HIV cross-sectional surveys require multi-layered testing with several tests to estimate HIV prevalence and HIV-1 incidence. We evaluated the performance and accuracy of the newly developed HIV Triplex assay to diagnose HIV-1 and HIV-2 and detect HIV-1 recent infections using plasma samples from the 2018 Nigeria AIDS Indicator and Impact Survey (NAIIS). Plasma samples from consenting HIV-positive (n=2,773) and a subset of HIV-negative samples (n=7,196), as determined by the national rapid testing algorithm, followed by Bio-Rad Geenius HIV-1/2 Supplemental Assay and Western Blot, aged 18 months - 64 years, were tested using the Luminex-based HIV Triplex assay. The assay classified specimens as HIV-1 positive, HIV-2 positive, dual (HIV-1 & 2) infections, or HIV-seronegative. All HIV-1 and dual infections were further classified as either HIV-1 recent (<6 months) or long-term (LT) based on mean fluorescent intensities and compared with the LAg-Avidity EIA as the reference. Multiplex results were analyzed and compared with the final NAIIS survey data for unweighted HIV prevalence and HIV-1 incidence. The diagnostic sensitivity and specificity of the HIV Triplex assay was 99.71% and 99.37%, respectively, with a kappa of 0.987 when compared to NAIIS survey results. Percent agreement between the HIV Triplex assay and the LAg-Avidity EIA for recent and LT classification was 98.86% with a kappa of 0.80 [CI: 0.71-0.89] and a Spearman-ranked correlation (ρ) of 0.689. A small number (n=45; 0.63%) of the subset of negatives tested were classified by the multiplex assay as either HIV-1 positive (n=35) or HIV-2 positive (n=10). Nevertheless, the HIV Triplex assay agreed with NAIIS HIV-negative survey results (99.37%). Using these results as they were, unweighted estimates of HIV prevalence for both HIV Triplex assay and NAIIS test results were similar (1.62% [95% CI: 1.56-1.68] and 1.60% [95% CI: 1.54-1.66], respectively) with overlapping confidence. After adjusting for viral load and anti-retroviral therapy, HIV-1 unweighted incidence for ages ≥15 years, using HIV Triplex assay data, was 0.70 per 1,000 [95% CI: 0.40-0.90]. This is similar to the unweighted incidence using the LAg-based RITA (recent infection testing algorithm) of 0.80 per 1,000 [95% CI: 0.60-1.10]. The HIV Triplex assay combines several assays in one, providing highly accurate results for estimating HIV prevalence and HIV-1 incidence in surveys. This assay has the potential to simplify cross-sectional surveys making them less expensive, easier, and quicker.

Pyrazinamide (PZA) is a key first-line antituberculosis drug that plays an important role in eradicating persister Mycobacterium tuberculosis (TB) bacilli and shortening the duration of tuberculosis treatment. However, PZA-resistance is on the rise, particularly among persons with multidrug-resistant (MDR) tuberculosis. This nationwide study was conducted to explore the prevalence of mutations conferring PZA resistance, catalogue mutation diversity, investigate the associations of PZA resistance with specific lineages, examine co-resistance to 13 first- and second-line drugs, and evaluate the diagnostic accuracy of sequencing pncA and panD genes for predicting PZA resistance. Whole genome sequencing was performed on 2,207 M. tuberculosis isolates from 25 States and 4 Union Territories of India. The majority of phenotypically PZA-resistant isolates (77%) harbored 171 distinct mutations in pncA; however, a small number of mutations in panD, rpsA and clpC1 were also observed. A set of novel mutations associated PZA resistance was uncovered, along with an additional 143 PZA resistance-conferring mutations in pncA based on application of WHO-endorsed grading rules. PZA resistance was predominately observed in Lineage 2 and eight lineage-specific resistance markers were identified. Mutations distributed across pncA correlate to 94% of PZA resistance and were the predominant drivers of phenotypic resistance; evidence generated herein substantiates sequencing the entire gene and promoter for comprehensive genotypic-based prediction of PZA resistance. This work provides key insights into the scope of PZA-resistance in India, a high drug-resistant TB burden country, and can support the effectiveness of TB prevention and control efforts.

The Sedia Biosciences Asanté rapid test for recent infection (RTRI) can identify HIV infections and characterize HIV-1 as recent or long-term infection via the positive verification (V) line and long-term line (LT) line, respectively. Tracking with Recency Assays to Control the Epidemic (TRACE) program uses RTRI assays. Successful implementation of TRACE requires high-quality test performance. The goal of this study is to evaluate the additional quality practices established for new kit lots prior to field use. Asanté lot quality control data from the manufacturer is reviewed by the Centers for Disease Control and Prevention International Laboratory Branch (CDC-ILB) in the Division of Global HIV and TB using. If a lot passes manufacturer quality control and CDC-ILB review, test kits are sent to CDC-ILB for further evaluation. Evaluation by CDC includes inter-rater reliability and linear regressions comparing the V and LT lines against reference data as well as V and LT line data between testers. A Bland-Altman analysis was conducted to assess bias and systematic error. Overall, CDC-ILB passed 29 (91%) out of 32 Sedia Biosciences Asanté kit lots that initially passed manufacturing quality control from July 2017 to May 2020. Regression analyses demonstrate that test kits are performing as expected with consistent R2≥0.92 for both V and LT lines. On average, inter-rater reliability kappa was 0.9, indicating a strong level of agreement. Bland-Altman analyses demonstrate high agreement with little to no systematic error and bias. Ongoing evaluation of new RTRI kit lots is important to ensure high quality test performance. Rejecting 9% of kit lots highlight the importance of continuing to work with manufacturers to ensure consistent kit production and quality assurance (QA) activities. Investing in effective QA measures, conducting both pre- and post-market performance data reviews, could help improve RTRI accuracy and outcomes in similar testing programs.

India has the largest number of multidrug-resistant TB | (MDR-TB) cases, defined as Mycobacterium tuberculosis | resistant to at least isoniazid (INH) and rifampicin (RIF).1 | However, less than half of all persons with MDR-TB in | India successfully complete treatment.1 Although initial | end-of-treatment outcomes offer a standardised time point | to assess the effect of treatment, these tend to | underestimate the overall burden of unfavourable longterm outcomes among persons treated for TB.2,3 The longterm outcomes of persons diagnosed with MDR-TB in | India, including the proportion with recurrent TB disease | or mortality, are unknown. This analysis was conducted | under programmatic conditions in a high-burden setting, | with no regular check-ups after treatment. The results can | be used to show the burden of recurrent illness and death | following treatment, and can be used as a benchmark to | measure improvement.

OBJECTIVES: In Malawi, a recent infection testing algorithm (RITA) is used to characterise infections of persons newly diagnosed with HIV as recent or long term. This paper shares results from recent HIV infection surveillance and describes distribution and predictors. SETTING: Data from 155 health facilities in 11 districts in Malawi were pooled from September 2019 to March 2020. PARTICIPANTS: Eligible participants were 13 years, and newly diagnosed with HIV. Clients had RITA recent infections if the rapid test for recent infection (RTRI) test result was recent and viral load (VL) 1000 copies/mL; if VL was <1000 copies/mL the RTRI result was reclassified as long-term. Results were stratified by age, sex, pregnancy/breastfeeding status and district. RESULTS: 13 838 persons consented to RTRI testing and 12 703 had valid RTRI test results and VL results after excluding clients not newly HIV-positive, RTRI negative or missing data (n=1135). A total of 12 365 of the 12 703 were included in the analysis after excluding those whose RTRI results were reclassified as long term (n=338/784 or 43.1%). The remainder, 446/12 703 or 3.5%, met the definition of RITA recent infection. The highest percentage of recent infections was among breastfeeding women (crude OR (COR) 3.2; 95% CI 2.0 to 5.0), young people aged 15-24 years (COR 1.6; 95% CI 1.3 to 1.9) and persons who reported a negative HIV test within the past 12 months (COR 3.3; 95% CI 2.6 to 4.2). Factors associated with recent infection in multivariable analysis included being a non-pregnant female (adjusted OR (AOR) 1.4; 95% CI 1.2 to 1.8), a breastfeeding female (AOR 2.2; 95% CI 1.4 to 3.5), aged 15-24 years (AOR 1.6; 95% CI 1.3 to 1.9) and residents of Machinga (AOR 2.0; 95% CI 1.2 to 3.5) and Mzimba (AOR 2.4; 95% CI 1.3 to 4.5) districts. CONCLUSIONS: Malawi's recent HIV infection surveillance system demonstrated high uptake and identified sub-populations of new HIV diagnoses with a higher percentage of recent infections.

We previously described development of a rapid test for recent infection (RTRI) that can diagnose HIV infection and detect HIV-1 recent infections in a single device. This technology was transferred to a commercial partner as Asante Rapid Recency Assay (ARRA). We evaluated performance of the ARRA kits in the laboratory using a well-characterized panel of specimens. The plasma specimen panel (N=1500) included HIV-1 (N=570), HIV-2 (N=10), and HIV-negatives (N=920) representing multiple subtypes and geographic locations. Reference diagnostic data were generated using the Bio-Rad HIV-1-2-O EIA/Western blot algorithm with further serotyping performed using the Multispot HIV-1/2 assay. The LAg-Avidity EIA was used to generate reference data on recent and long-term infection for HIV-1 positive specimens at a normalized optical density (ODn) cutoff of 2.0 corresponding to a mean duration of about 6 months. All specimens were tested with ARRA according to the manufacturer's recommendations. Test strips were also read for line intensities using a reader and results were correlated with visual interpretation. ARRA's positive verification line (PVL) correctly classified 575 of 580 HIV-positive and 910 of 920 negative specimens resulting in a sensitivity of 99.1% (95% CI: 98.0-99.6) and specificity of 98.9% (95% CI: 98.1-99.4), respectively. The reader-based classification was similar for PVL with sensitivity of 99.3% (576/580) and specificity of 98.8% (909/920). ARRA's long-term line (LTL) classified 109 of 565 HIV-1 specimens as recent and 456 as long-term compared to 98 as recent and 467 as long-term (LT) by LAg-Avidity EIA (cutoff ODn=2.0), suggesting a mean duration of recent infection (MDRI) close to 6 months. Agreement of ARRA with LAg recent cases was 81.6% (80/98) and LT cases was 93.8% (438/467), with an overall agreement of 91.7% (kappa=0.72). The reader (cutoff 2.9) classified 109/566 specimens as recent infections compared to 99 by the LAg-Avidity EIA for recency agreement of 81.8% (81/99), LT agreement of 9% (439/467) with overall agreement of 91.9% (kappa=0.72). The agreement between visual interpretation and strip reader was 99.9% (95% CI: 99.6-99.9) for the PVL and 98.1% (95% CI: 96.6-98.9) for the LTL. ARRA performed well with HIV diagnostic sensitivity >99% and specificity >98%. Its ability to identify recent infections is comparable to the LA-Avidity EIA corresponding to an MDRI of about 6 months. This point-of-care assay has implications for real-time surveillance of new infections among newly diagnosed individuals for targeted prevention and interrupting ongoing transmission thus accelerating epidemic control.

BACKGROUND: The Malawi Ministry of Health implemented a new surveillance activity in April 2019 to detect recent HIV infections using a rapid test for recent infection (RTRI) to identify areas of ongoing transmission and guide response activities. SETTING: At 23 health facilities in Blantyre District, healthcare workers (HCWs) were trained to conduct recent infection testing. In September 2019, we conducted a cross-sectional survey at these sites to explore the acceptability and feasibility of integrating this activity into routine HIV testing services (HTS). METHODS: Research assistants interviewed HCWs using a semi-structured survey. Descriptive statistics were used to summarize quantitative responses and thematic analysis was used to group open-ended text. RESULTS: We interviewed 119 HCWs. Eighty-two percent of participants reported the RTRI was easy-to-use. HCWs perceived high client acceptability; 100% reported clients as 'somewhat' or 'very accepting'. Challenges included 68% of HCWs estimating they spend 20min beyond routine HTS per client for this activity and 51% performing at least two additional finger pricks to complete the testing algorithm. HCWs differed in their perceptions of whether results should be returned to clients. CONCLUSION: This study assessed HCW experiences using point-of-care RTRIs for HIV recent infection surveillance. Overall, HCWs perceived RTRIs to be acceptable, easy-to-use, and valuable. Though only clients withnew HIV diagnoses are tested for recent infection, additional time may be substantial at high-volume health service delivery points. Providing response plans or aggregated recent infection results to HCWs and/or clients may support motivation and sustainability of this novel surveillance activity.

Persons infected with HIV are more likely to transmit the virus during the early stages (acute and recent) of infection, when viral load is elevated and opportunities to implement risk reduction are limited because persons are typically unaware of their status (1,2). Identifying recent HIV infections (acquired within the preceding 12 months)* is critical to understanding the factors and geographic areas associated with transmission to strengthen program intervention, including treatment and prevention (2). During June 2019, a novel recent infection surveillance initiative was integrated into routine HIV testing services in Malawi, a landlocked country in southeastern Africa with one of the world's highest prevalences of HIV infection.(†) The objectives of this initiative were to collect data on new HIV diagnoses, characterize the epidemic, and guide public health response (2). New HIV diagnoses were classified as recent infections based on a testing algorithm that included results from the rapid test for recent infection (RTRI)(§) and HIV viral load testing (3,4). Among 9,168 persons aged ≥15 years with a new HIV diagnosis who received testing across 103 facilities during October 2019-March 2020, a total of 304 (3.3%) were classified as having a recent infection. Higher proportions of recent infections were detected among females, persons aged <30 years, and clients at maternal and child health and youth clinics. Using a software application that analyzes clustering in spatially referenced data, transmission hotspots were identified with rates of recent infection that were significantly higher than expected. These near real-time HIV surveillance data highlighted locations across Malawi, allowing HIV program stakeholders to assess program gaps and improve access to HIV testing, prevention, and treatment services. Hotspot investigation information could be used to tailor HIV testing, prevention, and treatment to ultimately interrupt transmission.

India has a high burden of drug-resistant tuberculosis (DR TB) and many cases go undetected by current drug susceptibility tests (DSTs). This study was conducted to identify rifampicin (RIF) and isoniazid (INH) resistance associated genetic mutations undetected by current clinical diagnostics amongst persons with DR TB in Chennai, India. Retrospectively stored 166 DR TB isolates during 2013-2016 were retrieved and cultured in Löwenstein-Jensen medium. Whole genome sequencing (WGS) and MGIT DST for RIF and INH were performed. Discordant genotypic and phenotypic sensitivity results were repeated for confirmation and the discrepant results considered final. Further, drug resistance-conferring mutations identified through WGS were analyzed for their presence as targets in current WHO-recommended molecular diagnostics. WGS detected additional mutations for rifampicin and isoniazid resistance than WHO-endorsed line probe assays. For RIF, WGS was able to identify an additional 10% (15/146) of rpoB mutant isolates associated with borderline rifampicin resistance compared to MGIT DST. WGS could detect additional DR TB cases than commercially available and WHO-endorsed molecular DST tests. WGS results reiterate the importance of the recent WHO revised critical concentrations of current MGIT DST to detect low-level resistance to rifampicin. WGS may help inform effective treatment selection for persons at risk of, or diagnosed with, DR TB.

BACKGROUND: Zimbabwe has a high prevalence of children who have experienced abuse according to national data. OBJECTIVE: To understand how parents/caregivers and children describe child discipline, abuse, and neglect and what factors influence each, in order to inform the adaptation of a positive parenting/caregiving intervention in Chitungwiza, Zimbabwe. PARTICIPANTS: A total of eight focus groups were conducted, four with parents/caregivers (N = 40) and four with their children ages 10-14 (N = 40), separately, between June-July 2016. SETTING: Chitungwiza, Zimbabwe. METHODS: We used an inductive and deductive analytic approach to analyze focus group transcripts, using MAXQDA 12. RESULTS: There were similar themes across focus groups of children and parents/caregivers. Findings suggest that parents/caregivers and children may be somewhat aware of the differences between discipline and abuse, but they are not completely clear about what the definitions of discipline and abuse are, and where the boundaries between discipline and abuse lie. The use of both non-physical and physical forms of discipline were described in the community, however physical discipline was a reoccurring theme in the focus groups of both parents/caregivers and their children. There were several factors that influenced discipline and/or abuse of children in the community, including the child's gender and theseverity of the child's misbehavior/actions. Parents/caregivers shared that orphan/non-biological children were particularly vulnerable to forms of abuse and neglect committed by parents/caregivers in the community, for example, withholding food and overworking a child. CONCLUSIONS: Understanding the differences between discipline, abuse and neglect, as well as factors that influence occurrences of abuse/neglect and/or severity of abuse/neglect, need to be considered when assessing the vulnerability of children, in order to develop and refine parenting/caregiving interventions for the Zimbabwean context.

BACKGROUND: Pollution - unwanted waste released to air, water, and land by human activity - is the largest environmental cause of disease in the world today. It is responsible for an estimated nine million premature deaths per year, enormous economic losses, erosion of human capital, and degradation of ecosystems. Ocean pollution is an important, but insufficiently recognized and inadequately controlled component of global pollution. It poses serious threats to human health and well-being. The nature and magnitude of these impacts are only beginning to be understood. GOALS: (1) Broadly examine the known and potential impacts of ocean pollution on human health. (2) Inform policy makers, government leaders, international organizations, civil society, and the global public of these threats. (3) Propose priorities for interventions to control and prevent pollution of the seas and safeguard human health. METHODS: Topic-focused reviews that examine the effects of ocean pollution on human health, identify gaps in knowledge, project future trends, and offer evidence-based guidance for effective intervention. ENVIRONMENTAL FINDINGS: Pollution of the oceans is widespread, worsening, and in most countries poorly controlled. It is a complex mixture of toxic metals, plastics, manufactured chemicals, petroleum, urban and industrial wastes, pesticides, fertilizers, pharmaceutical chemicals, agricultural runoff, and sewage. More than 80% arises from land-based sources. It reaches the oceans through rivers, runoff, atmospheric deposition and direct discharges. It is often heaviest near the coasts and most highly concentrated along the coasts of low- and middle-income countries. Plastic is a rapidly increasing and highly visible component of ocean pollution, and an estimated 10 million metric tons of plastic waste enter the seas each year. Mercury is the metal pollutant of greatest concern in the oceans; it is released from two main sources - coal combustion and small-scale gold mining. Global spread of industrialized agriculture with increasing use of chemical fertilizer leads to extension of Harmful Algal Blooms (HABs) to previously unaffected regions. Chemical pollutants are ubiquitous and contaminate seas and marine organisms from the high Arctic to the abyssal depths. ECOSYSTEM FINDINGS: Ocean pollution has multiple negative impacts on marine ecosystems, and these impacts are exacerbated by global climate change. Petroleum-based pollutants reduce photosynthesis in marine microorganisms that generate oxygen. Increasing absorption of carbon dioxide into the seas causes ocean acidification, which destroys coral reefs, impairs shellfish development, dissolves calcium-containing microorganisms at the base of the marine food web, and increases the toxicity of some pollutants. Plastic pollution threatens marine mammals, fish, and seabirds and accumulates in large mid-ocean gyres. It breaks down into microplastic and nanoplastic particles containing multiple manufactured chemicals that can enter the tissues of marine organisms, including species consumed by humans. Industrial releases, runoff, and sewage increase frequency and severity of HABs, bacterial pollution, and anti-microbial resistance. Pollution and sea surface warming are triggering poleward migration of dangerous pathogens such as the Vibrio species. Industrial discharges, pharmaceutical wastes, pesticides, and sewage contribute to global declines in fish stocks. HUMAN HEALTH FINDINGS: Methylmercury and PCBs are the ocean pollutants whose human health effects are best understood. Exposures of infants in utero to these pollutants through maternal consumption of contaminated seafood can damage developing brains, reduce IQ and increase children's risks for autism, ADHD and learning disorders. Adult exposures to methylmercury increase risks for cardiovascular disease and dementia. Manufactured chemicals - phthalates, bisphenol A, flame retardants, and perfluorinated chemicals, many of them released into the seas from plastic waste - can disrupt endocrine signaling, reduce male fertility, damage the nervous system, and increase risk of cancer. HABs produce potent toxins that accumulate in fish and shellfish. When ingested, these toxins can cause severe neurological impairment and rapid death. HAB toxins can also become airborne and cause respiratory disease. Pathogenic marine bacteria cause gastrointestinal diseases and deep wound infections. With climate change and increasing pollution, risk is high that Vibrio infections, including cholera, will increase in frequency and extend to new areas. All of the health impacts of ocean pollution fall disproportionately on vulnerable populations in the Global South - environmental injustice on a planetary scale. CONCLUSIONS: Ocean pollution is a global problem. It arises from multiple sources and crosses national boundaries. It is the consequence of reckless, shortsighted, and unsustainable exploitation of the earth's resources. It endangers marine ecosystems. It impedes the production of atmospheric oxygen. Its threats to human health are great and growing, but still incompletely understood. Its economic costs are only beginning to be counted.Ocean pollution can be prevented. Like all forms of pollution, ocean pollution can be controlled by deploying data-driven strategies based on law, policy, technology, and enforcement that target priority pollution sources. Many countries have used these tools to control air and water pollution and are now applying them to ocean pollution. Successes achieved to date demonstrate that broader control is feasible. Heavily polluted harbors have been cleaned, estuaries rejuvenated, and coral reefs restored.Prevention of ocean pollution creates many benefits. It boosts economies, increases tourism, helps restore fisheries, and improves human health and well-being. It advances the Sustainable Development Goals (SDG). These benefits will last for centuries. RECOMMENDATIONS: World leaders who recognize the gravity of ocean pollution, acknowledge its growing dangers, engage civil society and the global public, and take bold, evidence-based action to stop pollution at source will be critical to preventing ocean pollution and safeguarding human health.Prevention of pollution from land-based sources is key. Eliminating coal combustion and banning all uses of mercury will reduce mercury pollution. Bans on single-use plastic and better management of plastic waste reduce plastic pollution. Bans on persistent organic pollutants (POPs) have reduced pollution by PCBs and DDT. Control of industrial discharges, treatment of sewage, and reduced applications of fertilizers have mitigated coastal pollution and are reducing frequency of HABs. National, regional and international marine pollution control programs that are adequately funded and backed by strong enforcement have been shown to be effective. Robust monitoring is essential to track progress.Further interventions that hold great promise include wide-scale transition to renewable fuels; transition to a circular economy that creates little waste and focuses on equity rather than on endless growth; embracing the principles of green chemistry; and building scientific capacity in all countries.Designation of Marine Protected Areas (MPAs) will safeguard critical ecosystems, protect vulnerable fish stocks, and enhance human health and well-being. Creation of MPAs is an important manifestation of national and international commitment to protecting the health of the seas.

We obtained the full-length genome of a simian foamy virus (SFV) from an infected human. This virus originated from a baboon (Papio species, strain SFVpxx_hu9406). The genome is 13,113 nucleotides long with the canonical SFV genome structure. Phylogenetically, SFVpxx_hu9406 clustered closely with SFVpan_V909/03F from a captive baboon and other Cercopithecidae SFVs.

Tenofovir disoproxil fumarate (TDF) genotypic resistance defined by K65R/N and/or K70E/Q/G occurs in 20% to 60% of individuals with virological failure (VF) on a WHO-recommended TDF-containing first-line regimen. However, the full spectrum of reverse transcriptase (RT) mutations selected in individuals with VF on such a regimen is not known. To identify TDF regimen-associated mutations (TRAMs), we compared the proportion of each RT mutation in 2873 individuals with VF on a WHO-recommended first-line TDF-containing regimen to its proportion in a cohort of 50,803 antiretroviral-naive individuals. To identify TRAMs specifically associated with TDF-selection pressure, we compared the proportion of each TRAM to its proportion in a cohort of 5805 individuals with VF on a first-line thymidine analog-containing regimen. We identified 83 TRAMs including 33 NRTI-associated, 40 NNRTI-associated, and 10 uncommon mutations of uncertain provenance. Of the 33 NRTI-associated TRAMs, 12 - A62V, K65R/N, S68G/N/D, K70E/Q/T, L74I, V75L, and Y115F - were more common among individuals receiving a first-line TDF-containing compared to a first-line thymidine analog-containing regimen. These 12 TDF-selected TRAMs will be important for monitoring TDF-associated transmitted drug-resistance and for determining the extent of reduced TDF susceptibility in individuals with VF on a TDF-containing regimen.

An accurate accessible test for early infant diagnosis (EID) is crucial for identifying HIV-infected infants and linking them to treatment. To improve EID services in Ukraine, dried blood spot (DBS) samples obtained from 237 HIV-exposed children (≤18 months of age) in six regions in Ukraine in 2012 to 2013 were tested with the AmpliSens DNA-HIV-FRT assay, the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 Qual test, and the Abbott RealTime HIV-1 Qualitative assay. In comparison with the paired whole-blood results generated from AmpliSens testing at the oblast HIV reference laboratories in Ukraine, the sensitivity was 0.99 (95% confidence interval [CI], 0.95 to 1.00) for the AmpliSens and Roche CAP/CTM Qual assays and 0.96 (95% CI, 0.90 to 0.98) for the Abbott Qualitative assay. The specificity was 1.00 (95% CI, 0.97 to 1.00) for the AmpliSens and Abbott Qualitative assays and 0.99 (95% CI, 0.96 to 1.00) for the Roche CAP/CTM Qual assay. McNemar analysis indicated that the proportions of positive results for the tests were not significantly different (P > 0.05). Cohen's kappa (0.97 to 0.99) indicated almost perfect agreement among the three tests. These results indicated that the AmpliSens DBS and whole-blood tests performed equally well and were comparable to the two commercially available EID tests. More importantly, the performance characteristics of the AmpliSens DBS test meets the World Health Organization EID test requirements; implementing AmpliSens DBS testing might improve EID services in resource-limited settings.

BACKGROUND: HIV-1 RNA viral load (VL) levels are used for monitoring disease progression and antiretroviral therapy outcomes in HIV-infected patients. To assess the performance of laboratories conducting HIV-1 VL testing in resource-limited settings, the US Centers for Disease Control and Prevention implemented a voluntary, free-of-charge, external quality assurance program using dried tube specimens (DTSs). METHODS: DTS proficiency test (PT) panels consisting of 5 specimens were distributed between 2010 and 2012 at ambient temperature to participants. The results from participants (N ≥ 6) using the same assay were grouped, analyzed, and graded as acceptable within a group mean +/- 3SDs. Mean proficiency scores were calculated by dividing the combined PT scores with the number of testing cycles using a linear regression model. RESULTS: Between 2010 and 2012, the number of participants enrolled increased from 32 in 16 countries to 114 in 44 countries. 78.2% of participants reported results using 10 different VL assays. The rates of participants reporting acceptable results were 96.6% (Abbott), 96.3% (Roche COBAS), 94.5% (Roche Amplicor), 93.0% (Biocentric), and 89.3% (NucliSENS). The overall mean proficiency scores improved over time (p = 0.024). CONCLUSION: DTSs are a good alternative specimen type to plasma specimens for VL PT programs as they do not require cold chain transportation and can be used on polymerase chain reaction (PCR)-based assays. Our data suggest that the CDC HIV-1 VL PT program using DTSs positively impacts the testing performance of the participants which might translate into better and accurate VL testing services to patients.

Timely diagnosis and treatment of infants infected with HIV are critical for reducing infant mortality. High-throughput automated diagnostic tests like Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Qual Test (Roche CAPCTM Qual) and the Abbott Real Time HIV-1 Qualitative (Abbott Qualitative) can be used to rapidly expand early infant diagnosis testing services. In this study, the performance characteristics of the Abbott Qualitative were evaluated using two hundred dried blood spots (DBSs) samples (100 HIV-1 positive and 100 HIV-1 negative) collected from infants attending the antenatal facilities in Kisumu, Kenya. The Abbott Qualitative results were compared to the diagnostic testing completed using the Roche CAPCTM Qual in Kenya. The sensitivity and specificity of the Abbott Qualitative were 99.0% (95% CI: 95.0-100.0) and 100.0% (95% CI: 96.0-100.0), respectively, and the overall reproducibility was 98.0% (95% CI: 86.0-100.0). The limits of detection for the Abbott Qualitative and Roche CAPCTM Qual were 56.5 and 6.9copies/mL at 95% CIs (p=0.005), respectively. The study findings demonstrate that the Abbott Qualitative test is a practical option for timely diagnosis of HIV in infants.

This report describes a pilot study, conducted in Nigeria, of the World Health Organization protocol for monitoring human immunodeficiency virus (HIV) drug resistance (HIVDR) and associated program factors among patients receiving first-line antiretroviral therapy (ART). In 2008, 283 HIV-infected patients starting ART were consecutively enrolled at 2 ART clinics in Abuja. Twelve months after ART initiation, 62% were alive and on first-line ART, 3% had died, 1% had transferred out of the program, and 34% were lost to follow-up. Among patients on first-line ART at 12 months, 90% had viral suppression. However, in view of the high loss to follow-up rate (34%), strategies for patient retention and tracking are critical to minimize possible HIVDR and optimize treatment outcomes.

Mutations associated with the use of protease (PR) and reverse transcriptase (RT) inhibitors have been mostly mapped for HIV-1 subtype B. The prevalence of these mutations in drug-naive HIV-1 subtype B infected individuals is low but occurs at high frequencies in treated individuals. To determine the prevalence of treatment-associated mutations in non-B viruses, we analyzed a 1613bp pol region of specimens collected from 57 HIV-1 infected treatment-naive individuals from Cameroon. Of the 57 HIV-1 sequences, 43 belonged to CRF02-AG, two to CRF11-cpx, six to subtype A, one to subtype D and five were unclassifiable. Of the 57 PR sequences, 100% contained at least one codon change giving substitutions at positions 10, 11, 16, 20, 33, 36, 60, 62, 64, 69, 77, and 89. These substitutions gave the following prevalence pattern, 36I/L (100%, 57/57) > 89M/I (98%, 56/57) > 69K/R (93%, 53/57) > 20I/R (89%, 51/57) > 16E (16%, 9/57) > 64M (12%, 7/57) > 10I (11%, 6/57) > 11V (5%, 3/57) = 62V (5%, 3/57) = 77I (5%, 3/57) > 233F/V (4%, 2/57) = 60E (4%), which differed significantly from subtype B at positions 20, 36, 69 and 89. All but one (98%) of the 57 RT sequences (438 amino acid residues) carried substitutions located at codons 39A (7%), 43E (7%), 122E (7%), 312Q (2%), 333E (2%), 335C/D (89%), 356K (89%), 358K (14%), 365I (2%), 371V (81%), 376S (11%) or 399D (4%); the frequency of these substitutions ranged from <0.5% to 4% in RT of subtype B. The high prevalence of minor mutations associated with protease inhibitors (PI) and reverse transcriptase inhibitors (RTI) represent natural polymorphisms. HIV-1 PR and RT sequences from ARV-naive HIV-infected persons in Cameroon are important for monitoring the development of resistance to PIs and RTIs as such mutations could lead to treatment failures in individuals undergoing ARV therapy.