Disengagement from Care Among People Co-Infected with HIV and HCV: A Scoping Review.

Disengagement from care among people with HIV (PWH) and hepatitis C (HCV) increases the risks of adverse health outcomes and poses significant barriers to achieving global HIV and HCV elimination goals. In accordance with the Joanna Briggs Institute framework, a scoping review was conducted to synthesize and highlight existing gaps in the literature on (dis)engagement in care among PWH and HCV. We searched for original studies on (dis)engagement in care among PWH and HCV in high-income countries using eight electronic databases from inception to May 2023. Our search yielded 4462 non-duplicated records, which were scoped to 27 studies. Definitions of (dis)engagement in care were diverse, with considerable heterogeneity in how retention was operationalized and temporally measured. Studies identified predictors of (dis)engagement to be related to drug and substance use (n = 5 articles), clinical factors (n = 5), social and welfare (n = 4), and demographic characteristics (n = 2). When engagement in care was treated as an exposure, it was associated with HCV treatment initiation (n = 3), achieving sustained virological response (n = 2), and maintaining HIV viral suppression (n = 1). Interventions to improve care engagement among PWH and HCV were limited to five studies using cash incentives (n = 1) and individual case management (n = 4). (Dis)engagement in care is a dynamic process influenced by shifting priorities that may 'tip the balance' towards or away from regularly interacting with healthcare professionals. However, inconsistent definitions render cross-study comparisons and meta-analyses virtually impossible. Further research needs to establish a standardized definition to identify patients at high risk of disengagement and develop interventions that leverage the nested HIV/HCV care cascades to retain and recover patients lost from care.

Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics.

Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.

Frequent Disengagement and Subsequent Mortality Among People With HIV and Hepatitis C in Canada: A Prospective Cohort Study.

Background: The cascade of care, commonly used to assess HIV and hepatitis C (HCV) health service delivery, has limitations in capturing the complexity of individuals' engagement patterns. This study examines the dynamic nature of engagement and mortality trajectories among people with HIV and HCV. Methods: We used data from the Canadian HIV-HCV Co-Infection Cohort, which prospectively follows 2098 participants from 18 centers biannually. Markov multistate models were used to evaluate sociodemographic and clinical factors associated with transitioning between the following states: (1) lost-to-follow-up (LTFU), defined as no visit for 18 months; (2) reengaged (reentry into cohort after being LTFU); (3) withdrawn from the study (ie, moved); (4) death; otherwise remained (5) engaged-in-care. Results: A total of 1809 participants met the eligibility criteria and contributed 12 591 person-years from 2003 to 2022. LTFU was common, with 46% experiencing at least 1 episode, of whom only 57% reengaged. One in 5 (n = 383) participants died during the study. Participants who transitioned to LTFU were twice as likely to die as those who were consistently engaged. Factors associated with transitioning to LTFU included detectable HCV RNA (adjusted hazards ratio [aHR], 1.37; 95% confidence interval [CI], 1.13-1.67), evidence of HCV treatment but no sustained virologic response result (aHR, 1.99; 95% CI, 1.56-2.53), and recent incarceration (aHR, 1.94; 95% CI, 1.58-2.40). Being Indigenous was a significant predictor of death across all engagement trajectories. Interpretation: Disengagement from clinical care was common and resulted in higher death rates. People LTFU were more likely to require HCV treatment highlighting a priority population for elimination strategies.

Enhancing Si3N4 Selectivity over SiO2 in Low-RF Power NF3-O2 Reactive Ion Etching: The Effect of NO Surface Reaction.

Highly selective etching of silicon nitride (Si3N4) and silicon dioxide (SiO2) has received considerable attention from the semiconductor community owing to its precise patterning and cost efficiency. We investigated the etching selectivity of Si3N4 and SiO2 in an NF3/O2 radio-frequency glow discharge. The etch rate linearly depended on the source and bias powers, whereas the etch selectivity was affected by the power and ratio of the gas mixture. We found that the selectivity can be controlled by lowering the power with a suitable gas ratio, which affects the surface reaction during the etching process. X-ray photoelectron spectroscopy of the Si3N4 and QMS measurements support the effect of surface reaction on the selectivity change by surface oxidation and nitrogen reduction with the increasing flow of O2. We suggest that the creation of SiOxNy bonds on the surface by NO oxidation is the key mechanism to change the etch selectivity of Si3N4 over SiO2.

Preparations and Thermal Properties of PDMS-AlN-Al2O3 Composites through the Incorporation of Poly(Catechol-Amine)-Modified Boron Nitride Nanotubes.

As one of the emerging nanomaterials, boron nitride nanotubes (BNNTs) provide promising opportunities for diverse applications due to their unique properties, such as high thermal conductivity, immense inertness, and high-temperature durability, while the instability of BNNTs due to their high surface induces agglomerates susceptible to the loss of their advantages. Therefore, the proper functionalization of BNNTs is crucial to highlight their fundamental characteristics. Herein, a simplistic low-cost approach of BNNT surface modification through catechol-polyamine (CAPA) interfacial polymerization is postulated to improve its dispersibility on the polymeric matrix. The modified BNNT was assimilated as a filler additive with AlN/Al2O3 filling materials in a PDMS polymeric matrix to prepare a thermal interface material (TIM). The resulting composite exhibits a heightened isotropic thermal conductivity of 8.10 W/mK, which is a ~47.27% increase compared to pristine composite 5.50 W/mK, and this can be ascribed to the improved BNNT dispersion forming interconnected phonon pathways and the thermal interface resistance reduction due to its augmented compatibility with the polymeric matrix. Moreover, the fabricated composite manifests a fire resistance improvement of ~10% in LOI relative to the neat composite sample, which can be correlated to the thermal stability shift in the TGA and DTA data. An enhancement in thermal permanence is stipulated due to a melting point (Tm) shift of ∼38.5 °C upon the integration of BNNT-CAPA. This improvement can be associated with the good distribution and adhesion of BNNT-CAPA in the polymeric matrix, integrated with its inherent thermal stability, good charring capability, and free radical scavenging effect due to the presence of CAPA on its surface. This study offers new insights into BNNT utilization and its corresponding incorporation into the polymeric matrix, which provides a prospective direction in the preparation of multifunctional materials for electric devices.

"Going vaccine hunting": Multilevel influences on COVID-19 vaccination among racialized sexual and gender minority adults-a qualitative study.

High levels of COVID-19 vaccine hesitancy have been reported among Black and Latinx populations, with lower vaccination coverage among racialized versus White sexual and gender minorities. We examined multilevel contexts that influence COVID-19 vaccine uptake, barriers to vaccination, and vaccine hesitancy among predominantly racialized sexual and gender minority individuals. Semi-structured online interviews explored perspectives and experiences around COVID-19 vaccination. Interviews were recorded, transcribed, uploaded into ATLAS.ti, and reviewed using thematic analysis. Among 40 participants (mean age, 29.0 years [SD, 9.6]), all identified as sexual and/or gender minority, 82.5% of whom were racialized. COVID-19 vaccination experiences were dominated by structural barriers: systemic racism, transphobia and homophobia in healthcare and government/public health institutions; limited availability of vaccination/appointments in vulnerable neighborhoods; absence of culturally-tailored and multi-language information; lack of digital/internet access; and prohibitive indirect costs of vaccination. Vaccine hesitancy reflected in uncertainties about a novel vaccine amid conflicting information and institutional mistrust was integrally linked to structural factors. Findings suggest that the uncritical application of "vaccine hesitancy" to unilaterally explain undervaccination among marginalized populations risks conflating structural and institutional barriers with individual-level psychological factors, in effect placing the onus on those most disenfranchised to overcome societal and institutional processes of marginalization. Rather, disaggregating structural determinants of vaccination availability, access, and institutional stigma and mistrust from individual attitudes and decision-making that reflect vaccine hesitancy, may support 1) evidence-informed interventions to mitigate structural barriers in access to vaccination, and 2) culturally-informed approaches to address decisional ambivalence in the context of structural homophobia, transphobia, and racism.

Covid-19 Vaccine Hesitancy and Under-Vaccination among Marginalized Populations in the United States and Canada: A Scoping Review.

BACKGROUND: Amid persistent disparities in Covid-19 vaccination and burgeoning research on vaccine hesitancy (VH), we conducted a scoping review to identify multilevel determinants of Covid-19 VH and under-vaccination among marginalized populations in the U.S. and Canada. METHODS: Using the scoping review methodology developed by the Joanna Briggs Institute, we designed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020-October 25, 2022. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 VH and under-vaccination among marginalized populations. RESULTS: The search captured 11,374 non-duplicated records, scoped to 103 peer-reviewed articles. Among 14 marginalized populations identified, African American/Black, Latinx, LGBTQ+, American Indian/Indigenous, people with disabilities, and justice-involved people were the predominant focus. Thirty-two factors emerged as influencing Covid-19 VH, with structural racism/stigma and institutional mistrust (structural)(n = 71) most prevalent, followed by vaccine safety (vaccine-specific)(n = 62), side effects (vaccine-specific)(n = 50), trust in individual healthcare provider (social/community)(n = 38), and perceived risk of infection (individual)(n = 33). Structural factors predominated across populations, including structural racism/stigma and institutional mistrust, barriers to Covid-19 vaccine access due to limited supply/availability, distance/lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally- and linguistically-appropriate information. DISCUSSION: We identified multilevel and complex drivers of Covid-19 under-vaccination among marginalized populations. Distinguishing vaccine-specific, individual, and social/community factors that may fuel decisional ambivalence, more appropriately defined as VH, from structural racism/structural stigma and systemic/institutional barriers to vaccination access may better support evidence-informed interventions to promote equity in access to vaccines and informed decision-making among marginalized populations.

Longitudinal Analysis of the Intestinal Microbiota among a Cohort of Children in Rural and Urban Areas of Pakistan.

The profile of the intestinal microbiota is known to be altered in malnourished young children in low- and middle-income countries. However, there are limited studies longitudinally evaluating the intestinal microbiota in malnourished young children in resource-limited settings over the first two years of life. In this longitudinal pilot study, we determined the effect of age, residential location, and intervention on the composition, relative abundance, and diversity of the intestinal microbiota in a representative sample of children under 24 months of age with no diarrhea in the preceding 72 h in the urban and rural areas of Sindh, Pakistan nested within a cluster-randomized trial evaluating the effect of zinc and micronutrients on growth and morbidity (ClinicalTrials.gov Identifier: NCT00705445). The major findings were age-related with significant changes in alpha and beta diversity with increasing age. There was a significant increase in the relative abundance of the Firmicutes and Bacteroidetes phyla and a significant decrease in that of the Actinobacteria and Proteobacteria phyla (p < 0.0001). There were significant increases in the relative abundances of the major genera Bifidobacterium, Escherichia/Shigella and Streptococcus (p < 0.0001), and no significant change in the relative abundance of Lactobacillus. Using the LEfSE algorithm, differentially abundant taxa were identified between children in the first and second years of age, between those residing in rural and urban areas, and those who received different interventions at different ages from 3 to 24 months. The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them. Further longitudinal studies with larger numbers of well-nourished and malnourished children are required to fully characterize the intestinal microbiota of children in this region.

Free satellite image data application for monitoring land use cover changes in the kon ha nung plateau, vietnam.

Remote sensing imagery is the most suitable tool for monitoring, managing, and evaluating land-use overlay fluctuations, especially forest cover for large areas. Free- and medium-resolution satellite imagery is a useful tool that allows scientific researchers and management organizations to monitor forest development in developing countries, such as Vietnam. In this study, we used SPOT 4 and Planet remote sensing data to assess land-use status fluctuations in the Kon Ha Nung Plateau area, Vietnam, between 2000 and 2021 (the overall accuracy was 90.52%, Kappa value = 0.89). The results showed that from 2000 to 2010, the rate of natural forest loss in this area was 0.32%/year, of which, more than 6500 ha were converted to other uses. Between 2010 and 2021, the rate of natural forest loss gradually decreased (0.09%/year) instead of fluctuating between different types of land use. The area of forests, perennial crop land, and annual crop land tended to increase from 2000 to 2010; however, from 2010 to 2021, the area of plantation forests decreased markedly, while the area of perennial crop land and annual crop land continued to expand. The analysis of the policies on forest management, exploitation, and protection was applied locally, to explain the causes of the change in spatiotemporal aspects of the types of land-use cover in the Kon Ha Nung Plateau. Restoring forest areas during 2010-2021 initially improved effectiveness in forest management and protection. Furthermore, the results provide a better understanding of the current position and role of the government apparatus, cadres, and ethnic minorities in socioeconomic development associated with forest protection and development on the Kon Ha Nung Plateau. The results of this study can help managers monitor annual forest-cover fluctuations based on free remote sensing imagery to reduce both the cost of management and surveying, yielding relatively accurate results.

Deployment of a Reservoir-Targeted Vaccine Against Borrelia burgdorferi Reduces the Prevalence of Babesia microti Coinfection in Ixodes scapularis Ticks.

In the Northeast and upper Midwest of the United States, Babesia microti and Borrelia burgdorferi use Ixodes scapularis ticks as vector and Peromyscus leucopus mice as major reservoir host. We previously established, in a 5-year field trial, that a reservoir-targeted outer surface protein A vaccine reduces the prevalence of B. burgdorferi-infected ticks. We accessed ticks and mouse blood samples collected during the trial, extracted total DNA, and amplified the B. microti 18S rRNA gene. Vaccine deployment reduced the prevalence of ticks coinfected with B. microti and that of mice infected with B. microti. Breaking the enzootic cycle of B. burgdorferi may reduce the incidence of babesiosis.

Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides.

BACKGROUND: Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R. toruloides to produce the polyketide triacetic acid lactone (TAL) directly from unfiltered hydrolysate deconstructed from biomass with minimal unit process operations. RESULTS: Introduction of the 2-pyrone synthase gene into R. toruloides enabled the organism to produce 2.4 g/L TAL from simple media or 2.0 g/L from hydrolysate produced from sorghum biomass. Both of these titers are on par with titers from other better-studied microbial hosts after they had been heavily engineered. We next demonstrate that filtered hydrolysates produced from ensiled sorghum are superior to those derived from dried sorghum for TAL production, likely due to the substantial organic acids produced during ensiling. We also demonstrate that the organic acids found in ensiled biomass can be used for direct synthesis of ionic liquids within the biomass pretreatment process, enabling consolidation of unit operations of in-situ ionic liquid synthesis, pretreatment, saccharification, and fermentation into a one-pot, separations-free process. Finally, we demonstrate this consolidation in a 2 L bioreactor using unfiltered hydrolysate, producing 3.9 g/L TAL. CONCLUSION: Many steps involved in deconstructing biomass into fermentable substrate can be combined into a distinct operation, and directly fed to cultures of engineered R. toruloides cultures for subsequent valorization into gram per liter titers of TAL in a cost-effective manner.

Differential Cytotoxicity of Curcumin-Loaded Micelles on Human Tumor and Stromal Cells.

Although curcumin in the form of nanoparticles has been demonstrated as a potential anti-tumor compound, the impact of curcumin and nanocurcumin in vitro on normal cells and in vivo in animal models is largely unknown. This study evaluated the toxicity of curcumin-loaded micelles in vitro and in vivo on several tumor cell lines, primary stromal cells, and zebrafish embryos. Breast tumor cell line (MCF7) and stromal cells (human umbilical cord vein endothelial cells, human fibroblasts, and human umbilical cord-derived mesenchymal stem cells) were used in this study. A zebrafish embryotoxicity (FET) assay was conducted following the Organisation for Economic Co-operation and Development (OECD) Test 236. Compared to free curcumin, curcumin PM showed higher cytotoxicity to MCF7 cells in both monolayer culture and multicellular tumor spheroids. The curcumin-loaded micelles efficiently penetrated the MCF7 spheroids and induced apoptosis. The nanocurcumin reduced the viability and disturbed the function of stromal cells by suppressing cell migration and tube formation. The micelles demonstrated toxicity to the development of zebrafish embryos. Curcumin-loaded micelles demonstrated toxicity to both tumor and normal primary stromal cells and zebrafish embryos, indicating that the use of nanocurcumin in cancer treatment should be carefully investigated and controlled.

Genetic diversity and population structure of Cinnamomum balansae Lecomte inferred by microsatellites.

Cinnamomum balansae Lecomte (Lauraceae), an economically important forest tree, is distributed in the tropical forests of central and northern Vietnam, which has been threatened in recent decades due to the destruction of its habitat and over-exploitation. The genetic diversity and population structure of the species have not been fully evaluated. We used a set of 15 microsatellites to analyze 161 adult trees from 9 different populations, representing the geographical distribution of C. balansae. Ninety-two different alleles were identified. Here our results showed a low genetic diversity level with an average H o = 0.246 and H e = 0.262, and a high level of genetic differentiation (F ST = 0.601). The bottleneck tests indicated evidence of a reduction in the population size of the two populations (TC and CP). Additionally, all three clustering methods (Bayesian analysis, principal coordinate analysis, and Neighbor-joining tree) were identified in the two genetic groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance (R 2 = 0.7331). This study will provide a platform for the conservation of C. balansae both in ex-situ and in-situ plans.

Effect of multiple rescatterings on continuum harmonics from asymmetric molecules in multicycle lasers.

A wide range of harmonics especially continuum harmonics is a prerequisite for attosecond pulse generation. One can use longer-wavelength lasers to push the cutoff to a higher order. However, this does not translate to the same amount of continuum range extension because multiple rescattering phenomena are also enhanced in the process, potentially affecting the lower end of the continuum harmonics. It is then important to understand exactly how multiple rescatterings affect the harmonic structure and their response to various laser parameters, which is the main theme of this paper. Particularly, by applying the synchrosqueezed time-frequency transform and classical electron trajectory analysis to the asymmetric molecule carbon monoxide (CO), we justify that the multiple rescatterings indeed influence the periodicity of the harmonic spectra and the stable periodicity is, in fact, bounded by the first- and third-order returns. Moreover, for the first time, we find that the high-order rescatterings are asymmetric regarding the molecular rotation of 180°, but always correlate with the first-order returns. Our last result is that by breaking the laser symmetry in an appropriate way, the contribution of multiple rescatterings is removed so that the continuum region is entirely defined by the first-order return energies.

Removal of ethyl acetate in air by using different types of corona discharges generated in a honeycomb monolith structure coated with Pd/γ-alumina.

A method based on the corona discharge produced by high voltage alternating current (AC) and direct current (DC) over a Pd/γ-Al2O3 catalyst supported on a honeycomb structure monolith was developed to eliminate ethyl acetate (EA) from the air at atmospheric pressure. The characteristics of the AC and DC corona discharge generated inside the honeycomb structure monolith were investigated by varying the humidity, gas hourly space velocity (GHSV), and temperature. The results showed that the DC corona discharge is more stable and easily operated at different operating conditions such as humidity, GHSV, and gas temperature compared to the AC discharge. At a given applied voltage, the EA conversion in the DC honeycomb catalyst discharge is, therefore, higher compared with that in the AC honeycomb catalyst discharge (e.g., 96% of EA conversion compared with approximately 68%, respectively, at 11.2 kV). These new results can open opportunities for wide applications of DC corona discharge combined with honeycomb catalysts to VOC treatment.

Zoogeographical barriers causing discontinuous osteometrical variations in the northern treeshrew skulls.

Morphological variation of the skull was examined in the northern treeshrew (Tupaia belangeri) from various localities across Southeast Asia. Through a multivariate analysis, the treeshrews from South Vietnam exhibited distinct morphological characteristics compared to other populations from Thailand and Laos, and Malaysia. The plots of the specimens of North Vietnam are not randomly mixed with Thailand plots segregation in the scatteregrams of canonical discriminant analysis. Since the skulls of the population from North Vietnam were morphologically similar to those form central Laos and northern and northeastern Thailand, the zoogeographical barrier effect of Mekong River was not clearly confirmed. The population of the Kanchanaburi in western Thailand is clearly smaller in size compared to the other populations. The southern border of the distribution of this species is determined by the Isthmus of Kra or Kangar-Pattani Line. In the northern treeshrew, which is distributed from southern China to Bangladesh and southern Thailand, we have detected osteometrical geographical variation driven by geography. These results indicate that the skull morphology in the Tupaia glis-belangeri complex distinctively differs in South Vietnam, western Thailand, and southern Thailand. The zoogeographical barrier and factor separating these districts are expected to clarify in the future.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

BACKGROUND: The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. METHODS: In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). RESULTS: Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. CONCLUSION: We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

Updates on metaQuantome Software for Quantitative Metaproteomics.

metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.