Early HIV-1 diagnosis using in-house real-time PCR amplification on dried blood spots for infants in remote and resource-limited settings

Antibiotic-Modified Nanoparticles Combined with Lysozyme for Rapid Extraction of Pathogenic Bacteria DNA in Blood

Rapid and precise identification of the pathogens causing sepsis remains a significant diagnostic challenge. Blood culture is time-consuming and insensitive, while molecular diagnostic techniques, such as the polymerase chain reaction (PCR), are fast but greatly influenced by template quality. Here, we present a new approach to separate trace amounts of pathogen DNA from blood, which utilizes lysozyme to destroy bacteria and release DNA, followed by enrichment and purification using magnetic nanoparticles (MNPs) modified with kanamycin (Kan) or tobramycin (TM). We demonstrate that the prepared Kan@MNPs and TM@MNPs can efficiently adsorb DNA, with the mechanism involving interaction with the minor groove of DNA. Notably, the adoption of lysozyme ensures bacterial lysis while avoiding damage to blood cells, minimizing the interference from human genomic DNA background and inhibitory components, thereby obtaining relatively pure bacterial DNA. For artificially infected whole blood samples, our method shortens the sample processing time to 35 min and achieves a 10-fold improvement in PCR sensitivity compared to a commercial kit. Through clinical evaluation of blood samples collected from suspected infected patients, we identified positive samples that were 100% consistent with the clinical practice. Therefore, this method holds promising potential for clinical application in advancing rapid sepsis diagnosis and earlier interventions.

Safety and Efficacy of Antiviral Drugs and Vaccines in Pregnant Women: Insights from Physiologically Based Pharmacokinetic Modeling and Integration of Viral Infection Dynamics

Addressing the complexities of managing viral infections during pregnancy is essential for informed medical decision-making. This comprehensive review delves into the management of key viral infections impacting pregnant women, namely Human Immunodeficiency Virus (HIV), Hepatitis B Virus/Hepatitis C Virus (HBV/HCV), Influenza, Cytomegalovirus (CMV), and SARS-CoV-2 (COVID-19). We evaluate the safety and efficacy profiles of antiviral treatments for each infection, while also exploring innovative avenues such as gene vaccines and their potential in mitigating viral threats during pregnancy. Additionally, the review examines strategies to overcome challenges, encompassing prophylactic and therapeutic vaccine research, regulatory considerations, and safety protocols. Utilizing advanced methodologies, including PBPK modeling, machine learning, artificial intelligence, and causal inference, we can amplify our comprehension and decision-making capabilities in this intricate domain. This narrative review aims to shed light on diverse approaches and ongoing advancements, this review aims to foster progress in antiviral therapy for pregnant women, improving maternal and fetal health outcomes.

A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix

Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.

Achieve Research Continuity During Social Distancing by Rapidly Implementing Individual and Group Videoconferencing with Participants: Key Considerations, Best Practices, and Protocols

The novel coronavirus has upended many traditional research procedures as universities and other research entities have closed to activate social distancing. Some social and behavioral research activities (e.g. data analysis, manuscript preparation) can be continued from other environments with appropriate security protocols in place. For studies involving in-person interactions, continuity may be more difficult. Phone-based interactions provide a low-tech solution that may suffice in some cases. Yet, videoconferencing platforms can nearly replicate in-person interactions, activating both auditory and visual senses and potentially resulting in more substantial engagement. Staff can meet with participants individually or in groups, each seeing and hearing one another in real time. This paper provides guidance for researchers transitioning in-person assessments and interventions to a synchronous videoconferencing platform. Best practices, key considerations, examples from the field, and sample protocols are presented to ease transition for ongoing studies and maximize the potential of videoconferencing—and social distancing.

Perinatal Antiretroviral Intensification to Prevent Intrapartum HIV Transmission When Antenatal Antiretroviral Therapy Is Initiated Less Than 8 Weeks Before Delivery

INTRODUCTION

Infants born to women living with HIV initiating combination antiretroviral therapy (cART) late in pregnancy are at high risk of intrapartum infection. Mother/infant perinatal antiretroviral intensification may substantially reduce this risk.

METHODS

In this single-arm Bayesian trial, pregnant women with HIV receiving standard of care antiretroviral prophylaxis in Thailand (maternal antenatal lopinavir-based cART; nonbreastfed infants 4 weeks' postnatal zidovudine) were offered "antiretroviral intensification" (labor single-dose nevirapine plus infant zidovudine-lamivudine-nevirapine for 2 weeks followed by zidovudine-lamivudine for 2 weeks) if their antenatal cART was initiated ≤8 weeks before delivery. A negative birth HIV-DNA polymerase chain reaction (PCR) followed by a confirmed positive PCR defined intrapartum transmission. Before study initiation, we modeled intrapartum transmission probabilities using data from 3738 mother/infant pairs enrolled in our previous trials in Thailand using a logistic model, with perinatal maternal/infant antiretroviral regimen and predicted viral load at delivery as main covariates. Using the characteristics of the women enrolled who received intensification, prior intrapartum transmission probabilities (credibility intervals) with/without intensification were estimated. After including the transmission data observed in the current study, the corresponding Bayesian posterior transmission probability was derived.

RESULTS

No intrapartum transmission of HIV was observed among the 88 mother/infant pairs receiving intensification. The estimated intrapartum transmission probability was 2·2% (95% credibility interval 0·5-6·1) without intensification versus 0·3% (0·0-1·6) with intensification. The probability of superiority of intensification over standard of care was 94·4%. Antiretroviral intensification appeared safe.

CONCLUSION

Mother/infant antiretroviral intensification was effective in preventing intrapartum transmission of HIV in pregnant women receiving ≤8 weeks antepartum cART.

HIV RNA measurement in dried blood spots of HIV-infected patients in Thailand using Abbott m2000 system

World Health Organization recommends using dried blood spots (DBS) for HIV RNA viral load (VL) measurement whenever plasma processing is not convenient or feasible. DBS collected from 80 treatment-naïve HIV-infected patients presenting in three hospitals of two different regions of Thailand were shipped to a central laboratory along with corresponding plasma specimens. Viral load was measured in both DBS and plasma using the Abbott m2000 system. HIV RNA levels were strongly correlated (r = 0.94) with a mean of differences of 0.23 log₁₀ copies/mL. Using the 1,000 copies/mL cut-off, the sensitivity of DBS was 97% (95%CI, 91–100%) and specificity was 75% (95%CI, 19–99%). DBS are useful to scale-up HIV RNA VL testing in settings with limited access to VL testing.

Killing of Latently HIV-Infected CD4 T Cells by Autologous CD8 T Cells Is Modulated by Nef

The role of HIV-specific CD8 T cell activity in the course of HIV infection and the way it affects the virus that resides in the latent reservoir resting memory cells is debated. The PBMC of HIV-infected patients contain HIV-specific CD8 T cells and their potential targets, CD4 T cells latently infected by HIV. CD4 T cells and CD8 T cells procured from PBMC of HIV-infected patients were co-incubated and analyzed: Formation of CD8 T cells and HIV-infected CD4 T cell conjugates and apoptosis of these CD4 T cells were observed by fluorescence microscopy with in situ PCR of HIV LTR DNA. Furthermore, conjugation of CD8 T cells with CD4 T cells and apoptosis of CD4 T cells was observed and quantified by imaging flow cytometry using anti-human activated caspase 3 antibody and TUNEL assay. The conjugation activity and apoptosis were found to be much higher in patients with acute HIV infection or AIDS compared to patients in chronic infection on antiretroviral therapy (ART) or not. Patients on ART had low grade conjugation and apoptosis of isolated CD69, CD25, and HLA-DR-negative CD4 T cells (latent reservoir cells) by CD8 T cells. Using in situ PCR The latent reservoir CD4 T cells were shown to contain most of the HIV DNA. We demonstrate in HIV-infected patients, that CD8 T cells conjugate with and kill HIV-infected CD4 T cells, including HIV-infected resting memory CD4 T cells, throughout the course of HIV infection. We propose that in HIV-infected patients CD4 T cell annihilation is caused in part by ongoing activity of HIV-specific CD8 T cells. HIV Nef protein interacts with ASK 1 and inhibits its pro-apoptotic death signaling by Fas/FasL, thus protecting HIV-infected cells from CD8 T cells killing. A peptide that interrupts Nef-ASK1 interaction that had been delivered into CD4 T cells procured from patients on ART resulted in the increase of their apoptosis inflicted by autologous CD8 T cells. We suggest that elimination of the HIV-infected latent reservoir CD4 T cells can be achieved by Nef inhibition.

The stability of HIV-1 nucleic acid in whole blood and improved detection of HIV-1 in alternative specimen types when compared to Dried Blood Spot (DBS) specimens

BACKGROUND

Commercially-available kits for HIV-1 detection include instructions for detecting HIV-1 in plasma and DBS, but don't support other specimen types.

OBJECTIVES

Show quantitative stability of HIV-1 total nucleic acid (TNA) in blood and improved HIV-1 detection in alternative specimen types.

STUDY DESIGN

Whole blood and DBS specimens, tested as part of an external quality assurance program for qualitative HIV-1 detection, were used to evaluated error rates (false negative [FN], false positive [FP] and indeterminant [IND] results) across assays (internally developed [IH], Roche Amplicor [RA], and Roche TaqMan Qual [TQ]) and specimen types (frozen whole blood [BLD], DBS and cell pellets [PEL]). A modified Roche TaqMan HIV-1 assay was used to quantify HIV-1 TNA.

RESULTS

Significantly higher error rates were noted in DBS across all of the assays (4% vs. 0% for DBS and PEL, IH, p = 0.005; 4% vs. 0.1% for DBS and PEL, RA, p < 0.001; 10% vs. 1% for DBS and PEL or BLD, TQ, p < 0.001). HIV TNA concentration is stable in BLD (day 1 vs. day 10, p = 0.39) and higher than DBS (p < 0.001).

CONCLUSIONS

Transporting refrigerated whole blood for centralized processing into alternative specimen types will improve the sensitivitiy of HIV-1 detection in samples with low virus loads.

Country of Birth of Children With Diagnosed HIV Infection in the United States, 2008-2014

BACKGROUND

Diagnoses of HIV infection among children in the United States have been declining; however, a notable percentage of diagnoses are among those born outside the United States. The impact of foreign birth among children with diagnosed infections has not been examined in the United States.

METHODS

Using the Centers for Disease Control and Prevention National HIV Surveillance System, we analyzed data for children aged <13 years with diagnosed HIV infection ("children") in the United States (reported from 50 states and the District of Columbia) during 2008-2014, by place of birth and selected characteristics.

RESULTS

There were 1516 children [726 US born (47.9%) and 676 foreign born (44.6%)]. US-born children accounted for 70.0% in 2008, declining to 32.3% in 2013, and 40.9% in 2014. Foreign-born children have exceeded US-born children in number since 2011. Age at diagnosis was younger for US-born than foreign-born children (0-18 months: 72.6% vs. 9.8%; 5-12 years: 16.9% vs. 60.3%). HIV diagnoses in mothers of US-born children were made more often before pregnancy (49.7% vs. 21.4%), or during pregnancy (16.6% vs. 13.9%), and less often after birth (23.7% vs. 41%). Custodians of US-born children were more often biological parents (71.9% vs. 43.2%) and less likely to be foster or nonrelated adoptive parents (10.4% vs. 55.1%). Of 676 foreign-born children with known place of birth, 65.5% were born in sub-Saharan Africa and 14.3% in Eastern Europe. The top countries of birth were Ethiopia, Ukraine, Uganda, Haiti, and Russia.

CONCLUSIONS

The increasing number of foreign-born children with diagnosed HIV infection in the United States requires specific considerations for care and treatment.

Miniaturized devices for point of care molecular detection of HIV

The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.

Early infant HIV diagnosis and entry to HIV care cascade in Thailand: an observational study

BACKGROUND

Early infant diagnosis of HIV is crucial for timely initiation of antiretroviral therapy (ART) in infected children who are at high risk of mortality. Early infant diagnosis with dried blood spot testing was provided by the National AIDS Programme in Thailand from 2007. We report ART initiation and vital status in children with HIV after 7 years of rollout in Thailand.

METHODS

Dried blood spot samples were collected from HIV-exposed children in hospitals in Thailand and mailed to the Faculty of Associated Medical Sciences, Chiang Mai University, where HIV DNA was assessed with real-time PCR to establish HIV infection. We linked data from children with an HIV infection to the National AIDS Programme database to ascertain ART and vital status.

FINDINGS

Between April 5, 2007, and Oct 1, 2014, 16 046 dried blood spot samples were sent from 8859 children in 364 hospitals in Thailand. Median age at first dried blood spot test was 2·1 (IQR 1·8-2·5) months. Of 7174 (81%) children with two or more samples, 223 (3%) were HIV positive (including five unconfirmed). Of 1685 (19%) children with one sample, 70 (4%) were unconfirmed positive. Of 293 (3%) children who were HIV positive, 220 (75%) registered for HIV care and 170 (58%) initiated ART. Median age at ART initiation decreased from 14·2 months (IQR 10·2-25·6) in 2007 to 6·1 months (4·2-9·2) in 2013, and the number of children initiating ART aged younger than 1 year increased from five (33%) of 15 children initiating ART in 2007 to ten (83%) of 12 initiating ART in 2013. 15 (9%) of 170 children who initiated ART died and 16 (32%) of 50 who had no ART record died.

INTERPRETATION

Early infant diagnosis with dried blood spot testing had high uptake in primary care settings. Further improvement of linkage to HIV care is needed to ensure timely treatment of all children with an HIV infection.

FUNDING

None.

Uptake of early infant diagnosis in Thailand's national program for preventing mother-to-child HIV transmission and linkage to care, 2008-2011

Introduction

Early infant diagnosis (EID) has been a component of Thailand's prevention of mother-to-child HIV transmission (PMTCT) programme since 2007. This study assessed the uptake, EID coverage, proportion of HIV-exposed infants receiving a definitive HIV diagnosis, mother-to-child transmission (MTCT) rates and linkage to HIV care and treatment.

Methods

Infant polymerase chain reaction (PCR) testing data from the National AIDS Program database were analyzed. EID coverage was calculated as the percentage of number of HIV-exposed infants receiving ≥1 HIV PCR test divided by the number of HIV-exposed infants estimated from HIV prevalence and live-birth registry data. Definitive HIV diagnosis was defined as having two concordant PCR results. MTCT rates were calculated based on infants tested with PCR and applied as a best-case scenario, and a sensitivity analysis was used to adjust these rates in average and worst scenarios. We defined linkage to HIV care as infants with at least one PCR-positive test who were registered with Thailand's National AIDS Program. Chi-squared tests for linear trend were used to analyze changes in programme coverage.

Results

For 2008 to 2011, the average EID coverage rate increased from 54 to 76% (p<0.001), with 65% coverage (13,761/21,099) overall. The number of hospitals submitting EID samples increased from 458 to 645, and the percentage of community hospitals submitting samples increased from 75 to 78% (p=0.044). A definitive HIV diagnosis was made for 10,854 (79%) infants during this period. The adjusted MTCT rates had significantly decreasing trends in all scenarios. Overall, an estimated 53% (429/804) of HIV-infected infants were identified through the EID programme, and 80% (341/429) of infants testing positive were linked to care. The overall rate of antiretroviral treatment (ART) initiation within one year of age was 37% (157/429), with an increasing trend from 28 to 52% (p<0.001).

Conclusions

EID coverage increased and MTCT rates decreased during 2008 to 2011; however, about half of HIV-infected infants still did not receive EID. Most HIV-infected infants were linked to care but less than half initiated ART within one year of age. Active follow-up of HIV-exposed infants to increase early detection of HIV infection and early initiation of ART should be more widely implemented.

Randomized noninferiority trial of two maternal single-dose nevirapine-sparing regimens to prevent perinatal HIV in Thailand

OBJECTIVES

Perinatal single-dose nevirapine (sdNVP) selects for resistance mutations. The objective of this trial was to compare two maternal sdNVP-sparing regimens with standard zidovudine (ZDV)/sdNVP prophylaxis.

DESIGN

PHPT-5 was a randomized, partially double-blind placebo-controlled, noninferiority trial in Thailand (NCT00409591). Study participants were women with CD4 of at least 250 cells/μl and their infants.

METHODS

All women received ZDV from 28 weeks' gestation and their newborn infants for one week. Women were also randomized to receive NVP-NVP (reference): maternal intrapartum sdNVP with a 7-day 'tail' of ZDV along with lamivudine, and infant NVP (one dose immediately, another 48 h later); infant-only NVP: maternal placebos for sdNVP and the 'tail', with infant NVP; LPV/r: maternal LPV/r starting at 28 weeks. Infants were formula-fed. HIV-diagnosis was determined by DNA-PCR.

RESULTS

Four-hundred and thirty-five women were randomized between January 2009 and September 2010. Accrual was terminated prematurely following a change in Thai guidelines recommending antiretroviral combination therapy for all pregnant women. Data on 405 mothers and 407 live-born children were analyzed. Baseline characteristics were similar between arms. Intent-to-treat transmission rates were 3.8% (95% confidence interval: 1.2-8.6) in NVP-NVP, 1.6% (0.2-5.6) in infant-only NVP, and 1.4% (0.4-5.1) in LPV/r arms. As-treated rates were 2.2% (0.5-6.4), 3.2% (0.9-7.9), and 1.5% (0.2-5.2), respectively. Factors independently associated with transmission were prophylaxis duration less than 8 weeks (adjusted odds ratio 15.5; 3.6-66.1) and viral load at baseline at least 4 log10copies/ml (adjusted odds ratio 10.9; 1.3-91.5). Regimens appeared well tolerated.

CONCLUSION

Transmission rates in all arms were low but noninferiority was not proven. Antiretroviral prophylaxis for at least 8 weeks before delivery is necessary to minimize transmission risk.

Community-Based HIV-1 Early Diagnosis and Risk Behavior Analysis of Men Having Sex with Men in Hong Kong

The increasing prevalence of HIV-1 among men having sex with men (MSM) calls for an investigation of HIV-1 prevalence and incidence in MSM by early diagnosis to assist with early preventive interventions in Hong Kong. The participants were recruited randomly from MSM communities within a one-year period. Rapid HIV Test (RHT) and real-time dried blood spot (DBS)-based quantitative polymerase chain reaction (DBS-qPCR) were used for the early diagnosis of 474 participants. Risk behavior analysis was performed by studying information obtained from the participants during the study period. The HIV-1 prevalence and incident rates in the studied MSM population were 4.01% (19/474) and 1.47% (7/474), respectively. Three infected participants were found at the acute phase of infection by DBS-qPCR. Only 46.4% (220/474) MSM were using condoms regularly for anal sex. HIV infection significantly correlated with unprotected receptive anal sex and syphilis infection. An increased number of infections was found among foreign MSM in Hong Kong. This study is the first to use DBS-qPCR to identify acutely infected individuals in a community setting and to provide both the prevalence and incident rates of HIV-1 infection among MSM in Hong Kong. The risk analysis provided evidence that behavior intervention strengthening is necessary to fight against the increasing HIV-1 epidemic among MSM in Hong Kong and surrounding regions in Asia.

The impact of a HIV prevention of mother to child transmission program in a nigerian early infant diagnosis centre

Background:

Mothers infected with human immunodeficiency virus (HIV) can transmit the virus to their babies in utero, intrapartum or postpartum through breastfeeding. Maternal to child transmission can be prevented through administration of antiretroviral drugs to mother and child, and through restriction of breastfeeding. This study evaluated the effectiveness of prevention of mother-to-child transmission (PMTCT) activities in reducing the incidence of HIV infection among exposed babies at the National Hospital Abuja, Nigeria.

Materials and Methods:

Early infant diagnosis laboratory records of 515 exposed babies aged below 18 months who had polymerase chain reaction (PCR) test between January 1^st 2011 and December 31^st 2012 were reviewed. The details of antiretroviral (ARV) therapy commencement for mother and baby, infant feeding choices, mode of delivery and HIV test results were analysed.

Results:

Of the 515 samples tested, 36 (7.0%) were found to be positive. The mean age of exposed children tested was 4 months. Highest prevalence was among children in the age group 6-18 months (16.1%). There was statistically significant association between HIV positive results and age. (P = 0.0000). If the mother and child pairs received ARVs, the prevalence was 1.3%, whereas if the mother only received ARV, then the prevalence was 4.6%, and when only the child received ARV the prevalence was 20.0%. When neither the mother nor the child received ARVs, the prevalence was 66.7%.

Conclusion:

There was a high prevalence of HIV among exposed children in our setting, especially if the mother and child pairs did not receive any form of antiretroviral prophylaxis. This further emphasises the usefulness of ARVs as the single most important intervention in PMTCT. Therefore, there is need to expand antiretroviral coverage, ensure access of the PMTCT program, and provide effective services to support infected children.

Cost-effectiveness of early infant HIV diagnosis of HIV-exposed infants and immediate antiretroviral therapy in HIV-infected children under 24 months in Thailand

Background

HIV-infected infants have high risk of death in the first two years of life if untreated. WHO guidelines recommend early infant HIV diagnosis (EID) of all HIV-exposed infants and immediate antiretroviral therapy (ART) in HIV-infected children under 24-months. We assessed the cost-effectiveness of this strategy in HIV-exposed non-breastfed children in Thailand.

Methods

A decision analytic model of HIV diagnosis and disease progression compared: EID using DNA PCR with immediate ART (Early-Early); or EID with deferred ART based on immune/clinical criteria (Early-Late); vs. clinical/serology based diagnosis and deferred ART (Reference). The model was populated with survival and cost data from a Thai observational cohort and the literature. Incremental cost-effectiveness ratio per life-year gained (LYG) was compared against the Reference strategy. Costs and outcomes were discounted at 3%.

Results

Mean discounted life expectancy of HIV-infected children increased from 13.3 years in the Reference strategy to 14.3 in the Early-Late and 17.8 years in Early-Early strategies. The mean discounted lifetime cost was $17,335, $22,583 and $29,108, respectively. The cost-effectiveness ratio of Early-Late and Early-Early strategies was $5,149 and $2,615 per LYG, respectively as compared to the Reference strategy. The Early-Early strategy was most cost-effective at approximately half the domestic product per capita per LYG ($4,420 in Thailand 2011). The results were robust in deterministic and probabilistic sensitivity analyses including varying perinatal transmission rates.

Conclusion

In Thailand, EID and immediate ART would lead to major survival benefits and is cost- effective. These findings strongly support the adoption of WHO recommendations as routine care.

Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification

Early diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in <20 min at a constant temperature, without the need for complex thermocycling equipment. Here we tested 63 HIV-1-specific primer and probe combinations and identified two RPA assays that target distinct regions of the HIV-1 genome (long terminal repeat [LTR] and pol) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. These pol and LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes.

Discrepant test findings in early infant diagnosis of HIV in a national reference laboratory in Kenya: challenges and opportunities for programs

BACKGROUND

In Kenya, the availability of a cheap diagnostic service for HIV-exposed infants has helped scale-up access to treatment, and provided a means by which programs that support Prevention of Mother to Child Transmission of HIV can be evaluated. As expected for any large testing program, discrepant and indeterminate results present a significant challenge.

METHODS

Dried Blood Spots were collected from health centers countrywide and couriered to four laboratories for tests. Results were dispatched either by email, telephone, GSM SMS printer or courier. Between 2006 and 2009, tests were conducted with the Manual Roche v. 1.5 Assay. In 2010 the labs switched fully to the Cobas® AmpliPrep/ Cobas® TaqMan® HIV-1 Qual automated Roche Test.

RESULTS

Between 2006 and 2010, the KEMRI CVR EID Lab conducted 64 591 HIV tests in on children <18 months of age. HIV tests (38 834) used the manual assay, while 17 133 tests used the automated assay. Overall, 10.7% (6915) of the samples tested positive, while 86.6% (55 967) tested negative. A total of 1.6% (1041) tested indeterminate and required a re-bleed of the infant. Two hundred positive tests by the manual assay were retrieved randomly and retested using the automated assay. Among them, 192 (96%) remained positive, 5 (2.5%) were negative while 3 (1.5%) failed. A total of 160 negative samples by the manual assay were retrieved and retested with the automated assay. Among them, 154 (96.24%) remained negative, 3 (1.88%) tested positive while 3 (1.88%) failed. A total of 215 samples that gave indeterminate results by the manual assay were retested using the automated system. Among them, 62 (28.8%) gave positive results, 144 (66.97%) negative and 6 (2.8%) samples still gave discrepant results. Three (1.4%) did not amplify successfully. A few infants who were apparently positive appeared to test HIV negative with age.

CONCLUSIONS

Indeterminate results are a significant challenge for HIV diagnostic services, as seen in the Kenyan EID Program. In our experience, they are more often negative than they are positive. False positive and false negative results can arise from clerical error, contamination and limitations of the technologies available. To forestall the consequences of such outcomes, the sensitivity and specificity of available assays must be further improved. All HIV positive samples should be retested for confirmation, and if confirmed, a new sample must be drawn and tested for DNA at the time the infant receives their initial results or starts antiretroviral therapy. Viral clearance is a phenomenon that requires further studies.

12-month mortality and loss-to-program in antiretroviral-treated children: The IeDEA pediatric West African Database to evaluate AIDS (pWADA), 2000-2008

Background

The IeDEA West Africa Pediatric Working Group (pWADA) was established in January 2007 to study the care and treatment of HIV-infected children in this region. We describe here the characteristics at antiretroviral treatment (ART) initiation and study the 12-month mortality and loss-to-program of HIV-infected children followed in ART programs in West Africa.

Methods

Standardized data from HIV-infected children followed-up in ART programs were included. Nine clinical centers from six countries contributed to the dataset (Benin, Côte d'Ivoire, Gambia, Ghana, Mali and Senegal). Inclusion criteria were the followings: age 0-15 years and initiated triple antiretroviral drug regimens. Baseline time was the date of ART initiation. WHO criteria was used to define severe immunosuppression based on CD4 count by age or CD4 percent < 15%. We estimated the 12-month Kaplan-Meier probabilities of mortality and loss-to-program (death or loss to follow-up > 6 months) after ART initiation and factors associated with these two outcomes.

Results

Between June 2000 and December 2007, 2170 children were included. Characteristics at ART initiation were the following: median age of 5 years (Interquartile range (IQR: 2-9) and median CD4 percentage of 13% (IQR: 7-19). The most frequent drug regimen consisted of two nucleoside reverse transcriptase inhibitors and one non-nucleoside reverse transcriptase inhibitors (62%). During the first 12 months, 169 (7.8%) children died and 461(21.2%) were lost-to-program. Overall, in HIV-infected children on ART, the 12-month probability of death was 8.3% (95% Confidence Interval (CI): 7.2-9.6%), and of loss-to-program was 23.1% (95% CI: 21.3-25.0%). Both mortality and loss-to program were associated with advanced clinical stage, CD4 percentage < 15% at ART initiation and year (> 2005) of ART initiation.

Conclusion

Innovative and sustainable approaches are needed to better document causes of death and increase retention in HIV pediatric clinics in West Africa.

RNA versus DNA (NucliSENS EasyQ HIV-1 v1.2 versus Amplicor HIV-1 DNA test v1.5) for early diagnosis of HIV-1 infection in infants in Senegal

The objective of this study was to compare the performance of the NucliSENS EasyQ HIV-1 v1.2 platform (bioMérieux, France) to the Amplicor HIV-1 DNA test v1.5 (Roche Molecular Systems, Switzerland) in detecting HIV-1 infection in infants using venipuncture-derived whole blood in tubes and dried blood spots. A total of 149 dried blood spots and 43 EDTA-anticoagulated peripheral blood samples were collected throughout Dakar and other areas in Senegal from infants and children aged 3 weeks to 24 months who were born to HIV-1-infected mothers. Samples were tested using the NucliSENS and Amplicor technologies. The NucliSENS and Amplicor results were 100% concordant using either EDTA-anticoagulated peripheral blood or dried blood spots. Compared to Amplicor, the sensitivity and specificity of the NucliSENS test were 100%. The NucliSENS EasyQ HIV-1 RNA assay performed as well as the Amplicor HIV-1 DNA test in detecting HIV-1 infection in infants. In addition, this platform can give an indication of the viral load baseline. The NucliSENS EasyQ platform is a good alternative for early infant diagnosis of HIV-1 infection.

Predictors of successful early infant diagnosis of HIV in a rural district hospital in Zambézia, Mozambique

BACKGROUND

A key challenge inhibiting the timely initiation of pediatric antiretroviral treatment is the loss to follow-up of mothers and their infants between the time of mothers' HIV diagnoses in pregnancy and return after delivery for early infant diagnosis of HIV. We sought to identify barriers to follow-up of HIV-exposed infants in rural Zambézia Province, Mozambique.

METHODS

We determined follow-up rates for early infant diagnosis and age at first test in a retrospective cohort of 443 HIV-infected mothers and their infants. Multivariable logistic regression models were used to identify factors associated with successful follow-up.

RESULTS

Of the 443 mother-infant pairs, 217 (49%) mothers enrolled in the adult HIV care clinic, and only 110 (25%) infants were brought for early infant diagnosis. The predictors of follow-up for early infant diagnosis were larger household size (odds ratio [OR], 1.29; 95% confidence interval [CI], 1.09-1.53), independent maternal source of income (OR, 10.8; 95% CI, 3.42-34.0), greater distance from the hospital (OR, 2.14; 95% CI, 1.01-4.51), and maternal receipt of antiretroviral therapy (OR, 3.15; 95% CI, 1.02-9.73). The median age at first test among 105 infants was 5 months (interquartile range, 2-7); 16% of the tested infants were infected.

CONCLUSIONS

Three of four HIV-infected women in rural Mozambique did not bring their children for early infant HIV diagnosis. Maternal receipt of antiretroviral therapy has favorable implications for maternal health that will increase the likelihood of early infant diagnosis. We are working with local health authorities to improve the linkage of HIV-infected women to HIV care to maximize early infant diagnosis and care.

Long-term survival of HIV-infected children receiving antiretroviral therapy in Thailand: a 5-year observational cohort study

BACKGROUND

There are scarce data on the long-term survival of human immunodeficiency virus (HIV)-infected children receiving antiretroviral therapy (ART) in lower-middle income countries beyond 2 years of follow-up.

METHODS

Previously untreated children who initiated ART on meeting immunological and/or clinical criteria were followed in a prospective cohort in Thailand. The probability of survival up to 5 years from initiation was estimated using Kaplan-Meier methods, and factors associated with mortality were assessed using Cox regression analyses.

RESULTS

Five hundred seventy-eight children received ART; of these, 111 (19.2%) were followed since birth. At start of ART (baseline), the median age was 6.7 years, 128 children (22%) were aged <2 years, and the median CD4 cell percentage was 7%. Median duration of follow-up was 53 months; 42 children (7%) died, and 38 (7%) were lost to follow-up. Age <12 months, low CD4 cell percentage, and low weight-for-height z score at ART initiation were independently associated with mortality (P < .001). The probability of survival among infants aged <12 months at baseline was 84.3% at 1 year and 76.7% at 5 years of ART, compared with 95.7% and 94.8%, respectively, among children aged ≥1 year. Low CD4 cell percentage and wasting at baseline had a strong association with mortality among older children but weak or no association among infants.

CONCLUSIONS

Children who initiated ART as infants after meeting immunological and/or clinical criteria had a high risk of mortality which persisted beyond the first year of therapy. Among older children, those with severe wasting or low CD4 cell percentage at treatment initiation were at high risk of mortality during the first 6 months of therapy. These findings support the scale-up of early HIV diagnosis and immediate treatment in infants, before advanced disease progression in older children.

Quantitative recovery of proviral HIV-1 DNA from leukocytes by the Dried Buffy Coat Spot method for real-time PCR determination

The current recommended method for diagnosing HIV-1 in newborns infected vertically and in adults, during the "window period", is the detection of proviral HIV-1 DNA within leukocytes (buffy coat). This study describes a new portable Dried Buffy Coat Spot (DBCS) assay able to provide a quantitative proviral HIV-1 DNA recovery from the buffy coat. Fifty blood samples were collected from HIV-positive children and processed for DBCSs. Total DNA and proviral DNA were normalised to β-globin and HIV-1 pol genes. Assay sensitivity and specificity were evaluated against the whole blood dried blood spot (DBS) method. Both procedures, using automatic DNA extraction, were compared to a standard whole blood DNA manual extraction. DNA recovery from whole blood was nearly equivalent to that of the DBCS-based extraction, while DBS-based extraction was 10-fold less sensitive. The detection rate of proviral HIV-1 DNA with DBCS assay was equivalent to whole blood manual extraction (100% concordance), but DBS-extracted samples showed limited concordance (44%). The DBCS assay may prove to be more feasible in resource-limited settings. It may represent a simple and robust point-of-care assay for HIV screening of children, for whom a reference test is still lacking.

Challenges for rapid molecular HIV diagnostics

The introduction of serological point-of-care assays 10 years ago dramatically changed the way that human immunodeficiency virus (HIV) infection was identified and diagnosed. Testing at the point of care has lead to a dramatic increase in the number of individuals who are screened and, most importantly, receive their HIV test result. As the AIDS epidemic continues to mature and scientific advances in prevention and treatment are evaluated and implemented, there is a need to identify acute (viremic preseroconversion) infections and to discriminate "window phase" infections from those that are serologically positive, especially in resource-limited settings, where the majority of vulnerable populations reside and where the incidence of HIV infection is highest. Rapid testing methods are now at a crossroads. There is opportunity to implement and evaluate the incremental diagnostic usefulness of new test modalities that are based on sophisticated molecular diagnostic technologies and that can be performed in settings where laboratory infrastructure is minimal. The way forward requires sound scientific judgment and an ability to further develop and implement these tests despite a variety of technical, social, and operational hurdles, to declare success.

Early versus deferred antiretroviral therapy in children in low-income and middle-income countries

PURPOSE OF REVIEW

We reviewed current literatures on early and deferred initiation of antiretroviral therapy in HIV-infected infants and children in low-income and middle-income countries.

RECENT FINDINGS

Data from children with HIV antiretroviral (Children with HIV Early Antiretroviral Therapy) study showed a significant reduction of 76% in mortality among infants who received antiretroviral therapy within 3 months of their life as opposed to those on deferred therapy. These data led World Health Organization to promptly revise the guideline to recommend initiation of antiretroviral therapy in all HIV-infected infants regardless of clinical or immunological status. The recommendation for older children is differed between guidelines of developed and developing countries. In general, higher CD4 cell count threshold is used for younger children and similar criteria to those used for adults are used once children are above 5 years of age. The randomized study of when to start antiretroviral therapy in children older than 1 year is ongoing.

SUMMARY

The current trend is to move toward early treatment to reduce morbidity and mortality, achieve immune recovery, normal growth, and development. Even though the antiretroviral rollout program has been successful in Asia and Africa, the challenges lie in diagnosing infants in a timely manner and maintaining infrastructure and resources to support life-long treatment.

A rapid real-time PCR assay for the detection of HIV-1 proviral DNA using double-stranded primer

In this study, a rapid real-time PCR assay to detect HIV-1 proviral DNA in whole blood was developed using a novel double-stranded primer that does not require a target-specific fluorescent probe or intercalating dye systems. Co-amplification of a human gene RNase P served as the internal control to monitor the efficiency of the DNA extraction and PCR amplification. The HIV-1 amplification efficiency was 100% and could amplify 1 copy of HIV-1 DNA 64% of the time and all attempts to amplify 4 copies were successful in less than 51 min. All 22 HIV-1 sero-positive and 20 sero-negative whole blood specimens tested were classified correctly by this assay. In addition, 22 cultured PBMC specimens infected with various HIV-1 subtypes or CRF (A=2, AC=1, B=4, C=3, D=3, AE=2, F=1, BF=2, G=4) were amplified equally well with a similar threshold cycle (C(t)) number (22.9+/-1.2). The high amplification efficiency and short PCR cycles were in part due to the short target sequence amplified by eliminating the probe-binding sequence between the primers. This assay may be useful as an alternative confirmation test in a variety of HIV testing venues.

Low-cost HIV-1 diagnosis and quantification in dried blood spots by real time PCR

Background

Rapid and cost-effective methods for HIV-1 diagnosis and viral load monitoring would greatly enhance the clinical management of HIV-1 infected adults and children in limited-resource settings. Recent recommendations to treat perinatally infected infants within the first year of life are feasible only if early diagnosis is routinely available. Dried blood spots (DBS) on filter paper are an easy and convenient way to collect and transport blood samples. A rapid and cost effective method to diagnose and quantify HIV-1 from DBS is urgently needed to facilitate early diagnosis of HIV-1 infection and monitoring of antiretroviral therapy.

Methods and Findings

We have developed a real-time LightCycler (rtLC) PCR assay to detect and quantify HIV-1 from DBS. HIV-1 RNA extracted from DBS was amplified in a one-step, single-tube system using primers specific for long-terminal repeat sequences that are conserved across all HIV-1 clades. SYBR Green dye was used to quantify PCR amplicons and HIV-1 RNA copy numbers were determined from a standard curve generated using serially diluted known copies of HIV-1 RNA. This assay detected samples across clades, has a dynamic range of 5 log₁₀, and %CV <8% up to 4 log₁₀ dilution. Plasma HIV-1 RNA copy numbers obtained using this method correlated well with the Roche Ultrasensitive (r = 0.91) and branched DNA (r = 0.89) assays. The lower limit of detection (95%) was estimated to be 136 copies. The rtLC DBS assay was 2.5 fold rapid as well as 40-fold cheaper when compared to commercial assays. Adaptation of the assay into other real-time systems demonstrated similar performance.

Conclusions

The accuracy, reliability, genotype inclusivity and affordability, along with the small volumes of blood required for the assay suggest that the rtLC DBS assay will be useful for early diagnosis and monitoring of pediatric HIV-1 infection in resource-limited settings.