Advancing genomics to improve health equity

Health equity is the state in which everyone has fair and just opportunities to attain their highest level of health. The field of human genomics has fallen short in increasing health equity, largely because the diversity of the human population has been inadequately reflected among participants of genomics research. This lack of diversity leads to disparities that can have scientific and clinical consequences. Achieving health equity related to genomics will require greater effort in addressing inequities within the field. As part of the commitment of the National Human Genome Research Institute (NHGRI) to advancing health equity, it convened experts in genomics and health equity research to make recommendations and performed a review of current literature to identify the landscape of gaps and opportunities at the interface between human genomics and health equity research. This Perspective describes these findings and examines health equity within the context of human genomics and genomic medicine.

Effect of a Digital Health Intervention on Receipt of Colorectal Cancer Screening in Vulnerable Patients: A Randomized Controlled Trial

BACKGROUND

Screening for colorectal cancer (CRC) reduces mortality, yet more than one third of age-eligible Americans are unscreened.

OBJECTIVE

To examine the effect of a digital health intervention, Mobile Patient Technology for Health-CRC (mPATH-CRC), on rates of CRC screening.

DESIGN

Randomized clinical trial. (ClinicalTrials.gov: NCT02088333).

SETTING

6 community-based primary care practices.

PARTICIPANTS

450 patients (223 in the mPATH-CRC group and 227 in usual care) scheduled for a primary care visit and due for routine CRC screening.

INTERVENTION

An iPad application that displays a CRC screening decision aid, lets patients order their own screening tests, and sends automated follow-up electronic messages to support patients.

MEASUREMENTS

The primary outcome was chart-verified completion of CRC screening within 24 weeks. Secondary outcomes were ability to state a screening preference, intention to receive screening, screening discussions, and orders for screening tests. All outcome assessors were blinded to randomization.

RESULTS

Baseline characteristics were similar between groups; 37% of participants had limited health literacy, and 53% had annual incomes less than $20 000. Screening was completed by 30% of mPATH-CRC participants and 15% of those receiving usual care (logistic regression odds ratio, 2.5 [95% CI, 1.6 to 4.0]). Compared with usual care, more mPATH-CRC participants could state a screening preference, planned to be screened within 6 months, discussed screening with their provider, and had a screening test ordered. Half of mPATH-CRC participants (53%; 118 of 223) "self-ordered" a test via the program.

LIMITATION

Participants were English speakers in a single health care system.

CONCLUSION

A digital health intervention that allows patients to self-order tests can increase CRC screening. Future research should identify methods for implementing similar interventions in clinical care.

PRIMARY FUNDING SOURCE

National Cancer Institute.

Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions

Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. Here, we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype-specific transmission pathways in a social carnivore. We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIV_Ple ) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIV_Ple molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father- and/or mother-offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype-specific FIV_Ple co-occurrence networks and assessed what combination of social networks, spatial networks or co-infection best structured the FIV_Ple network. While social organization (i.e., pride) was an important component of FIV_Ple transmission pathways at all scales, we find that FIV_Ple subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIV_Ple transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype-specific. Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.

Cost Analysis of Ceramic Heads in Primary Total Hip Arthroplasty

BACKGROUND

The advent of adverse local tissue reactions seen in metal-on-metal bearings, and the recent recognition of trunnionosis, have led many surgeons to recommend ceramic-on-polyethylene articulations for primary total hip arthroplasty. However, to our knowledge, there has been little research that has considered whether the increased cost of ceramic provides enough benefit over cobalt-chromium to justify its use. The primary purpose of this study was to compare the cost-effectiveness of ceramic-on-polyethylene implants and metal-on-polyethylene implants in patients undergoing total hip arthroplasty.

METHODS

Markov decision modeling was used to determine the ceramic-on-polyethylene implant revision rate necessary to be cost-effective compared with the revision rate of metal-on-polyethylene implants across a range of patient ages and implant costs. A different set of Markov models was used to estimate the national cost burden of choosing ceramic-on-polyethylene implants over metal-on-polyethylene implants for primary total hip arthroplasties. The Premier Research Database was used to identify 20,398 patients who in 2012 were ≥45 years of age and underwent a total hip arthroplasty with either a ceramic-on-polyethylene implant or a metal-on-polyethylene implant.

RESULTS

The cost-effectiveness of ceramic heads is highly dependent on the cost differential between ceramic and metal femoral heads and the age of the patient. At a cost differential of $325, ceramic-on-polyethylene bearings are cost-effective for patients <85 years of age. At a cost differential of $600, it is cost-effective to utilize ceramic-on-polyethylene bearings in patients <65 years of age, and, at a differential of $1,003, ceramic-on-polyethylene bearings are not cost-effective at any age.

CONCLUSIONS

The ability to recoup the initial increased expenditure of ceramic heads through a diminished lifetime revision cost is dependent on the price premium for ceramic and the age of the patient. A wholesale switch to ceramic bearings regardless of age or cost differential may result in an economic burden to the health system.

LEVEL OF EVIDENCE

Economic and decision analysis, Level III. See Instructions for Authors for a complete description of levels of evidence.

Does Increased Spending on Pharmaceutical Marketing Inhibit Pioneering Innovation?

The pharmaceutical industry has been criticized for developing and aggressively marketing drugs that do not provide significant health benefits relative to existing drugs but retain the benefits of patent protection. Critics argue that drug marketing increases health care expenditures and provides a disincentive for pioneering drug innovation. However, evidence that marketing expenditures have any relationship to new drug approvals has been anecdotal. We hypothesized that, at publicly traded pharmaceutical firms, increased marketing expenditures will result in a reduced volume of pioneering new drugs in comparison to less innovative new drugs. We also hypothesized that additional research and development spending will result in an increased volume of pioneering new drugs in comparison to less innovative drugs. Results confirm our hypotheses. Specific policy recommendations for altering firms' incentives for the development of pioneering drugs are provided.

Cost-effectiveness of quantitative pretest probability intended to reduce unnecessary medical radiation exposure in emergency department patients with chest pain and dyspnea

OBJECTIVES

Quantitative pretest probability (qPTP) incorporated into a decision support tool with advice can reduce unnecessary diagnostic testing among patients with symptoms suggestive of acute coronary syndrome (ACS) and pulmonary embolism (PE), reducing 30-day costs without an increase in 90-day adverse outcomes. This study estimates long-term (beyond 90-day) costs and outcomes associated with qPTP. The authors hypothesized that qPTP reduces lifetime costs and improves outcomes in low-risk patients with symptoms suggestive of ACS and PE.

METHODS

This was a cost-effectiveness analysis of a multicenter, randomized controlled trial of adult emergency patients with dyspnea and chest pain, in which a clinician encountering a low-risk patient with symptoms suggestive of ACS or PE conducted either the intervention (qPTP for ACS and PE with advice) or the sham (no qPTP and no advice). Effect of the intervention over a patient's lifetime was assessed using a Markov microsimulation model. Short-term costs and outcomes were from the trial; long-term outcomes and costs were from the literature. Outcomes included lifetime transition to PE, ACS, and intracranial hemorrhage (ICH); mortality from cancer, ICH, PE, ACS, renal failure, and ischemic stroke; quality-adjusted life-years (QALYs); and total medical costs compared between simulated intervention and sham groups.

RESULTS

Markov microsimulation for a 40-year-old patient receiving qPTP found lifetime cost savings of $497 for women and $528 for men, associated with small gains in QALYs (2 and 6 days, respectively) and lower rates of cancer mortality in both sexes, but a reduction in ICH only in males. Sensitivity analysis for patients aged 60 years predicted that qPTP would continue to save costs and also reduce mortality from both ICH and cancer. Use of qPTP significantly reduced the lifetime probability of PE diagnosis, with lower probability of death from PE in both sexes aged 40 to 60 years. However, use of qPTP reduced the rate of ACS diagnosis and death from ACS at age 40, but increased the death rate from ACS at age 60 for both sexes.

CONCLUSIONS

Widespread use of a combined qPTP for both ACS and PE has the potential to decrease costs by reducing diagnostic testing, while improving most long-term outcomes in emergency patients with chest pain and dyspnea.

Evolution of puma lentivirus in bobcats (Lynx rufus) and mountain lions (Puma concolor) in North America

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. Importance: An understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/recombination and host-imposed selection pressure.

A cost-utility analysis comparing the cost-effectiveness of simultaneous and staged bilateral total knee arthroplasty

BACKGROUND

The safety and efficacy of simultaneous or staged bilateral total knee arthroplasty have long been debated among orthopaedic surgeons. Advocates for simultaneous bilateral total knee arthroplasty posit that the benefits of decreased costs and recovery time, with no difference in functional outcomes, outweigh the economic costs of potential complications. The purpose of the study was to conduct a cost-utility analysis comparing simultaneous bilateral total knee arthroplasty with staged bilateral total knee arthroplasty.

METHODS

A Markov model was designed to compare the cost-effectiveness of simultaneous bilateral total knee arthroplasty with that of staged bilateral total knee arthroplasty. Nationwide Inpatient Sample data sets from 2004 to 2007 were used to identify 24,574 simultaneous and 382,496 unilateral procedures. On the basis of the codes of the International Classification of Diseases, Ninth Revision, Clinical Modification, perioperative complications were categorized as minor, major, and mortality, and respective probability values were calculated. Nationwide Inpatient Sample data were used to determine hospital costs conditional on procedure type and complications. Rehabilitation costs, anesthesia costs, and heath utilities were estimated from the literature. To minimize selection bias, propensity score matching was used to match the groups on comorbid conditions, socioeconomic variables, and hospital characteristics.

RESULTS

Using the matched sample, all complication rates were higher for the staged group. The estimated mean cost (in 2012 U.S. dollars) was $43,401 for simultaneous bilateral total knee arthroplasty compared with $72,233 for staged bilateral total knee arthroplasty. The quality-adjusted life years gained were 9.31 for simultaneous bilateral total knee arthroplasty and 9.29 for staged bilateral total knee arthroplasty. On the basis of these matched results, simultaneous bilateral total knee arthroplasty dominated staged bilateral total knee arthroplasty with lower costs and better outcomes.

CONCLUSIONS

On the basis of this analysis, simultaneous bilateral total knee arthroplasty is more cost-effective than staged bilateral total knee arthroplasty, with lower costs and better outcomes for the average patient. These data can inform shared medical decision-making when bilateral total knee arthroplasty is indicated.

Association between traditional nursing home quality measures and two sources of nursing home complaints

OBJECTIVE

To test for an association between traditional nursing home quality measures and two sources of resident- and caregiver-derived nursing home complaints.

DATA SOURCES

Nursing home complaints to the North Carolina Long-Term Care Ombudsman Program and state certification agency from October 2002 through September 2006 were matched with Online Survey Certification and Reporting data and Minimum Data Set Quality Indicators (MDS-QIs).

STUDY DESIGN

We examine the association between the number of complaints filed against a facility and measures of inspection violations, staffing levels, and MDS-QIs.

DATA EXTRACTION

One observation per facility per quarter is constructed by matching quarterly data on complaints to OSCAR data from the same or most recent prior quarter and to MDS-QIs from the same quarter. One observation per inspection is obtained by matching OSCAR data to complaint totals from both the same and the immediate prior quarter.

PRINCIPAL FINDINGS

There is little relationship between MDS-QIs and complaints. Ombudsman complaints and inspection violations are generally unrelated, but there is a positive relationship between state certification agency complaints and inspection violations.

CONCLUSIONS

Ombudsman and state certification agency complaint data are resident- and caregiver-derived quality measures that are distinctive from and complement traditional quality measures.

Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition

BACKGROUND

To date, only mutations in CCR5 have been shown to confer resistance to human immunodeficiency virus type 1 (HIV-1) infection, and these explain only a small fraction of the observed variability in HIV susceptibility.

METHODS

We performed a meta-analysis between 2 independent European genomewide association studies, each comparing HIV-1 seropositive cases with normal population controls known to be HIV uninfected, to identify single-nucleotide polymorphisms (SNPs) associated with the HIV-1 acquisition phenotype. SNPs exhibiting P < 10(-5) in this first stage underwent second-stage analysis in 2 independent US cohorts of European descent.

RESULTS

After the first stage, a single highly significant association was revealed for the chromosome 8 rs6996198 with HIV-1 acquisition and was replicated in both second-stage cohorts. Across the 4 groups, the rs6996198-T allele was consistently associated with a significant reduced risk of HIV-1 infection, and the global meta-analysis reached genomewide significance: P(combined) = 7.76 × 10(-8).

CONCLUSIONS

We provide strong evidence of association for a common variant with HIV-1 acquisition in populations of European ancestry. This protective signal against HIV-1 infection is the first identified outside the CCR5 nexus. First clues point to a potential functional role for a nearby candidate gene, CYP7B1, but this locus warrants further investigation.

Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured-exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

The effect of medical nutrition therapy on changes in dietary knowledge and DASH diet adherence in older adults with cardiovascular disease

OBJECTIVE

To examine the effect of MNT on dietary knowledge of older adults at baseline, 6 months and 12 months and to assess the effect of dietary knowledge on change in DASH diet adherence from baseline to 12 months.

DESIGN

Data for the analysis come from a controlled, randomized prospective design conducted from 2003-2005 with the outcome measures taken pre-, mid-, and post-intervention.

SETTING

Data were collected from participants in their homes in an urban community in North Carolina.

PARTICIPANTS

Participants (N=147) were adults aged 60+ with a diagnosis of hypertension and/or hyperlipidemia.

INTERVENTION

Intervention recipients received three sessions of MNT throughout the 1 year study period. The control group received nutrition information at enrollment.

MEASUREMENTS

Participants completed a dietary knowledge questionnaire and a 24 dietary recall at baseline, 6 months, and 12 months. Instrumental variables models with participant fixed effects were used to determine the impact of MNT on dietary knowledge and dietary knowledge on DASH diet adherence.

RESULTS

Among those who received MNT, dietary knowledge increased from baseline to twelve months (p<.01). Changes in dietary knowledge were not associated with changes in DASH adherence from baseline to 12 months (p=0.44).

CONCLUSIONS

The MNT administered was effective at improving dietary knowledge, but not at improving DASH adherence. Three MNT sessions may be insufficient to change behavior. Integrating behavioral change theory and cultural sensitivity to MNT may improve diet adherence among diverse older adults.

Trends in potentially avoidable hospitalizations among adults in Tennessee, 1998-2006

BACKGROUND

Potentially avoidable hospitalizations are inpatient admissions for certain conditions, called Ambulatory Care Sensitive Conditions (ACSCs), which can potentially be prevented by effective outpatient treatment of individuals who actively participate in their own care and engage in responsible personal behavior. Changes in the rates of ACSC hospitalizations over time may signal an improvement or deterioration in the quality and effectiveness of ambulatory care. These long-term trends may also suggest changes in the underlying factors such as lifestyle choices and dietary practices of individuals and families.

OBJECTIVE

This study presents data from the Tennessee Hospital Discharge Datasets on changes in ACSC hospitalizations as a percent of all hospitalizations for 1998-2006.

METHODS

Retrospective analysis of administrative data based on the UB-92 claims forms submitted by all short-term acute-care hospitals in Tennessee.

RESULTS

Total ACSC hospitalizations in Tennessee increased by 4.2 percent between 1998 and 2006, while the total costs for ACSC hospitalizations decreased by 1.8 percent in constant 2006 dollars. In comparison, total admissions for all conditions increased by 15 percent during 1998-2006 while total hospital costs for all conditions increased by 21 percent. The rate of increase in ACSC hospitalization varied according to patient's race, insurance type, and whether the patient's health plan is managed care or fee-for-service. ACSC patients admitted through an emergency department outnumbered their counterparts who were not admitted through an emergency department by a factor of more than two throughout 1998-2006.

CONCLUSIONS

Our analysis of long-term trends of ACSC hospitalizations in Tennessee reveals a mixed bag of good news and bad news. In 1998-2006, ACSC hospitalizations rose at a much lower rate than overall hospitalizations for all conditions. Meanwhile, the costs of ACSC hospitalization in 2006 constant dollars decreased while the costs of overall hospitalizations increased. Minority groups such as blacks and patients insured under TennCare did not experience much decline in ACSC hospitalizations, especially in the rates of chronic ambulatory-care sensitive conditions, when compared with their white and commercially-insured counterparts. Patients whose care was managed experienced smaller declines in ACSC hospitalizations than those not under managed care. Finally, the number of ACSC hospitalizations admitted through an ED outnumbered those admitted through the regular hospital admission department during the study period, and the gap between the two sources of admissions grew larger over time.

Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia

Chromosome 3p21–22 harbors two clusters of chemokine receptor genes, several of which serve as major or minor coreceptors of HIV-1. Although the genetic association of CCR5 and CCR2 variants with HIV-1 pathogenesis is well known, the role of variation in other nearby chemokine receptor genes remain unresolved. We genotyped exonic single nucleotide polymorphisms (SNPs) in chemokine receptor genes: CCR3, CCRL2, and CXCR6 (at 3p21) and CCR8 and CX3CR1 (at 3p22), the majority of which were non-synonymous. The individual SNPs were tested for their effects on disease progression and outcomes in five treatment-naïve HIV-1/AIDS natural history cohorts. In addition to the known CCR5 and CCR2 associations, significant associations were identified for CCR3, CCR8, and CCRL2 on progression to AIDS. A multivariate survival analysis pointed to a previously undetected association of a non-conservative amino acid change F167Y in CCRL2 with AIDS progression: 167F is associated with accelerated progression to AIDS (RH = 1.90, P = 0.002, corrected). Further analysis indicated that CCRL2-167F was specifically associated with more rapid development of pneumocystis pneumonia (PCP) (RH = 2.84, 95% CI 1.28–6.31) among four major AIDS–defining conditions. Considering the newly defined role of CCRL2 in lung dendritic cell trafficking, this atypical chemokine receptor may affect PCP through immune regulation and inducing inflammation.

Human chemokine receptors are cell surface proteins that may be utilized by HIV-1 for entry into host cells. DNA variation in the HIV-1 major coreceptor CCR5 affects HIV-1 infection and progression. This study comprehensively assesses the role of genetic variation of multiple chemokine receptor genes clustered in the chromosome 3p21 and 3p22 on HIV-1 disease outcomes in HIV-1 natural history cohorts. The multivariate survival analyses identified functional variants that altered disease progression rate in CCRL2, CCR3, and CCR8. CCRL2-F167Y affects the rate to AIDS development through a specific protection against pneumocystis pneumonia (PCP), a common AIDS–defining condition. Our study identified this atypical chemokine receptor CCRL2 as a key factor involved in PCP, possibly through inducing inflammation in the lung.

FIV diversity: FIV Ple subtype composition may influence disease outcome in African lions

Feline immunodeficiency virus (FIV) infects domestic cats and at least 20 additional species of non-domestic felids throughout the world. Strains specific to domestic cat (FIV(Fca)) produce AIDS-like disease progression, sequelae and pathology providing an informative model for HIV infection in humans. Less is known about the immunological and pathological influence of FIV in other felid species although multiple distinct strains of FIV circulate in natural populations. As in HIV-1 and HIV-2, multiple diverse cross-species infections may have occurred. In the Serengeti National Park, Tanzania, three divergent subtypes of lion FIV (FIV(Ple)) are endemic, whereby 100% of adult lions are infected with one or more of these strains. Herein, the relative distribution of these subtypes in the population are surveyed and, combined with observed differences in lion mortality due to secondary infections based on FIV(Ple) subtypes, the data suggest that FIV(Ple) subtypes may have different patterns of pathogenicity and transmissibility among wild lion populations.

Association of host genetic risk factors with the course of cytomegalovirus retinitis in patients infected with human immunodeficiency virus

PURPOSE

To evaluate the effects of previously reported host genetics factors that influence cytomegalovirus (CMV) retinitis incidence, progression to acquired immune deficiency syndrome (AIDS), and efficacy of highly active antiretroviral therapy (HAART) for mortality, retinitis progression, and retinal detachment in patients with CMV retinitis and AIDS in the era of HAART.

DESIGN

Prospective, multicenter, observational study.

METHODS

Cox proportional hazards model based genetic association tests examined the influence of IL-10R1_S420L, CCR5-Δ32, CCR2-V64I, CCR5 promoter, and SDF-3'A polymorphisms among patients with mortality, retinitis progression, and retinal detachment. Participants were 203 European-American and 117 African-American patients with AIDS and CMV retinitis.

RESULTS

European-American patients with the CCR5 +.P1.+ promoter haplotype showed increased risk for mortality (hazard ratio [HR] = 1.83; 95% confidence interval [CI]: 1.00-3.40; P = .05). Although the same haplotype also trended for increased risk for mortality in African-American patients, the result was not significant (HR = 2.28; 95% CI: 0.93-5.60; P = .07). However, this haplotype was associated with faster retinitis progression in African Americans (HR = 5.22; 95% CI: 1.54-17.71; P = .007). Increased risk of retinitis progression was also evident for African-American patients with the SDF1-3'A variant (HR = 3.89; 95% CI: 1.42-10.60; P = .008). In addition, the SDF1-3'A variant increased the retinal detachment risk in this patient group (HR = 3.05; 95% CI: 1.01-9.16; P = .05).

CONCLUSION

Besides overall immune health, host genetic factors influence mortality, retinitis progression, and retinal detachment in patients with AIDS and CMV retinitis that are receiving HAART.

Complaints against nursing homes: comparing two sources of complaint information and predictors of complaints

PURPOSE OF THE STUDY

Two consumer-derived measures of nursing home quality that have been underutilized by researchers are consumer complaints to the state certification agency between inspections and complaints to the Long-Term Care Ombudsman Program. This article describes these complaints, considers facility-level predictors of complaints, and examines how complaints to the 2 entities are related.

DESIGN AND METHODS

This article uses North Carolina complaint data from the state certification agency and Ombudsman from 2002 to 2006. First, we outline the similarities and differences in the 2 complaint sources by considering descriptive statistics and examining the structure of the 2 agencies. Second, we examine the relationship between complaints and facility characteristics that have been predictive of traditional quality measures. Finally, we examine the relationships between the 2 types of complaints.

RESULTS

We find that complaints to the 2 agencies exhibit distinct differences in substantiation rates, although the top complaint category for both agencies is quality of care. Having a higher proportion of Medicaid residents is generally not predictive of complaint volume, whereas having a higher proportion of Medicare residents is associated with higher complaint levels.

IMPLICATIONS

We find a lack of association between complaints to the 2 agencies when examining specific matched categories of complaints in many cases, suggesting that the 2 entities are not duplicating efforts in these categories.

Genome-wide association study implicates PARD3B-based AIDS restriction

BACKGROUND

Host genetic variation influences human immunodeficiency virus (HIV) infection and progression to AIDS. Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression.

METHODS

European American HIV seroconverters (n = 755) were interrogated for single-nucleotide polymorphisms (SNPs) (n = 700,022) associated with progression to AIDS 1987 (Cox proportional hazards regression analysis, co-dominant model).

RESULTS

Association with slower progression was observed for SNPs in the gene PARD3B. One of these, rs11884476, reached genome-wide significance (relative hazard = 0.3; P =3. 370 × 10(-9)) after statistical correction for 700,022 SNPs and contributes 4.52% of the overall variance in AIDS progression in this study. Nine of the top-ranked SNPs define a PARD3B haplotype that also displays significant association with progression to AIDS (hazard ratio, 0.3; P = 3.220 × 10(-8)). One of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the expression profile of PARD3B splicing transcripts was observed in B cell lines with alternate rs10185378 genotypes. This SNP was typed in European cohorts of rapid progressors and was found to be protective for AIDS 1993 definition (odds ratio, 0.43, P = .025).

CONCLUSIONS

These observations suggest a potential unsuspected pathway of host genetic influence on the dynamics of AIDS progression.

Cost-effectiveness of medical nutrition therapy and therapeutically designed meals for older adults with cardiovascular disease

BACKGROUND

Many older adults experience hyperlipidemia and hypertension, but there is little information about whether medical nutrition therapy (MNT) or therapeutic meals have independent or joint beneficial effects on older adults with these diagnoses.

OBJECTIVE

To assess the cost-effectiveness of MNT and therapeutic meals for older adults with hyperlipidemia and/or hypertension.

DESIGN

A 1-year prospective four-arm controlled randomized community-based clinical trial.

SUBJECTS/SETTING

Participants were people ages 60 years or older residing in community settings who were medically diagnosed with either hypertension or hyperlipidemia. They were recruited through a number of venues beginning in May 2003.

INTERVENTION

The 321 eligible individuals were assigned to one of four arms: (a) a literature control group, (b) a therapeutic meal group that received seven diagnosis-appropriate therapeutic meals a week, (c) an MNT group, and (d) an MNT-plus-therapeutic meal group.

MAIN OUTCOME MEASURE

The outcome measure was quality-adjusted life-years (QALYs). Costs included both intervention and medical costs.

STATISTICAL ANALYSES

Estimations of separate models of costs and QALYs facilitated the construction of incremental cost-effectiveness ratios. Net benefit analysis produced the probability that each intervention was cost-effective given different values for society's willingness to pay for a QALY.

RESULTS

Therapeutic meals are cost-effective. Using the net benefit approach and a willingness to pay of $109,000 per QALY, the probability that the therapeutic meal delivery program is cost-effective is 95% and for MNT the probability is 90%. However, the combination of MNT and therapeutic meals did not have an independent significant effect on QALYs.

CONCLUSIONS

Results inform the debate about extending Medicare funding for MNT to individuals with hypertension and hyperlipidemia. Future research should include more individuals who are not currently receiving medications for these diseases.

Accounting for multiple comparisons in a genome-wide association study (GWAS)

Background

As we enter an era when testing millions of SNPs in a single gene association study will become the standard, consideration of multiple comparisons is an essential part of determining statistical significance. Bonferroni adjustments can be made but are conservative due to the preponderance of linkage disequilibrium (LD) between genetic markers, and permutation testing is not always a viable option. Three major classes of corrections have been proposed to correct the dependent nature of genetic data in Bonferroni adjustments: permutation testing and related alternatives, principal components analysis (PCA), and analysis of blocks of LD across the genome. We consider seven implementations of these commonly used methods using data from 1514 European American participants genotyped for 700,078 SNPs in a GWAS for AIDS.

Results

A Bonferroni correction using the number of LD blocks found by the three algorithms implemented by Haploview resulted in an insufficiently conservative threshold, corresponding to a genome-wide significance level of α = 0.15 - 0.20. We observed a moderate increase in power when using PRESTO, SLIDE, and simpleℳ when compared with traditional Bonferroni methods for population data genotyped on the Affymetrix 6.0 platform in European Americans (α = 0.05 thresholds between 1 × 10^-7 and 7 × 10^-8).

Conclusions

Correcting for the number of LD blocks resulted in an anti-conservative Bonferroni adjustment. SLIDE and simpleℳ are particularly useful when using a statistical test not handled in optimized permutation testing packages, and genome-wide corrected p-values using SLIDE, are much easier to interpret for consumers of GWAS studies.

Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection

BACKGROUND

High-throughput genome-wide techniques have facilitated the identification of previously unknown host proteins involved in cellular human immunodeficiency virus (HIV) infection. Recently, 3 independent studies have used small interfering RNA technology to silence each gene in the human genome to determine the importance of each in HIV infection. Genes conferring a significant effect were termed HIV-dependency factors (HDFs).

METHODS

We assembled high-density panels of 6380 single-nucleotide polymorphisms (SNPs) in 278 HDF genes and tested for genotype associations with HIV infection and AIDS progression in 1633 individuals from clinical AIDS cohorts.

RESULTS

After statistical correction for multiple tests, significant associations with HIV acquisition were found for SNPs in 2 genes, NCOR2 and IDH1. Weaker associations with AIDS progression were revealed for SNPs within the TM9SF2 and EGFR genes.

CONCLUSIONS

This study independently verifies the influence of NCOR2 and IDH1 on HIV transmission, and its findings suggest that variation in these genes affects susceptibility to HIV infection in exposed individuals.

Effect of host genetics on the development of cytomegalovirus retinitis in patients with AIDS

BACKGROUND

Cytomegalovirus (CMV) retinitis is a common opportunistic infection among patients with AIDS and still causes visual morbidity despite the wide spread usage of highly active antiretroviral therapy (HAART). The ubiquitous CMV pathogen contains a human interleukin-10 (IL-10) homolog in its genome and utilizes it to evade host immune reactions through an IL-10 receptor mediated immune-suppression pathway.

METHODS

Effects of IL-10R1, IL-10 and previously described AIDS restriction gene variants are investigated on the development of CMV retinitis in the Longitudinal Study of the Ocular Complications of AIDS (LSOCA) cohort (N = 1284).

RESULTS

In European Americans (n = 750), a haplotype carrying an amino acid changing variation in the cytoplasmic domain (S420L) of IL-10R1 can be protective (OR, 0.14; 95% CI, 0.02-0.94; P = .04) against, whereas another haplotype carrying an amino acid changing variation in the extracellular domain (I224V) of IL-10R1 can be more susceptible (OR, 6.21; 95% CI, 1.22- 31.54; P = .03) to CMV retinitis. In African Americans (n = 534), potential effects of IL-10 variants are observed.

CONCLUSION

Host genetics may have a role in the occurrence of CMV retinitis in patients infected with HIV.

The effect of home-delivered Dietary Approach to Stop Hypertension (DASH) meals on the diets of older adults with cardiovascular disease

BACKGROUND

Many older adults with hyperlipidemia or hypertension participate in the Older Americans Act Nutrition Program, which serves meals in community settings and delivers meals to homes. However, there is little information regarding whether therapeutic meals designed around Dietary Approach to Stop Hypertension (DASH) principles have a beneficial effect on the diets of these older adults.

OBJECTIVE

The objective of this study was to determine the degree to which dietary change is influenced by providing 7 home-delivered therapeutic meals weekly to adults aged > or = 60 y.

DESIGN

We conducted a 1-y randomized controlled trial in 298 persons with hyperlipidemia or hypertension, in which 50% of participants received 7 therapeutic meals per week for 12 mo. Those in need of dietary change at baseline (n = 210) were examined. Changes in intermediate DASH accordance, DASH accordance, and the nutrients that make up the DASH diet were measured by using 24-h food recalls at baseline, 6 mo, and 12 mo. Chi-square tests, t tests, and multiple regression were used to examine the association between receipt of meals and dietary change over time.

RESULTS

Participants who received meals were 20% (P = 0.001) more likely to reach intermediate DASH accordance at 6 mo and were 18% (P = 0.007) more likely to meet saturated fat accordance at 12 mo than were those who did not receive meals. When stratified by race and income, gains were marginally larger for whites and higher-income individuals.

CONCLUSION

Delivery of 7 DASH meals per week was found to increase compliance with dietary recommendations among noncompliant older adults with cardiovascular disease.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS

BACKGROUND

A mean of 9-10 years of human immunodeficiency virus type 1 (HIV-1) infection elapse before clinical AIDS develops in untreated persons, but this rate of disease progression varies substantially among individuals. To investigate host genetic determinants of the rate of progression to clinical AIDS, we performed a multistage genomewide association study.

METHODS

The discovery stage comprised 156 individuals from the Multicenter AIDS Cohort Study, enriched with rapid and long-term nonprogressors to increase statistical power. This was followed by replication tests of putatively associated genotypes in an independent population of 590 HIV-1-infected seroconverters.

RESULTS

Significant associations with delayed AIDS progression were observed in a haplotype located at 1q41, 36 kb upstream of PROX1 on chromosome 1 (relative hazard ratio, 0.69; Fisher's combined P = 6.23 X 10(-7)). This association was replicated further in an analysis stratified by transmission mode, with the effect consistent in sexual or mucosal and parenteral transmission (relative hazard ratios, 0.72 and 0.63, respectively; combined P = 1.63 X 10(-6)).

CONCLUSIONS

This study identified and replicated a locus upstream of PROX1 that is associated with delayed progression to clinical AIDS. PROX1 is a negative regulator of interferon-gamma expression in T cells and also mitigates the advancement of vascular neoplasms, such as Kaposi sarcoma, a common AIDS-defining malignancy. This study adds to the cumulative polygenic host component that effectively regulates the progression to clinical AIDS among HIV-1-infected individuals, raising prospects for potential new avenues for therapy and improvements in AIDS prognosis.

Genetics and pathogenesis of feline infectious peritonitis virus

Coronavirus sequence analyses demonstrate distinctive circulating strains in natural populations.

Feline coronavirus (FCoV) is endemic in feral cat populations and cat colonies, frequently preceding outbreaks of fatal feline infectious peritonitis (FIP). FCoV exhibits 2 biotypes: the pathogenic disease and a benign infection with feline enteric coronavirus (FECV). Uncertainty remains regarding whether genetically distinctive avirulent and virulent forms coexist or whether an avirulent form mutates in vivo, causing FIP. To resolve these alternative hypotheses, we isolated viral sequences from FCoV-infected clinically healthy and sick cats (8 FIP cases and 48 FECV-asymptomatic animals); 735 sequences from 4 gene segments were generated and subjected to phylogenetic analyses. Viral sequences from healthy cats were distinct from sick cats on the basis of genetic distances observed in the membrane and nonstructural protein 7b genes. These data demonstrate distinctive circulating virulent and avirulent strains in natural populations. In addition, 5 membrane protein amino acid residues with functional potential differentiated healthy cats from cats with FIP. These findings may have potential as diagnostic markers for virulent FIP-associated FCoV.

Feline immunodeficiency virus (FIV) in wild Pallas' cats

Feline immunodeficiency virus (FIV), a feline lentivirus related to HIV, causes immune dysfunction in domestic and wild cats. The Pallas' cat is the only species from Asia known to harbor a species-specific strain of FIV designated FIV(Oma) in natural populations. Here, a 25% seroprevalence of FIV is reported from 28 wild Mongolian Pallas' cats sampled from 2000 to 2008. Phylogenetic analysis of proviral RT-Pol from eight FIV(Oma) isolates from Mongolia, Russia, China and Kazakhstan reveals a unique monophyletic lineage of the virus within the Pallas' cat population, most closely related to the African cheetah and leopard FIV strains. Histopathological examination of lymph node and spleen from infected and uninfected Pallas' cats suggests that FIV(Oma) causes immune depletion in its' native host.

Pathological manifestations of feline immunodeficiency virus (FIV) infection in wild African lions

Feline immunodeficiency virus (FIV) causes AIDS in the domestic cat (Felis catus) but has not been explicitly associated with AIDS pathology in any of the eight free-ranging species of Felidae that are endemic with circulating FIV strains. African lion (Panthera leo) populations are infected with lion-specific FIV strains (FIVple), yet there remains uncertainty about the degree to which FIV infection impacts their health. Reported CD4+ T-lymphocyte depletion in FIVple-infected lions and anecdotal reports of lion morbidity associated with FIV seroprevalence emphasize the concern as to whether FIVple is innocuous or pathogenic. Here we monitored clinical, biochemical, histological and serological parameters among FIVple-positive (N=47) as compared to FIVple-negative (N=17) lions anesthetized and sampled on multiple occasions between 1999 and 2006 in Botswana. Relative to uninfected lions, FIVple-infected lions displayed a significant elevation in the prevalence of AIDS-defining conditions: lymphadenopathy, gingivitis, tongue papillomas, dehydration, and poor coat condition, as well as displaying abnormal red blood cell parameters, depressed serum albumin, and elevated liver enzymes and gamma globulin. Spleen and lymph node biopsies from free-ranging FIVple-infected lions (N=9) revealed evidence of lymphoid depletion, the hallmark pathology documented in immunodeficiency virus infections of humans (HIV-1), macaques, and domestic cats. We conclude that over time FIVple infections in free-ranging lions can lead to adverse clinical, immunological, and pathological outcomes in some individuals that parallel sequelae caused by lentivirus infection in humans (HIV), Asian macaques (SIV) and domestic cats (FIVfca).

Association of Y chromosome haplogroup I with HIV progression, and HAART outcome

The host genetic basis of differential outcomes in HIV infection, progression, viral load set point and highly active retroviral therapy (HAART) responses was examined for the common Y haplogroups in European Americans and African Americans. Accelerated progression to acquired immune deficiency syndrome (AIDS) and related death in European Americans among Y chromosome haplogroup I (Y-I) subjects was discovered. Additionally, Y-I haplogroup subjects on HAART took a longer time to HIV-1 viral suppression and were more likely to fail HAART. Both the accelerated progression and longer time to viral suppression results observed in haplogroup Y-I were significant after false-discovery-rate corrections. A higher frequency of AIDS-defining illnesses was also observed in haplogroup Y-I. These effects were independent of the previously identified autosomal AIDS restriction genes. When the Y-I haplogroup subjects were further subdivided into six I subhaplogroups, no one subhaplogroup accounted for the effects on HIV progression, viral load or HAART response. Adjustment of the analyses for population stratification found significant and concordant haplogroup Y-I results. The Y chromosome haplogroup analyses of HIV infection and progression in African Americans were not significant. Our results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans.

The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics

The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV_Ple), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Φ_ST = 0.92; nDNA F_ST = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV_Ple subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (∼324,000–169,000 years ago), which expanded during the Late Pleistocene (∼100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (∼14,000–7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV_Ple variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

The lion Panthera leo, a formidable carnivore with a complex cooperative social system, has fascinated humanity since pre-historical times, inspiring hundreds of religious and cultural allusions. Here, we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and Asia. We assayed appropriately informative autosomal, Y-chromosome, and mitochondrial genetic markers, and assessed the prevalence and genetic variation of the lion-specific feline immunodeficiency virus (FIV_Ple), a lentivirus analogous to human immunodeficiency virus (HIV) that causes AIDS-like immunodeficiency disease in domestic cats. We compare the large multigenic dataset from lions with patterns of genetic variation of the FIV_Ple to characterize the population-genomic legacy of lions. We refute the hypothesis that African lions consist of a single panmictic population, highlighting the importance of preserving populations in decline rather than prioritizing larger-scale conservation efforts. Interestingly, lion and FIV_Ple variation revealed evidence of unsuspected genetic diversity even in the well-studied lion population of the Serengeti Ecosystem, which consists of recently admixed animals derived from three distinct genetic groups.

Prevention of immunodeficiency virus induced CD4+ T-cell depletion by prior infection with a non-pathogenic virus

Immune dysregulation initiated by a profound loss of CD4+ T-cells is fundamental to HIV-induced pathogenesis. Infection of domestic cats with a non-pathogenic lentivirus prevalent in the puma (puma lentivirus, PLV or FIV(pco)) prevented peripheral blood CD4+ T-cell depletion caused by subsequent virulent FIV infection. Maintenance of this critical population was not associated with a significant decrease in FIV viremia, lending support to the hypothesis that direct viral cytopathic effect is not the primary cause of immunodeficiency. Although this approach was analogous to immunization with a modified live vaccine, correlates of immunity such as a serum-neutralizing antibody or virus-specific T-cell proliferative response were not found in protected animals. Differences in cytokine transcription profile, most notably in interferon gamma, were observed between the protected and unprotected groups. These data provide support for the importance of non-adaptive enhancement of the immune response in the prevention of CD4+ T-cell loss.

Evolution of feline immunodeficiency virus in Felidae: implications for human health and wildlife ecology

Genetic analyses of feline immunodeficiency viruses provide significant insights on the worldwide distribution and evolutionary history of this emerging pathogen. Large-scale screening of over 3000 samples from all species of Felidae indicates that at least some individuals from most species possess antibodies that cross react to FIV. Phylogenetic analyses of genetic variation in the pol-RT gene demonstrate that FIV lineages are species-specific and suggest that there has been a prolonged period of viral-host co-evolution. The clinical effects of FIV specific to species other than domestic cat are controversial. Comparative genomic analyses of all full-length FIV genomes confirmed that FIV is host specific. Recently sequenced lion subtype E is marginally more similar to Pallas cat FIV though env is more similar to that of domestic cat FIV, indicating a possible recombination between two divergent strains in the wild. Here we review global patterns of FIV seroprevalence and endemnicity, assess genetic differences within and between species-specific FIV strains, and interpret these with patterns of felid speciation to propose an ancestral origin of FIV in Africa followed by interspecies transmission and global dissemination to Eurasia and the Americas. Continued comparative genomic analyses of full-length FIV from all seropositive animals, along with whole genome sequence of host species, will greatly advance our understanding of the role of recombination, selection and adaptation in retroviral emergence.

Genetic characterization of feline leukemia virus from Florida panthers

The emergent strain of FeLV, a novel subgroup A, was probably transmitted to panthers by a domestic cat.

From 2002 through 2005, an outbreak of feline leukemia virus (FeLV) occurred in Florida panthers (Puma concolor coryi). Clinical signs included lymphadenopathy, anemia, septicemia, and weight loss; 5 panthers died. Not associated with FeLV outcome were the genetic heritage of the panthers (pure Florida vs. Texas/Florida crosses) and co-infection with feline immunodeficiency virus. Genetic analysis of panther FeLV, designated FeLV-Pco, determined that the outbreak likely came from 1 cross-species transmission from a domestic cat. The FeLV-Pco virus was closely related to the domestic cat exogenous FeLV-A subgroup in lacking recombinant segments derived from endogenous FeLV. FeLV-Pco sequences were most similar to the well-characterized FeLV-945 strain, which is highly virulent and strongly pathogenic in domestic cats because of unique long terminal repeat and envelope sequences. These unique features may also account for the severity of the outbreak after cross-species transmission to the panther.

Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild

BACKGROUND

Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus) and serves as a natural model for HIV infection in humans. In African lions (Panthera leo) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion.

RESULTS

In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIVPle subtype B (9891 bp) from lions in the Serengeti National Park in Tanzania and FIVPle subtype E (9899 bp) isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, gag, pol, vif, orfA, env, rev and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIVFca, Pallas cat FIVOma and two puma FIVPco subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIVPle gene regions except env, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIVOma than to other FIV. Sequence analyses indicate the SU and TM regions of env vary substantially between subtypes, with FIVPle subtype E more related to domestic cat FIVFca than to FIVPle subtype B and FIVOma likely reflecting recombination between strains in the wild.

CONCLUSION

This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion lentiviruses are integral to the advancement of comparative genomics of human pathogens, as well as emerging disease in wild populations of endangered species.

FIV cross-species transmission: an evolutionary prospective

Feline and primate immunodeficiency viruses (FIVs, SIVs, and HIV) are transmitted via direct contact (e.g. fighting, sexual contact, and mother–offspring transmission). This dynamic likely poses a behavioral barrier to cross-species transmission in the wild. Recently, several host intracellular anti-viral proteins that contribute to species-specificity of primate lentiviruses have been identified revealing adaptive mechanisms that further limit spread of lentiviruses between species. Consistent with these inter-species transmission barriers, phylogenetic evidence supports the prediction that FIV transmission is an exceedingly rare event between free-ranging cat species, though it has occurred occasionally in captive settings. Recently we documented that puma and bobcats in Southern California share an FIV strain, providing an opportunity to evaluate evolution of both viral strains and host intracellular restriction proteins. These studies are facilitated by the availability of the 2× cat genome sequence annotation. In addition, concurrent viral and host genetic analyses have been used to track patterns of migration of the host species and barriers to transmission of the virus within the African lion. These studies illustrate the utility of FIV as a model to discover the variables necessary for establishment and control of lentiviral infections in new species.

Frequent transmission of immunodeficiency viruses among bobcats and pumas

With the exception of human immunodeficiency virus (HIV), which emerged in humans after cross-species transmissions of simian immunodeficiency viruses from nonhuman primates, immunodeficiency viruses of the family Lentiviridae represent species-specific viruses that rarely cross species barriers to infect new hosts. Among the Felidae, numerous immunodeficiency-like lentiviruses have been documented, but only a few cross-species transmissions have been recorded, and these have not been perpetuated in the recipient species. Lentivirus seroprevalence was determined for 79 bobcats (Lynx rufus) and 31 pumas (Puma concolor) from well-defined populations in Southern California. Partial genomic sequences were subsequently obtained from 18 and 12 seropositive bobcats and pumas, respectively. Genotypes were analyzed for phylogenic relatedness and genotypic composition among the study set and archived feline lentivirus sequences. This investigation of feline immunodeficiency virus infection in bobcats and pumas of Southern California provides evidence that cross-species infection has occurred frequently among these animals. The data suggest that transmission has occurred in multiple locations and are most consistent with the spread of the virus from bobcats to pumas. Although the ultimate causes remain unknown, these transmission events may occur as a result of puma predation on bobcats, a situation similar to that which fostered transmission of HIV to humans, and likely represent the emergence of a lentivirus with relaxed barriers to cross-species transmission. This unusual observation provides a valuable opportunity to evaluate the ecological, behavioral, and molecular conditions that favor repeated transmissions and persistence of lentivirus between species.

Neurologic disease in captive lions (Panthera leo) with low-titer lion lentivirus infection

Lion lentivirus (LLV; also known as feline immunodeficiency virus of lion, Panthera leo [FIVPle]) is present in free-ranging and captive lion populations at a seroprevalence of up to 100%; however, clinical signs are rarely reported. LLV displays up to 25% interclade sequence diversity, suggesting that it has been in the lion population for some time and may be significantly host adapted. Three captive lions diagnosed with LLV infection displayed lymphocyte subset alterations and progressive behavioral, locomotor, and neuroanatomic abnormalities. No evidence of infection with other potential neuropathogens was found. Antemortem electrodiagnostics and radiologic imaging indicated a diagnosis consistent with lentiviral neuropathy. PCR was used to determine a partial lentiviral genomic sequence and to quantify the proviral burden in eight postmortem tissue specimens. Phylogenetic analysis demonstrated that the virus was consistent with the LLV detected in other captive and free-ranging lions. Despite progressive neurologic signs, the proviral load in tissues, including several regions of the brain, was low; furthermore, gross and histopathologic changes in the brain were minimal. These findings suggest that the symptoms in these animals resulted from nonspecific encephalopathy, similar to human immunodeficiency virus, FIV, and simian immunodeficiency virus (SIV) neuropathies, rather than a direct effect of active viral replication. The association of neuropathy and lymphocyte subset alterations with chronic LLV infection suggests that long-term LLV infection can have detrimental effects for the host, including death. This is similar to reports of aged sootey mangabeys dying from diseases typically associated with end-stage SIV infection and indicates areas for further research of lentiviral infections of seemingly adapted natural hosts, including mechanisms of host control and viral adaptation.

Environmental contexts of ultimate decisions: why White nursing home residents are twice as likely as African American residents to have an advance directive

OBJECTIVES

The purpose of this study was to determine the extent to which observed differences between White and African American nursing home residents in having an advance directive are attributable to differences between the groups in personal characteristics, the organizational environment of the nursing home, and the geographical environment of the counties in which the nursing homes are located.

METHODS

By using the Medical Expenditure Panel Survey Nursing Home Component matched with county-level measures from the Area Resource File, we modeled the probability of having an advance directive as a function of nursing home resident, facility, and county characteristics for African American and White residents.

RESULTS

The probability of having an advance directive was 27.0% for African American residents and 63.6% for White residents. Nearly half of this 36.6 percentage point gap could be explained by group differences in personal, facility, and county characteristics.

DISCUSSION

County characteristics play a more prominent role than do personal or facility measures in explaining the observed ethnic gap in the prevalence of advance directives. Additional studies should focus further on geographic, health status, and attitudinal variations among nursing home residents that may account for the remaining ethnic difference in the prevalence of advance directives among nursing home residents.

Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS

Research studies of infectious disease outbreaks in wild species of the cat family Felidae have revealed unusual details regarding forces that shape population survival and genetic resistance in these species. A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. Widespread prevalence of species specific feline immunodeficiency virus (FIV), a relative of HIV-AIDS, occurs with little pathogenesis in felid species, except in domestic cats, suggesting immunological adaptation in species where FIV is endemic. Resolving the interaction of host and pathogen genomes can shed new light on the process of disease outbreak in wildlife and in humankind. The role of disease in endangered populations and species is difficult to access as opportunities to monitor outbreaks in natural populations are limited. Conservation management may benefit greatly from advances in molecular genetic tools developed for human biomedical research to assay the biodiversity of both host species and emerging pathogen. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach.

Medicaid enrollee switching among managed care plans

This case-study (n=41,969) of voluntary switching among Mecklenburg County, North Carolina Medicaid managed care plans showed a low switching rate of 14.5 per 100 member-years over 33 months, or 5.3 averaged annually. Population, plan and plan characteristics, claims and telephone survey data were examined to better understand this important behavioral measure. Switching in Medicaid managed care, which is little studied, is contrasted with the extensive literature on middle class switching. Policy implications included the suitability of Medicaid populations for managed care and the need for more research on switching and disenrollment and the Medicaid innovation of neutral health benefits advising.

Feline lentiviruses demonstrate differences in receptor repertoire and envelope structural elements

Feline immunodeficiency virus (FIV) causes fatal disease in domestic cats via T cell depletion-mediated immunodeficiency. Pumas and lions are hosts for apparently apathogenic lentiviruses (PLV, LLV) distinct from FIV. We compared receptor use among these viruses by: (1) evaluating target cell susceptibility; (2) measuring viral replication following exposure to specific and non-specific receptor antagonists; and (3) comparing Env sequence and structural motifs. Most isolates of LLV and PLV productively infected domestic feline T cells, but differed from domestic cat FIV by infecting cells independent of CXCR4, demonstrating equivalent or enhanced replication following heparin exposure, and demonstrating substantial divergence in amino acid sequence and secondary structure in Env receptor binding domains. PLV infection was, however, inhibited by CD134/OX40 antibody. Thus, although PLV and LLV infection interfere with FIV superinfection, we conclude that LLV and PLV utilize novel, more promiscuous mechanisms for cell entry than FIV, underlying divergent tropism and biological properties of these viruses.

Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species

Feline immunodeficiency virus (FIV) infects numerous wild and domestic feline species and is closely related to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). Species-specific strains of FIV have been described for domestic cat (Felis catus), puma (Puma concolor), lion (Panthera leo), leopard (Panthera pardus), and Pallas' cat (Otocolobus manul). Here, we employ a three-antigen Western blot screening (domestic cat, puma, and lion FIV antigens) and PCR analysis to survey worldwide prevalence, distribution, and genomic differentiation of FIV based on 3,055 specimens from 35 Felidae and 3 Hyaenidae species. Although FIV infects a wide variety of host species, it is confirmed to be endemic in free-ranging populations of nine Felidae and one Hyaenidae species. These include the large African carnivores (lion, leopard, cheetah, and spotted hyena), where FIV is widely distributed in multiple populations; most of the South American felids (puma, jaguar, ocelot, margay, Geoffroy's cat, and tigrina), which maintain a lower FIV-positive level throughout their range; and two Asian species, the Pallas' cat, which has a species-specific strain of FIV, and the leopard cat, which has a domestic cat FIV strain in one population. Phylogenetic analysis of FIV proviral sequence demonstrates that most species for which FIV is endemic harbor monophyletic, genetically distinct species-specific FIV strains, suggesting that FIV transfer between cat species has occurred in the past but is quite infrequent today.

Examining Differences in Death Rates for Medicaid and Non-Medicaid Nursing Home Residents

OBJECTIVES

The purpose of this work was to examine differences in the probability of death for Medicaid and privately funded nursing home residents, controlling for differences in facility, market, and resident characteristics.

METHODS

Given that Medicaid residents are more likely to die in nursing facilities, the probability of dying within 1 or 2 years is estimated using a series of probit models, controlling for whether a resident is Medicaid-funded or privately-funded. As resident characteristics, market attributes, facility characteristics, and facility fixed effects are sequentially added to the specifications, the gap in the probability of death between Medicaid and private-pay residents is considered.

RESULTS

The overall mortality rate for Medicaid residents was 14.8% points higher than the death rate for privately funded residents. When considering death within 1 year and 2 years, Medicaid resident death rates were 4.2% and 7.8% higher, respectively. The apparent difference in mortality declines as one controls for resident, market, and facility characteristics. Both facility characteristics and facility fixed effects are relatively important in explaining differences in death rates between Medicaid and private-pay residents.

CONCLUSIONS

Differences in death rates between Medicaid and private-pay residents are relatively small, suggesting that residents with different payment sources are not treated differently in nursing homes in ways that impact the probability of death. However, policymakers may want to look more closely at whether Medicaid residents are segregated into lower-quality facilities.

Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions

Feline immunodeficiency virus (FIV) is a lentivirus that causes AIDS-like immunodeficiency disease in domestic cats. Free-ranging lions, Panthera leo, carry a chronic species-specific strain of FIV, FIV-Ple, which so far has not been convincingly connected with immune pathology or mortality. FIV-Ple, harboring the three distinct strains A, B, and C defined by pol gene sequence divergences, is endemic in the large outbred population of lions in the Serengeti ecosystem in Tanzania. Here we describe the pattern of variation in the three FIV genes gag, pol-RT, and pol-RNase among lions within 13 prides to assess the occurrence of FIV infection and coinfection. Genome diversity within and among FIV-Ple strains is shown to be large, with strain divergence for each gene approaching genetic distances observed for FIV between different species of cats. Multiple in fections with two or three strains were found in 43% of the FIV-positive individuals based on pol-RT sequence analysis, which may suggest that antiviral immunity or interference evoked by one strain is not consistently protective against infection by a second. This comprehensive study of FIV-Ple in a free-ranging population of lions reveals a dynamic transmission of virus in a social species that has historically adapted to render the virus benign.

The impact of litigation on nursing home quality

Government reports indicate that regulations have been ineffective in improving quality of care in many nursing homes. Some analysts feel that litigation against nursing homes may be the result of quality problems that are monitored during the inspection process, some contend litigation merely causes quality problems by diverting financial resources away from patient care, and some argue that litigation is duplicating the efforts of the inspection process. Given that the relationship between litigation and inspection-oriented measures of quality is not clear, this article explores the relationship empirically. When a significant relationship is found, the empirical results suggest that litigation is associated with a decline in inspection-oriented measured quality in the nursing home facing the legal claim. In contrast, litigation against a chain has a very different relationship to firm-level quality, where firms within a chain that is being sued have higher levels of inspection-oriented quality. Our results suggest that legal claims may result from quality problems that go unmeasured during the inspection process. However, more research in this area is warranted.