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DOE OSTI2024

Elemental profiling and genomewide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

Samples were collected from a population of 1,089 black cottonwood genotypes (P. trichocarpa) assembled from native stands to encompass the central portion of the natural range of the species, stretching from 38.8° to 54.3° N Q13 latitude from California, USA, to British Columbia, Canada. Establishment of the common garden, growth conditions, and site maintenance have been described by Muchero et al (2015). In this study, leaf samples for ionomic profiling were collected from 4-year-old trees, during the growing season, in July 2012, from a field located in Clatskanie, Oregon, USA (46°6′11″N 123°12′13″W). The field site was located in a protected alluvial floodplain containing a uniform Wauna-Locoda silt loam soil area characterized by an acidic pH, in Columbia County, Oregon. A subset of 584 out of the 1,089 P. trichocarpa genotypes were represented in this sampling. These genotypes were randomly selected to represent the geographical distribution of the population. A single fully mature (LPI 7-9) leaf on the south side of the tree exposed to full sunlight conditions was removed from the tree within a 6-hour window centering on solar noon and immediately frozen under dry ice before processing. Leaf samples of 584 P. trichocarpa genotypes were finely ground to 40 mm particle size using a mortar and pestle, and ionomic composition was analyzed using ICP-MS. In total, 20 elements were profiled, including aluminum (Al27), arsenic (As75), boron (B11), cadmium (Cd111), calcium (Ca43), cobalt (Co), copper (Cu), iron (Fe57), magnesium (Mg25), manganese (Mn55), molybdenum (Mo), nickel (Ni60), phosphorus (P31), potassium (K39), rubidium (Rb85), selenium (Se82), sodium (Na23), strontium (Sr88), sulfur (S34), and zinc (Zn66), following a protocol established by Ziegler et al. (2013). For each sample, 75mg of powder was digested overnight in 2.5 mL HNO3 containing 20 parts per billion (ppb) indium as an internal standard, following the protocol described in Ziegler et al. (2013). Following a dilution, concentration of the 20 elements was measured using an Elan 6000 DRC-e mass spectrometer (Perkin-Elmer SCIEX) connected to a PFA microflow nebulizer (Elemental Scientific) and Apex HF desolvator (Elemental Scientific). One measurement per sample per genotype was done. For subsequent analyses, the quantifications were converted to total element concentration.

CBI ionomics, GWAS, plasma-mass spectrometry, neut↗

DOE OSTI2025

April 2024 Semiannual Composite Salt Waste Processing Facility (SWPF) Decontaminated Salt Solution (DSS) Toxicity Characteristic Leaching Procedure (TCLP) Results

The aqueous waste from the Salt Waste Processing Facility (SWPF) is sampled semiannually for transfers to the Saltstone Production Facility (SPF). Salt solution is treated at SPF and disposed of in the Saltstone Disposal Facility (SDF). Per request of customer, X-TTR-Z-00027, Revision 0, one SDF waste form (saltstone) sample was prepared in the Savannah River National Laboratory (SRNL) from the SWPF Decontaminated Salt Solution (DSS) Waste Acceptance Criteria (WAC) sample and Z-area premix material for the April 2024 semiannual Toxicity Characteristic Leaching Procedure (TCLP) sample. The sample contained 60:40 (by weight) of slag and fly ash (referred to as the “Cement-Free grout sample”). Results from the technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request (TTR) prepared by Savannah River Mission Completion (SRMC). After at least 28 days cured, a sample of the SDF waste form was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure (TCLP). The April 2024 semiannual Cement-Free grout sample met the South Carolina (SC) Code of Regulations for Hazardous Waste Management Regulations (HWMR) 61-79.261.24 and 61-79.268.48 requirements for a non-hazardous waste form with respect to the Resource Conservation and Recovery Act (RCRA) metals and Underlying Hazardous Constituents (UHCs), and met the SPF WAC that was in effect at the time of the tank sampling.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

The Chicago Carnegie Hubble Program: Improving the Calibration of Type Ia Supernovae with JWST Measurements of the Tip of the Red Giant Branch

We present distances to 10 supernova (SN) host galaxies determined via the tip of the red giant branch using JWST/NIRCam and the F115W, F356W, and F444W bandpasses. The majority of the analysis was conducted on photometric catalogs that had their absolute zero-points randomized to mask information on distance. The new F115W TRGB distances, anchored by the geometric maser distance to NGC 4258, agree well with our previously derived Hubble Space Telescope (HST) TRGB distances, differing by only 1% on average and 4% on a per-galaxy basis. The color-corrected F115W TRGB is therefore equally precise a method of distance measurement as, and offers unique advantages over, its color-insensitive, I-band counterpart. We use these distances to update four published H 0 calibrations and evaluate how different SN analyses, both within and across independent groups, yield different H 0 values. For our JWST sample of 11 SNe, we find consistent values of H 0 ≃ 69 km s −1 Mpc −1 , with a dispersion of just 0.6 km s −1 Mpc −1 across the updated calibrations. When we expand the sample to 24 by combining with HST TRGB measurements, the results from different SN analyses begin to diverge, with the H 0 based on Pantheon+ and the Carnegie Supernova Project II (CSP-II), respectively, increasing by +2.0 km s −1 Mpc −1 (3.1σ significance) and +0.8 km s −1 Mpc −1 (1.4σ significance). More independent analyses of low-redshift SNe and JWST observations of the TRGB are needed to improve our understanding of systematics in distance ladder determinations of H 0 .

Hoyt, Taylor J. [Lawrence Berkeley National Labora↗

DOE OSTI2024

Plastic additives in the ocean: Use of a comprehensive dataset for meta-analysis and method development

In excess of 13,000 chemicals are added to plastics (‘additives’) to improve performance, durability, and production of plastic products. They are categorized into numerous chemical classes including flame retardants, light stabilizers, antioxidants, and plasticizers. While research on plastic additives in the marine environment has increased over the past decade, there is a lack of methodological standardization. To direct future measurement of plastic additives, we compiled a first-of-its-kind dataset of literature assessing plastic additives in marine environments, delineated by sample type (plastic debris, seawater, sediment, biota). Using this dataset, we performed a meta-analysis to summarize the state of the science. Currently, our dataset includes 217 publications published between 1978 and May 2023. The majority of publications analyzed plastic additives in biota collected from Europe and Asia. Analyses concentrated on plasticizers, brominated flame retardants, and bisphenols. Common sample preparation techniques included Solvent - Agitation extraction for plastic, sediment, and biota samples, and Solid Phase Extraction for seawater samples with dichloromethane and solvent mixtures including dichloromethane as the organic extraction solvent. Finally, most analyses were performed utilizing gas chromatography/mass spectrometry. There are a variety of data gaps illuminated by this meta-analysis, most notably the small number of compounds that have been targeted for detection compared to the large number of additives used in plastic production. The provided dataset facilitates future investigation of trends in plastic additive concentration data in the marine environment (allowing for comparison to toxicity thresholds) and acts as a starting point for optimizing and harmonizing plastic additive analytical methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Validating sequential Monte Carlo for gravitational-wave inference

Nested sampling (NS) is the preferred stochastic sampling algorithm for gravitational-wave inference for compact binary coalescences. It can handle the complex nature of the gravitational-wave likelihood surface and provides an estimate of the Bayesian model evidence. However, there is another class of algorithms that meets the same requirements, but has not been used for gravitational-wave analyses: sequential Monte Carlo (SMC), an extension of importance sampling that maps samples from an initial density to a target density via a series of intermediate densities. In this work, we validate a type of SMC algorithm, called persistent sampling (PS), for gravitational-wave inference. We consider a range of different scenarios including binary black holes and binary neutron stars and real and simulated data and show that PS produces results that are consistent with NS whilst being, on average, 2 times more efficient and 2.74 times faster. This demonstrates that PS is a viable alternative to NS that should be considered for future gravitational-wave analyses.

black hole mergers↗

DOE OSTI2025

The XMM Cluster Survey: automating the estimation of hydrostatic mass for large samples of galaxy clusters – I. Methodology, validation, and application to the SDSSRM-XCS sample

ABSTRACT We describe features of the X-ray: Generate and Analyse (xga) open-source software package that have been developed to facilitate automated hydrostatic mass ($M_{\rm hydro}$) measurements from XMM X-ray observations of clusters of galaxies. This includes describing how xga measures global, and radial, X-ray properties of galaxy clusters. We then demonstrate the reliability of xga by comparing simple X-ray properties, namely the X-ray temperature and gas mass, with published values presented by the XMM Cluster Survey (XCS), the Ultimate XMM eXtragaLactic survey project (XXL), and the Local Cluster Substructure Survey (LoCuSS). xga measured values for temperature are, on average, within 1 per cent of the values reported in the literature for each sample. xga gas masses for XXL clusters are shown to be ${\sim }$10 per cent lower than previous measurements (though the difference is only significant at the $\sim 1.8\sigma$ level), LoCuSS $R_{2500}$ and $R_{500}$ gas mass re-measurements are 3 per cent and 7 per cent lower, respectively (representing 1.5$\sigma$ and 3.5$\sigma$ differences). Like-for-like comparisons of hydrostatic mass are made to LoCuSS results, which show that our measurements are $10{\pm }3~{{\rm per\ cent}}$ ($19{\pm }7~{{\rm per\ cent}}$) higher for $R_{2500}$ ($R_{500}$). The comparison between $R_{500}$ masses shows significant scatter. Finally, we present new $M_{\rm hydro}$ measurements for 104 clusters from the Sloan Digital Sky Survey (SDSS) DR8 redMaPPer XCS sample (SDSSRM-XCS). Our SDSSRM-XCS hydrostatic mass measurements are in good agreement with multiple literature estimates, and represent one of the largest samples of consistently measured hydrostatic masses. We have demonstrated that xga is a powerful tool for X-ray analysis of clusters; it will render complex-to-measure X-ray properties accessible to non-specialists.

Turner, D. J. (ORCID:0000000196581396)↗

DOE OSTI2025

Elephant range and population, strontium isotopes, and genetics combine to give local-scale specificity to ivory hotspot tracking

We use Sr isotopes to increase the precision of DNA-based origin estimates of wildlife products. Population information is used to develop Sr isotope Elephant Polygons that are overlaid onto the region of origin identified by DNA assignment to determine the sources of seized ivory samples. Our approach is cognizant of isotope mixing due to isotope turnover within animals and also of the large home range of elephants or other mobile species. Genetic information from 3 different law enforcement ivory seizures suggests a region of origin confined to Kenya and Tanzania in eastern Africa. We determine characteristic 87 Sr/ 86 Sr ratios for each of 25 different Elephant Polygons within this region using analyses of more the 600 known-origin reference samples. Using both the 87 Sr/ 86 Sr ratios of the seized ivory samples and elephant population estimates from individual Elephant Polygons we find that at least 75 % of the samples likely came from a single Elephant Polygon which includes the Tsavo National Parks in Kenya and the Mkomazi National Park in Tanzania. A few samples may have come from other regions, most likely from Tanzania. This study illustrates the value of combining genetics, isotope geochemistry, and population surveys in wildlife forensics studies.

Africa↗

DOE OSTI2026

Opportunities and Limitations of Nuclear Magnetic Resonance Spectroscopy in Astrobiology

For decades, Nuclear Magnetic Resonance (NMR) spectroscopy has been utilized as a powerful tool in various scientific disciplines, most prominently in chemistry, to determine molecular structures or monitor reactions. While well established in various fields, NMR applications in astrobiology are still unclear. This work aims to explore the potential of NMR in astrobiology, highlighting strengths but also weaknesses. We illustrate capabilities of NMR with two applications: (1) recently developed methods for position-specific carbon isotope analysis of complex organics; and (2) well-established tools for performing quantitative compositional analysis of complex organic mixtures. By utilizing samples relevant to astrobiology, specifically the amino acid valine and analogue mixtures of organics, we showcase that molecules retain a source dependent and distinct intramolecular carbon isotope fingerprint. We demonstrate that compositional sample analysis provides an independent and complementary line of evidence pointing towards the origin of a molecule or mixture. Together, these NMR tools have the potential to support life detection efforts, and aid in distinguishing between biotic and abiotic samples. Finally, we discuss sensitivity, detection limits, the portability of NMR, and propose how integration with mass-spectrometry techniques will be imperative to enable more targeted and comprehensive analyses relevant to astrobiology, including in-situ analysis but also sample return missions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Quantifying the resonant photoemission of radiation damaged Pu

Here, the resonant photoelectron spectroscopy (ResPes) of new and aged δ-Pu(Ga) is reassessed by using the small oxygen contaminant peaks as an independent and quantitative check upon conventional cross-photon-energy normalization. Good agreement is found between the measured oxygen intensities and the atomic cross section calculations. Consistent with earlier analyses, the radiation induced damage in the aged samples is found to compress and sharpen the 5f peaks. This is associated with increased localization of the 5f bands, corresponding to the 5f density of states calculations that show a narrowing of 5f bandwidth with cluster size diminishment.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Statistically-driven Experimental Design to Improve Reference-free Quantification of Small Molecules by Liquid Chromatography-Mass Spectrometry

Non-targeted analysis of small molecules and metabolites in unknown, complex samples using liquid chromatography-tandem mass spectrometry remains challenging. One of the main bottlenecks is the extensive unannotated regions of metabolomics mass spectrometry data, resulting in knowledge gaps. Small molecule annotation in mass spectrometry data has conventionally relied on reference standards and libraries for compound identification and confirmation, which can constrain compound identification to those molecules already known, thus limiting the ability to discover new knowledge and new markers. Retention time prediction can facilitate and expedite unknown compound identification in non-targeted analysis of complex metabolomics samples. Additionally, accurate retention time predictions can also inform sample mixture design for LC-MS/MS analyses. However, current machine learning-based methods for retention time prediction are typically developed for specific chromatographic platforms and are not generalizable across scales. And while technologies and methods to improve reference-free metabolite identification for more comprehensive annotation of unknowns has received much attention, development of the same for quantitation without reference standards has been much more limited, despite its importance in toxicological, environmental, food safety, forensics, and clinical applications. We believe that a reference-free quantitation strategy that exploits mass spectrometry data already collected for reference-free identification can provide much more insight on unknowns, and move the metabolomics field for more complete unknowns characterization. As such, we pursue two efforts to improve upon current state-of-the-art methods in non-targeted analysis: (1) machine learning-based retention time prediction and (2) statistical design of experiments framework for reference-free quantitation. In this work, we develop and demonstrate (1) a generalizable retention time prediction capability across chromatographic conditions and scales, and (2) a statistical design-based framework for response factor contribution elucidation and reference-free quantitation. Evaluation of our retention time prediction model, PrediToR, showed approximately 24% improvement over current models, and we observed approximately 10X improvement in concentration estimation accuracy from our statistical design-based response factor model over a primarily ionization efficiency-based model. We expect that future efforts to improve upon these new capabilities will further advance non-targeted analysis of small molecules towards truly reference-free metabolomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

High-Resolution Computed Tomography Dataset of Mount Simon Sandstone

The Illinois Basin is a critical structure for subsurface energy related activities and their implementation in the United States. The Mount Simon Sandstone has been identified as a storage target for permanent and transient storage of fluids in the basin. Known for its exceptional thickness, depth, porosity, and sealing properties of overlying formations, this saline reservoir is crucial for long-term subsurface energy efforts. We present an extensive Computed Tomography (CT) dataset on a high porosity and permeability zone in the lower Mount Simon Sandstone available on the Energy Data eXchange® (EDX). This publicly accessible database comprises over 500 GB of high-resolution CT scans of six core samples, with resolutions ranging from 14.8 µm to 0.7 µm per pixel. The scans include both dry sandstone samples and those saturated with multiple fluids, allowing for comparative analyses across different conditions and resolutions. Coarser scans capture the bedding structure of the sandstone, while finer resolutions reveal detailed pore infill and throat characteristics. Metadata on location, depth, and saturation state enhance usability, enabling quick identification and cross-sample comparisons. By providing a robust resource for research and collaboration, the database contributes to domestic energy advancement by supporting continued progress in the use of the subsurface for energy solutions.

characterization↗

DOE OSTI2025

LBNF Material Activation Study

This poster presents a study on material activation at the Fermilab Long-Baseline Neutrino Facility (LBNF), focusing on understanding how high-energy beams interact with surrounding materials to produce radioactive isotopes. Using a simplified model of the LBNF-20 bunker and the FLUKA Monte Carlo simulation tool, the project quantifies isotope production at key locations inside and outside the shielding structures. The study employs a two-step simulation process, tracking primary and secondary particles, and explores the impact of different geometric and material configurations on activation rates. Results include preliminary comparisons of simulated activation rates and suggest methods for refining geometry, improving accuracy, and efficiently simulating future configurations. This work informs the design and operation of the LBNF facility, aiding in radiation safety and shielding optimization. Future efforts will focus on sample iteration, automated simulations, and detailed residual isotope analyses to further enhance the understanding of material activation in high-energy physics environments.

Pietraszek, Jacob [Unlisted, US]↗

DOE OSTI2025

Probabilistic Predictions for Fastener Failure in the Sandia Mechanics Challenge Using the Discrete-Direct Uncertainty Quantification Approach

This paper documents the blind and post-blind analysis predictions for the 2023 Sandia Mechanics Challenge (SMC), which involved predicting the behavior of a threaded fastener joint structure subjected to shock loading. Utilizing repeat sets of fastener calibration data from various experimental configurations including tension, double shear, and joint tension, we developed a library of calibrated models which were propagated through the application model using the Discrete-Direct (DD) uncertainty quantification (UQ) approach. Although the initial blind predictions did not incorporate spare-sample processing to quantify fastener failure probabilities, the analyses yielded reasonable conclusions aligned with experimental results. In the post-blind analysis phase, we focused on enhancing the fidelity of the aluminum constitutive model and innovating the DD approach to obtain probabilistic predictions for fastener failure, particularly when quantities of interest (QoIs) approach their bounds. The improved aluminum model captures the behavior of the cantilever under shock loading more accurately, predicting both partial and complete cracks, although it tends to underpredict failure propagation. The enhanced DD approach facilitates probabilistic predictions that reflect the interdependent failure mechanisms of the fasteners and the cantilever, revealing that while certain fasteners are more likely to fail, the failure does not necessarily follow a progressive pattern. Overall, the post-blind analyses significantly improved the predictive capabilities of the model, providing valuable insights into the SMC application and establishing a robust foundation for informed engineering decisions. The methodology demonstrates a cost-effective and extensible approach suitable for a wide range of applications, highlighting the importance of uncertainty quantification to provide context for engineering decision making.

42 ENGINEERING↗

DOE OSTI2025

The Dark Energy Bedrock All-sky Supernova Program: Cross Calibration, Simulations, and Cosmology Forecasts

Type Ia supernovae (SNe Ia) have been essential for probing the nature of dark energy; however, most SN analyses rely on the same low-redshift sample, which may lead to shared systematics. In a companion paper, we introduce the Dark Energy Bedrock All-Sky Supernova (DEBASS) program, which has already collected more than 500 low-redshift SNe Ia on the Dark Energy Camera, and present an initial release of 77 SNe Ia within the Dark Energy Survey (DES) footprint observed between 2021 and 2024. Here, we examine the systematics, including photometric calibration and selection effects. We find agreement at the 10 mmag level among the tertiary standard stars of DEBASS, DES, and Pan-STARRS1. Our simulations reproduce the observed distributions of DEBASS SN light-curve properties, and we measure a bias-corrected Hubble residual scatter of 0.08 mag, which, while small, is found in 10% of our simulations. We compare the DEBASS SN distances to the Foundation sample and find consistency with a median residual offset of 0.016 ± 0.019 mag. Selection effects have negligible impacts on distances, but a different photometric calibration solution shifts the median residual −0.015 ± 0.019 mag, highlighting calibration sensitivity. Using conservative simulations, we forecast that replacing historical low-redshift samples with the full DEBASS sample will improve the statistical uncertainties on dark energy parameters w 0 and w a by 30% and 24%, respectively, enhance the dark energy Figure of Merit by up to 60%, and enable a measurement of fσ 8 at the 25% level.

Acevedo, Maria [Duke Univ., Durham, NC (United Sta↗

DOE OSTI2025

Fabrication of surrogate oxide spent fuel with various cracking patterns and design of an axial gas transport apparatus

In this article, understanding gas transport behavior in nuclear fuel rods is important for the design, performance, and safety of nuclear fuels. Surrogate materials help enable efficient research by reducing both the costs and the amount of time required. A parametric study using Darcy’s law is completed that demonstrates the feasibility of observing pressure decay over short 13-to-15-cm specimens to enable full characterization of the fabricated specimens using x-ray computed tomography. This paper demonstrates that thermally shocked and mechanically compressed alumina pellets produce surrogate samples whose various cracking patterns are representative of the severity of cracking observed as a function of burnup in irradiated nuclear fuels. Furthermore, image analyses of the cracking patterns—in conjunction with gas transport testing using surrogate samples—affords a valuable accelerated basis for developing gas transport simulations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

A comparison of compact, presumably young with extended, evolved radio active galactic nuclei

Context.The triggering and evolution of active galactic nuclei (AGNs) and the interaction of the AGN with its host galaxy is an important topic in extragalactic astrophysics. Radio sources with peaked spectra (peaked spectrum sources, PSS) and compact symmetric objects (CSO) are powerful, compact, and presumably young AGNs and therefore particularly suitable to study aspects of the AGN-host connection. Aims.We use a statistical approach to investigate properties of a PSS-CSO sample that are related to host galaxies and could potentially shed light on the link between host galaxies and AGNs. The main goal is to compare the PSS-CSO sample with a matching comparison sample of extended sources (ECS) to see if the two have significant differences. Methods.We analysed composite spectra, diagnostic line diagrams, multi-band spectral energy distributions (MBSEDs), star formation (SF) indicators, morphologies, and cluster environments for a sample of 121 PSSs and CSOs for which spectra are available from the Sloan Digital Sky Survey (SDSS). The statistical results were compared with those of the ECS sample, where we generally considered the two subsamples of quasi-stellar objects (QSOs) and radio galaxies separately. The analysis is based on a large set of archival data in the spectral range from the ultraviolet to mid-infrared. Results.We find significant differences between the PSS-CSO and the ECS sample. In particular, we find that the ECS sample has a higher proportion of passive galaxies with a lower star formation activity. This applies to both sub-samples (QSOs or radio galaxies) as well as to the entire sample. The star formation rates of the PSS-CSO host galaxies with available data are typically in the range ∼0 to 5 ℳ ⊙ yr −1 , and the stellar masses are in the range 3 × 10 11 to 10 12 ℳ ⊙ . Secondly, in agreement with previous results, we find a remarkably high proportion of PSS-CSO host galaxies with merger signatures. The merger fraction of the PSS-CSO sample is 0.61 ± 0.07, which is significantly higher than that of the comparison sample (0.15 ± 0.06). We suggest that this difference can be explained by assuming that the majority of the PSSs and CSOs cannot evolve to extended radio sources and are therefore not represented in our comparison sample.

Astronomy & Astrophysics↗

DOE OSTI2026

Reducing systematic bias in machine learning applications to J/ψ signal extraction in high-energy nuclear physics

Machine learning techniques are increasingly used in high-energy nuclear physics because they can exploit multivariate correlations more efficiently than conventional cut-based analyses. A central challenge is the construction of training samples that faithfully reproduce the detector response observed in data. Signal samples are usually derived from detector simulations; therefore, mismatches between simulation and data can degrade classifier performance and introduce systematic biases. This work presents two practical correction procedures, namely cumulative distribution function (CDF) mapping and a shift-and-scale transformation, to align simulated signal features with those measured in data. Their performance is demonstrated with $J$/$\psi$ yield measurements in $\sqrt{s_{nn}}$ = 200 GeV Ru+Ru and Zr+Zr collisions recorded by STAR. A set of self-consistency tests shows that these procedures substantially suppress the systematic bias associated with data-simulation discrepancies in machine-learning-based signal extraction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012–19: a population-based, longitudinal study

Background With scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, increasing pretreatment HIV drug resistance has been reported; however, the broader effect of ART expansion on population-level resistance patterns remains insufficiently quantified. We aimed to estimate the longitudinal prevalence of drug resistance and resistance-conferring mutations. Methods This study used data collected as part of the Rakai Community Cohort Study (RCCS), an open population-based census and cohort study conducted in southern Uganda. At each survey round, residents aged 15–49 years are invited to participate and receive a structured questionnaire that obtains sociodemographic, behavioural, and health information, including self-reported past and current ART use. Voluntary HIV testing is conducted using a rapid test algorithm and a venous blood sample. People with HIV provide samples for viral load quantification and deep sequencing. We analysed RCCS survey, HIV viral load, and deep sequencing (which was used to predict resistance) data from five survey rounds. The key outcomes were the population prevalence of viraemic people with HIV with non-nucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), protease inhibitor, or multiclass resistance among all participants (regardless of HIV serostatus) in the 2015 and 2017 surveys. Prevalence of class-specific resistance and resistance-conferring substitutions were estimated using robust log-Poisson regression. Findings Between Aug 10, 2011, and Nov 4, 2020, there were 43 361 participants in the RCCS and 7923 (18·27%) people with HIV. Over five survey rounds, 93 622 participant visits occurred, among which 17 460 (18·65%) were from people with HIV. Over the analysis period, the median age of study participants remained similar (28 years [22–35] in 2012 and 29 years [21–38] in 2019). Sufficient data were available to reliably genotype 4072 (90·03%) of 4523 participant visits from 3407 people with HIV for at least one drug. Overall population prevalence of resistance contributed by viraemic pretreatment people with HIV decreased between 2012 and 2017 from 0·56% (95% CI 0·42–0·75) to 0·25% (0·18–0·33) for NNRTI and from 0·24% (0·15–0·37) to 0·05% (0·02–0·10) for NRTI (prevalence ratio 0·44 [0·29–0·68] for NNRTI and 0·21 [0·09–0·47] for NRTI). Between 2012 and 2017, NNRTI resistance among viraemic pretreatment people with HIV increased from 4·86% (3·69–6·42) to 9·61% (7·27–12·7; prevalence ratio 1·98 [1·34–2·91]). The prevalence of NNRTI and NRTI resistance was substantially higher among viraemic treatment-experienced people with HIV (51·49% [46·24–57·34] for NNRTI and 36·46% [30·06–44·22] for NRTI in 2017) than among pretreatment people with HIV. NNRTI and NRTI resistance was predominantly attributable to rtK103N and rtM184V. inT97A was observed at a similar prevalence among viraemic treatment-experienced (9·96% [6·41–15·48]) and viraemic pretreatment (10·56% [8·01–13·93]) people with HIV; no major dolutegravir resistance mutations were observed. Interpretation Despite rising NNRTI resistance among pretreatment people with HIV, overall population prevalence of pretreatment HIV drug-resistant viraemia decreased due to increasing ART uptake and viral suppression. This finding underscores the crucial role of achieving and maintaining high ART coverage in reducing transmission of drug-resistant HIV. The high prevalence of mutations conferring resistance to components of first-line ART regimens among viraemic people with HIV is potentially concerning. Funding National Institutes of Health, Johns Hopkins University Center for AIDS Research, Bill & Melinda Gates Foundation, and the US Centers for Disease Control and Prevention.

59 BASIC BIOLOGICAL SCIENCES↗