime and recombinant adenovirus boost regime significantly varies between rhesus macaques of Chinese and Indian origins

BACKGROUND

Due to an ever increasing shortage of rhesus macaques of Indian origin (InR) that have been generally used for preclinical AIDS vaccine trials in non-human primates, demand is rising for Chinese rhesus macaques (ChR). However, the immunogenicity of an AIDS vaccine candidate has not been compared in parallel in both rhesus macaque subspecies.

METHODS

ChR and InR were immunized with SIV/HIV DNA and adenovirus vaccine and their immune responses to SIV and HIV evaluated.

RESULTS

SIV Gag- and Env-specific T-cell responses and SIV-specific lymphoproliferative responses measured in ChR were significantly weaker than those in InR (P < 0.05). By contrast, antibody responses to SIV Env, Tat, and Nef in ChR were stronger than those in InR (P < 0.05).

CONCLUSIONS

Immunogenicity of an AIDS vaccine can vary significantly depending on the geographic origin implying genetic differences of macaques. This must be considered when describing and interpreting results of such vaccine studies.

High prevalence of the CCR5Delta32 HIV-resistance mutation among Estonian HIV type 1-infected individuals

The aim of this survey was to investigate human immunodeficiency virus type 1 (HIV-1) coreceptor, chemokine receptor 5 (CCR5), polymorphism among Estonian HIV-1-infected individuals. Homozygous CCR5Delta32 genotypes have been associated with resistance to HIV-1 infection; however, inconsistent evidence exists as to whether a single copy of a mutant allele among heterozygotes confers protection from HIV-1 infection. In an Estonian population the frequency of the CCR5Delta32 allele has been found to be among the greatest observed to date. Ironically, Estonia is concomitantly characterized by a very high HIV-1 prevalence. We compared the allele frequencies in a healthy control population to the HIV-positive group. The frequency of heterozygous individuals did not differ significantly between the HIV-positive group and the control population. Allele frequencies were analyzed among different risk groups as well as groups with different HIV genetic backgrounds. We did not find a difference between CCR5Delta32 allele frequencies among intravenous drug users (IDUs) and sexually infected persons. Likewise, the distribution of CCR5Delta32 allele frequencies among patients infected with different subtypes did not differ while data from "pure" subtypes A, B, and CRF06_cpx were pooled and evaluated against unique recombinant forms.

From the Old World to the New World: an ecologic study of population susceptibility to HIV infection

It remains unclear why the global distribution of human immunodeficiency virus (HIV), between and within continents, is so heterogeneous. This ecologic study of 34 populations of the Americas explored the hypothesis that populations differ in their intrinsic, biological susceptibility to HIV which, together with exposure, might determine the ultimate 'mature' prevalence. If true, national HIV prevalence in populations of the Americas should be predictable from each country's ethnic mosaic, inter-racial admixture and HIV prevalence in regions of Africa, Europe and Asia from where their ancestors migrated. For each country, the adult population (15-49 years) was multiplied by the proportion corresponding to each ethnic group by HIV prevalence in the country/region of origin of each group, yielding the predicted prevalences, which were then compared with observed prevalences documented by UNAIDS for 2001. Predicted and observed HIV prevalences were highly correlated (r = 0.70, P < 0.001). In North America, predicted prevalences were within 0.5% of the observed values, except for African-Americans and African-Canadians. In Central and South America, differences between predicted and observed prevalences were <1.0% except in Honduras and Guyana. Some Caribbean countries had a predicted prevalence identical to the observed one, but there were outliers. Overall, predicted prevalence was 0.93% and observed prevalence 0.64%; two-thirds of this difference was attributed to Brazil. Although it was not possible to adjust to the confounding effects of sexual behaviour and cofactors of transmission (such as sexually transmitted infections) because of the lack of nationally representative data for each and every country, a number of arguments reviewed in the paper suggest that confounders cannot explain all this association and that differential susceptibility might be an important determinant of steady-state HIV prevalence.

Functional analysis of naturally occurring mutations in the open reading frame of CCR5 in HIV-infected Chinese patients and healthy controls

We studied polymorphism of the HIV coreceptor CC chemokine receptor (CCR) 5 in 1099 Chinese adults residing in Hong Kong, including 785 HIV-negative healthy donors and 314 HIV-positive patients. Ten mutants in the CCR5 open reading frame were identified, 7 of which were nonsynonymous. The frequencies of these alleles did not show a significant difference between HIV patients and healthy controls. G106R, Delta32, R223Q, 299(FS), and S336I were cloned from prevalent mutant genes, and their effects on HIV infection were analyzed by a series of in vitro experiments to determine their transcription levels, expression levels, conformational changes, and HIV coreceptor function. R223Q is the most prevalent CCR5 mutant in ethnic Chinese, with a frequency of 0.046, which does not affect HIV infection in vitro, however. The S336I mutant also does not affect its transcription, expression, or HIV coreceptor function. Similar to 299(FS), the mutant G106R located in the third transmembrane domain results in diminished HIV coreceptor function in vitro through conformation changes in ECL2.

Frequency-dependent incidence in models of sexually transmitted diseases: portrayal of pair-based transmission and effects of illness on contact behaviour

We explore the transmission process for sexually transmitted diseases (STDs). We derive the classical frequency-dependent incidence mechanistically from a pair-formation model, using an approximation that applies to populations with rapid pairing dynamics (such as core groups or non-pair-bonding animals). This mechanistic derivation provides a framework to assess how accurately frequency-dependent incidence portrays the pair-based transmission known to underlie STD dynamics. This accuracy depends strongly on the disease being studied: frequency-dependent formulations are more suitable for chronic less-transmissible infections than for transient highly transmissible infections. Our results thus support earlier proposals to divide STDs into these two functional classes, and we suggest guidelines to help assess under what conditions each class can be appropriately modelled using frequency-dependent incidence. We then extend the derivation to include situations where infected individuals exhibit altered pairing behaviour. For four cases of increasing behavioural complexity, analytic expressions are presented for the generalized frequency-dependent incidence rate, basic reproductive number (R0) and steady-state prevalence (i infinity) of an epidemic. The expression for R0 is identical for all cases, giving refined insights into determinants of invasibility of STDs. Potentially significant effects of infection-induced changes in contact behaviour are illustrated by simulating epidemics of bacterial and viral STDs. We discuss the application of our results to STDs (in humans and animals) and other infectious diseases.

Genetic variants in the CCR gene cluster and spontaneous viral elimination in hepatitis C-infected patients

Hepatitis C virus (HCV) infection results in chronic hepatitis in more than 80% of infected patients while 10-20% of patients recover spontaneously. Host genetic factors may influence the ability to clear the virus after infection. Six single nucleotide polymorphisms and a 32 bp deletion in the genes coding for CCR3, CCR2 and CCR5 (which are all located in a cluster on chromosome 3) were investigated in 465 consecutively recruited patients infected with HCV and 370 matched controls. Genetic variants were tested for association with spontaneous viral elimination and, in the chronically infected patients, stage of fibrosis and response to antiviral therapy. The G190A polymorphism (variant allele Ile64) in the first transmembrane domain of CCR2 was under-represented in the 29 patients who had cleared the hepatitis C virus spontaneously (P = 0.018). None of the other variants in the CCR gene cluster showed association with the natural course of the infection, stage of fibrosis or response to therapy.

Allelic histories: positive selection on a HIV-resistance allele

The CCR5-Delta32 allele crucially determines the course of HIV infection and appears to be highly protective against the disease. Population genetic studies suggest that the allele has been under positive selection in Europe in the past. In a recent paper, Alison Galvani and Montgomery Slatkin collate the available evidence and use a mathematical model to strongly suggest that smallpox could have exerted sufficient selection pressure to explain the distribution of the allele across Europe. This is a beautiful example of the power of mathematical models in evolutionary genetics.

On treatment of tuberculosis in heterogeneous populations

Global eradication of tuberculosis (TB) is an international agenda. Thus understanding effects of treatment of TB in different settings is crucial. In previous work, we introduced the framework for a mathematical model of epidemic TB in demographically distinct, heterogeneous populations. Simulations showed the importance of genetic susceptibility in determining endemic prevalence levels. In the work presented here, we include treatment and investigate different strategies for treatment of latent and active TB disease in heterogeneous populations. We illustrate how the presence of a genetically susceptible subpopulation dramatically alters effects of treatment in the same way a core population does in the setting of sexually transmitted diseases. In addition, we evaluate treatment strategies that focus specifically on this subpopulation, and our results indicate that genetically susceptible subpopulations should be accounted for when designing treatment strategies to achieve the greatest reduction in disease prevalence.

CC chemokine receptor 5 genotype and susceptibility to transmission of human immunodeficiency virus type 1 in women

The human gene for CC chemokine receptor 5, a coreceptor for human immunodeficiency virus type 1 (HIV-1), affects susceptibility to infection. Most studies of predominantly male cohorts found that individuals carrying a homozygous deleted form of the gene, Delta 32, were protected against transmission, but protection did not extend to Delta 32 heterozygotes. The role played by this mutation in HIV-1 transmission to women was studied in 2605 participants in the Women's Interagency HIV Study. The Delta 32 gene frequency was 0.026 for HIV-1-seropositive women and 0.040 for HIV-1-seronegative women, and statistical analyses showed that Delta 32 heterozygotes were significantly less likely to be infected (odds ratio, 0.63 [95% confidence interval, 0.44-0.90]). The CCR5 Delta 32 heterozygous genotype may confer partial protection against HIV-1 infection in women. Because Delta 32 is rare in Africans and Asians, it seems plausible that differential genetic susceptibility, in addition to social and behavioral factors, may contribute to the rapid heterosexual spread of HIV-1 in Africa and Asia.

Interrogating a high-density SNP map for signatures of natural selection

Identifying genomic regions that have been targets of natural selection remains one of the most important and challenging areas of research in genetics. To this end, we report an analysis of 26,530 single nucleotide polymorphisms (SNPs) with allele frequencies that were determined in three populations. Specifically, we calculated a measure of genetic differentiation, F(ST), for each locus and examined its distribution at the level of the genome, the chromosome, and individual genes. Through a variety of analyses, we have found statistically significant evidence supporting the hypothesis that selection has influenced extant patterns of human genetic variation. Importantly, by contrasting the F(ST) of individual SNPs to the empirical genome-wide distribution of F(ST), our results are not confounded by tenuous assumptions of population demographic history. Furthermore, we have identified 174 candidate genes with distribution of genetic variation that indicates that they have been targets of selection. Our work provides a first generation natural selection map of the human genome and provides compelling evidence that selection has shaped extant patterns of human genomic variation.

Comparing epidemic tuberculosis in demographically distinct heterogeneous populations

There is wide variation in endemic tuberculosis (TB) levels between countries and we seek to identify possible causes of these differences. In this study we present an epidemiological model of Mycobacterium tuberculosis infection to investigate the effects of host genetics and demographic factors on epidemic TB. We discuss the general framework for this approach and present analytical results to identify important parameters affecting steady-state prevalence and incidence rates of TB disease. We then use numerical simulations of our model to observe the effects of a genetically susceptible subpopulation on TB disease dynamics at the population level. Finally, we simulate infection within a genetically heterogeneous population in two demographic settings: India (a typical population with high TB prevalence) and the USA (a typical population with low TB prevalence). Results show that changes in transmission parameters, the fraction of the population genetically susceptible to infection, and demographic factors strongly affect TB prevalence and incidence rates.