Case report: mechanisms of HIV elite control in two African women

Tuberculosis infection control practice among healthcare workers in Ethiopia: a protocol for systematic review and meta-analysis

BACKGROUND

Tuberculosis (TB) is a main concern of health care workers in sub-Saharan Africa. Healthcare workers have the potential to have contact with TB patients and are the main stakeholders in healthcare settings to implement TB infection control, and the poor practice of TB infection control may increase the risk of transmission of TB in healthcare settings. However, there is no consistent conclusion on the TB infection control practice among healthcare workers in Ethiopia. Thus, this study aimed to determine the pooled magnitude of TB infection control practice and associated factors among healthcare workers in Ethiopia.

METHODS

This systematic review and meta-analysis will be done by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. The following databases will be used to search for articles: PubMed, Cochrane Library, Google Scholar and grey literatures. The quality of studies will be assessed using the Joanna Briggs Institute (JBI) critical appraisal checklist. The data from included studies will be extracted using Microsoft Excel V.2016, and the extracted data will be analysed using STATA V.16. Forest plot and I2 statistics will be done for heterogeneity. A funnel plot and Egger's regression test will be conducted to check for publication bias. Potential sources of bias will be identified by subgroup analysis and meta-regression. Any type of study design conducted in Ethiopia and in English language will be included.

ETHICS AND DISSEMINATION

Ethics approval is not required, and the findings will be published in peer-reviewed journal.

PROSPERO REGISTRATION NUMBER

CRD42023393580.

Comparison of the Biological Basis for Non-HIV Transmission to HIV-Exposed Seronegative Individuals, Disease Non-Progression in HIV Long-Term Non-Progressors and Elite Controllers

HIV-exposed seronegative individuals (HESIs) are a small fraction of persons who are multiply exposed to human immunodeficiency virus (HIV), but do not exhibit serological or clinical evidence of HIV infection. In other words, they are groups of people maintaining an uninfected status for a long time, even after being exposed to HIV several times. The long-term non-progressors (LTNPs), on the other hand, are a group of HIV-infected individuals (approx. 5%) who remain clinically and immunologically stable for an extended number of years without combination antiretroviral therapy (cART). Meanwhile, elite controllers are comprise a much lower number (0.5%) of HIV-infected persons who spontaneously and durably control viremia to below levels of detection for at least 12 months, even when using the most sensitive assays, such as polymerase chain reaction (PCR) in the absence of cART. Despite the fact that there is no universal agreement regarding the mechanisms by which these groups of individuals are able to control HIV infection and/or disease progression, there is a general consensus that the mechanisms of protection are multifaceted and include genetic, immunological as well as viral factors. In this review, we analyze and compare the biological factors responsible for the control of HIV in these unique groups of individuals.

High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes

Background

Combatting the tuberculosis (TB) epidemic caused by Mycobacterium tuberculosis ( Mtb ) necessitates a better understanding of the factors contributing to patient clinical outcomes and transmission. While host and environmental factors have been evaluated, the impact of Mtb genetic background and phenotypic diversity is underexplored. Previous work has made associations between Mtb genetic lineages and some clinical and epidemiological features, but the bacterial traits underlying these connections are largely unknown.

Methods

We developed a high-throughput functional genomics platform for defining genotype-phenotype relationships across a panel of Mtb clinical isolates. These phenotypic fitness profiles function as intermediate traits which can be linked to Mtb genetic variants and associated with clinical and epidemiological outcomes. We applied this approach to a collection of 158 Mtb strains from a study of Mtb transmission in Ho Chi Minh City, Vietnam. Mtb strains were genetically tagged in multiplicate, which allowed us to pool the strains and assess in vitro competitive fitness using deep sequencing across a set of 14 host-relevant antibiotic and metabolic conditions. Phylogenetic and monogenic associations with these intermediate traits were identified and then associated with clinical outcomes.

Findings

Mtb clinical strains have a broad range of growth and drug response dynamics that can be clustered by their phylogenetic relationships. We identified novel monogenic associations with Mtb fitness in various metabolic and antibiotic conditions. Among these, we find that mutations in Rv1339 , a phosphodiesterase, which were identified through their association with slow growth in glycerol, are further associated with treatment failure. We also identify a previously uncharacterized subclade of Lineage 1 strains (L1.1.1.1) that is phenotypically distinguished by slow growth under most antibiotic and metabolic stress conditions in vitro . This clade is associated with cavitary disease, treatment failure, and demonstrates increased transmission potential.

Interpretation

High-throughput phenogenotyping of Mtb clinical strains enabled bacterial intermediate trait identification that can provide a mechanistic link between Mtb genetic variation and patient clinical outcomes. Mtb strains associated with cavitary disease, treatment failure, and transmission potential display intermediate phenotypes distinguished by slow growth under various antibiotic and metabolic conditions. These data suggest that Mtb growth regulation is an adaptive advantage for host bacterial success in human populations, in at least some circumstances. These data further suggest markers for the underlying bacterial processes that govern these clinical outcomes.

Funding

National Institutes of Allergy and Infectious Diseases: P01 AI132130 (SS, SMF); P01 AI143575 (XW, SMF); U19 AI142793 (QL, SMF); 5T32AI132120-03 (SS); 5T32AI132120-04 (SS); 5T32AI049928-17 (SS) Wellcome Trust Fellowship in Public Health and Tropical Medicine: 097124/Z/11/Z (NTTT) National Health and Medical Research Council (NHMRC)/A*STAR joint call: APP1056689 (SJD) The funding sources had no involvement in study methodology, data collection, analysis, and interpretation nor in the writing or submission of the manuscript.

Research in context

Evidence before this study: We used different combinations of the words mycobacterium tuberculosis, tuberculosis, clinical strains, intermediate phenotypes, genetic barcoding, phenogenomics, cavitary disease, treatment failure, and transmission to search the PubMed database for all studies published up until January 20 th , 2022. We only considered English language publications, which biases our search. Previous work linking Mtb determinants to clinical or epidemiological data has made associations between bacterial lineage, or less frequently, genetic polymorphisms to in vitro or in vivo models of pathogenesis, transmission, and clinical outcomes such as cavitary disease, treatment failure, delayed culture conversion, and severity. Many of these studies focus on the global pandemic Lineage 2 and Lineage 4 Mtb strains due in part to a deletion in a polyketide synthase implicated in host-pathogen interactions. There are a number of Mtb GWAS studies that have led to novel genetic determinants of in vitro drug resistance and tolerance. Previous Mtb GWAS analyses with clinical outcomes did not experimentally test any predicted phenotypes of the clinical strains. Published laboratory-based studies of Mtb clinical strains involve relatively small numbers of strains, do not identify the genetic basis of relevant phenotypes, or link findings to the corresponding clinical outcomes. There are two recent studies of other pathogens that describe phenogenomic analyses. One study of 331 M. abscessus clinical strains performed one-by-one phenotyping to identify bacterial features associated with clearance of infection and another details a competition experiment utilizing three barcoded Plasmodium falciparum clinical isolates to assay antimalarial fitness and resistance. Added value of this study: We developed a functional genomics platform to perform high-throughput phenotyping of Mtb clinical strains. We then used these phenotypes as intermediate traits to identify novel bacterial genetic features associated with clinical outcomes. We leveraged this platform with a sample of 158 Mtb clinical strains from a cross sectional study of Mtb transmission in Ho Chi Minh City, Vietnam. To enable high-throughput phenotyping of large numbers of Mtb clinical isolates, we applied a DNA barcoding approach that has not been previously utilized for the high-throughput analysis of Mtb clinical strains. This approach allowed us to perform pooled competitive fitness assays, tracking strain fitness using deep sequencing. We measured the replicative fitness of the clinical strains in multiplicate under 14 metabolic and antibiotic stress condition. To our knowledge, this is the largest phenotypic screen of Mtb clinical isolates to date. We performed bacterial GWAS to delineate the Mtb genetic variants associated with each fitness phenotype, identifying monogenic associations with several conditions. We then defined Mtb phenotypic and genetic features associated with clinical outcomes. We find that a subclade of Mtb strains, defined by variants largely involved in fatty acid metabolic pathways, share a universal slow growth phenotype that is associated with cavitary disease, treatment failure and increased transmission potential in Vietnam. We also find that mutations in Rv1339 , a poorly characterized phosphodiesterase, also associate with slow growth in vitro and with treatment failure in patients. Implications of all the available evidence: Phenogenomic profiling demonstrates that Mtb strains exhibit distinct growth characteristics under metabolic and antibiotic stress conditions. These fitness profiles can serve as intermediate traits for GWAS and association with clinical outcomes. Intermediate phenotyping allows us to examine potential processes by which bacterial strain differences contribute to clinical outcomes. Our study identifies clinical strains with slow growth phenotypes under in vitro models of antibiotic and host-like metabolic conditions that are associated with adverse clinical outcomes. It is possible that the bacterial intermediate phenotypes we identified are directly related to the mechanisms of these outcomes, or they may serve as markers for the causal yet unidentified bacterial determinants. Via the intermediate phenotyping, we also discovered a surprising diversity in Mtb responses to the new anti-mycobacterial drugs that target central metabolic processes, which will be important in considering roll-out of these new agents. Our study and others that have identified Mtb determinants of TB clinical and epidemiological phenotypes should inform efforts to improve diagnostics and drug regimen design.

Cohort profile: CareConekta: a pilot study of a smartphone application to improve engagement in postpartum HIV care in South Africa

PURPOSE

Pregnant and postpartum women living with HIV in South Africa are at high risk of dropping out of care, particularly after delivery. Population mobility may contribute to disruptions in HIV care, and postpartum women are known to be especially mobile. To improve engagement in HIV care during the peripartum period, we developed CareConekta, a smartphone application (app) that uses GPS coordinates to characterise mobility and allow for real-time intervention. We conducted a randomised controlled pilot study to assess feasibility, acceptability and initial efficacy of the app intervention to improve engagement in HIV care. This cohort profile describes participant enrolment and follow-up, describes the data collected and provides participant characteristics.

PARTICIPANTS

We enrolled 200 pregnant women living with HIV attending routine antenatal care at the Gugulethu Midwife Obstetric Unit in Cape Town, South Africa. Eligible women must have owned smartphones that met the app's technical requirements. Seven participants were withdrawn near enrolment, leaving 193 in the cohort.

FINDINGS TO DATE

Data were collected from detailed participant questionnaires at enrolment and follow-up (6 months after delivery), as well as GPS data from the app, and medical records. Follow-up is complete; initial analyses have explored smartphone ownership, preferences and patterns of use among women screened for eligibility and those enrolled in the study.

FUTURE PLANS

Additional planned analyses will characterise mobility in the population using the phone GPS data and participant self-reported data. We will assess the impact of mobility on engagement in care for the mother and infant. We also will describe the acceptability and feasibility of the study, including operational lessons learnt. By linking this cohort to the National Health Laboratory Service National HIV Cohort in South Africa, we will continue to assess engagement in care and mobility outcomes for years to come. Collaborations are welcome.

TRIAL REGISTRATION NUMBER

NCT03836625.

CD8 + T-cell responses in HIV controllers: potential implications for novel HIV remission strategies

PURPOSE OF REVIEW

Immunological studies of spontaneous HIV and simian virus (SIV) controllers have identified virus-specific CD8 +  T cells as a key immune mechanism of viral control. The purpose of this review is to consider how knowledge about the mechanisms that are associated with CD8 +  T cell control of HIV/SIV in natural infection can be harnessed in HIV remission strategies.

RECENT FINDINGS

We discuss characteristics of CD8 +  T-cell responses that may be critical for suppressing HIV replication in spontaneous controllers comprising HIV antigen recognition including specific human leukocyte antigen types, broadly cross-reactive T cell receptors and epitope targeting, enhanced expansion and antiviral functions, and localization of virus-specific T cells near sites of reservoir persistence. We also discuss the need to better understand the timing of CD8 +  T-cell responses associated with viral control of HIV/SIV during acute infection and after treatment interruption as well as the mechanisms by which HIV/SIV-specific CD8 +  T cells coordinate with other immune responses to achieve control.

SUMMARY

We propose implications as to how this knowledge from natural infection can be applied in the design and evaluation of CD8 +  T-cell-based remission strategies and offer questions to consider as these strategies target distinct CD8 +  T-cell-dependent mechanisms of viral control.

Seroprevalence of syphilis and its predictors among pregnant women in Buno Bedele zone, southwest Ethiopia: a community-based cross-sectional study

OBJECTIVES

The study was aimed at assessing the prevalence of syphilis and associated factors among pregnant women with antenatal care follow-up.

DESIGN

A health facility-based, cross-sectional study.

SETTING

The study was conducted in 12 health facilities in Buno Bedele zone, southwest Ethiopia.

PARTICIPANTS

Randomly selected 920 pregnant women who came to health facilities in the Buno Bedele zone for antenatal care services from May to August 2021 were included in the study. Women with previously diagnosed syphilis and those on treatment were excluded from the study.

OUTCOME MEASURES

Blood samples and data on sociodemographic and other risk factors for syphilis were collected. Sera were screened for syphilis using the one-step rapid syphilis diagnostic test kit, and positive tests were retested using the rapid plasma reagin test. Data were analysed using SPSS V.22. Bivariate and multivariate logistic regression analyses were used to identify risk factors for maternal syphilis at a p value less than 0.05.

RESULTS

The prevalence of syphilis among pregnant women was found to be 1.4% (95% CI: 0.8% to 2.3%, p=0.002). Women with no formal education (adjusted OR (AOR)=3.6; 95% CI: 1.02 to 13.2, p=0.047), husbands with a history of substance use (AOR=3.3, 95% CI: 1.04 to 10.7, p=0.042), more than one antenatal care visit (AOR=3.5, 95% CI: 1.07 to 10.5, p=0.038), age at marriage under 18 years (AOR=4.3, 95% CI: 2.2 to 7.9, p=0.045) and a woman's poor knowledge of syphilis (AOR=3.3, 95% CI: 1.04 to 10.4, p=0.042) were significantly associated with syphilis.

CONCLUSION

The prevalence of maternal syphilis in this study area was found to be comparable with the national prevalence. Women's educational status, husbands' history of substance use, antenatal care, age at marriage and knowledge about syphilis were the independent predictors of syphilis. Emphasis shall be given to screening all pregnant women, education of women, lifestyle factors and avoiding early marriage.

Type 2 diabetes and hypertension in Vietnam: a systematic review and meta-analysis of studies between 2000 and 2020

OBJECTIVES

The objective of this study was to determine the level of type 2 diabetes (T2DM) and hypertension (HTN) in Vietnam and to assess the trend and recommend the future direction of prevention research efforts.

DESIGN

We searched scientific literature, databases including PubMed, EMBASE, CINHAL and Google Scholar; grey literature and reference lists for primary research published, nation database websites between 1 January 2000 and 30 September 2020. We adapted the modified Newcastle Ottawa Scale for assessing the quality of the study, as recommended by the Cochrane Collaboration.

RESULTS

In total, 83 studies met our inclusion criteria, representing data of approximately 239 034 population of more than 15 years of age in Vietnam. The findings show that prevalence rates varied widely across studies, from 1.0% to 29.0% for T2DM and 2.0% to 47.0% for HTN. For the total study period, pooled prevalence of T2DM and HTN in Vietnam for all studies was 6.0% (95% CI: 4.0% to 7.0%) and 25% (95% CI: 19% to 31%), respectively. Prevalence rate of both T2DM and HTN was higher among the male population compared with female counterpart.

CONCLUSION

There is evidence of a rising trend of HTN and T2DM prevalence in Vietnam. Future research should focus on the major drivers, incidence and prognosis of T2DM and HTN. Policy approaches should base upon the trends of T2DM and HTN in Vietnam over the last 20 years and pay more attention on the effective interventions to combat T2DM and HTN. In our study, we included both English and Vietnamese language articles and seems that majority of the articles came from Vietnamese language.

PROSPERO REGISTRATION NUMBER

CRD42020182959.

Intestinal perforation due to miliary tuberculosis in a patient with myasthenia gravis

A man in his early 70s presented to the emergency department with a fall, following a history of fatigue and malodorous urine. On presentation, he was feverish, tachycardic and confused and was treated for presumed urinary sepsis. A chest radiograph showed increased opacification in the left upper lobe with calcification. CT imaging and bronchoalveolar lavage demonstrated miliary tuberculosis infection. His background included myasthenia gravis, which led to challenges in selecting appropriate antituberculosis treatment. During his stay, he developed sudden-onset abdominal pain due to intestinal perforation. He subsequently deteriorated and underwent multiple interventions, including a Hartmann's procedure and ileocaecal resection. Histological examination of his sigmoid colon revealed abundant acid-fast bacilli. Unfortunately, the patient died due to multiorgan failure in the context of several complications. This case highlights intestinal perforation as a rare complication of miliary tuberculosis and emphasises the importance of being vigilant for this potential complication.

Different drugs, different sides: injection use of opioids alone, and not stimulants alone, predisposes to right-sided endocarditis

Objectives

Many studies suggest that infective endocarditis (IE) in people who inject drugs is predominantly right sided, while other studies suggest left sided disease; few have differentiated by class of drug used. We hypothesised that based on differing physiological mechanisms, opioids but not stimulants would be associated with right sided IE.

Methods

A retrospective case series of 290 adult (age ≥18) patients with self-reported recent injection drug use, admitted for a first episode of IE to one of three hospitals in London Ontario between April 2007 and March 2018, stratified patients by drug class used (opioid, stimulant or both), and by site of endocarditis. Other outcomes captured included demographics, causative organisms, cardiac and non-cardiac complications, referral to addiction services, medical versus surgical management, and survival.

Results

Of those who injected only opioids, 47/71 (69%) developed right-sided IE, 17/71 (25%) developed left-sided IE and 4/71 (6%) had bilateral IE. Of those who injected only stimulants, 11/24 (46%) developed right-sided IE, 11/24 (46%) developed left-sided IE and 2/24 (8%) had bilateral IE. Relative to opioid-only users, stimulant-only users were 1.75 (95% CI 1.05 to 2.93; p=0.031) times more likely to have a left or bilateral IE versus right IE.

Conclusions

While injection use of opioids is associated with a strong predisposition to right-sided IE, stimulants differ in producing a balanced ratio of right and left-sided disease. As the epidemic of crystal methamphetamine injection continues unabated, the rate of left-sided disease, with its attendant higher morbidity and mortality, may also grow.

Using nasal sprays to prevent respiratory tract infections: a qualitative study of online consumer reviews and primary care patient interviews

OBJECTIVES

Nasal sprays could be a promising approach to preventing respiratory tract infections (RTIs). This study explored lay people's perceptions and experiences of using nasal sprays to prevent RTIs to identify barriers and facilitators to their adoption and continued use.

DESIGN

Qualitative research. Study 1 thematically analysed online consumer reviews of an RTI prevention nasal spray. Study 2 interviewed patients about their reactions to and experiences of a digital intervention that promotes and supports nasal spray use for RTI prevention (reactively: at 'first signs' of infection and preventatively: following possible/probable exposure to infection). Interview transcripts were analysed using thematic analysis.

SETTING

Primary care, UK.

PARTICIPANTS

407 online customer reviews. 13 purposively recruited primary care patients who had experienced recurrent infections and/or had risk factors for severe infections.

RESULTS

Both studies identified various factors that might influence nasal spray use including: high motivation to avoid RTIs, particularly during the COVID-19 pandemic; fatalistic views about RTIs; beliefs about alternative prevention methods; the importance of personal recommendation; perceived complexity and familiarity of nasal sprays; personal experiences of spray success or failure; tolerable and off-putting side effects; concerns about medicines; and the nose as unpleasant and unhygienic.

CONCLUSIONS

People who suffer disruptive, frequent or severe RTIs or who are vulnerable to RTIs are interested in using a nasal spray for prevention. They also have doubts and concerns and may encounter problems. Some of these may be reduced or eliminated by providing nasal spray users with information and advice that addresses these concerns or helps people overcome difficulties.

Mechanism of Viral Suppression among HIV Elite Controllers and Long-Term Nonprogressors in Nigeria and South Africa

A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall into this category, and a large sample of this group can be found in areas with a high prevalence of HIV infection such as Nigeria and South Africa. Understanding the mechanism underpinning the nonprogressive phenotype in this subgroup may provide insights into the control of the global HIV epidemic. This work provides mechanisms of the elite control and nonprogressive phenotype among PLHIV in Nigeria and South Africa and identifies research gaps that will contribute to a better understanding on HIV controllers among PLHIV.

Rabies mortality and morbidity associated with animal bites in Africa: a case for integrated rabies disease surveillance, prevention and control: a scoping review

OBJECTIVE

The objective of this scoping review was to map the current situation and available evidence and gaps on rabies morbidity, mortality, integrated rabies surveillance programmes, and existing prevention and control strategies in Africa.

METHODS

We conducted a systematic scoping review following the Joanna Briggs methodology and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews checklist. Medline, Embase, CINAHL (EBSCOHost), Scopus, Web of Science and rabies web conferences were used to search for peer-reviewed publications between January 1946 and May 2020. Two researchers reviewed the studies and extracted data based on author (year) and region, study design and data collection duration, participants/comparators, interventions, control conditions/exposures and outcomes (rabies mortality and morbidity) and key findings/gaps/challenges. The results were reported narratively using Arksey and O'Malley's methodological framework.

RESULTS

Electronic search yielded 2775 records, of which 43 studies were included. A total of 543 714 bite victims were censored through the included studies. Most of the victims were less than 15 years of age. The studies included rabies morbidity (21) and mortality (15) fluctuating in space and time across Africa depending on countries' rabies prevention and control practices (16). Others were surveillance (nine studies); surveillance and prevention (five studies); management and control (seven studies); and surveillance, prevention and control (six studies). We found challenges in rabies reporting, existing dog vaccination programmes and post-exposure prophylaxis availability or compliance.

CONCLUSION

This study found challenges for dog rabies control and elimination in Africa and the need for a policy to drive the goal of zero dog-transmitted rabies to humans by 2030.This is an open-access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build on this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated and the use is non-commercial (see http://creativecommons.org/licenses/by-nc/4.0/).

HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy

Curing HIV will require eliminating the reservoir of integrated, replication-competent proviruses that persist despite antiretroviral therapy (ART). Understanding the burden, genetic diversity, and longevity of persisting proviruses in diverse individuals with HIV is critical to this goal, but these characteristics remain understudied in some groups. Among them are viremic controllers—individuals who naturally suppress HIV to low levels but for whom therapy is nevertheless recommended. We reconstructed within-host HIV evolutionary histories from longitudinal single-genome amplified viral sequences in four viremic controllers who eventually initiated ART and used this information to characterize the age and diversity of proviruses persisting on therapy. We further leveraged these within-host proviral age distributions to estimate rates of proviral turnover prior to ART. This is an important yet understudied metric, since pre-ART proviral turnover dictates reservoir composition at ART initiation (and thereafter), which is when curative interventions, once developed, would be administered. Despite natural viremic control, all participants displayed significant within-host HIV evolution pretherapy, where overall on-ART proviral burden and diversity broadly reflected the extent of viral replication and diversity pre-ART. Consistent with recent studies of noncontrollers, the proviral pools of two participants were skewed toward sequences that integrated near ART initiation, suggesting dynamic proviral turnover during untreated infection. In contrast, proviruses recovered from the other two participants dated to time points that were more evenly spread throughout infection, suggesting slow or negligible proviral decay following deposition. HIV cure strategies will need to overcome within-host proviral diversity, even in individuals who naturally controlled HIV replication before therapy.

A recombinant measles virus vaccine strongly reduces SHIV viremia and virus reservoir establishment in macaques

Replicative vectors derived from live-attenuated measles virus (MV) carrying additional non-measles vaccine antigens have long demonstrated safety and immunogenicity in humans despite pre-existing immunity to measles. Here, we report the vaccination of cynomolgus macaques with MV replicative vectors expressing simian-human immunodeficiency virus Gag, Env, and Nef antigens (MV-SHIV Wt) either wild type or mutated in the immunosuppressive (IS) domains of Nef and Env antigens (MV-SHIV Mt). We found that the inactivation of Nef and Env IS domains by targeted mutations led to the induction of significantly enhanced post-prime cellular immune responses. After repeated challenges with low doses of SHIV-SF162p3, vaccinees were protected against high viremia, resulting in a 2-Log reduction in peak viremia, accelerated viral clearance, and a decrease -even complete protection for nearly half of the monkeys- in reservoir cell infection. This study demonstrates the potential of a replicative viral vector derived from the safe and widely used measles vaccine in the development of a future human vaccine against HIV-1.

The influence of HLA/HIV genetics on the occurrence of elite controllers and a need for therapeutics geotargeting view

The interaction of HIV-1, human leukocyte antigen (HLA), and elite controllers (EC) compose a still intricate triad. Elite controllers maintain a very low viral load and a normal CD4 count, even without antiretrovirals. There is a lot of diversity in HIV subtypes and HLA alleles. The most common subtype in each country varies depending on its localization and epidemiological history. As we know EC appears to maintain an effective CD8 response against HIV. In this phenomenon, some alleles of HLAs are associated with a slow progression of HIV infection, others with a rapid progression. This relationship also depends on the virus subtype. Epitopes of Gag protein-restricted by HLA-B*57 generated a considerable immune response in EC. However, some mutations allow HIV to escape the CD8 response, while others do not. HLA protective alleles, like HLA-B*27, HLA-B*57 and HLA-B*58:01, that are common in Caucasians infected with HIV-1 Clade B, do not show the same protection in sub-Saharan Africans infected by HIV-1 Clade C. Endogenous pathway of antigen processing and presentation is used to present intracellular synthesized cellular peptides as well as viral protein fragments via the MHC class I molecule to the cytotoxic T-lymphocytes (CTLs). Some epitopes are immunodominant, which means that they drive the immune reaction to some virus. Mutation on an anchor residue of epitope necessary for binding on MHC class I is used by HIV to escape the immune system. Mutations inside or flanking an epitope may lead to T cell lack of recognition and CTL escape. Studying how immunodominance at epitopes drives the EC in a geographically dependent way with genetics and immunological elements orchestrating it may help future research on vaccines or immunotherapy for HIV.

Additive quantile mixed effects modelling with application to longitudinal CD4 count data

Quantile regression offers an invaluable tool to discern effects that would be missed by other conventional regression models, which are solely based on modeling conditional mean. Quantile regression for mixed-effects models has become practical for longitudinal data analysis due to the recent computational advances and the ready availability of efficient linear programming algorithms. Recently, quantile regression has also been extended to additive mixed-effects models, providing an efficient and flexible framework for nonparametric as well as parametric longitudinal forms of data analysis focused on features of the outcome beyond its central tendency. This study applies the additive quantile mixed model to analyze the longitudinal CD4 count of HIV-infected patients enrolled in a follow-up study at the Centre of the AIDS Programme of Research in South Africa. The objective of the study is to justify how the procedure developed can obtain robust nonlinear and linear effects at different conditional distribution locations. With respect to time and baseline BMI effect, the study shows a significant nonlinear effect on CD4 count across all fitted quantiles. Furthermore, across all fitted quantiles, the effect of the parametric covariates of baseline viral load, place of residence, and the number of sexual partners was found to be major significant factors on the progression of patients' CD4 count who had been initiated on the Highly Active Antiretroviral Therapy study.

Impact of the gate-keeping policies of China's primary healthcare model on the future burden of tuberculosis in China: a protocol for a mathematical modelling study

INTRODUCTION

In the past three decades, China has made great strides in the prevention and treatment of tuberculosis (TB). However, the TB burden remains high. In 2019, China accounted for 8.4% of global incident cases of TB, the third highest in the world, with a higher prevalence in rural areas. The Healthy China 2030 highlights the gate-keeping role of primary healthcare (PHC). However, the impact of PHC reforms on the future TB burden is unclear. We propose to use mathematical models to project and evaluate the impacts of different gate-keeping policies.

METHODS AND ANALYSIS

We will develop a deterministic, population-level, compartmental model to capture the dynamics of TB transmission within adult rural population. The model will incorporate seven main TB statuses, and each compartment will be subdivided by service providers. The parameters involving preference for healthcare seeking will be collected using discrete choice experiment (DCE) method. We will solve the deterministic model numerically over a 20-year (2021-2040) timeframe and predict the TB prevalence, incidence and cumulative new infections under the status quo or various policy scenarios. We will also conduct an analysis following standard protocols to calculate the average cost-effectiveness for each policy scenario relative to the status quo. A numerical calibration analysis against the available published TB prevalence data will be performed using a Bayesian approach.

ETHICS AND DISSEMINATION

Most of the data or parameters in the model will be obtained based on secondary data (eg, published literature and an open-access data set). The DCE survey has been reviewed and approved by the Ethics Committee of the School of Public Health, Sun Yat-sen University. The approval number is SYSU [2019]140. Results of the study will be disseminated through peer-reviewed journals, media and conference presentations.

A high prevalence of potential HIV elite controllers identified over 30 years in Democratic Republic of Congo

Background

In-depth analysis of the HIV pandemic at its epicenter in the Congo basin has been hampered by 40 years of political unrest and lack of functional public health infrastructure. In recent surveillance studies (2017-18), we found that the prevalence of HIV in Kinshasa, Democratic Republic of Congo (11%) far exceeded previous estimates.

Methods

10,457 participants were screened in Kinshasa with rapid tests from 2017-2019. Individuals confirmed as reactive by the Abbott ARCHITECT HIV Ag/Ab Combo assay (n=1968) were measured by the Abbott RealTime HIV-1 viral load assay. Follow up characterization of samples was performed with alternate manufacturer viral load assays, qPCR for additional blood borne viruses, unbiased next generation sequencing, and HIV Western blotting.

Findings

Our data suggested the existence of a significant cohort (n=429) of HIV antibody positive/viral load negative individuals. We systematically eliminated collection site bias, sample integrity, and viral genetic diversity as alternative explanations for undetectable viral loads. Mass spectroscopy unexpectedly detected the presence of 3TC antiviral medication in approximately 60% of those tested (209/354), and negative Western blot results indicated false positive serology in 12% (49/404). From the remaining Western blot positives (n=53) and indeterminates (n=31) with reactive Combo and rapid test results, we estimate 2.7-4.3% of infections in DRC to be potential elite controllers. We also analyzed samples from the DRC collected in 1987 and 2001-03, when antiretroviral drugs were not available, and found similarly elevated trends.

Interpretation

Viral suppression to undetectable viral loads without therapy occurs infrequently in HIV-1 infected patients around the world. Mining of global data suggests a unique ability to control HIV infection arose early in central Africa and occurs in <1% of founder populations. Identification of this group of elite controllers presents a unique opportunity to study potentially novel genetic mechanisms of viral suppression.

Funding

Abbott Laboratories funded surveillance in DRC and subsequent research efforts. Additional funding was received from a MIZZOU Award from the University of Missouri. Research was supported in part by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH.

Geographical Distribution and Risk Factors of Low Birth Weight in Nigeria

BACKGROUND

Low birth weight (LBW) directly or indirectly accounts for 60% to 80% of all neonatal deaths globally, and it has become an issue of serious health concern with Nigeria with one of the highest infant mortality rates (74/1,000) in the world. Despite the severe health impact, little is understood on the geographical differences in maternal socioeconomic and environmental factors that affect LBW across the states in Nigeria.

METHOD

Using the spatial epidemiological approach, this study examined the geographical variations in LBW and associated risk factors in Nigeria with the aid of spatial statistics.

RESULTS

There was a regional LBW corridor in the extreme north with Yobe state with the highest prevalence rate. Maternal educational attainment and acute maternal malnutrition explained 65.4% (ordinary least squares model) and 70.5% (spatial error model, SEM) of the variation in the geographical pattern of LBW.

CONCLUSION

LBW remains an issue of serious health concern in Nigeria. The finding of this study would shed more light on the spatial epidemiology of LBW in Nigeria and also guide public health programs in curtailing the high prevalence rate of LBW.

RECOMMENDATIONS

The study recommends health education on nutrition in pregnancy and the need to improve health literacy among women so as to check the high LBW prevalence.

Modelling CD4 counts before and after HAART for HIV infected patients in KwaZulu-Natal South Africa

BACKGROUND

This study aims to make use of a longitudinal data modelling approach to analyze data on the number of CD4+cell counts measured repeatedly in HIV-1 Subtype C infected women enrolled in the Acute Infection Study of the Centre for the AIDS Programme of Research in South Africa.

METHODOLOGY

This study uses data from the CAPRISA 002 Acute Infection Study, which was conducted in South Africa. This cohort study observed N=235 incident HIV-1 positive women whose disease biomarkers were measured repeatedly at least four times on each participant.

RESULTS

From the findings of this study, post-HAART initiation, baseline viral load, and the prevalence of obese nutrition status were found to be major significant factors on the prognosis CD4+ count of HIV-infected patients.

CONCLUSION

Effective HAART initiation immediately after HIV exposure is necessary to suppress the increase of viral loads to induce potential ART benefits that accrue over time. The data showed evidence of strong individual-specific effects on the evolution of CD4+ counts. Effective monitoring and modelling of disease biomarkers are essential to help inform methods that can be put in place to suppress viral loads for maximum ART benefits that can be accrued over time at an individual level.

Viral reservoirs in elite controllers of HIV-1 infection: Implications for HIV cure strategies

Elite controllers are HIV-1 positive subjects who control viral replication without antiretroviral therapy. Many of these subjects have replication-competent virus and thus represent a model of a functional cure. Peripheral CD4+ T cells in these subjects have small reservoirs with a low frequency of intact proviruses. Furthermore, recent studies suggest that many of these intact proviruses are disproportionally integrated at sites that have limited transcriptional activity raising the possibility that replication-competent viruses do not replicate because they are in a “blocked and locked” state. However, this feature is probably a consequence rather than a cause of elite control. Additionally, evolution of plasma virus has been detected in many elites suggesting that there continues to be ongoing viral replication in other compartments. While exceptional elite controllers with very limited viral reservoirs have recently been described, more work is needed to determine whether these patients have achieved a sterilizing cure.

Estimating the establishment of local transmission and the cryptic phase of the COVID-19 pandemic in the USA

We use a global metapopulation transmission model to study the establishment of sustained and undetected community transmission of the COVID-19 pandemic in the United States. The model is calibrated on international case importations from mainland China and takes into account travel restrictions to and from international destinations. We estimate widespread community transmission of SARS-CoV-2 in February, 2020. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 in the West and East Coast metropolitan areas that could have been seeded as early as late-December, 2019. For most of the continental states the largest contribution of imported infections arrived through domestic travel flows.

Increased expression of CDKN1A/p21 in HIV-1 controllers is correlated with upregulation of ZC3H12A/MCPIP1

BACKGROUND

Some multifunctional cellular proteins, as the monocyte chemotactic protein-induced protein 1 (ZC3H12A/MCPIP1) and the cyclin-dependent kinase inhibitor CDKN1A/p21, are able to modulate the cellular susceptibility to the human immunodeficiency virus type 1 (HIV-1). Several studies showed that CDKN1A/p21 is expressed at high levels ex vivo in cells from individuals who naturally control HIV-1 replication (HIC) and a recent study supports a coordinate regulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in a model of renal carcinoma cells. Here, we explored the potential associations between mRNA expression of ZC3H12A/MCPIP1 and CDKN1A/p21 in HIC sustaining undetectable (elite controllers-EC) or low (viremic controllers-VC) viral loads.

RESULTS

We found a selective upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in PBMC from HIC compared with both ART-suppressed and HIV-negative control groups (P≤ 0.02) and higher MCPIP1 and p21 proteins levels in HIC than in HIV-1 negative subjects. There was a moderate positive correlation (r ≥ 0.57; P ≤ 0.014) between expressions of both transcripts in HIC and in HIC combined with control groups. We found positive correlations between the mRNA level of CDKN1A/p21 with activated CD4+ T cells levels in HIC (r ≥ 0.53; P ≤ 0.017) and between the mRNA levels of both CDKN1A/p21 (r = 0.74; P = 0.005) and ZC3H12A/MCPIP1 (r = 0.58; P = 0.040) with plasmatic levels of sCD14 in EC. Reanalysis of published transcriptomic data confirmed the positive association between ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in CD4+ T cells and monocytes from disparate cohorts of HIC and other HIV-positive control groups.

CONCLUSIONS

These data show for the first time the simultaneous upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in the setting of natural suppression of HIV-1 replication in vivo and the positive correlation of the expression of these cellular factors in disparate cohorts of HIV-positive individuals. The existence of a common regulatory pathway connecting ZC3H12A/MCPIP1 and CDKN1A/p21 could have a synergistic effect on HIV-1 replication control and pharmacological manipulation of these multifunctional host factors may open novel therapeutic perspectives to prevent HIV-1 replication and disease progression.

Barriers to and enablers of uptake of and adherence to antiretroviral therapy in the context of integrated HIV and tuberculosis treatment among adults in sub-Saharan Africa: a protocol for a systematic literature review

INTRODUCTION

The scale-up of integrated Human Immunodeficiency Virus (HIV) and tuberculosis (TB) treatment has been an important intervention to curb the burden of HIV and TB co-infection worldwide. Uptake of and adherence to antiretroviral therapy (ART) are key determinants of the quality and therapeutic endpoints of this intervention. This study aims to conduct an up-to-date collection and synthesis of evidence on barriers to and facilitators of uptake of and adherence to ART in HIV/TB integrated treatment programs in sub-Saharan Africa (SSA).

METHOD

A systematic review of peer-reviewed literature on the uptake of and adherence to ART in the context of integrated therapy for HIV and TB in SSA will be performed. We will review qualitative and quantitative studies reporting on the uptake of and adherence to ART during integrated treatment for TB and HIV among adults. These will include studies that involve HIV-infected TB patients initiating ART and studies involving PLWHA already on ART who are newly diagnosed with TB. Qualitative studies, quantitative studies, randomised trials and observational studies will be included. Six databases including Medline and Embase will be searched for relevant studies published from March 2004 to July 2019. Two authors will independently screen the search output and retrieve full texts of eligible studies. Disagreements between the two authors will be resolved by arbitration by a third author. Data will be abstracted from the eligible studies and synthesis will be done through descriptive synthesis for qualitative data and meta-analysis for quantitative data.

ETHICS AND DISSEMINATION

This study will be a review of the literature and will not involve primary collection of individuals' data. Amendments to the protocol will be documented in the final review. The final study will be published in a peer-reviewed journal and presented at conferences. The review is expected to contribute to improving strategies to enhance uptake of and adherence to ART in integrated care.

PROSPERO REGISTRATION NUMBER

CRD42019131933.

Rapid development of HIV elite control in a patient with acute infection

Background

Elite controllers (EC), a small subset of the HIV-positive population (< 1%), suppress HIV viremia below the limit of quantification of clinical viral load assays in the absence of antiretroviral therapy (ART). However, there is a paucity of longitudinal data detailing the viral and immune dynamics or HIV reservoir seeding during acute infection in individuals that go on to become Elite Controllers.

Case presentation

In this report, we describe a case of a 42 year old woman diagnosed during acute infection who rapidly and permanently suppressed her viremia in the absence of antiretroviral therapy (ART). Rapid antibody/antigen testing was either negative or equivocal during acute infection, despite subsequent viral load testing at that time point with 71,550 plasma HIV RNA copies/mL, making initial diagnosis challenging. The patient subsequently developed detectable anti-HIV antibodies and an increase in HIV-specific CD8+ T cell responses to overlapping subtype C HIV gag peptide; very low-level plasma viremia (0.84 RNA copies/mL) was detected by an ultrasensitive assay 2 years following infection. Subsequently, she was started on ART for multifocal furunculosis despite continued suppression of virus and stable CD4+ T cell counts. Following ART initiation, HIV specific antibody levels and CD8+ T cell responses increased, but no HIV DNA or RNA was able to be isolated from large numbers of peripheral blood CD4+ T cells.

Conclusion

This case provides important information regarding the establishment of elite HIV control during acute infection and also demonstrates an increase in HIV-specific immune responses following ART despite undetectable peripheral blood cellular measures of HIV persistence. This case also highlights the challenges in diagnosing acute HIV infection without the use of viral load testing in this rare elite controller phenotype.

A rare pulmonary pathology complicated with an unusual condition

A 73-year-old male presented to the emergency department complaining about fatigue, night sweats, lack of appetite and weight loss for the past 2 months. His baseline weight was 47 kg and his height was 1.78 m (body mass index of 14.83 kg·m⁻²), while at presentation he weighed 39 kg. From his history, he underwent gastrectomy 31 years ago for stomach cancer. He was a smoker (55 pack-years), with no history of alcohol consumption or any other known pathological condition. Despite his gastrectomy, he did not suffer from symptoms suggesting reflux disease. 2 years ago, his daughter suffered from pulmonary tuberculosis, but he was not checked at that time with either a Mantoux test or chest radiograph. Physical examination revealed crackles in both lungs. His heart rate and blood pressure were normal. Because of his gastrectomy, he was on treatment with B12 and folic acid supplements and on presentation he did not reveal megaloblastic anaemia. From his laboratory examinations, his white blood cells were normal (9780 cells·μL⁻¹ (68.4% neutrophils, 21.7% lymphocytes)) while his C-reactive protein was elevated (8.87 mg·dL⁻¹). Despite his obviously impaired nutritional status his serum albumin was slightly above the lower normal level (3.67 g·dL⁻¹). His chest computed tomography (CT) revealed infiltrations bilaterally, signs of incipient pulmonary fibrosis with thickened interlobular septa, centrilobular nodules and loss of volume of the left lower lobe (figure 1). His blood gas analysis revealed hypoxaemia; therefore, he was admitted to hospital and initiated intravenous antibiotic treatment with ampicillin/sulbactam plus azithromycin.

Differential diagnosis should never be limited to the obvious diagnoseshttp://ow.ly/ybTM30obh6H

An integrative genomic analysis of transcriptional profiles identifies characteristic genes and patterns in HIV-infected long-term non-progressors and elite controllers

Background

Despite that most HIV-infected individuals experience progressive CD4+ T cell loss and develop AIDS, a minority of HIV-infected individuals remain asymptomatic and maintain high level CD4+ T cell counts several years after seroconversion. Efforts have been made to understand the determinants of the nonprogressive status, exemplified by the clinical course of elite controllers (ECs) who maintain an undetectable viremia and viremic nonprogressors (VNPs) who have a normal CD4+ count in spite of circulating viral load. However, the intrinsic mechanism underlying nonprogression remained elusive. In this study, we performed an integrative analysis of transcriptional profiles to pinpoint the underlying mechanism for a naturally occurring viral control.

Methods

Three microarray datasets, reporting mRNA expression of the LTNPs or ECs in HIV-infected patients, were retrieved from Gene Expression Ominbus (GEO) or Arrayexpress databases. These datasets, profiled on the same type of microarray chip, were selected and merged by a bioinformatic approach to build a meta-analysis derived transcriptome (MADNT). In addition, we investigated the different transcriptional pathways and potential biomarkers in CD4+ and CD8+ cells in ECs and whole blood in VNPs compared to HIV progressors. The combined transcriptome and each subgroup was subject to gene set enrichment analysis and weighted co-expression network analysis to search potential transcription patterns related to the non-progressive status.

Results

30 up-regulated genes and 83 down-regulated genes were identified in lymphocytes from integrative meta-analysis of expression data. The interferon response and innate immune activation was reduced in both CD4+ and CD8+ T cells from ECs. Several characteristic genes including CMPK1, CBX7, EIF3L, EIF4A and ZNF395 were indicated to be highly correlated with viremic control. Besides that, we indicated that the reduction of ribosome components and blockade of translation facilitated AIDS disease progression. Most interestingly, among VNPs who have a relatively high viral load, we detected a two gene-interaction networks which showed a strong correlation to immune control even with a rigorous statistical threshold (p value = 2−e4 and p value = 0.004, respectively) by WGCNA.

Conclusions

We have identified differentially expressed genes and transcriptional patterns in ECs and VNPs compared to normal chronic HIV-infected individuals. Our study provides new insights into the pathogenesis of HIV and AIDS and clues for the therapeutic strategies for anti-retroviral administration.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1777-7) contains supplementary material, which is available to authorized users.

Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants

Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8⁺ T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML_180–188) in the context of the protective allele B*81:01 and the less protective allele B*42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B*81:01 and B*42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B*42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation.

Closely related HLA alleles presenting similar HIV-1 epitopes can be associated with variable clinical outcome. Here the authors report their findings on CD8+ T cell responses to the HIV-1 Gag-p24 TL9 immunodominant epitope in the context of closely related protective and less protective HLA alleles, and their differential effect on viral control

HIV control: Is getting there the same as staying there?

In this brief review and perspective, we address the question of whether the immune responses that bring about immune control of acute HIV infection are the same as, or distinct from, those that maintain long-term viral suppression once control of viremia has been achieved. To this end, we describe the natural history of elite and post-treatment control, noting the lack of data regarding what happens acutely. We review the evidence suggesting that the two clinical phenotypes may differ in terms of the mechanisms required to achieve and maintain control, as well as the level of inflammation that persists once a steady state is achieved. We then describe the evidence from longitudinal studies of controllers who fail and studies of biologic sex (male versus female), age (children versus adults), and simian immunodeficiency virus (SIV) (pathogenic/experimental versus nonpathogenic/natural infection). Collectively, these studies demonstrate that the battle between the inflammatory and anti-inflammatory pathways during acute infection has long-term consequences, both for the degree to which control is maintained and the health of the individual. Potent and stringent control of HIV may be required acutely, but once control is established, the chronic inflammatory response can be detrimental. Interventional approaches designed to bring about HIV cure and/or remission should be nuanced accordingly.

Understanding the CD8 T-cell response in natural HIV control

HIV-infected individuals who maintain control of virus without antiretroviral therapy (ART) are called HIV controllers. The immune responses of these individuals suppress HIV viral replication to low levels or, in the case of elite controllers, to undetectable levels. Although some research indicates a role for inferior virulence of the infecting viral strain in natural control, perhaps by way of defective Nef protein function, we find that the majority of research in HIV controllers highlights CD8 T cells as the main suppressor of viral replication. The most convincing evidence for this argument lies in the strong correlation between certain HLA-I alleles, especially B*57, and HIV control status, a finding that has been replicated by many groups. However, natural control can also occur in individuals lacking these specific HLA alleles, and our understanding of what constitutes an effective CD8 T-cell response remains an incomplete picture. Recent research has broadened our understanding of natural HIV control by illustrating the interactions between different immune cells, including innate immune effectors and antigen-presenting cells. For many years, the immune responses of the natural HIV controllers have been studied for clues on how to achieve functional cure in the rest of the HIV-infected population. The goal of a future functional cure to HIV is one where HIV-infected individuals’ immune responses are able to suppress virus long-term without requiring ART. This review highlights recent advances in our understanding of how HIV controllers’ natural immune responses are able to suppress virus.