The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs.

BACKGROUND: Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. METHODS: We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. RESULTS: Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. CONCLUSIONS: In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.

The role of diet and non-pharmacologic supplements in the treatment of chronic neuropathic pain: A systematic review.

BACKGROUND/IMPORTANCE: Dietary interventions, vitamins, and nutritional supplementation are playing an increasingly important role in the management of neuropathic pain. Current pharmacological treatments are poorly tolerated and ineffective in many cases. OBJECTIVE: This systematic review aims to study the efficacy of dietary interventions, vitamins, and nutritional supplementation in the management of chronic neuropathic pain in adults. EVIDENCE REVIEW: The review followed PRISMA guidelines and was registered with PROSPERO (#CRD42022300312). Ten databases and gray literature, including Embase.com, MEDLINE and Web of Science, were systematically searched using a combination of keywords and controlled vocabulary related to chronic neuropathic pain and oral non-pharmacological supplements. Studies on adult humans published between 2000 and 2021 were considered for inclusion. The Cochrane Handbook was used to assess risk of bias, and Grading of Recommendations Assessment, Development, and Evaluation was used to determine overall quality of evidence. FINDINGS: Forty studies were included in the final review, and results were categorized according to pain type including pain related to chemotherapy-induced peripheral neuropathy (CIPN, 22 studies, including 3 prospective cohorts), diabetic peripheral neuropathy (DPN, 13 studies, including 2 prospective), complex regional pain syndrome (CRPS-I, 3 studies, including 1 prospective), and other (2 studies, both RCT). The CIPN studies used various interventions including goshajinkigan (4 studies), vitamin E (5), vitamin B12 (3), glutamine (3), N-acetyl-cysteine (2), acetyl-l-carnitine (2), guilongtonluofang (1), ninjin'yoeito (1), alpha-lipoic acid (1), l-carnosine (1), magnesium and calcium (1), crocin (1), and antioxidants (1), with some studies involving multiple interventions. All CIPN studies involved varying cancers and/or chemotherapies, advising caution for generalizability of results. Interventions for DPN included alpha-lipoic acid (5 studies), vitamin B12 (3), acetyl-l-carnitine (3), vitamin E (1), vitamin D (2), and a low-fat plant-based diet (1). Vitamin C was studied to treat CRPS-I (3 studies, including 1 prospective). Magnesium (1) and St. John's wort (1) were studied for other or mixed neuropathologies. CONCLUSIONS: Based on the review, we cannot recommend any supplement use for the management of CIPN, although further research into N-acetyl-cysteine, l-carnosine, crocin, and magnesium is warranted. Acetyl-l-carnitine was found to be likely ineffective or harmful. Alpha-lipoic acid was not found effective. Studies with goshajinkigan, vitamin B12, vitamin E, and glutamine had conflicting results regarding efficacy, with one goshajinkigan study finding it harmful. Guilongtonluofang, ninjin'yoeito, and antioxidants showed various degrees of potential effectiveness. Regarding DPN, our review supports the use of alpha-lipoic acid, acetyl-l-carnitine, and vitamin D. The early use of vitamin C prophylaxis for the development of CRPS-I also seems promising. Further research is warranted to confirm these findings.

Prevalence of SARS-CoV-2 in hemoglobinopathies is modified by age and race.

Prior literature has established a positive association between sickle cell disease and risk of contracting SARS-CoV-2. Data from a cross-sectional study evaluating COVID-19 testing devices (n = 10,567) was used to examine the association between underlying health conditions and SARS-CoV-2 infection in an urban metropolis in the southern United States. Firth's logistic regression was used to fit the model predicting SARS-CoV-2 positivity using vaccine status and different medical conditions commonly associated with COVID-19. Another model using the same method was built using SARS-CoV-2 positivity as the outcome and hemoglobinopathy presence, age (<16 Years vs. ≥16 Years), race/ethnicity and comorbidities, including hemoglobinopathy, as the factors. Our first model showed a significant association between hemoglobinopathy and SARS-CoV-2 infection (OR: 2.28, 95 % CI: (1.17,4.35), P = 0.016). However, in the second model, this association was not maintained (OR: 1.35, 95 % CI: (0.72,2.50), P = 0.344). We conclude that the association between SARS-CoV-2 positivity and presence of hemoglobinopathies like sickle cell disease is confounded by race, age, and comorbidity status. Our results illuminate previous findings by identifying underlying clinical/demographic factors that confound the reported association between hemoglobinopathies and SARS-CoV-2. These findings demonstrate how social determinants of health may influence disease manifestations more than genetics alone.

Predictive Value of Isolated Symptoms for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Children Tested During Peak Circulation of the Delta Variant.

BACKGROUND: Coronavirus disease 2019 (COVID-19) testing policies for symptomatic children attending US schools or daycare vary, and whether isolated symptoms should prompt testing is unclear. We evaluated children presenting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing to determine if the likelihood of having a positive SARS-CoV-2 test differed between participants with 1 symptom vs ≥2 symptoms, and to examine the predictive capability of isolated symptoms. METHODS: Participants aged <18 years presenting for clinical SARS-CoV-2 molecular testing in 6 sites in urban/suburban/rural Georgia (July-October, 2021; Delta variant predominant) were queried about individual symptoms. Participants were classified into 3 groups: asymptomatic, 1 symptom only, or ≥2 symptoms. SARS-CoV-2 test results and clinical characteristics of the 3 groups were compared. Sensitivity, specificity, positive predictive values (PPVs), and negative predictive values (NPVs) for isolated symptoms were calculated by fitting a saturated Poisson model. RESULTS: Of 602 participants, 21.8% tested positive and 48.7% had a known or suspected close contact. Children reporting 1 symptom (n = 82; odds ratio [OR], 6.00 [95% confidence interval {CI}, 2.70-13.33]) and children reporting ≥2 symptoms (n = 365; OR, 5.25 [95% CI, 2.66-10.38]) were significantly more likely to have a positive COVID-19 test than asymptomatic children (n = 155), but they were not significantly different from each other (OR, 0.88 [95% CI, .52-1.49]). Sensitivity and PPV were highest for isolated fever (33% and 57%, respectively), cough (25% and 32%), and sore throat (21% and 45%); headache had low sensitivity (8%) but higher PPV (33%). Sensitivity and PPV of isolated congestion/rhinorrhea were 8% and 9%, respectively. CONCLUSIONS: With high Delta variant prevalence, children with isolated symptoms were as likely as those with multiple symptoms to test positive for COVID-19. Isolated fever, cough, sore throat, or headache, but not congestion/rhinorrhea, offered the highest predictive value.

Correlation of SARS-CoV-2 Subgenomic RNA with Antigen Detection in Nasal Midturbinate Swab Specimens.

Among symptomatic outpatients, subgenomic RNA of severe acute respiratory syndrome coronavirus 2 in nasal midturbinate swab specimens was concordant with antigen detection but remained detectable in 13 (82.1%) of 16 nasopharyngeal swab specimens from antigen-negative persons. Subgenomic RNA in midturbinate swab specimens might be useful for routine diagnostics to identify active virus replication.

Arsenic exposure and risk of nonalcoholic fatty liver disease (NAFLD) among U.S. adolescents and adults: an association modified by race/ethnicity, NHANES 2005-2014.

BACKGROUND: While associated with obesity, the cause of the rapid rise in prevalence of nonalcoholic fatty liver disease (NAFLD) in children, which is highest among Hispanics, is not well understood. Animal experiments have demonstrated that arsenic exposure contributes to liver injury. Our objective was to examine the association between arsenic exposure and NAFLD in humans and to determine if race/ethnicity modifies the association. METHODS: Urinary inorganic arsenic concentrations among those ≥12 years in the National Health and Nutrition Examination Survey, 2005-2014 were used to assess the cross-sectional association with serum alanine aminotransferase (ALT) levels, a marker of liver dysfunction. We excluded high alcohol consumers (>4-5 drinks/day; n = 939), positive hepatitis B or C (n = 2330), those missing body mass index (n = 100) and pregnant women (n = 629) for a final sample of 8518. Arsenic was measured using liquid chromatography coupled with mass spectrometry and ALT was measured using standard methods. Sampling weights were used to obtain national estimates. Due to lack of normality, estimates were log transformed and are presented as geometric means. Logistic regression models controlling for age, sex, income, and weight category estimate adjusted odd ratios (aOR) of elevated ALT by quartile of arsenic and tested for effect modification by race/ethnicity and weight. Elevated ALT was defined as >25 IU/L and >22 IU/L for boys and girls ≤17 years, respectively and >30 IU/L and >19 IU/L for men and women, respectively. RESULTS: Among all, aOR of elevated ALT were higher among those in the highest vs. lowest arsenic quartile (referent), 1.4 (95% confidence interval [CI]: 1.1, 1.7) with a borderline significant interaction (p = 0.07) by race/ethnicity but not weight (p = 0.4). In analysis stratified by race/ethnicity, aOR of elevated ALT among those in the 4th quartile were higher among Mexican Americans, 2.0 (CI: 1.3, 3.1) and non-Hispanic whites only, aOR 1.4 (CI: 1.1, 1.8) despite the fact that obesity prevalence was highest among non-Hispanic blacks. CONCLUSIONS: Our findings demonstrate a positive association between urinary arsenic exposure and risk of NAFLD among U.S. adolescents and adults that is highest among Mexican Americans and among those obese, regardless of race/ethnicity.

Development and evaluation of a Nutrition Transition-FFQ for adolescents in South India.

OBJECTIVE: To develop and evaluate a Nutrition Transition-FFQ (NT-FFQ) to measure nutrition transition among adolescents in South India. DESIGN: We developed an interviewer-administered NT-FFQ comprising a 125-item semi-quantitative FFQ and a twenty-seven-item eating behaviour survey. The reproducibility and validity of the NT-FFQ were assessed using Spearman correlations, intra-class correlation coefficients (ICC), and levels of agreement using Bland-Altman and cross-classification over 2 months (NT-FFQ1 and NT-FFQ2). Validity of foods was evaluated against three 24-h dietary recalls (24-HR). Face validity of eating behaviours was evaluated through semi-structured cognitive interviews. The reproducibility of eating behaviours was assessed using weighted kappa (κ w) and cross-classification analyses. SETTING: Vijayapura, India. SUBJECTS: A representative sample of 198 adolescents aged 14-18 years. RESULTS: Reproducibility of NT-FFQ: Spearman correlations ranged from 0·33 (pulses) to 0·80 (red meat) and ICC from 0·05 (fruits) to 1·00 (tea). On average, concordance (agreement) was 60 % and discordance was 7 % for food groups. For eating behaviours, κ w ranged from 0·24 (eating snacks while watching television) to 0·67 (eating lunch at home) with a mean of 0·40. Validity of NT-FFQ: Spearman correlations ranged from 0·11 (fried traditional foods) to 0·70 (tea) and ICC ranged from 0·02 (healthy global foods) to 1·00 (grains). The concordance and discordance were 48 % and 8 %, respectively. Bland-Altman plots showed acceptable agreement between NT-FFQ2 and 24-HR. The eating behaviours had acceptable face validity. CONCLUSIONS: The NT-FFQ has good reproducibility and acceptable validity for food intake and eating behaviours. The NT-FFQ can quantify the nutrition transition among Indian adolescents.

Changes in Diabetes Care and Management Practices during the COVID-19 Pandemic.

Background: Evidence suggests diabetes management was negatively impacted early in the pandemic. However, the impact of the pandemic on key healthcare services for diabetes control and diabetes self-management practices is less known. We examined changes in diabetes care and management practices before and during the COVID-19 pandemic. Methods: Population-based data regarding 4 diabetes-related healthcare engagement and 4 self-management indicators were obtained from adults with diabetes surveyed in 19 US States and Washington DC through the Behavioral Risk Factor Surveillance System. Using logistic regression, we estimated changes in the prevalence of each indicator, overall and by sociodemographic subgroups, before (2019; n = 15,307) and during (2021; n = 13,994) the COVID-19 pandemic. Results: Between 2019 and 2021, the prevalence of biannual HbA1c tests reduced by 2.6 percentage points (pp, 95% CI :-4.8, -0.4), from 75.4-73.1%, and prevalence of annual eye exams fell by 4.0 pp (-6.2, -2.8), from 72.2-68.7%. The composite indicator of engagement with healthcare for diabetes control fell by 3.5 pp (-5.9, -1.1), from 44.9-41.9%. Reductions in engagement with healthcare were largely seen across sex, age, education, employment status, marital status, insurance status, and urbanicity; and were more pronounced among those aged 18-34 and the uninsured. Reductions in engagement with healthcare were seen in several states, with Delaware and Washington DC reporting the largest decrease. Of self-management behaviors, we only observed change in avoidance of smoking, an increase of 2.0 pp (0.4, 3.6) from 84.7-87.1%. Conclusions: The pandemic had mixed impacts on diabetes care and self-management. The findings suggest a deterioration of the uptake of evidence-based, preventive health services requiring laboratory services and clinical examination for diabetes control during the pandemic. On the other hand, smoking rates decreased, suggesting potential positive impacts of the pandemic on health behaviors in people with diabetes.

Lessons Learned from Community Partnership During the COVID-19 Pandemic.

Underserved communities have been disproportionately affected by the COVID-19 pandemic. The Project Promoting Engagement and COVID-19 Testing for Health (PEACH) study was designed to understand the attitudes, beliefs, and infrastructure associated with COVID-19 risk, testing, and prevention behaviors in people living with, caring for, or at risk for type 2 diabetes. The purpose of this joint community-academic partnered manuscript is to share lessons learned for maintaining community partnerships through the challenging times of a pandemic. New and existing community partners were invited to share their perceptions about the facilitators and barriers of partnering with academia during the COVID-19 public health crisis. Key facilitators included those partners felt heard and their input valued. And the changing nature and demands in response to the pandemic on the partners' responsibilities were among the key challenges. Successful maintenance of the partnerships required flexibility, creativity, and a willingness to adapt engagement as community partners responded to the needs of their communities.

Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests.

Genomic epidemiology offers important insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 antigen tests to identify a wide range of respiratory viruses and generate full genome sequences, offering a streamlined mechanism for broad respiratory virus genomic surveillance.

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant.

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.

Quality and adequacy of dietary intake in a southern urban heart failure population.

BACKGROUND: Few studies have examined the quality and adequacy of dietary intake in patients attempting to limit sodium. OBJECTIVE: The aim of this study was to provide a comprehensive analysis of the dietary intake of persons with heart failure (HF) in the Southern United States who have been advised to limit their sodium intake. METHODS: Three-day food diaries were completed by 114 New York Heart Association class II and III persons with HF enrolled in a family partnership intervention study, which were reviewed by a dietitian and analyzed using validated nutritional software. The Harris-Benedict equation for sedentary adults was used to determine macronutrient intake adequacy. Demographic information and clinical data were obtained through patient report and medical record review. RESULTS: Dietary sodium ingestion ranged from 522 to 9251 mg/d (mean [SD], 2671 [1432] mg/d), with 38 (33.3%) individuals consuming the recommended 2000 mg/d or less in this sample (age, 28-78 years; 64.0% men; 57.0% African American). Mean (SD) caloric intake for the total sample was 1674 (636) kcal/d, with participants eating 99% of the recommended daily allowance (RDA) of protein, 63% of the RDA of carbohydrates, and 89% of the RDA of fat. Participants eating 2000 mg or less of sodium consumed significantly less calories (P < .001), protein (P < .001), carbohydrates (P = .008), and fat (P < .001), but not fiber (P = .103), compared with those consuming more than 2000 mg of sodium after adjusting for body mass index. When analyzed by amount of sodium consumption, persons ingesting 2000 mg or less of sodium per day ate significantly less grains (P = .001) and meat and beans (P = .004) and had less intake of the micronutrients calcium (P < .001), zinc (P = .002), and thiamine (P = .05). CONCLUSION: Only one-third of participants with HF who have been instructed on a low-sodium diet reported consuming the RDA of 2000 mg or less, indicating the need for further dietary instruction with a particular focus on modifying the Southern US diet.

Psychosocial factors associated with diet quality in a working adult population.

The associations between specific intra- and inter-personal psychosocial factors and dietary patterns were explored in a healthy, working adult sample of university and health center employees (N = 640) who were enrolled in a prospective predictive health study. Participants had a mean age of 48 (SD = 11) years and were 67% women and 30% minority. Baseline psychosocial measures of perceived stress, depressive symptoms, social support, and family functioning were examined for their relationships with three diet quality indices-AHEI, DASH, and the Mediterranean. Dietary intake was of moderate quality in this high-income, well-educated, psychosocially healthy population. Social support was positively associated with better diet quality for all three indices (p < .01). Further research should focus on socio-environmental factors associated with diet quality.

The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs.

Background: Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods: We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results: Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions: In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points: In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.

Food group intake patterns and nutrient intake vary across low-income Hispanic and African American preschool children in Atlanta: a cross sectional study.

BACKGROUND: The food group intake patterns of low income Hispanic and African American preschool children are not well documented. The aim of this study was to perform a food group intake analysis of low income minority preschool children and evaluate how macronutrient and micronutrient intake compares to Dietary Reference Intakes (DRI). METHODS: A cross sectional study design using three-day food diaries analyzed by dietary analysis software (Nutrient Database System for Research) was used. Children were recruited from well-child clinics at Children's Healthcare of Atlanta at Hughes Spalding and North Dekalb Grady Satellite Clinic, Atlanta, GA. Low-income, African American and Hispanic preschool age children (n = 291) were enrolled. A total of 105 completed and returned the 3-day food diaries. Chi-squared tests were used to assess demographic variables. The mean percentage of intake per day of specific food groups and sub-groups were obtained (servings of given food group/total daily servings). Food intake data and proportion of children meeting DRIs for macro- and micronutrients were stratified by race/ethnicity, nutritional status, and caloric intake, and were compared using t-tests. Regression models controlling for age, BMI and sex were obtained to assess the effect of total caloric intake upon the proportional intake of each studied food group. RESULTS: The mean age of African American children was 2.24 ± 1.07 years and Hispanic children 2.84 ± 1.12 years. African Americans consumed more kcal/kg/day than Hispanics (124.7 ± 51 vs. 96.9 ± 33, p < 0.05). Hispanics consumed more fruits (22.0 ± 10.7% vs. 14.7 ± 13.7%, p < 0.05), while African Americans consumed more grains (25.7 ± 7.8% vs. 18.1 ± 6.4%, p < 0.05), meats (20.7 ± 9.0% vs. 15.4 ± 6.1%, p < 0.05), fats (9.8 ± 5.4% vs. 7.0 ± 5.8%, p < 0.05), sweet drinks (58.7 ± 17.1% vs. 41.3 ± 14.8%, p < 0.05) and low-fat dairy products (39.5 ± 19.3% vs. 28.9 ± 12.6%, p < 0.05). Among Hispanics, the proportional intake of fruits, fats and grains varied by total caloric intake, while no difference by total caloric intake was found for the dietary patterns of African Americans. Micronutrient intake also differed significantly between African American and Hispanic children. CONCLUSIONS: Food group intake patterns among low-income children differ by ethnic group. There is a need for more research to guide program design and target nutritional interventions for this population.

Machine Learning Approaches to Identify Discriminative Signatures of Volatile Organic Compounds (VOCs) from Bacteria and Fungi Using SPME-DART-MS.

Point-of-care screening tools are essential to expedite patient care and decrease reliance on slow diagnostic tools (e.g., microbial cultures) to identify pathogens and their associated antibiotic resistance. Analysis of volatile organic compounds (VOC) emitted from biological media has seen increased attention in recent years as a potential non-invasive diagnostic procedure. This work explores the use of solid phase micro-extraction (SPME) and ambient plasma ionization mass spectrometry (MS) to rapidly acquire VOC signatures of bacteria and fungi. The MS spectrum of each pathogen goes through a preprocessing and feature extraction pipeline. Various supervised and unsupervised machine learning (ML) classification algorithms are trained and evaluated on the extracted feature set. These are able to classify the type of pathogen as bacteria or fungi with high accuracy, while marked progress is also made in identifying specific strains of bacteria. This study presents a new approach for the identification of pathogens from VOC signatures collected using SPME and ambient ionization MS by training classifiers on just a few samples of data. This ambient plasma ionization and ML approach is robust, rapid, precise, and can potentially be used as a non-invasive clinical diagnostic tool for point-of-care applications.

Metabolomics profiling in acute liver transplant rejection in a pediatric population.

Pediatric liver transplantation rejection affects 20% of children. Currently, liver biopsy, expensive and invasive, is the best method of diagnosis. Discovery and validation of clinical biomarkers from blood or other biospecimens would improve clinical care. For this study, stored plasma samples were utilized from two cross-sectional cohorts of liver transplant patients at Children's Healthcare of Atlanta. High resolution metabolic profiling was completed using established methods. Children with (n = 18) or without (n = 25) acute cellular rejection were included in the analysis (n = 43 total). The mean age of these racially diverse cohorts ranged from 12.6 years in the rejection group and 13.6 years in the no rejection group. Linear regression provided 510 significantly differentiating metabolites between groups, and OPLS-DA showed 145 metabolites with VIP > 2. A total of 95 overlapping significant metabolites between OPLS-DA and linear regression analyses were detected. Pathway analysis (p < 0.05) showed bile acid biosynthesis and tryptophan metabolism as the top two differentiating pathways. Network analysis also identified tryptophan and clustered with liver enzymes and steroid use. We conclude metabolic profiling of plasma from children with acute liver transplant rejection demonstrates > 500 significant metabolites. This result suggests that development of a non-invasive biomarker-based test is possible for rejection screening.

SARS-CoV-2 reliably detected in frozen saliva samples stored up to one year.

Viability of saliva samples stored for longer than 28 days has not been reported in the literature. The COVID-19 pandemic has spawned new research evaluating various sample types, thus large biobanks have been started. Residual saliva samples from university student surveillance testing were retested on SalivaDirect and compared with original RT-PCR (cycle threshold values) and quantitative antigen values for each month in storage. We conclude that saliva samples stored at -80°C are still viable in detecting SARS-CoV-2 after 12 months of storage, establishing the validity of these samples for future testing.

Severe acute respiratory syndrome coronavirus 2 vaccine breakthrough infections: A single metro-based testing network experience.

Objectives: Understanding the incidence and characteristics that influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine breakthrough infections (VBIs) is imperative for developing public health policies to mitigate the coronavirus disease of 2019 (COVID-19) pandemic. We examined these factors and post-vaccination mitigation practices in individuals partially and fully vaccinated against SARS-CoV-2. Materials and methods: Adults >18 years old were voluntarily enrolled from a single metro-based SARS-CoV-2 testing network from January to July 2021. Participants were categorized as asymptomatic or symptomatic, and as unvaccinated, partially vaccinated, or fully vaccinated. All participants had confirmed SARS-CoV-2 infection based on standard of care (SOC) testing with nasopharyngeal swabs. Variant analysis by rRT-PCR was performed in a subset of time-matched vaccinated and unvaccinated individuals. A subgroup of partially and fully vaccinated individuals with a positive SARS-CoV-2 rRT-PCR was contacted to assess disease severity and post-vaccination mitigation practices. Results: Participants (n = 1,317) voluntarily underwent testing for SARS-CoV-2 during the enrollment period. A total of 29.5% of the population received at least one SARS-CoV-2 vaccine (n = 389), 12.8% partially vaccinated (n = 169); 16.1% fully vaccinated (n = 213). A total of 21.3% of partially vaccinated individuals tested positive (n = 36) and 9.4% of fully vaccinated individuals tested positive (n = 20) for SARS-CoV-2. Pfizer/BioNTech mRNA-1273 was the predominant vaccine received (1st dose = 66.8%, 2nd dose = 67.9%). Chronic liver disease and immunosuppression were more prevalent in the vaccinated (partially/fully) group compared to the unvaccinated group (p = 0.003, p = 0.021, respectively). There were more asymptomatic individuals in the vaccinated group compared to the unvaccinated group [n = 6 (10.7%), n = 16 (4.1%), p = 0.045]. CT values were lower for the unvaccinated group (median 24.3, IQR 19.1-30.5) compared to the vaccinated group (29.4, 22.0-33.7, p = 0.004). In the vaccinated group (n = 56), 18 participants were successfully contacted, 7 were lost to follow-up, and 2 were deceased. A total of 50% (n = 9) required hospitalization due to COVID-19 illness. Adherence to nationally endorsed mitigation strategies varied post-vaccination. Conclusion: The incidence of SARS-CoV-2 infection at this center was 21.3% in the partially vaccinated group and 9.4% in the fully vaccinated group. Chronic liver disease and immunosuppression were more prevalent in the vaccinated SARS-CoV-2 positive group, suggesting that these may be risk factors for VBIs. Partially and fully vaccinated individuals had a higher incidence of asymptomatic SARS-CoV-2 and higher CT values compared to unvaccinated SARS-CoV-2 positive individuals.