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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

U-Net Decoder CRF v0.1.0

We introduce a new encoder-decoder system that overcomes adaptability and scalability issues. We adapt multiple CNNs as encoders, allowing for the definition of multiple function parameter arguments to structure the models according to the targeted datasets and scientific problem. We leverage the flexibility of the U-Net architecture to act as a scalable decoder. The CRF-RNN layer is integrated into the decoder as an optional final layer, keeping the entire system fully compatible with back-propagation.

Avaylon, Matthew↗
DOE OSTI2025

Seasonality and Albedo Dependence of Cloud Radiative Forcing in the Upper Colorado River Basin

Mountains create and enhance their own clouds, which both scatter and absorb shortwave radiation from the sun and absorb and re-emit land surface and atmospheric longwave radiation. However, the impacts of clouds on the surface radiation balance in high elevation snowy mountain terrain are poorly explored. In this study, we use data collected by the SAIL field campaign and partner organizations in the upper elevations (2,880 m.a.s.l) of the Upper Colorado River Basin (UCRB) over a 21-month period from September 2021 to June 2023 to estimate Cloud Radiative Forcing (CRF) in the shortwave, longwave, and the net effect. Longwave warming effects dominate during the winter when snow albedos are high (0.8–0.9) and the background atmospheric precipitable water vapor is low (<0.5 cm), yielding a maximum monthly average net CRF of +34.7 W·m -2 , meaning that clouds increase the net radiation relative to clear skies during this time period. The sign of net CRF switches in the warm season as snow recedes, sun-angles increase, and the North American monsoon arrives, yielding a minimum monthly average net CRF of -47.6 W·m -2 with hourly minima of -600 W·m -2 . The sign of net CRF is typically positive, even at solar noon, when the surface is snow covered, except for a brief period over melting, low-albedo snow (0.5–0.6) impacted by dust impurities. Sensitivity tests elucidate the role of the surface albedo on the net CRF. The results suggest that net CRF will increase in magnitude and lead to a more persistent cooling effect on the surface net radiation budget as the snow cover declines.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The Influence of Cloud Types on Cloud–Radiative Forcing During DYNAMO/AMIE

Cloud-radiative feedback is known to be an important process for the Madden-Julian Oscillation (MJO) and its accurate representation in general circulation models. The MJO is known to have a stronger cloud-radiative feedback compared to higher frequency convectively coupled equatorial waves (CCEW), for reasons that remain unclear. The objective of this study is to use data from the Dynamics of the MJO/Atmospheric Radiation Measurement MJO Investigation Experiment field campaign to investigate how cloud type evolution and their associated cloud-radiative forcing (CRF) differ between the MJO and CCEWs and their application to MJO dynamics under moisture mode theory. This study finds that the amplitude of CRF is the largest within the MJO compared to the higher frequency CCEWs, and CRF maximizes after the maximum precipitation (enhanced phase) of the MJO. We suggest this delay in the timing of maximum CRF occurs because most cloud types (congestus, deep, anvil, and cirrus) simultaneously maximize in frequency after the enhanced phase of the MJO, which is not seen for the higher frequency CCEWs. These specific cloud types help maintain the MJO through their radiatively-driven moistening which acts to prolong the enhanced phase of the MJO. The decomposition of radiatively-driven moistening by cloud types shows that simultaneous moistening by deep, anvil, and congestus clouds are particularly responsible for the maintenance of the MJO under moisture mode theory. Further, this analysis suggests the importance of capturing the correct evolution of different cloud types and their associated radiative effects to better understand the thermodynamics of the MJO.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Text Mining for Process–Structure–Properties Relationships in Metals

With the advent of large language models (LLMs), the vast unstructured text within millions of academic papers is increasingly accessible for materials discovery—although significant challenges remain. While LLMs offer promising few- and zero-shot learning capabilities, particularly valuable in the materials domain where expert annotations are scarce, general-purpose LLMs often fail to address key materials-specific queries without further adaptation. To bridge this gap, fine-tuning LLMs on human-labeled data is essential for effective structured knowledge extraction (Liu in The Importance of Human-Labeled Data in the Era of LLMs, 2023). Here, in this study, we introduce a novel annotation schema designed to extract generic process–structure–properties relationships from scientific literature. We demonstrate the utility of this approach using a dataset of 128 abstracts, with annotations drawn from two distinct domains: high-temperature materials (Domain I) and uncertainty quantification in simulating materials microstructure (Domain II). Initially, we developed a conditional random field (CRF) model based on MatBERT—a domain-specific BERT variant—and evaluated its performance on Domain I. Subsequently, we compared this model with a fine-tuned LLM (GPT-4o from OpenAI) under identical conditions. Our results indicate that fine-tuning LLMs can significantly improve entity extraction performance over the BERT-CRF baseline on Domain I. However, when additional examples from Domain II were incorporated, the performance of the BERT-CRF model became comparable to that of the GPT-4o model. These findings underscore the potential of our schema for structured knowledge extraction and highlight the complementary strengths of both modeling approaches.

Materials science↗
DOE OSTI2022

A Systematic Review and Meta-Analysis of Tai Chi Training in Cardiorespiratory Fitness of Elderly People

Objectives. The purpose of this study was to investigate the influence of Tai Chi on cardiorespiratory fitness (CRF) in elderly people using meta-analysis. Methods. This study used seven electronic databases and data retrieved from randomized controlled trials (RCTs) investigating the role of Tai Chi on CRF in the elderly. All these 24 RCTs were screened and selected from 7 literature databases. The Stata 11.2 software (StataCorp, USA) was used for the meta-analysis, subgroup analysis, and bias test, while the Cochrane Collaboration’s tool was used for the assessment of the risk of bias (RoB). 4 researchers independently participated in sample selection, data extraction, and RoB assessment. Results. Following the inclusion criteria, 24 eligible studies were included in our analysis. The meta-analysis indicated that Tai Chi practice significantly increased the maximum rate of oxygen consumption (VO2 max) (weighted mean difference (WMD) = 3.76, 95% CI: 1.25 to 6.26, P < 0.1 ), leading to an overall reduction in the heart rate (HR) (WMD = −1.84, 95% CI: −2.04 to −1.63, P ≤ 0.001 ) and an increase in the O2 pulse (WMD = 0.94, 95% CI: 0.60 to 1.28, P ≤ 0.001 ) in individuals who practiced Tai Chi regularly compared with those who did not. The subgroup analysis suggested that overall in those who practiced Tai Chi, males (WMD = 1.48, 95% CI: 0.85 to 2.12, P ≤ 0.001 ) had higher O2 pulse than females (WMD = 0.73, 95% CI: 0.33 to 1.12, P ≤ 0.001 ). The subgroup analysis also showed an increase in the vital capacity (VC) (WMD = 316.05, 95% CI: 239.74 to 392.35, P ≤ 0.001 ) in individuals practicing Tai Chi. When the samples were further stratified by Tai Chi practicing time, the subgroup analysis suggested that individuals practicing Tai Chi over a period of 24 weeks showed no significant difference in VC (WMD = 82.95, 95% CI: -98.34 to 264.23, P = 0.370 ), while those practicing Tai Chi over a period of 48 weeks showed a significant increase (WMD = 416.62, 95% CI: 280.68 to 552.56, P ≤ 0.001 ). Furthermore, the subgroup analysis demonstrated that the increase in VC is significantly correlated with the Tai Chi practicing time (WMD = 344.97, 95% CI: 227.88 to 442.06, P ≤ 0.001 ). Conclusion. Regular Tai Chi practice could improve the CRF in the elderly, as indicated by significant improvement in indicators including VO2max, O2pulse, VC, and HR. However, gender and practice time might influence the overall beneficial outcomes.

Tan, Tianyang↗
DOE OSTI2022

Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol -infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Effect of metal fluorides on the corrosion of structural materials in molten LiF-NaF-KF

The corrosion of structural materials in molten fluoride salts is predominantly caused by the presence of impurities in the salt. Here, this study focuses on understanding the corrosion behavior of selected alloys in molten FLiNaK salt with addition of similar quantities of metal fluoride impurities such as CrF 2 , CrF 3 , FeF 2 , FeF 3 , and NiF 2 . The results show that the presence of selected metal fluoride impurities increases the extent of corrosion of the selected alloys in molten FLiNaK salt, with the exact effect depending on the thermodynamic stability of the fluoride impurity added as well as the composition of the structural alloy studied.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Insights on the corrosion thermodynamics of chromium in molten LiF-NaF-KF eutectic salts

The thermodynamic stability of chromium in the Cr 0 , Cr 2+ , and Cr 3+ oxidation states considering various F - ion coordination compounds was investigated in molten LiF–NaF-KF (FLiNaK) eutectic salt. Potential fluoride ion activity (F - and CrF 3 - ) diagrams were constructed to predict the most stable Cr oxidation states as a function of anion activity, solvation state of chromium ions and potential at 600 °C. The Gibbs free energies of these compounds were estimated by utilizing a combined cyclic voltammetry – Nernst theory analysis approach in FLiNaK salt. To verify the constructed diagrams, X-ray diffraction was utilized after exposure of Cr at various applied potentials to determine whether compounds detected in solidified FLiNaK salts agreed with thermodynamic calculations. This work aims to identify key thermodynamic factors that are significant to chromium corrosion for molten salt nuclear reactor applications. The F - stability region spans the entire region where spontaneous corrosion of Cr occurs. Cr may be oxidized to Cr 2+ and Cr 3+ in the presence HF (due to moisture as an impurity) spontaneously except some conditions of p 1/2 H 2 /a HF etc. This situation is not changed qualitatively for various states of solvation between oxidized Cr solute in F - solvent and this aspect is substantially similar for the two cases (pair 1: Cr 0 /CrF 3 - / CrF 6 3- ; pair 2: Cr 0 /CrF 4 2- /CrF 5 2- ) considered in this work.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A pre-training and self-training approach for biomedical named entity recognition

Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training data in order to be effective. This severely limits the effectiveness of NER models in applications where expert annotations are difficult and expensive to obtain. In this work, we explore the effectiveness of transfer learning and semi-supervised self-training to improve the performance of NER models in biomedical settings with very limited labeled data (250-2000 labeled samples). We first pre-train a BiLSTM-CRF and a BERT model on a very large general biomedical NER corpus such as MedMentions or Semantic Medline, and then we fine-tune the model on a more specific target NER task that has very limited training data; finally, we apply semi-supervised self-training using unlabeled data to further boost model performance. We show that in NER tasks that focus on common biomedical entity types such as those in the Unified Medical Language System (UMLS), combining transfer learning with self-training enables a NER model such as a BiLSTM-CRF or BERT to obtain similar performance with the same model trained on 3x-8x the amount of labeled data. We further show that our approach can also boost performance in a low-resource application where entities types are more rare and not specifically covered in UMLS.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Impacts of active satellite sensors' low-level cloud detection limitations on cloud radiative forcing in the Arctic

Previous studies revealed that satellites sensors with the best detection capability identify 25 %–40 % and 0 %–25 % fewer clouds below 0.5 and between 0.5–1.0 km, respectively, over the Arctic. Quantifying the impacts of cloud detection limitations on the radiation flux are critical especially over the Arctic Ocean considering the dramatic changes in Arctic sea ice. In this study, the proxies of the space-based radar, CloudSat, and lidar, CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations), cloud masks are derived based on simulated radar reflectivity with QuickBeam and cloud optical thickness using retrieved cloud properties from surface-based radar and lidar during the Surface Heat Budget of the Arctic Ocean (SHEBA) experiment. Limitations in low-level cloud detection by the space-based active sensors, and the impact of these limitations on the radiation fluxes at the surface and the top of the atmosphere (TOA), are estimated with radiative transfer model Streamer. The results show that the combined CloudSat and CALIPSO product generally detects all clouds above 1 km, while detecting 25 % (9 %) fewer in absolute values below 600 m (600 m to 1 km) than surface observations. These detection limitations lead to uncertainties in the monthly mean cloud radiative forcing (CRF), with maximum absolute monthly mean values of 2.5 and 3.4 Wm –2 at the surface and TOA, respectively. Cloud information from only CALIPSO or CloudSat lead to larger cloud detection differences compared to the surface observations and larger CRF uncertainties with absolute monthly means larger than 10.0 Wm –2 at the surface and TOA. The uncertainties for individual cases are larger – up to 30 Wm –2 . These uncertainties need to be considered when radiation flux products from CloudSat and CALIPSO are used in climate and weather studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Programmable bionanocomposite coated fertilizers for prolonged controlled release of nitrogen

Controlled-release fertilizers (CRFs) present a promising solution for alleviating food and nutrient scarcity. However, their development has been mainly hindered by both rapid and unsynchronized nutrient release and unsustainable coating materials. In this study, we address this issue by developing a new coating layer for CRFs using a programmable biopolyurethane nanocomposite. This nanocomposite is prepared from diphenylmethane diisocyanate (MDI)-functionalized bentonite nanoclay (BNT-MDI) and a biopolyol from biomass waste. The results show that the BNT-MDI-doped CRFs (BCRFs) exhibit an impressive nitrogen (N)-release longevity of approximately 120 days at a 4 wt% coating ratio, surpassing previous CRF formulations. In a 30-day snap bean cultivation study, BCRF significantly improved root length (1000%), leaf length (257%), leaf width (400%), and plant height (1400%) compared to the control. The superior performance of BCRF is attributed to the PU-nanoclay biocomposite film, with full nano-exfoliation, controllable porosity, and high crosslinking density. Furthermore, we introduce a new dynamic release mechanism and establish a quantitative relationship between the nanostructure, property, and release performance of BCRF by combining the multiplicative and diffusion models for porous materials. Finally, this study provides a theoretical framework and a straightforward methodology for designing programmable nanocomposite structures for future biobased CRFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Investigation of impurity driven corrosion behavior in molten 2LiF-BeF 2 salt

A 1000 -h corrosion experiment of 316H stainless steel at 700 °C investigated the role of metal fluoride impurities CrF 2 and FeF 2 in LiF-BeF 2 (66-34 mole %) (FLiBe) salt. Inductively coupled plasma-optical emission spectroscopy (ICP-OES) demonstrated the ability to measure changes in the concentration of these fluorides in FLiBe salt. Cyclic voltammetry (CV) showed the potential for real-time quantitative concentration measurement of corrosion products in the molten salt. Materials characterization revealed that both impurity species influence the dissolution of Cr from the alloy. The collective results from these analysis methods advance the understanding of the influence impurities have on materials corrosion.

2LiF-BeF2↗
DOE OSTI2024

Emulation and detection of physical faults and cyber-attacks on building energy systems through real-time hardware-in-the-loop experiments

The increasing use of remote or mobile access, integrated wearable technologies, data exchange, and cloud-based data analytics in modern smart buildings is steering the building industry towards open communication technologies. The increased connectivity and accessibility could lead to more cyber-attacks in smart buildings. On the other hand, physical faults (e.g., HVAC -heating, ventilation, and air-conditioning faults) may have similar adverse impacts as those from the cyber-attacks on building energy systems, such as occupant discomfort, energy wastage, and equipment downtime. However, current physical behavior-based anomaly detection methods fail to differentiate between cyber-attacks and physical faults in building energy systems. Moreover, the challenge in collecting real-world threat data with ground truth has led researchers to rely on numerical models with user-defined assumptions, which may not accurately reflect real-world conditions due to the lack of in-situ experimental datasets. To address these challenges and gaps, this paper presents a flexible hardware-in-the-loop (HIL) testbed for generating cyber-attack and physical fault datasets and demonstrating threat detection algorithms in a real building automation system (BAS) environment. This testbed combines hardware (i.e., real BAS with local HVAC controllers and a physical network) with software (i.e., high-fidelity models to represent behaviors of building envelope and HVAC energy systems), enabling emulations of realistic threats. Five HIL experiments, including one baseline without any threats, two with physical faults, and two with cyber-attacks, were conducted to generate datasets containing detailed network traffic and system states. A joint classification framework, incorporating a network analyzer and a physical HVAC fault detector, was proposed to automatically detect cyber-physical abnormalities on BAS at both the network and the physical HVAC levels. The network analyzer comprises a conditional random fields (CRF) based command validator and a statistics-based detection strategy. The fault detector employs a weather and schedule-based pattern matching and feature-based principal component analysis (WPM-FPCA) method. Evaluation of the classification using four metrics from the multi-class confusion matrix revealed an average accuracy of 90.2%, recall of 89.7%, precision of 88.5% and F1-score of 89.2%. Finally, these results demonstrate that the proposed joint classification framework can effectively differentiate between specific types of cyber-attacks (e.g., device reinitialization attack, network Denial-of-Service attack) and physical faults (e.g., air handling unit operational fault, cooling coil valve stuck) in real time for improved building energy management.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Assessing outdoor air quality and public health impact attributable to residential black carbon emissions in rural China

Black carbon (BC) is a significant component of particulate matter (PM) that relates to air pollution, climate forcing, and further implications for public health. BC is predominantly released from the combustion of solid fuels. Combustion of low-quality fuels in rural China may induce severe respiratory and cardiopulmonary health outcomes for residents, which have however been inadequately assessed. One major reason for the limited understanding is the lack of a high-resolution inventory. An improved method of estimating the BC-associated public health burden is needed. This work quantified premature mortalities due to residential BC emissions in rural China. Domestic BC emissions at 1×1 km resolution were compiled based on previous field investigation, which were further configured for air quality simulation. A chemistry transport model, WRF–CMAQ v5.2, was employed for simulating BC concentrations. The consequent premature mortalities were quantified by a BC-specific concentration-response function (CRF) derived from an epidemiological study. Results show that residential combustion of solid fuel in rural China emitted 648.0 Gg (95%CI: 361.0–965.9) BC in 2014, after dispersion, accounting for 51.8% of annual mean ground-level BC concentration in China. Such impact was most severe in North and Northeast China, and the Sichuan Basin. The further investigation estimated 171,000 (95%CI: 69,000–387,000) premature mortalities that were attributable to exposure to rural residential BC. These findings reveal the major contribution of rural residential BC emissions to air pollution formation and public health impacts. Our findings are anticipated to provide useful information for enacting the next-stage environmental strategy for the residential sector in China.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Estimating the Acute Health Impacts of Fire-Originated PM 2.5 Exposure During the 2017 California Wildfires: Sensitivity to Choices of Inputs

Exposure to wildfire smoke increases the risk of respiratory and cardiovascular hospital admissions. Health impact assessments, used to inform decision-making processes, characterize the health impacts of environmental exposures by combining preexisting epidemiological concentration–response functions (CRFs) with estimates of exposure. These two key inputs influence the magnitude and uncertainty of the health impacts estimated, but for wildfire-related impact assessments the extent of their impact is largely unknown. We first estimated the number of respiratory, cardiovascular, and asthma hospital admissions attributable to fire-originated PM 2.5 exposure in central California during the October 2017 wildfires, using Monte Carlo simulations to quantify uncertainty with respect to the exposure and epidemiological inputs. We next conducted sensitivity analyses, comparing four estimates of fire-originated PM 2.5 and two CRFs, wildfire and nonwildfire specific, to understand their impact on the estimation of excess admissions and sources of uncertainty. We estimate the fires accounted for an excess 240 (95% CI: 114, 404) respiratory, 68 (95% CI: -10, 159) cardiovascular, and 45 (95% CI: 18, 81) asthma hospital admissions, with 56% of admissions occurring in the Bay Area. Although differences between impact assessment methods are not statistically significant, the admissions estimates' magnitude is particularly sensitive to the CRF specified while the uncertainty is most sensitive to estimates of fire-originated PM 2.5 . Not accounting for the exposure surface's uncertainty leads to an underestimation of the uncertainty of the health impacts estimated. Employing context-specific CRFs and using accurate exposure estimates that combine multiple data sets generates more certain estimates of the acute health impacts of wildfires.

58 GEOSCIENCES↗
DOE OSTI2022

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.

60 APPLIED LIFE SCIENCES↗