The immunopathogenesis of human immunodeficiency virus infection

Risk of breakthrough infection and hospitalisation after COVID-19 primary vaccination by HIV status in four Italian regions during 2021

BACKGROUND

As of 2024, vaccination remains the main mitigation measure against COVID-19, but there are contradictory results on whether people living with HIV (PLWH) are less protected by vaccines than people living without HIV (PLWoH). In this study we compared the risk of SARS-CoV-2 infection and COVID-19 hospitalisation following full vaccination in PLWH and PLWoH.

METHODS

We linked data from the vaccination registry, the COVID-19 surveillance system and from healthcare/pharmacological registries in four Italian regions. We identified PLWH fully vaccinated (14 days post completion of the primary cycle) and matched them at a ratio of 1:4 with PLWoH by week of vaccine administration, age, sex, region of residence and comorbidities. Follow-up started on January 24, 2021, and lasted for a maximum of 234 days. We used the Kaplan-Meier estimator to calculate the cumulative incidence of infection and COVID-19 hospitalisation in both groups, and we compared risks using risk differences and ratios taking PLWoH as the reference group.

RESULTS

We matched 42,771 PLWH with 171,084 PLWoH. The overall risk of breakthrough infection was similar in both groups with a rate ratio (RR) of 1.10 (95% confidence interval (CI):0.80-1.53). The absolute difference between groups at the end of the study period was 8.28 events per 10,000 person-days in the PLWH group (95%CI:-18.43-40.29). There was a non-significant increase the risk of COVID-19 hospitalisation among PLWH (RR:1.90; 95%CI:0.93-3.32) which corresponds to 6.73 hospitalisations per 10,000 individuals (95%CI: -0.57 to 14.87 per 10,000).

CONCLUSIONS

Our findings suggest PLWH were not at increased risk of breakthrough SARS-CoV-2 infection or COVID-19 hospitalisation following a primary cycle of mRNA vaccination.

Glutathione Modulates Efficacious Changes in the Immune Response against Tuberculosis

Glutathione (GSH) is an antioxidant in human cells that is utilized to prevent damage occurred by reactive oxygen species, free radicals, peroxides, lipid peroxides, and heavy metals. Due to its immunological role in tuberculosis (TB), GSH is hypothesized to play an important part in the immune response against M. tb infection. In fact, one of the hallmark structures of TB is granuloma formation, which involves many types of immune cells. T cells, specifically, are a major component and are involved in the release of cytokines and activation of macrophages. GSH also serves an important function in macrophages, natural killer cells, and T cells in modulating their activation, their metabolism, proper cytokine release, proper redox activity, and free radical levels. For patients with increased susceptibility, such as those with HIV and type 2 diabetes, the demand for higher GSH levels is increased. GSH acts as an important immunomodulatory antioxidant by stabilizing redox activity, shifting of cytokine profile toward Th1 type response, and enhancing T lymphocytes. This review compiles reports showing the benefits of GSH in improving the immune responses against M. tb infection and the use of GSH as an adjunctive therapy for TB.

The Problem of Host and Pathogen Genetic Variability for Developing Strategies of Universally Efficacious Vaccination against and Personalised Immunotherapy of Tuberculosis: Potential Solutions?

Rational vaccination against and immunotherapy of any infectious disease requires knowledge of how protective and non-protective immune responses differ, and how immune responses are regulated, so their nature can be controlled. Strong Th1 responses are likely protective against M tuberculosis. Understanding how immune class regulation is achieved is pertinent to both vaccination and treatment. I argue that variables of infection, other than PAMPs, primarily determine the class of immunity generated. The alternative, non-PAMP framework I favour, allows me to propose strategies to achieve efficacious vaccination, transcending host and pathogen genetic variability, to prevent tuberculosis, and personalised protocols to treat disease.

Is the definition of late diagnosis correct?

BACKGROUND

The study analysed 1711 patients of the Hospital for Infectious Diseases in Warsaw diagnosed with HIV infection in 2008-2010 and 2016-2018. Research was conducted examining the changes in CD4 cell counts before starting antiretroviral (ARV) treatment in order to find people who were misclassified as late-diagnosed.

METHODS

Patients with late diagnosis were distinguished on the basis of the consensus definition. The Mann-Whitney U-test was used to analyse the change in CD4 cell counts before starting ARV treatment.

RESULTS

In the years 2008-2010, the CD4 count was remeasured before starting ARV treatment in 90 late-diagnosed patients. The median change in the CD4 count was 22 cells/μL. In 49 of these, the number of CD4 cells spontaneously increased before the start of treatment. We can suspect that these patients were misclassified as late-diagnosed.

CONCLUSIONS

The consensus definition of late diagnosis often leads to overestimation of the number of late-diagnosed patients. The crucial problem is a transient decline in the CD4 lymphocyte count in the acute phase of HIV infection. A potential solution is to introduce serum HIV viral load measurement into the definition.

Host Molecule Incorporation into HIV Virions, Potential Influences in HIV Pathogenesis

During the last phase of HIV viral production, nascent HIV virions acquire a fraction of the cellular lipid membrane to create the external lipid envelope, a process by which cellular proteins present on the surface of the infected cell can be incorporated along with Env trimers. Interestingly, several studies indicated that these incorporated host molecules could conserve their biological activity and consequently contribute to HIV pathogenesis either by enhancing the infectivity of HIV virions, their tissue tropism or by affecting immune cell functions. The following review will describe the main approaches used to characterize membrane bound host molecule incorporation into HIV virions, the proposed mechanisms involved, and the role of a non-exhaustive list of incorporated molecules.

Analyzing some concepts of immune regulation of the last three decades: Fostering greater research resilience despite the information overload. A personal view

There is considerable interest in whether increased investment in science, made by society, pays dividends. Some plausibly argue the increased rate of production of information results in an ossification of the canon. Reports, challenging the canon, fall by the wayside. The field thus becomes increasingly complex, reflecting not so much the reality of nature but how we investigate the subject. I suggest that focusing on and resolving the paradoxes evident within a canon will free the logjam, resulting in more resilient research. Immunology is among the fastest growing of biological sciences and is, I suggest, an appropriate case study. I examine the commonly accepted frameworks employed over the last three decades to address two major, related immunological questions: what determines whether antigen activates or inactivates CD4 T cells, and so whether immune responses are initiated or this potential ablated; secondly, what determines the Th subset to which the activated Th cells belong, thus determining the class of immunity generated. I show there are major paradoxes within these frameworks, neglected for decades. I propose how research focused on resolving paradoxes can be better fostered, and so support the evolution of the canon. This perspective is pertinent in facing critical issues on how immune responses are regulated, and to more general issues of both the philosophy of science and of science policy.The last section is in response to questions and comments of the reviewers. It brings together several considerations to express my view: the same frameworks, formulated in response to the two questions, are useful in understanding the regulation of the immune response against model antigens, against self and foreign antigens, those of tumors and of pathogens.

Temporal and Spatial Distribution of Opportunistic Infections Associated with the Human Immunodeficiency Virus (HIV) in Uganda

The human immunodeficiency virus (HIV) remains one of the greatest challenges of the twenty-first century in the absence of an effective vaccine or cure. It is estimated globally that close to 38 million people are currently living with the HIV virus and more than 36 million have succumbed to this deadly virus from the time the first case was reported in early 1980s. The virus degrades the human body immunity and makes it more vulnerable to different kinds of opportunistic infections (OIs). However, with the introduction of highly active anti-retroviral therapy (HAART) in 2003, the pattern and frequency of OIs has been progressively changing though with variations in the different parts of the World. So this chapter discusses the temporal and spatial patterns of OIs in Uganda.

Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam

Background

More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, we aimed to estimate the number and proportion of Amsterdam HIV infections that originated within the city, from Amsterdam residents. We also aimed to estimate the proportion of recent HIV infections during the 5-year period 2014-2018 in Amsterdam that remained undiagnosed.

Methods

We located diagnosed HIV infections in Amsterdam using postcode data (PC4) at time of registration in the ATHENA observational HIV cohort, and used HIV sequence data to reconstruct phylogeographically distinct, partially observed Amsterdam transmission chains. Individual-level infection times were estimated from biomarker data, and used to date the phylogenetically observed transmission chains as well as to estimate undiagnosed proportions among recent infections. A Bayesian Negative Binomial branching process model was used to estimate the number, size, and growth of the unobserved Amsterdam transmission chains from the partially observed phylogenetic data.

Results

Between 1 January 2014 and 1 May 2019, there were 846 HIV diagnoses in Amsterdam residents, of whom 516 (61%) were estimated to have been infected in 2014-2018. The rate of new Amsterdam diagnoses since 2014 (104 per 100,000) remained higher than the national rates excluding Amsterdam (24 per 100,000), and in this sense Amsterdam remained a HIV hotspot in the Netherlands. An estimated 14% [12-16%] of infections in Amsterdan MSM in 2014-2018 remained undiagnosed by 1 May 2019, and 41% [35-48%] in Amsterdam heterosexuals, with variation by region of birth. An estimated 67% [60-74%] of Amsterdam MSM infections in 2014-2018 had an Amsterdam resident as source, and 56% [41-70%] in Amsterdam heterosexuals, with heterogeneity by region of birth. Of the locally acquired infections, an estimated 43% [37-49%] were in foreign-born MSM, 41% [35-47%] in Dutch-born MSM, 10% [6-18%] in foreign-born heterosexuals, and 5% [2-9%] in Dutch-born heterosexuals. We estimate the majority of Amsterdam MSM infections in 2014-2018 originated in transmission chains that pre-existed by 2014.

Conclusions

This combined phylogenetic, epidemiologic, and modelling analysis in the UNAIDS Fast-Track City Amsterdam indicates that there remains considerable potential to prevent HIV infections among Amsterdam residents through city-level interventions. The burden of locally acquired infection remains concentrated in MSM, and both Dutch-born and foreign-born MSM would likely benefit most from intensified city-level interventions.

Funding

This study received funding as part of the H-TEAM initiative from Aidsfonds (project number P29701). The H-TEAM initiative is being supported by Aidsfonds (grant number: 2013169, P29701, P60803), Stichting Amsterdam Dinner Foundation, Bristol-Myers Squibb International Corp. (study number: AI424-541), Gilead Sciences Europe Ltd (grant number: PA-HIV-PREP-16-0024), Gilead Sciences (protocol numbers: CO-NL-276-4222, CO-US-276-1712, CO-NL-985-6195), and M.A.C AIDS Fund.

Hepatitis B Virus and Tuberculosis Are Associated with Increased Noncommunicable Disease Risk among Treatment-Naïve People with HIV: Opportunities for Prevention, Early Detection and Management of Comorbidities in Sierra Leone

Noncommunicable diseases (NCDs) are a growing public health concern in low- and middle-income countries and disproportionately affect people living with HIV (PWH). Hepatitis B virus (HBV) and tuberculosis (TB) coinfection are presumed risk factors in endemic settings; however, supporting evidence is conflicting. We analyzed baseline data of newly diagnosed PWH prospectively enrolled in the Sierra Leone HIV Cohort Study in Freetown, Sierra Leone, from March to September 2021. Logistic regression was used to identify associations between NCDs, HBV and TB. A total of 275 PWH aged ≥18 years were studied (55% female, median age 33 years, median CD4 307 cells/mm3, 15.3% HIV/HBV, 8.7% HIV/TB). NCDs were bimodally distributed, with 1 in 4 PWH clustered around liver disease (fibrosis/cirrhosis), diabetes/prediabetes and obesity/preobesity, while 1 in 8 had renal impairment or hypertension (HTN). Overall, 41.5% had ≥1 NCD, while 17.5% were multimorbid (≥2 NCDs). After adjusting for age, sex, sociodemographic factors and CD4 count, liver fibrosis/cirrhosis was strongly associated with HBV (aOR 8.80, 95% CI [2.46−31.45]; p < 0.001) and diabetes/prediabetes (aOR 9.89, 95% CI [1.14−85.67]; p < 0.037). TB independently predicted diabetes/prediabetes (aOR 7.34, 95% CI [1.87−28.74]; p < 0.004), while renal impairment was associated with proteinuria (aOR 9.34, 95% CI [2.01−43.78]; p < 0.004) and HTN (aOR 6.00, 95% CI [1.10−35.39]; p < 0.049). Our findings warrant the implementation of NCD-aware HIV programs for the prevention, early detection and management of comorbidities.

A Tale of Two Viruses: Immunological Insights Into HCV/HIV Coinfection

Nearly 2.3 million individuals worldwide are coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Odds of HCV infection are six times higher in people living with HIV (PLWH) compared to their HIV-negative counterparts, with the highest prevalence among people who inject drugs (PWID) and men who have sex with men (MSM). HIV coinfection has a detrimental impact on the natural history of HCV, including higher rates of HCV persistence following acute infection, higher viral loads, and accelerated progression of liver fibrosis and development of end-stage liver disease compared to HCV monoinfection. Similarly, it has been reported that HCV coinfection impacts HIV disease progression in PLWH receiving anti-retroviral therapies (ART) where HCV coinfection negatively affects the homeostasis of CD4⁺ T cell counts and facilitates HIV replication and viral reservoir persistence. While ART does not cure HIV, direct acting antivirals (DAA) can now achieve HCV cure in nearly 95% of coinfected individuals. However, little is known about how HCV cure and the subsequent resolution of liver inflammation influence systemic immune activation, immune reconstitution and the latent HIV reservoir. In this review, we will summarize the current knowledge regarding the pathogenesis of HIV/HCV coinfection, the effects of HCV coinfection on HIV disease progression in the context of ART, the impact of HIV on HCV-associated liver morbidity, and the consequences of DAA-mediated HCV cure on immune reconstitution and HIV reservoir persistence in coinfected patients.

Serum electrolytes and renal alterations in HIV-seropositive Mexican subjects

To examine potential risk factors associated with biochemical alterations in renal function in a population diagnosed with HIV/AIDS undergoing antiretroviral treatment.This is an observational, transversal, and relational design study that included 179 HIV-seropositive subjects. Glucose serum, cholesterol, triglycerides, total proteins, albumin, creatine, urea, blood urea nitrogen (BUN), and electrolytes levels were determined for each individual. Renal function was evaluated through the glomerular filtration rate (GFR), using the CKD-EPI equation. Chronic kidney disease (CKD) was defined as estimated glomerular filtration rate  < 60 mL/min/1.73 m2. Univariate model significant variables, with a 95% confidence interval (CI), were included in a multivariate logistic regression analysis.CKD prevalence in patients was 7.3%, with comorbidities of 7.8% for type 2 diabetes mellitus, 7.3% for arterial hypertension, and 35.2% for dyslipidemia. Additionally, both hypernatremia and hypophosphatemia were detected in 57% (n = 102) of the patients. Multivariate logistic regression suggested that CD4+ T cell count < 200 (P = .02; OR 0.2; CI 95% 0.08-0.8) was associated to hyponatremia; similarly, detectable viral load was associated to hypokalemia (P = .02; OR 5.1; CI 95% 1.2-21.3), hypocalcemia (P = .01; OR 4.1; CI 95% 1.3-12.3), and hypermagnesemia (OR 3.9; CI 95% 1.1-13.6). Patient age was associated to both hypophosphatemia (P = .01; OR 2.4; CI 95% 1.1-5.0) and hypermagnesemia (P = .01; OR 2.8; IC 95% 1.1-7.0), and high creatinine levels were associated to nucleoside reverse transcriptase inhibitor treatment (P = .001; OR 42.5; CI 95% 2.2-806.9). Lastly, high BUN levels were associated to age (P = .03; OR 3.8; CI 95% 1.0-14.4), while GFR 60 to 89 mL/min/1.73 m2 was associated to dyslipidemia (P = .02; OR 2.2; CI 95% 1.1-4.5).CD4+ T cell and viral load were the main factors associated with renal biochemical alterations.

Brazilian Protocol for Sexually Transmitted Infections, 2020: HIV infection in adolescents and adults

HIV infection is presented in the chapters of the Clinical Protocol and Therapeutic Guidelines for Comprehensive Care for People with Sexually Transmitted Infections, published by the Brazilian Ministry of Health in 2020. Health professionals and managers must learn the signs and symptoms of HIV infection and know how to diagnose it to provide appropriate treatment and reduce complications. HIV infection has become a chronic disease. Its treatment includes addressing common comorbidities such as arterial hypertension, diabetes, and dyslipidemia, in addition to cardiac risk assessment, cancer prevention, and guidance on immunization. Initiation of treatment for HIV patients is recommended regardless of clinical or immunological criteria as adopted by the Ministry of Health since 2013. Lately, it has been simplified with more tolerable first-line medications and fewer drug interactions, making its management easy to implement, including by primary health care.

HIV cases are concentrated in specific population groups, such as sex workers, men who have sex with men, transexuals, people who use alcohol or other drugs, and vulnerable people, such as black, incarcerated, or people living on the streets.

[Brazilian Protocol for Sexually Transmitted Infections 2020: HIV infection in adolescents and adults]

HIV infection is the subject of one of the chapters of the "Clinical Protocol and Therapeutic Guidelines for Comprehensive Care for People with Sexually Transmitted Infections", published by the Brazilian Ministry of Health in 2020. It is important that health professionals and managers learn the signs and symptoms of HIV infection and know how to diagnose it, in order to provide appropriate treatment and reduce complications. HIV infection has become a chronic disease and its treatment includes addressing common comorbidities in clinical practice such as arterial hypertension, diabetes and dyslipidemia, in addition to cardiac risk assessment, cancer prevention and guidance on immunization. Initiation of treatment for all HIV patients, regardless of clinical or immunological criteria, adopted by the Ministry of Health since 2013, has now been simplified with more tolerable first-line medications and with fewer drug interactions, which makes its management easy to implement, including by Primary Health Care.

HIV integrase inhibitors that inhibit strand transfer interact with RAG1 and hamper its activities

Multiple steps of the retroviral infection process have been targeted over the years to develop therapeutic approaches, starting from the entry of the virus into the cell till the viral DNA integration to host genome. Inhibitors against the Human Immunodeficiency Virus (HIV) integrase is the newest among the therapies employed against HIV. Recombination activating gene 1 (RAG1) is an integral protein involved in the generation of diversity of antibodies and T-cell receptors and is one of the partners of the RAG complex. Studies have shown structural and functional similarities between the HIV integrase and RAG1. Recently, we and others have shown that some of the integrase inhibitors can interfere with RAG binding and cleavage, hindering its physiological functions. This mini review focuses on the HIV integrase, integrase inhibitors and their effect on RAG activities.

Understanding the Impact of Resistance to Influenza Antivirals

Influenza poses a significant burden on society and health care systems. Although antivirals are an integral tool in effective influenza management, the potential for the emergence of antiviral-resistant viruses can lead to uncertainty and hesitation among front-line prescribers and policy makers. Here, we provide an overview of influenza antiviral resistance in context, exploring the key concepts underlying its development and clinical impact. Due to the acute nature of influenza in immunocompetent patients, resistant viruses that develop during antiviral treatment of a single patient ("treatment-emergent resistance") are usually cleared in a relatively short time, with no impact on future antiviral efficacy. In addition, although available data are limited by small numbers of patients, they show that antiviral treatment still provides clinical benefit to the patient within whom resistance emerges. In contrast, the sustained community transmission of resistant variants in the absence of treatment ("acquired resistance") is of greater concern and can potentially render front-line antivirals ineffective. Importantly, however, resistant viruses are usually associated with reduced fitness such that their widespread transmission is relatively rare. Influenza antivirals are an essential part of effective influenza management due to their ability to reduce the risk of complications and death in infected patients. Although antiviral resistance should be taken seriously and requires continuous careful monitoring, it is not comparable to antibiotic resistance in bacteria, which can become permanent and widespread, with far-reaching medical consequences. The benefits of antiviral treatment far outweigh concerns of potential resistance, which in the vast majority of cases does not have a significant clinical impact.

People living with HIV and fracture risk

PLHIV have an increased risk of osteoporosis and fractures when compared with people of the same age and sex. In this review, we address the epidemiology and the pathophysiology of bone disease and fractures in PLHIV. The assessment of fracture risk and fracture prevention in these subjects is also discussed. The spectrum of HIV-associated disease has changed dramatically since the introduction of potent antiretroviral drugs. Today, the survival of people living with HIV (PLHIV) is close to that of the general population. However, the longer life-span in PLHIV is accompanied by an increased prevalence of chronic diseases. Detrimental effects on bone health are well recognised, with an increased risk of osteoporosis and fractures, including vertebral fractures, compared to the general population. The causes of bone disease in PLHIV are not fully understood, but include HIV-specific risk factors such as use of antiretrovirals and the presence of chronic inflammation, as well as traditional risk factors for fracture. Current guidelines recommend the use of FRAX to assess fracture probability in PLHIV age ≥ 40 years and measurement of bone mineral density in those at increased fracture risk. Vitamin D deficiency, if present, should be treated. Bisphosphonates have been shown to increase bone density in PLHIV although fracture outcomes are not available.

[Benign lymphoid hyperplasia associated with HIV: An exceptional orbital location]

HIV-related lymphoid hyperplasia has been exceptionally described outside lymph nodes. To our knowledge, 3 cases of nasopharyngeal localisation have been described in the literature. We report here an intracranial localisation with an important ophthalmological clinical impact. Our observation allows us to approach the differential diagnoses of intracranial lesions in the HIV-positive patient, to analyse the differential diagnoses of benign lymphoid hyperplasia and to discuss the therapeutic options.

The Prevalence of HIV-Positive Infants Born to HIV-Positive Mothers Attended at the University of Gondar Specialized Hospital Anti-Retroviral Therapy Services, Northwest Ethiopia, 2018

Introduction

The human immunodeficiency virus (HIV) attacks the human immune cells and affects their function. It is the highest burden that occurs in a developing country. Ethiopia is one of the top ten countries in the world, which has a high burden of HIV-infected children. Even if the country works hard on the PMCT program, still there is challenging on MTCT reduction.

Objective

The purpose of this study was to assess the prevalence of HIV-positive infants born to HIV-positive mothers attending anti-retroviral treatment (ART) services at the University of Gondar specialized hospital, Gondar, northwest Ethiopia, 2018.

Methods

A retrospective chart review study was conducted from February to April 2018, among HIV-exposed infants who born to HIV-positive mothers in ART service at the University of Gondar specialized hospital. A systematic sampling method was applied to select study participants. Data were entered into EPI info version 7 statistical software and transferred to SPSS version 20 for analysis.

Results

In this study, 239 participants were enrolled, with a 98.8% response rate. The prevalence of HIV-positive infants born to HIV-positive mothers was 5.5% with a 95% CI (3.0–8.5%). Of the mothers, 77.1% were within 25–35 years of age range. Of the total infants, 56.8% were males. From these HIV-positive infants, 13 (5.5%) were born from age ranges of 25–35years old mothers, 9(3.8%) were females, 8(3.4%) were 6–11 months old, 13 (5.5%) were post-term gestation, and 13 (5.5%) were maternal CD4+ less than 350/mm³.

Conclusion and Recommendations

The prevalence of HIV-positive infants born to HIV-positive mothers in this study was lower than the previous 10.2%. To reduce such infant HIV infection to zero, it needs proactive action from stakeholders, health professionals, and the community at large.

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

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

Clinical efficacy of photodynamic therapy in the treatment of necrotizing ulcerative periodontitis among HIV seropositive patients: A randomized controlled clinical trial

AIM

To evaluate clinical periodontal and microbiological parameters after the treatment with adjunctive antimicrobial photodynamic therapy (APDT) among HIV seropositive and seronegative patients with necrotizing ulcerative periodontitis (NUP).

MATERIALS AND METHODS

Seropositive patients (Group-I) and health controls (Group-II) with NUP were randomized into two groups and further underwent APDT and scaling and root planing (SRP), respectively. Clinical periodontal parameters including full mouth plaque index (FMPI), bleeding on probing (FMBOP), probing depth (PD) and clinical attachment level (CAL) gain were assessed. Levels of bacteria including Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg) and Tannerella forsythia (Tf) were assessed using PCR technique. All assessments were done at baseline, 3 months and 6 months.

RESULTS

All periodontal parameters including FMPI, FMBOP, PD and CAL significantly improved in both HIV seropositive and seronegative patients. The reduction in mean PD was higher only with the APDT treatment among group II patients compared to group I patients at follow-up (p < 0.05). The gain in mean CAL was higher only with the APDT treatment among group I and group II patients at follow-up (p < 0.05). All bacterial levels reduced from baseline to follow-up with both APDT and SRP treatments in both groups (p < 0.05). APDT showed significantly reduced counts of Aa and Tf at 3 months, and only Aa at 6 months among HIV seropositive patients, while the levels of Pg and Tf significantly reduced at 3 months and only Aa at 6 months in the seronegative patients, respectively (p < 0.05).

CONCLUSION

Application of antimicrobial photodynamic therapy as an adjunct to scaling and root planing was effective in improving clinical periodontal parameters and bacterial levels among HIV positive patients with NUP. However, the improvement was not greater when compared with HIV seronegative patients.

Myeloid and CD4 T Cells Comprise the Latent Reservoir in Antiretroviral Therapy-Suppressed SIVmac251-Infected Macaques

Human immunodeficiency virus (HIV) eradication or long-term suppression in the absence of antiretroviral therapy (ART) requires an understanding of all viral reservoirs that could contribute to viral rebound after ART interruption. CD4 T cells (CD4s) are recognized as the predominant reservoir in HIV type 1 (HIV-1)-infected individuals. However, macrophages are also infected by HIV-1 and simian immunodeficiency virus (SIV) during acute infection and may persist throughout ART, contributing to the size of the latent reservoir. We sought to determine whether tissue macrophages contribute to the SIVmac251 reservoir in suppressed macaques. Using cell-specific quantitative viral outgrowth assays (CD4-QVOA and MΦ-QVOA), we measured functional latent reservoirs in CD4s and macrophages in ART-suppressed SIVmac251-infected macaques. Spleen, lung, and brain in all suppressed animals contained latently infected macrophages, undetectable or low-level SIV RNA, and detectable SIV DNA. Silent viral genomes with potential for reactivation and viral spread were also identified in blood monocytes, although these cells might not be considered reservoirs due to their short life span. Additionally, virus produced in the MΦ-QVOA was capable of infecting healthy activated CD4s. Our results strongly suggest that functional latent reservoirs in CD4s and macrophages can contribute to viral rebound and reestablishment of productive infection after ART interruption. These findings should be considered in the design and implementation of future HIV cure strategies.IMPORTANCE This study provides further evidence that the latent reservoir is comprised of both CD4+ T cells and myeloid cells. The data presented here suggest that CD4+ T cells and macrophages found throughout tissues in the body can contain replication-competent SIV and contribute to rebound of the virus after treatment interruption. Additionally, we have shown that monocytes in blood contain latent virus and, though not considered a reservoir themselves due to their short life span, could contribute to the size of the latent reservoir upon entering the tissue and differentiating into long-lived macrophages. These new insights into the size and location of the SIV reservoir using a model that is heavily studied in the HIV field could have great implications for HIV-infected individuals and should be taken into consideration with the development of future HIV cure strategies.

The potential impact of initiating antiretroviral therapy with integrase inhibitors on HIV transmission risk in British Columbia, Canada

BACKGROUND

Available agents within the integrase strand-transfer inhibitor (INSTI) class have been shown to lead to a faster decay in viral load than other regimens. Therefore, we estimated the potential reduction in HIV transmission risk among antiretroviral-naïve individuals initiating on INSTI-based antiretroviral therapy (ART), focusing on the gay, bisexual and other men who have sex with men (gbMSM) population and various degrees of sexual activity.

METHODS

Using two mathematical models that estimate the HIV transmission risk corresponding to different viral loads, we estimated the average probability of HIV transmission per risky contact for gbMSM during the six months post-ART initiation, stratified by stage of HIV infection, viral load at ART initiation and type of first-line ART (i.e., INSTI or non-INSTI-based ART). This study focused individuals who initiated ART between 2011 and 2016 with at least one year of follow-up in British Columbia, Canada.

FINDINGS

Time to first virologic suppression for INSTI-based regimens was 21.4 days (95% credible interval (CI) 19.9-23.2), compared to 58.6 days (95% CI 54.1-62.2) for non-INSTI regimens. We showed that INSTI-based regimens could reduce the HIV transmission risk by at least 25% among those with viral load ≥ 5 log₁₀ copies/mL at ART initiation.

INTERPRETATION

Initiating ART on INSTI-based regimens has the potential to reduce HIV transmission risk among individuals with high baseline viral load levels, especially among those with high levels of sexual activity.

FUNDING

The British Columbia Ministry of Health, the Canadian Institutes of Health Research, and the Michael Smith Foundation for Health Research.

Cytokine gene polymorphisms among North Indians: Implications for genetic predisposition?

Variations in the production and activity of cytokines influence the susceptibility and/or resistance to various infectious agents, autoimmune diseases, as well as the post-transplant engraftment/ rejection. Differences in the production of cytokines between individuals have been correlated to single nucleotide polymorphisms (SNPs) in the promoter, coding or non-coding regions of cytokine genes. The present study aimed at understanding distribution of cytokine gene variants among HIV seropositive subjects including HIV + TB+ subjects of Indian origin. Our findings indicate significant association of pro-inflammatory (IL2, IFN-γ, TNF-α) and anti-inflammatory cytokine gene variants (IL4, IL10) with the risk to acquire the HIV infection and development of AIDS related illness in Indian population. Since distribution of genetic polymorphisms varies significantly across different populations, different genotypes might exhibit different disease-modifying effects. An understanding of the immunogenetic factors or AIDS restriction genes is important not only for elucidating the mechanisms of disease pathogenesis but also for vaccine design and its application.

Comparing the Diagnostics Accuracy of CD4+ T-Lymphocyte Count and Percent as a Surrogate Markers of Pediatric HIV Disease

The percentage CD4+ T-lymphocytes is used to monitor pediatric HIV disease. However, in resource-limited settings, enumerating the percentage of CD4+ T-lymphocytes is hampered by the lack of laboratory infrastructure and trained technicians. In this paper, we investigated the performances of the percentage and absolute CD4+ T-lymphocytes as markers of pediatric HIV disease progression using data from HIV-infected children enrolled through the Yale Prospective Longitudinal Pediatric Cohort study. A Lehmann family of Receiver Operating Characteristic (ROC) curves were used to estimate and compare the performance of the two biomarkers in monitoring pediatric HIV disease progression. The area under the ROC (AUC) curve and its empirical estimator have previously been used to assess the performance of biomarkers for a cross-sectional data. However, there is a paucity of literature on the AUC for correlated longitudinal biomarkers. Previous works on the estimation and inference of the AUC for longitudinal biomarkers have largely focused on independent biomarkers or failed to consider the effect of covariates. The Lehmann approach allowed us to estimate the AUC of the aforementioned correlated longitudinal biomarkers as functions of explanatory variables. We found that the overall performance of the two biomarkers was comparable. The area under the ROC curves for CD4+ T cell count and percentage were 0.681 [SE = 0.029; 95% CI: 0.624-0.737] and 0.678 [SE = 0.024; 95% CI:0.630-0.725], respectively. Our results suggest that absolute CD4+ T-lymphocyte counts could be used as a proxy for percentage of CD4+ T-lymphocytes in monitoring pediatric HIV in resource-limited settings.

Prevalence of antiretroviral therapy treatment failure among HIV-infected pregnant women at first antenatal care: PMTCT Option B+ in Malawi

BACKGROUND

In Malawi's PMTCT Option B+ program, HIV-infected pregnant women who are already receiving ART are continued on their current therapy regimen without testing for treatment failure at the first antenatal care (ANC) visit. HIV RNA screening at ANC may identify women with treatment failure and ensure that viral suppression is maintained throughout the pregnancy.

METHODS

We conducted a cross-sectional study of HIV-infected pregnant women who had been receiving ART for at least 6 months at the first ANC visit under the PMTCT Option B+ program at Bwaila Hospital in Lilongwe, Malawi from June 2015 to December 2017. Poisson regression models with robust variance were used to investigate the predictors of ART treatment failure defined as viral load ≥1000 copies/ml.

RESULTS

The median age of 864 women tested for ART failure was 31.1 years (interquartile range: 26.9-34.5). The prevalence of treatment failure was 7.6% (95% confidence interval (CI): 6.0-9.6). CD4 cell count (adjusted prevalence ratio (aPR) = 0.57; 95% CI: 0.50-0.65) was strongly associated with treatment failure.

CONCLUSION

The low prevalence of treatment failure among women presenting for their first ANC in urban Malawi demonstrates success of Option B+ in maintaining viral suppression and suggests progress towards the last 90% of the UNAIDS 90-90-90 targets. Women failing on ART should be identified early for adherence counseling and may require switching to an alternative ART regimen.

The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection

Background

Microbial flora in several organs of HIV-infected individuals have been characterized; however, the palatine tonsil bacteriome and mycobiome and their relationship with each other remain unclear. Determining the palatine tonsil microbiome may provide a better understanding of the pathogenesis of oral and systemic complications in HIV-infected individuals. We conducted a cross-sectional study to characterize the palatine tonsil microbiome in HIV-infected individuals.

Results

Palatine tonsillar swabs were collected from 46 HIV-infected and 20 HIV-uninfected individuals. The bacteriome and mycobiome were analyzed by amplicon sequencing using Illumina MiSeq. The palatine tonsil bacteriome of the HIV-infected individuals differed from that of HIV-uninfected individuals in terms of the decreased relative abundances of the commensal genera Neisseria and Haemophilus. At the species level, the relative abundances and presence of Capnocytophaga ochracea, Neisseria cinerea, and Selenomonas noxia were higher in the HIV-infected group than those in the HIV-uninfected group. In contrast, fungal diversity and composition did not differ significantly between the two groups. Microbial intercorrelation analysis revealed that Candida and Neisseria were negatively correlated with each other in the HIV-infected group. HIV immune status did not influence the palatine tonsil microbiome in the HIV-infected individuals.

Conclusions

HIV-infected individuals exhibit dysbiotic changes in their palatine tonsil bacteriome, independent of immunological status.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1274-9) contains supplementary material, which is available to authorized users.

Total Joint Arthroplasty in Patients with Human Immunodeficiency Virus

With the advent of highly active antiretroviral therapy (HAART), total joint arthroplasty has become a safe and effective procedure for patients infected with the human immunodeficiency virus (HIV). A correlation between a low CD4+ count (<200 cells/mm3) and major postoperative complications such as deep joint infection has been postulated, although high-level studies are not available in the literature. As most studies have not demonstrated an increase in the incidence of deep-vein thrombosis in patients with HIV/AIDS (acquired immunodeficiency syndrome), our recommendation is to use the standard prophylaxis that is followed by the operating surgeon.

The Hidden Burden of Fractures in People Living With HIV

The survival of people living with human immunodeficiency virus (HIV) has increased markedly since the advent of antiretroviral therapy (ART). However, other morbidities have emerged, including osteoporosis. The estimated incidence of fractures at any site in people living with HIV ranges from 0.1 per 1000 person‐years to 8.4 per 1000 person‐years: at least twice that of people without HIV. This increased risk seems to be related to HIV itself and its treatment. Risk factors for bone disease in HIV‐positive (HIV⁺) subjects include both classical risk factors for osteoporosis and fracture and factors linked to HIV itself, such as inflammation, reconstitution syndrome, low CD4, ART, and co‐infection with hepatitis B and C viruses. The risk of fractures in these individuals can be at least partially assessed by measurement of BMD and the Fracture Risk Assessment Tool (FRAX™). Only alendronate and zoledronic acid have been studied in HIV⁺ individuals; both show beneficial effects on BMD, although data on fracture reduction are not available. © 2018 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Single-molecule techniques to quantify and genetically characterise persistent HIV

Antiretroviral therapy effectively suppresses, but does not eradicate HIV-1 infection. Persistent low-level HIV-1 can still be detected in plasma and cellular reservoirs even after years of effective therapy, and cessation of current treatments invariably results in resumption of viral replication. Efforts to eradicate persistent HIV-1 require a comprehensive examination of the quantity and genetic composition of HIV-1 within the plasma and infected cells located in the peripheral blood and tissues throughout the body. Single-molecule techniques, such as the single-copy assay and single-genome/proviral sequencing assays, have been employed to further our understanding of the source and viral dynamics of persistent HIV-1 during long-term effective therapy. The application of the single-copy assay, which quantifies plasma HIV-1 RNA down to a single copy, has revealed that viremia persists in the plasma and CSF after years of effective therapy. This low-level HIV-1 RNA also persists in the plasma following treatment intensification, treatment with latency reversing agents, cancer-related therapy, and bone marrow transplantation. Single-genome/proviral sequencing assays genetically characterise HIV-1 populations after passing through different selective pressures related to cell type, tissue type, compartment, or therapy. The application of these assays has revealed that the intracellular HIV-1 reservoir is stable and mainly located in CD4+ memory T cells. Moreover, this intracellular HIV-1 reservoir is primarily maintained by cellular proliferation due to homeostasis and antigenic stimulation, although cryptic replication may take place in anatomic sites where treatment is sub-optimal. The employment of single-genome/proviral sequencing showed that latency reversing agents broadly activate quiescent proviruses but do not clear the intracellular reservoir. Recently, full-length individual proviral sequencing assays have been developed and the application of these assays has revealed that the majority of intracellular HIV-1 DNA is genetically defective. In addition, the employment of these assays has shown that genetically intact proviruses are unequally distributed in memory T cell subsets during antiretroviral therapy. The application of single-molecule assays has enhanced the understanding of the source and dynamics of persistent HIV-1 in the plasma and cells of HIV-infected individuals. Future studies of the persistent HIV-1 reservoir and new treatment strategies to eradicate persistent virus will benefit from the utilization of these assays.

Role of Monocyte/Macrophages during HIV/SIV Infection in Adult and Pediatric Acquired Immune Deficiency Syndrome

Monocytes/macrophages are a diverse group of cells that act as first responders in innate immunity and then as mediators for adaptive immunity to help clear infections. In performing these functions, however, the macrophage inflammatory responses can also contribute to pathogenesis. Various monocyte and tissue macrophage subsets have been associated with inflammatory disorders and tissue pathogeneses such as occur during HIV infection. Non-human primate research of simian immunodeficiency virus (SIV) has been invaluable in better understanding the pathogenesis of HIV infection. The question of HIV/SIV-infected macrophages serving as a viral reservoir has become significant for achieving a cure. In the rhesus macaque model, SIV-infected macrophages have been shown to promote pathogenesis in several tissues resulting in cardiovascular, metabolic, and neurological diseases. Results from human studies illustrated that alveolar macrophages could be an important HIV reservoir and humanized myeloid-only mice supported productive HIV infection and viral persistence in macrophages during ART treatment. Depletion of CD4+ T cells is considered the primary cause for terminal progression, but it was reported that increasing monocyte turnover was a significantly better predictor in SIV-infected adult macaques. Notably, pediatric cases of HIV/SIV exhibit faster and more severe disease progression than adults, yet neonates have fewer target T cells and generally lack the hallmark CD4+ T cell depletion typical of adult infections. Current data show that the baseline blood monocyte turnover rate was significantly higher in neonatal macaques compared to adults and this remained high with disease progression. In this review, we discuss recent data exploring the contribution of monocytes and macrophages to HIV/SIV infection and progression. Furthermore, we highlight the need to further investigate their role in pediatric cases of infection.

HIV-1-infected T-cells dynamics and prognosis: An evolutionary game model

BACKGROUND AND OBJECTIVE

Understanding the dynamics of human immunodeficiency virus (HIV) is essential for depicting, developing, and investigating effective treatment strategies. HIV infects several types of immune cells, but its main target is to destroy helper T-cells. In the lymph nodes, the infected T-cells interact with each other and their environment to obtain more resources. According to infectivity and replicative capacity of T-cells in the HIV infection process, they can be divided into four phenotypes. Although genetic mutations in the reverse transcription that beget these phenotypes are random, the framework by which a phenotype become favored is affected by the environment and neighboring phenotypes. Moreover, the HIV disease has all components of an evolutionary process, including replication, mutation, and selection.

METHODS

We propose a novel structure-based game-theoretic model for the evolution of HIV-1-Infected CD4+T-cells and invasion of the immune system. We discuss the theoretical basis of the stable equilibrium states of the evolutionary dynamics of four T-cells types as well as its significant results to understand and control HIV infection. The results include the importance of genetic variations and the process of establishing evolutionary dynamics of the virus quasispecies.

RESULTS

Our results show that there is a direct dependency between some parameters such as mutation rates and the stability of equilibrium states in the HIV infection. This is an interesting result because these parameters can be changed by some pharmacotherapies and alternative treatments. Our model indicates that in an appropriate treatment the relative frequency of the wild type of virus quasispecies can be decreased in the population. Consequently, this can cause delaying the emergence of the AIDS phase. To assess the model, we investigate two new treatments for HIV. The results show that our model can predict the treatment results.

CONCLUSIONS

The paper shows that a structured-based evolutionary game theory can model the evolutionary dynamics of the infected T-cells and virus quasispecies. The model predicts certain aspects of the HIV infection process under several treatments.

Cell-Mediated Immune Predictors of Vaccine Effect on Viral Load and CD4 Count in a Phase 2 Therapeutic HIV-1 Vaccine Clinical Trial

Background

In a placebo-controlled trial of the peptide-based therapeutic HIV-1 p24^Gag vaccine candidate Vacc-4x, participants on combination antiretroviral therapy (cART) received six immunizations over 18 weeks, followed by analytical treatment interruption (ATI) between weeks 28 and 52. Cell-mediated immune responses were investigated as predictors of Vacc-4x effect (VE) on viral load (VL) and CD4 count during ATI.

Methods

All analyses of week 28 responses and fold-changes relative to baseline considered per-protocol participants (Vacc-4x:placebo = 72:32) resuming cART after week 40. Linear regression models with interaction tests were used. VE was estimated as the Vacc-4x–placebo difference in log₁₀-transformed VL (VE^VL) or CD4 count (VE^CD4).

Findings

A lower fold-change of CD4+ T-cell proliferation was associated with VE^CD4 at week 48 (p = 0.036, multiplicity adjusted q = 0.036) and week 52 (p = 0.040, q = 0.080). A higher fold-change of IFN-γ in proliferation supernatants was associated with VE^VL at week 44 (p = 0.047, q = 0.07). A higher fold-change of TNF-α was associated with VE^VL at week 44 (p = 0.045, q = 0.070), week 48 (p = 0.028, q = 0.070), and week 52 (p = 0.037, q = 0.074). A higher fold-change of IL-6 was associated with VE^VL at week 48 (p = 0.017, q = 0.036). TNF-α levels (> median) were associated with VE^CD4 at week 48 (p = 0.009, q = 0.009).

Interpretation

These exploratory analyses highlight the potential value of investigating biomarkers in T-cell proliferation supernatants for VE in clinical studies.

•

Ex vivo CD4+ T-cell proliferation was predictive of Vacc-4x effect.

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IFN-γ, TNF-α and IL-6 secretion in T-cell proliferation supernatants were predictive of Vacc-4x effect.

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Such immune predictors could be utilized to mitigate risks associated with cART interruption towards HIV cure.

No immune correlates or predictors of therapeutic vaccine effect (i.e. a reduction in viral load compared to placebo on treatment interruption) for human immunodeficiency virus (HIV)-1 are known. We investigated a broad array of cytokines/chemokines produced in T-cell proliferation supernatants from a placebo-controlled clinical study of a therapeutic HIV vaccine. Although such supernatants do not provide cell type-specific readouts, the cytokines/chemokines studied included T-helper (Th)1, Th2, growth factor, immuno-modulatory and pro-inflammatory functions. Specifically, we found that, IFN-γ, TNF-α and IL-6 secretion correlated with vaccine effect, suggesting such supernatants could represent important sample material not previously considered for the identification of immune markers of vaccine effect.

Limiting Cumulative HIV Viremia Copy-Years by Early Treatment Reduces Risk of AIDS and Death

Supplemental Digital Content is Available in the Text.

Background:

Viremia copy-years (VCY), a time-updated measure of cumulative HIV exposure, predicts AIDS/death; although its utility in deciding when to start combination antiretroviral therapy (cART) remains unclear. We aimed to assess the impact of initiating versus deferring cART on risk of AIDS/death by levels of VCY both independent of and within CD4 cell count strata ≥500 cells per cubic millimeter.

Methods:

Using Concerted Action on Seroconversion to AIDS and Death in Europe (CASCADE) data, we created a series of nested “trials” corresponding to consecutive months for individuals ≥16 years at seroconversion after 1995 who were cART-naive and AIDS-free. Pooling across all trials, time to AIDS/death by CD4, and VCY strata was compared in those initiating vs. deferring cART using Cox models adjusted for: country, sex, risk group, seroconversion year, age, time since last HIV-RNA, and current CD4, VCY, HIV-RNA, and mean number of previous CD4/HIV-RNA measurements/year.

Results:

Of 9353 individuals, 5312 (57%) initiated cART and 486 (5%) acquired AIDS/died. Pooling CD4 strata, risk of AIDS/death associated with initiating vs. deferring cART reduced as VCY increased. In patients with high CD4 cell counts, ≥500 cells per cubic millimeter, there was a trend for a greater reduction for those initiating vs. deferring with increasing VCY (P = 0.09), with the largest benefit in the VCY ≥100,000 copy-years/mL group [hazard ratio (95% CI) = 0.41 (0.19 to 0.87)].

Conclusions:

For individuals with CD4 ≥500 cells per cubic millimeter, limiting the cumulative HIV burden to <100,000 copy-years/mL through cART may reduce the risk of AIDS/death.

Gut Mucosal Barrier Dysfunction, Microbial Dysbiosis, and Their Role in HIV-1 Disease Progression

Distinct pathological events occur within the gastrointestinal (GI) tract of Asian macaques with progressive simian immunodeficiency virus (SIV) infection and humans with human immunodeficiency virus type 1 (HIV-1) infection that are critical in shaping disease course. These events include depletion and functional alteration of GI-resident CD4(+) T cells, loss of antigen-presenting cells, loss of innate lymphocytes, and possible alterations to the composition of the gut microbiota. These contribute to structural damage to the GI tract and systemic translocation of GI tract microbial products. These translocated microbial products directly stimulate the immune system, and there is now overwhelming evidence that this drives chronic immune activation in HIV-1 and SIV infection. While combined antiretroviral therapy (cART) in HIV-1-infected subjects generally allows for immune reconstitution in peripheral blood, reconstitution of the GI tract occurs at a much slower pace, and both immunological and structural abnormalities persist in the GI tract. Importantly, studies of large cohorts of individuals have linked suboptimal GI reconstitution to residual inflammation and heightened morbidities in HIV-1-infected cART recipients. As a result, current era treatments aimed at augmenting restoration of the GI tract hold promise in returning cART recipients to full health.

Preservation affinity in consensus modules among stages of HIV-1 progression

Background

Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding.

Methods

HIV-1 disease provides a well-documented progression pattern through three stages of infection: acute, chronic and non-progressor. In this article, we have developed a novel framework to describe the relationship among the consensus (or shared) co-expression modules for each pair of HIV-1 infection stages. The consensus modules are identified to assess the preservation of network properties. We have investigated the preservation patterns of co-expression networks during HIV-1 disease progression through an eigengene-based approach.

Results

We discovered that the expression patterns of consensus modules have a strong preservation during the transitions of three infection stages. In particular, it is noticed that between acute and non-progressor stages the preservation is slightly more than the other pair of stages. Moreover, we have constructed eigengene networks for the identified consensus modules and observed the preservation structure among them. Some consensus modules are marked as preserved in two pairs of stages and are analyzed further to form a higher order meta-network consisting of a group of preserved modules. Additionally, we observed that module membership (MM) values of genes within a module are consistent with the preservation characteristics. The MM values of genes within a pair of preserved modules show strong correlation patterns across two infection stages.

Conclusions

We have performed an extensive analysis to discover preservation pattern of co-expression network constructed from microarray gene expression data of three different HIV-1 progression stages. The preservation pattern is investigated through identification of consensus modules in each pair of infection stages. It is observed that the preservation of the expression pattern of consensus modules remains more prominent during the transition of infection from acute stage to non-progressor stage. Additionally, we observed that the module membership values of genes are coherent with preserved modules across the HIV-1 progression stages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1590-3) contains supplementary material, which is available to authorized users.

What Are Clinically Relevant Levels of Cellular and Biomolecular Analytes?

The ultimate goal of developing sensors for biomolecular analytes is to offer new tools for the analysis of clinical specimens for biomarkers of disease. It is thus important to understand the types of samples that are routinely used in the clinic for specific indications, and what the typical levels of relevant analytes are in these specimens. This Sensor Issues article summarizes information concerning levels of target molecules and cells that are of interest for the development of new diagnostics for infectious disease and cancer. Having this information in hand helps better define the "needle-in-a-haystack" challenge associated with developing robust sensors with the needed levels of sensitivity and specificity.

Diagnosing Acute HIV Infection

Acute HIV infection (AHI) represents the first 6 to 12 weeks of the disease process, when the virus is aggressively replicating in the lymphoid tissues. Accordingly, high viral loads are often present during this phase, with declining lymphocyte levels, as the CD4+ T-cell subset is preferentially commandeered to facilitate viral reproduction. Detection at this stage is imperative-the affected are often unaware, but highly infectious. Unfortunately, correct diagnosis of AHI can be challenging because the more traditional, frequently used tests, which rely on antibody detection, will often produce false-negative results during the "window period" (usually 3 to 4 weeks from infection) due to slow production of HIV antibodies. Consequently, testing with fourth-generation antibody-antigen and viral nucleic acid polymerase chain reaction modalities, which can yield positive results within 5 to 7 days of infection, is vital in the context of any significant concern for AHI. [Pediatr Ann. 2017;46(2):e47-e50.].

Personalized life expectancy and treatment benefit index of antiretroviral therapy

BACKGROUND

The progression of Human Immunodeficiency Virus (HIV) within host includes typical stages and the Antiretroviral Therapy (ART) is shown to be effective in slowing down this progression. There are great challenges in describing the entire HIV disease progression and evaluating comprehensive effects of ART on life expectancy for HIV infected individuals on ART.

METHODS

We develop a novel summative treatment benefit index (TBI), based on an HIV viral dynamics model and linking the infection and viral production rates to the Weibull function. This index summarizes the integrated effect of ART on the life expectancy (LE) of a patient, and more importantly, can be reconstructed from the individual clinic data.

RESULTS

The proposed model, faithfully mimicking the entire HIV disease progression, enables us to predict life expectancy and trace back the timing of infection. We fit the model to the longitudinal data in a cohort study in China to reconstruct the treatment benefit index, and we describe the dependence of individual life expectancy on key ART treatment specifics including the timing of ART initiation, timing of emergence of drug resistant virus variants and ART adherence.

CONCLUSIONS

We show that combining model predictions with monitored CD4 counts and viral loads can provide critical information about the disease progression, to assist the design of ART regimen for maximizing the treatment benefits.

Effect of Korean Red Ginseng intake on the survival duration of human immunodeficiency virus type 1 patients

Background

Long-term ginseng intake can increase longevity in healthy individuals. Here, we examined if long-term treatment with Panax ginseng Meyer (Korean Red Ginseng, KRG) can also enhance survival duration (SD) in patients with human immunodeficiency virus type 1 (HIV-1) infection.

Methods

We retrospectively analyzed 252 HIV-1 patients diagnosed from 1986 to 2013 prior to the initiation of antiretroviral therapy. Overall, 162 patients were treated with KRG (3,947 ± 4,943 g) for 86 ± 63 mo. The effects of KRG on SD were analyzed according to the KRG intake level and the length of the follow-up period.

Results

There were significant correlations between the total amount of KRG and SD in the KRG intake group (r = 0.64, p < 0.0001) as well as between total amount of KRG and mean annual decrease in CD4⁺ T-cell count in all 252 patients (r = −0.17, p < 0.01). The annual decrease in CD4⁺ T-cell count (change in cells/μL) was significantly slower in KRG-treated patients than in patients receiving no KRG (48 ± 40 vs. 106 ± 162; p < 0.001). The SD (in months) was also significantly longer in the KRG group than in the no-KRG group (101 ± 64 vs. 59 ± 40, p < 0.01).

Conclusion

KRG prolongs survival in HIV-1 patients, possibly by slowing the decrease in CD4⁺ T-cell count.

The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency

The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.

Skin aging in patients with acquired immunodeficiency syndrome

To evaluate the histomorphometric skin changes over aging patients with autopsied acquired immunodeficiency syndrome (AIDS). In 29 skin fragments of autopsied elderly (older than 50 years) and nonelderly patients with AIDS, epidermal thickness, the number of layers, the diameter of cells, the percentage of collagen and elastic fibers in the dermis, and the number and morphology of Langerhans cells were assessed. Statistical analysis was performed by SigmaStat 2.03 program. The thickness of the epidermis (92.55 × 158.94 μm), the number of layers (7 × 9 layers), and the diameter of the cells (13.27 × 17.6 μm) were statistically lower among the elderly. The quantity of collagen fibers (9.68 × 14.11%) and elastic fibers (11.89 × 15.31%) was also significantly lower in the elderly. There was a decrease in total (10.61 × 12.38 cel/mm(2)) and an increase in immature Langerhans cells (6.31 × 4.98 cel/mm(2)) in elderly patients with AIDS. The aging of the skin of patients with AIDS is amended in different histomorphometric aspects, the epidermis constituents suffer less pronounced changes in normal aging, and the dermis has more intense changes in elastic fibers and collagen.

ILC You Later: Early and Irreparable Loss of Innate Lymphocytes in HIV Infection

Loss of IL-17-producing cells in the gut during HIV infection is linked to GI barrier damage. Kløverpris et al. (2016) find that circulating ILCs are lost early and irreversibly during HIV infection. Early ART administration protects against the ILC loss, and this might be clinically beneficial to HIV-infected individuals.