Prevalence of Potential Drug Interactions With Direct-Acting Antivirals for COVID-19 Among Hospitalized Patients.

PURPOSE: Clinicians consider polypharmacy, comorbidities, and other factors including the potential for drug-drug interactions (DDIs) when evaluating therapeutic options for specific clinical diagnoses. Contemporary treatment for coronavirus disease 2019 (COVID-19) includes direct-acting antivirals (DAAs). We sought to characterize patients' characteristics, comorbidities, and medications received during their hospitalization for COVID-19 and quantify potential DDIs that clinicians consider in selecting appropriate DAAs. METHODS: Patients hospitalized with a primary diagnosis of COVID-19 between May 2020 and December 2022 from the PINC AI Healthcare Database were identified. Medications administered during the hospitalization with the potential to cause DDIs with nirmatrelvir/ritonavir, remdesivir, or molnupiravir (per the Emergency Use Authorization factsheet or package insert) were assessed. For DDIs with nirmatrelvir/ritonavir, medications are categorized as "Contraindicated," "Avoid Concomitant Use," or "Other DDIs" (includes recommendation for dose modification or clinical and laboratory monitoring). For remdesivir, coadministration with chloroquine phosphate and hydroxychloroquine sulfate was not recommended. For molnupiravir, no drugs are listed as having potential DDIs. In a subset of patients, a multivariable logistic regression model was used to examine the association between documented patient/hospital characteristics and the likelihood of being "Contraindicated" to receive nirmatrelvir/ritonavir. FINDINGS: Of the 788,238 patients hospitalized for COVID-19 in 920 hospitals, 53% were ≥ 65 years old, and 31% had Charlson Comorbidity Index (CCI) ≥ 3. During the study period, about half of the patients received medications categorized as "Contraindicated" (11%) and/or "Avoid Concomitant Use" (41%) with nirmatrelvir/ritonavir. The frequency of administered drugs was higher in those aged ≥ 65 years (68%), CCI ≥ 3 (78%), with high-risk underlying conditions (55%). About 1% of patients received medications that were not recommended to be coadmistered with remdesivir. Among a subset of patients hospitalized for COVID-19 in 2022, those who were older, had higher CCI, high-risk underlying conditions, severe hepatic impairment, Medicare insurance, and hospitalized in larger hospitals were significantly more likely to be categorized as "Contraindicated" when considering nirmatrelvir/ritonavir as a therapeutic option to manage COVID-19. IMPLICATIONS: A significant proportion of patients hospitalized for COVID-19 receive medications for other conditions that have the potential to result in DDIs with DAAs; most predominantly with nirmatrelvir/ritonavir, a strong CYP3A enzyme inhibitor, fewer with remdesivir, and none with molnupiravir. Higher age and comorbidity burden were significantly associated with a higher likelihood of receiving medications that are "Contraindicated" with nirmatrelvir/ritonavir. In the evolving COVID-19 era, these findings provide insights into patients hospitalized for COVID-19, and the polypharmacy evaluations that clinicians may encounter when selecting among DAAs to manage COVID-19.

Epidemiology, clinical characteristics, and outcomes of nontuberculous mycobacterial skin, soft tissue, and bone infections from a single center over a 10-year period.

Introduction: Non-tuberculous mycobacteria (NTM) cause a wide variety of clinical syndromes. Data guiding diagnosis and treatment of NTM skin and soft tissue infections (SSTI) and bone infections are limited. We sought to better understand SSTI and bone infections caused by NTM. Methods: All NTM clinical isolates recovered at Brooke Army Medical Center from 2012 to 2022 were screened; SSTI and bone isolates were included. Electronic health records were reviewed for epidemiologic, microbiologic, and clinical data. Infections were defined as recovery of one or more NTM isolate from skin, soft tissue, or bone cultures with a corresponding clinical syndrome. Results: Forty isolates of skin, soft tissue, or bone origin from 29 patients were analyzed. Twenty (69 %) patients, majority female (14/20, 70 %), had infecting isolates, most commonly secondary to surgery (35 %) or trauma (35 %). Six of 20 (30 %) had bone infections. Time from symptom onset to isolate recovery was a median 61 days (IQR 43-95). Eight (40 %) had combined medical/surgical therapy, 8 (40 %) had surgery alone, and 4 (20 %) had medical therapy alone. M. abscessus was more frequently isolated from patients with true infections. Conclusions: Data supporting diagnosis and treatment decisions in NTM SSTI/bone infections is sparse. In this study the majority of NTM isolated were true infections. We confirm that surgery and trauma are the most common routes of exposure. The delay between symptom onset and directed therapy and the wide variety of treatment regimens highlight a need for additional studies delineating criteria for diagnosis and treatment.

Provider uptake of extragenital screening for gonorrhea and chlamydia in a cohort of Air Force members with incident HIV diagnosis.

The prevalence of Neisseria gonorrhea (GC) and Chlamydia trachomatis (CT) is higher at extragenital anatomic sites among men who have sex with men (MSM) with HIV infection. Although national guidelines recommend that all MSM with HIV infection undergo screening for extragenital sexually transmitted infections (EG-STIs), uptake is low in many primary care settings. We evaluated EG-STI screening by primary care providers (PCPs) for US Air Force (USAF) members with incident HIV infection. All USAF members with incident HIV infection who received initial HIV specialty care with Infectious Disease (ID) providers at Brooke Army Medical Center from 2016 to 2018 (n = 98) were included. A retrospective chart review was conducted to evaluate STI screening performed by PCPs within 1 week of HIV diagnosis compared to screening at entry into ID care. Demographic, clinical, laboratory and behavioral risk data were collected. STI screening included GC/CT EG-STIs, urethral GC/CT, syphilis, and hepatitis B and C. Patients were predominantly male (98%) with a median age of 26 (IQR 23, 32) years at HIV diagnosis. A previous history of STIs was reported in 53 (54%) patients and the majority of males self-identified as MSM (66%) or bisexual (23%). The median time from HIV diagnosis to ID evaluation was 26 days (IQR 9, 33). PCPs performed any STI screening in 61 (62%) patients. EG-STI screening was conducted in 3 (3%) patients overall and in (3%) MSM/bisexuals. A total of 31 (32%) patients had missed STIs; the majority due to EG-STIs of the rectum (59%) and pharynx (19%). All EG-STIs would have been missed by urethral GC/CT screening alone. EG-STI screening uptake was low among PCPs evaluating USAF members with incident HIV infection. Underutilization of EG-STI screening can result in missed infections and forward transmission of GC/CT. Barriers to low uptake need to be explored.

Patients with HIV-associated cancers have evidence of increased T cell dysfunction and exhaustion prior to cancer diagnosis.

BACKGROUND: People living with HIV (PLWH) have increased risk of developing cancers after controlling traditional risk factors and viral suppression. This study explores whether T cells can serve as a marker of risk for cancer among HIV-infected virally suppressed patients. METHODS: A nested case control study design was pursued with 17 cancer cases and 73 controls (PLWH without cancer)ouidentified among the US Military HIV Natural History Study cohort, and were matched for CD4 + count, duration of HIV infection, and viral suppression. Cells were obtained from PLWH on an average of 12 months prior to clinical cancer diagnosis. Expression of inhibitory receptors (PD-1, CD160, CD244, Lag-3, and TIGIT), and transcription factors (T-bet, Eomesodermin, TCF-1, and (TOX) was measured on CD8 +T cells from that early time point. RESULTS: We found that cases have increased expression of PD-1 +CD160+CD244+ ('triple positive') on total and effector CD8 + compared with controls (p=0.02). Furthermore, CD8 +T cells that were both PD-1 +CD160+CD244+ and T-betdimEomeshi were significantly elevated in cases at time point before cancer detection, compared with controls without cancer (p=0.008). This was driven by the finding that transcriptional factor profile of cells was altered in cancers compared with controls. Triple-positive cells were noted to retain the ability for cytotoxicity and cytokine secretion mediated by expression of CD160 and PD-1, respectively. However, triple-positive cells demonstrated high expression of TOX-1, a transcription factor associated with T cell exhaustion. CONCLUSION: In conclusion, we have found a subset of dysfunctional CD8 +T cells, PD-1 +CD160+CD244+T-betdimEomeshi, that is elevated 12 months before cancer diagnosis, suggesting that peripheral T cell alterations may serve as a biomarker of increased cancer risk among PLWH.

Immunologic resilience and COVID-19 survival advantage.

BACKGROUND: The risk of severe coronavirus disease 2019 (COVID-19) varies significantly among persons of similar age and is higher in males. Age-independent, sex-biased differences in susceptibility to severe COVID-19 may be ascribable to deficits in a sexually dimorphic protective attribute that we termed immunologic resilience (IR). OBJECTIVE: We sought to examine whether deficits in IR that antedate or are induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection independently predict COVID-19 mortality. METHODS: IR levels were quantified with 2 novel metrics: immune health grades (IHG-I [best] to IHG-IV) to gauge CD8+ and CD4+ T-cell count equilibrium, and blood gene expression signatures. IR metrics were examined in a prospective COVID-19 cohort (n = 522); primary outcome was 30-day mortality. Associations of IR metrics with outcomes in non-COVID-19 cohorts (n = 13,461) provided the framework for linking pre-COVID-19 IR status to IR during COVID-19, as well as to COVID-19 outcomes. RESULTS: IHG-I, tracking high-grade equilibrium between CD8+ and CD4+ T-cell counts, was the most common grade (73%) among healthy adults, particularly in females. SARS-CoV-2 infection was associated with underrepresentation of IHG-I (21%) versus overrepresentation (77%) of IHG-II or IHG-IV, especially in males versus females (P < .01). Presentation with IHG-I was associated with 88% lower mortality, after controlling for age and sex; reduced risk of hospitalization and respiratory failure; lower plasma IL-6 levels; rapid clearance of nasopharyngeal SARS-CoV-2 burden; and gene expression signatures correlating with survival that signify immunocompetence and controlled inflammation. In non-COVID-19 cohorts, IR-preserving metrics were associated with resistance to progressive influenza or HIV infection, as well as lower 9-year mortality in the Framingham Heart Study, especially in females. CONCLUSIONS: Preservation of immunocompetence with controlled inflammation during antigenic challenges is a hallmark of IR and associates with longevity and AIDS resistance. Independent of age, a male-biased proclivity to degrade IR before and/or during SARS-CoV-2 infection predisposes to severe COVID-19.

Mediastinal Actinomycosis After Esophagogastroduodenoscopy.

Actinomycosis is an uncommon bacterial infection that presents as an indolent, progressive disease that can affect multiple organ systems. We describe the case of a 66-year-old female with end-stage renal disease who presented to the emergency department after developing acute dyspnea and chest pain two weeks after undergoing a diagnostic esophagogastroduodenoscopy (EGD). A CT scan was obtained that revealed a large mediastinal mass, which was initially concerning for a potential malignancy. Biopsy of the mass and Gram stain was consistent with mediastinal actinomycosis. The patient was subsequently treated with an extended course of antibiotics that resulted in significant clinical improvement. Previously reported cases describing a correlation between EGD and mediastinal actinomycosis have been associated with invasive procedures such as esophageal stent placement and transesophageal biopsy. We describe a case of an uncommon infectious complication of a diagnostic EGD that was not associated with intentional mucosal disruption.

Hepatitis B seroprevalence in the U.S. military and its impact on potential screening strategies.

INTRODUCTION: Knowledge of the contemporary epidemiology of hepatitis B virus (HBV) infection among military personnel can inform potential Department of Defense (DoD) screening policy and infection and disease control strategies. MATERIALS AND METHODS: HBV infection status at accession and following deployment was determined by evaluating reposed serum from 10,000 service members recently deployed to combat operations in Iraq and Afghanistan in the period from 2007 to 2010. A cost model was developed from the perspective of the Department of Defense for a program to integrate HBV infection screening of applicants for military service into the existing screening program of screening new accessions for vaccine-preventable infections. RESULTS: The prevalence of chronic HBV infection at accession was 2.3/1,000 (95% CI: 1.4, 3.2); most cases (16/21, 76%) identified after deployment were present at accession. There were 110 military service-related HBV infections identified. Screening accessions who are identified as HBV susceptible with HBV surface antigen followed by HBV surface antigen neutralization for confirmation offered no cost advantage over not screening and resulted in a net annual increase in cost of $5.78 million. However, screening would exclude as many as 514 HBV cases each year from accession. CONCLUSIONS: Screening for HBV infection at service entry would potentially reduce chronic HBV infection in the force, decrease the threat of transfusion-transmitted HBV infection in the battlefield blood supply, and lead to earlier diagnosis and linkage to care; however, applicant screening is not cost saving. Service-related incident infections indicate a durable threat, the need for improved laboratory-based surveillance tools, and mandate review of immunization policy and practice.

HIV Care Continuum and Meeting 90-90-90 Targets: Cascade of Care Analyses of a U.S. Military Cohort.

INTRODUCTION: The new initiative by the Department of Health and Human Services (DHHS) aims to decrease new HIV infections in the U.S. by 75% within 5 years and 90% within 10 years. Our objective was to evaluate whether the U.S. military provides a good example of the benefits of such policies. MATERIALS AND METHODS: We conducted an analysis of a cohort of 1,405 active duty military personnel with HIV enrolled in the Natural History Study who were diagnosed between 2003 and 2015 at six U.S. military medical centers. The study was approved by institutional review boards at the Uniformed Services University of the Health Sciences and each of the sites. We evaluated the impact of Department of Defense (DoD) HIV care policies, including screening, linkage to care, treatment eligibility, and combined antiretroviral therapy (cART) initiation on achieving viral suppression (VS) within 3 years of diagnosis. As a secondary outcome, we evaluated the DoD's achievement of UNAIDS 90-90-90 targets. RESULTS: Nearly all (99%) were linked to care within 60 days. Among patients diagnosed in 2003-2009, 77.5% (95% confidence intervals (CI) 73.9-80.6%) became eligible for cART within 3 years of diagnosis, 70.6% (95% CI 66.6-74.1%) overall initiated cART, and 64.2% (95% CI 60.1-68.0%) overall achieved VS. Among patients diagnosed in 2010-2015, 98.7% (95% CI 96.7-99.5%) became eligible for cART within 3 years of diagnosis, 98.5% (95% CI 96.4-99.4%) overall initiated cART, and 89.8% (95% CI 86.0-92.5%) overall achieved VS. CONCLUSIONS: U.S. military HIV policies have been highly successful in achieving VS goals, exceeding the UNAIDS 90-90-90 targets. In spite of limitations, including generalizability, this example demonstrates the feasibility of the DHHS initiative to decrease new infections through testing, early treatment, and retention in care.

The US Military HIV Natural History Study: Informing Military HIV Care and Policy for Over 30 Years.

INTRODUCTION: In October 1985, 4 years after the initial descriptions of the acquired immunodeficiency syndrome (AIDS), the U.S. Department of Defense (DoD) began routine screening for human immunodeficiency virus (HIV) infection to prevent infected recruits from exposure to live virus vaccines, implemented routine active-duty force screening to ensure timely care and help protect the walking blood bank, and initiated the U.S. Military HIV Natural History Study (NHS) to develop epidemiologic, clinical, and basic science evidence to inform military HIV policy and establish a repository of data and specimens for future research. Here, we have reviewed accomplishments of the NHS over the past 30 years and sought to describe relevant trends among NHS subjects over this time, with emphasis on combination antiretroviral therapy (cART) use and non-AIDS comorbidities. METHODS: Subjects who were prospectively enrolled in the NHS from 1986 through 2015 were included in this analysis. Time periods were classified by decade of study conduct, 1986-1995, 1996-2005, and 2006-2015, which also correlate approximately with pre-, early-, and late-combination ART (cART) eras. Analyses included descriptive statistics and comparisons among decades. We also evaluated mean community log10 HIV viral load (CVL) and CD4 counts for each year. RESULTS: A total of 5,758 subjects were enrolled between 1986 and 2015, of whom 92% were male with a median age of 28 years, and 45% were African-American, 42% Caucasian, and 13% Hispanic/other. The proportion of African-Americans remained stable over the decades (45%, 47%, and 42%, respectively), while the proportion of Hispanic/other increased (10%, 13%, and 24%, respectively). The CD4 count at HIV diagnosis has remained high (median 496 cells/uL), while the occurrence of AIDS-defining conditions (excluding low CD4 count) has decreased by decade (36.7%, 5.4%, and 2.9%, respectively). Following the introduction of effective cART in 1996, CVL declined through 2000 as use increased and then plateaued until guidelines changed. After 2004, cART use again increased and CVL declined further until 2012-15 when the vast majority of subjects achieved viral suppression. Non-AIDS comorbidities have remained common, with approximately half of subjects experiencing one or more new diagnoses overall and nearly half of subjects diagnosed between 2006 and 2015, in spite of their relatively young age, shorter median follow-up, and wide use of cART. CONCLUSIONS: The US Military HIV NHS has been critical to understanding the impact of HIV infection among active-duty service members and military beneficiaries, as well as producing insights that are broadly relevant. In addition, the rich repository of NHS data and specimens serves as a resource to investigators in the DoD, NIH, and academic community, markedly increasing scientific yield and identifying novel associations. Looking forward, the NHS remains relevant to understanding host factor correlates of virologic and immunologic control, biologic pathways of HIV pathogenesis, causes and consequences of residual inflammation in spite of effective cART, identifying predictors of and potential approaches to mitigation of excess non-AIDS comorbidities, and helping to understand the latent reservoir.

Refractive surgery in the HIV-positive U.S. Military Natural History Study Cohort: complications and risk factors.

PURPOSE: This study sought to assess the frequency of refractive surgery complications in HIV+ individuals and related risk factors. SETTINGS: Multiple centers in the United States. DESIGN: Prospective observational cohort study. METHODS: The U.S. Military HIV Natural History Study is a prospective observational cohort study of HIV+ service members and beneficiaries. Participants were selected who had Current Procedural Terminology codes for laser in situ keratomileusis (LASIK), photorefractive keratectomy (PRK), and other refractive surgeries. The frequency of complications was determined using International Classification of Diseases-9 codes. Covariates included age, sex, antiretroviral therapy, time since HIV diagnosis, history of AIDS, and CD4 (T lymphocytes) count and viral load. Statistical analysis was completed using univariate (χ2 and Wilcoxon-Mann-Whitney tests) and multivariate analyses. RESULTS: Seventy-nine of 2073 participants had refractive surgery. Fifty-three patients underwent PRK, 23 LASIK, 2 radial keratotomy (RK), and 1 astigmatic correction. Complications occurred in 6 (7.6%) of 79 participants, including 5 patients who underwent PRK and 1 after RK, occurring between 8 and 217 days after surgery. Five ulcers and 1 unspecified keratitis were noted. In the univariate analysis, type of surgery (P = .02) and history of AIDS (P = .02) were risk factors for complications. In logistic regression analysis, no variables were found to be risk factors for complications. CONCLUSION: Complications were infrequent among HIV+ participants after refractive surgery. Point estimates suggest that PRK might have more complications than LASIK and that advanced HIV, reflected by previous AIDS, might be associated with an increased risk for complications. Further study will be required to confirm these findings.

Preemptive Tecovirimat Use in an Active Duty Service Member Who Presented With Acute Myeloid Leukemia After Smallpox Vaccination.

Smallpox vaccine is contraindicated in immunosuppression due to increased risk for adverse reactions (eg, progressive vaccinia). We describe the first-ever use of tecovirimat as a preemptive vaccinia virus treatment strategy during induction chemotherapy in an active duty service member who presented with acute leukemia and inadvertent autoinoculation after smallpox vaccination.

Herpes Zoster Rates Continue to Decline in People Living With Human Immunodeficiency Virus but Remain Higher Than Rates Reported in the General US Population.

In the antiretroviral therapy era, herpes zoster incidence continued to decline in people living with HIV (PLWH). However, at 0.9 cases/100 person-years, rates in PLWH are substantially higher than the general US population; emphasizing the needs for studies of the subunit vaccine in PLWH.

Inflammation-Related Morbidity and Mortality Among HIV-Positive Adults: How Extensive Is It?

OBJECTIVE: To determine the rate of grade 4, potentially life-threatening events not attributable to AIDS, cardiovascular disease (CVD), or non-AIDS cancer among participants on antiretroviral therapy and to describe associations of these events with interleukin-6 (IL-6) and D-dimer. DESIGN: Cohort study. METHODS: HIV-infected participants on antiretroviral therapy (N = 3568) with an HIV-RNA level ≤ 500 copies/mL were followed for grade 4, AIDS, CVD, non-AIDS cancer, and all-cause mortality events. Grade 4 events were further classified masked to biomarker levels as reflecting chronic inflammation-related disease (ChrIRD) or not (non-ChrIRD). Associations of baseline IL-6 and D-dimer with events were studied using Cox models. RESULTS: Over a median follow-up of 4.3 years, 339 participants developed a grade 4 event (22.9 per 1000 person-years); 165 participants developed a ChrIRD grade 4 event (10.7 per 1000 person-years). Grade 4 events were more common than AIDS (54 participants), CVD (132), and non-AIDS cancer (80) events, any of which developed in 252 participants (17.1 per 1000 person-years). Grade 4 and AIDS events were associated with similar risks of death. Higher IL-6 [hazard ratio (HR) = 1.19 per doubling of biomarker; P = 0.003] and D-dimer (HR = 1.23; P < 0.001) levels were associated with an increased risk of grade 4 events. IL-6 associations were stronger for ChrIRD (HR = 1.38; P < 0.001) than non-ChrIRD grade 4 events (HR = 1.11; P = 0.21). CONCLUSIONS: Morbidity and mortality associated with activation of inflammatory and coagulation pathways include conditions other than AIDS, CVD, and non-AIDS cancer events. Effective inflammation-dampening interventions could greatly affect the health of people with HIV.

Health-related quality of life among military HIV patients on antiretroviral therapy.

OBJECTIVE: The aims of this study were: (i) to determine the factors associated with HRQOL at baseline in our cohort, and (ii) to evaluate if there are differences in baseline HRQOL measures by antiretroviral treatment. METHODS: The Short Form 36 (SF-36) was administered between 2006 and 2010 among members of the United States HIV Natural History Study cohort (NHS), and participants who completed the SF-36 were included in the study. Physical component summary (PCS) and mental component summary (MCS) scores were computed based on standard algorithms. Multivariate linear regression models were constructed for PCS and MCS to estimate the association between selected variables and HRQOL scores. RESULTS: Antiretroviral therapy (ART) was not independently associated with HRQOL scores. Factors associated with PCS were CD4+ count < 200 cells/mm3 (ß = -5.84, 95% CI: -7.63, -4.06), mental comorbidity (ß = -2.82, 95% CI: -3.79, -1.85), medical comorbidity (ß = -2.51, 95% CI: -3.75, -1.27), AIDS diagnosis (ß = -2.38, 95% CI: -3.79, -0.98). Others were gender, military rank, marital status, and age. Factors independently associated with MCS were CD4+ count < 200 cells/mm3 (ß = -1.93, 95% CI: -3.85, -0.02), mental comorbidity (ß = -6.25, 95% CI: -7.25, -5.25), age (ß = 0.37, 95% CI: 0.14, 0.60), and being African American (ß = 1.55, 95% CI: 0.63, 2.47). CONCLUSION: Among military active duty and beneficiaries with HIV, modifiable factors associated with HRQOL measures included advanced HIV disease, and mental or medical comorbidity. Addressing these factors may improve quality of life of HIV-infected individuals in the NHS cohort.

Cancers in elite controllers: appropriate follow-up is essential.

Elite controllers may have non-AIDS-defining comorbidities. We describe here 18 cases of cancers diagnosed in two cohorts of controllers, elite and viremic. Cancers are similar to those commonly described in antiretroviral therapy treated patients but also in HIV-negative patients, which underlines the necessity of an appropriate regular follow-up.

D-Dimer Levels before HIV Seroconversion Remain Elevated Even after Viral Suppression and Are Associated with an Increased Risk of Non-AIDS Events.

The mechanism underlying the excess risk of non-AIDS diseases among HIV infected people is unclear. HIV associated inflammation/hypercoagulability likely plays a role. While antiretroviral therapy (ART) may return this process to pre-HIV levels, this has not been directly demonstrated. We analyzed data/specimens on 249 HIV+ participants from the US Military HIV Natural History Study, a prospective, multicenter observational cohort of >5600 active duty military personnel and beneficiaries living with HIV. We used stored blood specimens to measure D-dimer and Interleukin-6 (IL-6) at three time points: pre-HIV seroconversion, ≥6 months post-HIV seroconversion but prior to ART initiation, and ≥6 months post-ART with documented HIV viral suppression on two successive evaluations. We evaluated the changes in biomarker levels between time points, and the association between these biomarker changes and future non-AIDS events. During a median follow-up of 3.7 years, there were 28 incident non-AIDS diseases. At ART initiation, the median CD4 count was 361cells/mm3; median duration of documented HIV infection 392 days; median time on ART was 354 days. Adjusted mean percent increase in D-dimer levels from pre-seroconversion to post-ART was 75.1% (95% confidence interval 24.6-148.0, p = 0.002). This increase in D-dimer was associated with a significant 22% increase risk of future non-AIDS events (p = 0.03). Changes in IL-6 levels across time points were small and not associated with future non-AIDS events. In conclusion, ART initiation and HIV viral suppression does not eliminate HIV associated elevation in D-dimer levels. This residual pathology is associated with an increased risk of future non-AIDS diseases.

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.

Next-Generation Sequencing (NGS) has transformed our understanding of the dynamics and diversity of virus populations for human pathogens and model systems alike. Due to the sensitivity and depth of coverage in NGS, it is possible to measure the frequency of mutations that may be present even at vanishingly low frequencies within the viral population. Here, we describe a simple bioinformatic pipeline called CoVaMa (Co-Variation Mapper) scripted in Python that detects correlated patterns of mutations in a viral sample. Our algorithm takes NGS alignment data and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides in the viral genome or amino acids in the chosen open reading frame. These tables are then analysed using classical linkage disequilibrium to detect and report evidence of epistasis. We test our analysis with simulated data and then apply the approach to find epistatically linked loci in Flock House Virus genomic RNA grown under controlled cell culture conditions. We also reanalyze NGS data from a large cohort of HIV infected patients and find correlated amino acid substitution events in the protease gene that have arisen in response to anti-viral therapy. This both confirms previous findings and suggests new pairs of interactions within HIV protease. The script is publically available at http://sourceforge.net/projects/covama.

Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease.

While the role of drug resistance mutations in HIV protease has been studied comprehensively, mutations in its substrate, Gag, have not been extensively cataloged. Using deep sequencing, we analyzed a unique collection of longitudinal viral samples from 93 patients who have been treated with therapies containing protease inhibitors (PIs). Due to the high sequence coverage within each sample, the frequencies of mutations at individual positions were calculated with high precision. We used this information to characterize the variability in the Gag polyprotein and its effects on PI-therapy outcomes. To examine covariation of mutations between two different sites using deep sequencing data, we developed an approach to estimate the tight bounds on the two-site bivariate probabilities in each viral sample, and the mutual information between pairs of positions based on all the bounds. Utilizing the new methodology we found that mutations in the matrix and p6 proteins contribute to continued therapy failure and have a major role in the network of strongly correlated mutations in the Gag polyprotein, as well as between Gag and protease. Although covariation is not direct evidence of structural propensities, we found the strongest correlations between residues on capsid and matrix of the same Gag protein were often due to structural proximity. This suggests that some of the strongest inter-protein Gag correlations are the result of structural proximity. Moreover, the strong covariation between residues in matrix and capsid at the N-terminus with p1 and p6 at the C-terminus is consistent with residue-residue contacts between these proteins at some point in the viral life cycle.

Short Communication: HIV RNA Levels Predict AIDS-Defining and Non-AIDS-Defining Cancers After Antiretroviral Therapy Initiation Among HIV-Infected Adults.

Whether poor virologic control is associated with incident cancers after initiation of combination antiretroviral therapy (ART) remains unclear. In a large cohort, time-updated HIV RNA levels ≥1,000 copies/ml predicted AIDS-defining cancers (ADCs), non-AIDS-defining cancers (NADCs), and skin cancers. Virologic control may be an important strategy in reducing cancer events among HIV-infected persons.