Eosinophilic Gastritis and Enteritis Are Increased in Families With Eosinophilic Esophagitis.

INTRODUCTION: There are limited data on the familial risk of distal eosinophilic gastrointestinal diseases (EGIDs) in patients with eosinophilic esophagitis (EoE). We analyzed the risk of eosinophilic gastritis/gastroenteritis (EG/EGE) and eosinophilic colitis (EC) as forms of distal EGIDs using International Disease Classification-9/10 codes in subjects with EoE and their relatives. METHODS: The Utah Population Database is a resource that links genealogy information and medical records in Utah. We identified EGIDs in probands and their first-degree (FDRs), second-degree (SDRs), and third-degree (TDRs) relatives in the Utah Population Database. Relative risk and 95% confidence intervals were estimated. All individuals with inflammatory bowel disorder were eliminated to avoid misdiagnosis with EGIDs. RESULTS: We included 8,455 subjects with EoE, 396 with EG/EGE, and 172 with EC. Probands with EoE were at increased risk of EG/EGE and EC. Risks of EG/EGE were increased among FDRs and SDRs of probands with EoE , even without concomitant EoE in the relatives. Increased risk of EG/EGE in FDRs and SDRs was also present for EoE probands without EG/EGE or EC. We observed no isolated familial aggregation of EG/EGE after excluding cases with comorbid EoE. EC probands without EoE were at increased risk of EG/EGE, but no evidence of familial risk of EC was observed. DISCUSSION: The relative risk of EG/EGE is significant among relatives of patients with EoE, suggesting that shared genetic factors exist among these EGIDs. EG/EGE and EC showed limited familial clustering, although sample sizes were small.

A Novel Method to Detect Copy Number Variation in Melanoma: Droplet Digital PCR for Quantitation of the CDKN2A Gene, a Proof-of-Concept Study.

ABSTRACT: A definitive diagnosis of nevus or melanoma is not always possible for histologically ambiguous melanocytic neoplasms. In such cases, ancillary molecular testing can support a diagnosis of melanoma if certain chromosomal aberrations are detected. Current technologies for copy number variation (CNV) detection include chromosomal microarray analysis (CMA) and fluorescence in situ hybridization. Although CMA and fluorescence in situ hybridization are effective, their utilization can be limited by cost, turnaround time, and inaccessibility outside of large reference laboratories. Droplet digital polymerase chain reaction (ddPCR) is a rapid, automated, and relatively inexpensive technology for CNV detection. We investigated the ability of ddPCR to quantify CNV in cyclin-dependent kinase inhibitor 2A ( CDKN2A ), the most commonly deleted tumor suppressor gene in melanoma. CMA data were used as the gold standard. We analyzed 57 skin samples from 52 patients diagnosed with benign nevi, borderline lesions, primary melanomas, and metastatic melanomas. In a training cohort comprising 29 randomly selected samples, receiver operator characteristic curve analysis revealed an optimal ddPCR cutoff value of 1.73 for calling CDKN2A loss. In a validation cohort comprising the remaining 28 samples, ddPCR detected CDKN2A loss with a sensitivity and specificity of 94% and 90%, respectively. Significantly, ddPCR could also identify whether CDKN2A losses were monoallelic or biallelic. These pilot data suggest that ddPCR can detect CDKN2A deletions in melanocytic tumors with accuracy comparable with CMA. With further validation, ddPCR could provide an additional CNV assay to aid in the diagnosis of challenging melanocytic neoplasms.

Targeted and Suspect Screening of Per- and Polyfluoroalkyl Substances in Cosmetics and Personal Care Products.

Per- and polyfluoroalkyl substances (PFAS) are anthropogenic chemicals reported in cosmetics and personal care products as ingredients, possible impurities in the raw material manufacturing process, or degradation products. The purpose of this study was to further delineate contributions of these varying PFAS sources to these products. Thirty-eight cosmetics and personal care products were selected and analyzed for polyfluoroalkyl phosphates (PAPs), perfluoroalkyl carboxylic acids (PFCAs), fluorotelomer sulfonic acids (FTSAs), and perfluoroalkyl sulfonic acids (PFSAs) using targeted liquid chromatography tandem mass spectrometry (LC-MS/MS). A subset of products was also subjected to suspect screening using LC-high resolution mass spectrometry (HRMS) for >200 compounds. Results of LC-MS/MS and LC-HRMS indicated a predominant and ubiquitous presence of PAPs (detection frequency 99.7%, mean and median ΣPAPs 1 080 000 and 299 ng/g). Total median PFCA and PFSA concentrations were 3 and 38 times lower, respectively. There were significant correlations (Spearman's correlation coefficients = 0.60-0.81, p < 0.05) between 6:2 PAPs and their biotransformation products. Low levels of other PFAS classes were detected, including those previously measured in wastewater and human blood (e.g., hydrido-PFCAs), and five compounds associated with aqueous film-forming foams. Overall, these data highlight that cosmetics and personal care products can contain a breadth of PFAS at extremely high levels, leading to human and environmental exposure.

Differential Neurotoxicity Related to Tetracycline Transactivator and TDP-43 Expression in Conditional TDP-43 Mouse Model of Frontotemporal Lobar Degeneration.

Frontotemporal lobar degeneration (FTLD) is among the most prevalent dementias of early-onset. Pathologically, FTLD presents with tauopathy or TAR DNA-binding protein 43 (TDP-43) proteinopathy. A biallelic mouse model of FTLD was produced on a mix FVB/129SVE background overexpressing wild-type human TDP-43 (hTDP-43) using tetracycline transactivator (tTA), a system widely used in mouse models of neurological disorders. tTA activates hTDP-43, which is placed downstream of the tetracycline response element. The original study on this transgenic mouse found hippocampal degeneration following hTDP-43 expression, but did not account for independent effects of tTA protein. Here, we initially analyzed the neurotoxic effects of tTA in postweaning age mice of either sex using immunostaining and area measurements of select brain regions. We observed tTA-dependent toxicity selectively in the hippocampus affecting the dentate gyrus significantly more than CA fields, whereas hTDP-43-dependent toxicity in bigenic mice occurred in most other cortical regions. Atrophy was associated with inflammation, activation of caspase-3, and loss of neurons. The atrophy associated with tTA expression was rescuable by the tetracycline analog, doxycycline, in the diet. MRI studies corroborated the patterns of atrophy. tTA-induced degeneration was strain-dependent and was rescued by moving the transgene onto a congenic C57BL/6 background. Despite significant hippocampal atrophy, behavioral tests in bigenic mice revealed no hippocampally mediated memory impairment. Significant atrophy in most cortical areas due solely to TDP-43 expression indicates that this mouse model remains useful for providing critical insight into co-occurrence of TDP-43 pathology, neurodegeneration, and behavioral deficits in FTLD.SIGNIFICANCE STATEMENT The tTA expression system has been widely used in mice to model neurological disorders. The technique allows investigators to reversibly turn on or off disease causing genes. Here, we report on a mouse model that overexpresses human TDP-43 using tTA and attempt to recapitulate features of TDP-43 pathology present in human FTLD. The tTA expression system is problematic, resulting in dramatic degeneration of the hippocampus. Thus, our study adds a note of caution for the use of the tTA system. However, because FTLD is primarily characterized by cortical degeneration and our mouse model shows significant atrophy in most cortical areas due to human TDP-43 overexpression, our animal model remains useful for providing critical insight on this human disease.

Heterotrophic Aurantiochytrium sp. supplementation to layer diets sustainably increases the omega-3 concentration of eggs.

1. The consumption of adequate amounts of the long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) has been associated with beneficial effects on human health. Eggs are commonly consumed worldwide, and their omega-3 content can be easily altered by changing the diets of laying hens and so represent an important target for enrichment. 2. In this study, the effect of supplementing laying hens with DHA-rich, Aurantiochytrium limacinum at three different inclusion levels was investigated over a 24-week period. 3. Significant increases in egg DHA concentrations were observed after four weeks and were maintained for the duration of the 24-week study. The supplemented eggs in the current study had a DHA content of 82, 101, and 129 mg/yolk when supplemented with 0.25%, 0.5% and 1% treatments, respectively, which meets the EU criteria to be considered 'high in omega-3'. 4. Using the sustainably grown protist Aurantiochytrium limacinum to supplement layer diets increased the egg DHA concentration and decreased the n-6/n-3 ratio, improving the nutritional value of the eggs for human consumers.

Redressing the balance: including DHA-rich Aurantiochytrium limacinum in broiler diets increases tissue omega-3 fatty acid content and lowers the n-6:n-3 ratio.

1. The consumption of sufficient quantities of long chain omega-3 fatty acids (n-3 LCPUFA) from meat and other animal products can lead to a variety of health benefits in humans. The fatty acid content of poultry meat can be increased by feeding birds ingredients that are rich in n-3 LCFUFA 2. The effect of feeding a docosahexaenoic acid (DHA) rich Aurantiochytrium limacinum biomass (AURA) on the fatty acid content of breast and thigh tissues was investigated in a feeding trial with 2880 male Ross 308 broilers. The broiler diets were supplemented with either 0, 0.25, 0.5 or 1% AURA from day 21 to 42 of age. 3. Supplementation significantly increased the DHA content of both breast and thigh meat at an inclusion rate of 1% in the diet, leading to a total of 42 and 46 mg DHA/100 g of fresh breast or thigh tissue respectively. Significant increases in the tissue eicosapentaenoic acid (EPA) concentration were seen alongside a reduced omega-6/omega-3 ratio, improving the nutritional value of the meat for consumers and identifying supplementation of broiler diets with A. limacinum as an effective and sustainable method to increase n-3 LCPUFA consumption in the human population.

Candidate genetic modifiers of retinitis pigmentosa identified by exploiting natural variation in Drosophila.

Individuals carrying the same pathogenic mutation can present with a broad range of disease outcomes. While some of this variation arises from environmental factors, it is increasingly recognized that the background genetic variation of each individual can have a profound effect on the expressivity of a pathogenic mutation. In order to understand this background effect on disease-causing mutations, studies need to be performed across a wide range of backgrounds. Recent advancements in model organism biology allow us to test mutations across genetically diverse backgrounds and identify the genes that influence the expressivity of a mutation. In this study, we used the Drosophila Genetic Reference Panel, a collection of ∼200 wild-derived strains, to test the variability of the retinal phenotype of the Rh1(G69D) Drosophila model of retinitis pigmentosa (RP). We found that the Rh1(G69D) retinal phenotype is quite a variable quantitative phenotype. To identify the genes driving this extensive phenotypic variation, we performed a genome-wide association study. We identified 106 candidate genes, including 14 high-priority candidates. Functional testing by RNAi indicates that 10/13 top candidates tested influence the expressivity of Rh1(G69D). The human orthologs of the candidate genes have not previously been implicated as RP modifiers and their functions are diverse, including roles in endoplasmic reticulum stress, apoptosis and retinal degeneration and development. This study demonstrates the utility of studying a pathogenic mutation across a wide range of genetic backgrounds. These candidate modifiers provide new avenues of inquiry that may reveal new RP disease mechanisms and therapies.

The effect of dietary supplementation with Aurantiochytrium limacinum on lactating dairy cows in terms of animal health, productivity and milk composition.

The aim of this study was to investigate the effect of dietary supplementation with the docosahexaenoic acid (DHA)-rich microalgae, Aurantiochytrium limacinum (AURA), on a variety of health and productivity parameters in lactating cows. Twenty-four cows were blocked by parity and number of days in milk and then randomly assigned to a control (CON; n = 12) group with no algal supplementation, or a treatment group (AURA; n = 12) provided with 100 g AURA cow-1  day-1 or 16 g DHA cow-1  day-1 . A variety of health and productivity measurements were taken, and results indicated that supplementation had no negative effects on animal health in terms of somatic cell count, haematological and biochemical blood parameters, while body condition was marginally improved by algal supplementation. No differences were found for the various production parameters measured; however, a tendency towards increased milk production was observed for the AURA group during the final stage of the study (+4.5 kg cow-1  day-1 , day 78-84). The fatty acid profile of milk was improved by supplementation, with significantly lower saturated fatty acids, significantly higher omega-3 fatty acids and an improved omega-3/omega-6 ratio observed when compared to the control group. The amount of DHA in the milk of cows provided 105 g AURA head-1  day-1 was 4.7 mg/100 g milk with a peak transfer efficiency from feed to milk at day 49 of 8.3%. These results indicate that supplementation with 105 g AURA head-1  day-1 resulted in the successful enrichment of milk with DHA without negatively impacting the health or productivity of the animals.

Effects of a DHA-rich unextracted microalgae as a dietary supplement on performance, carcass traits and meat fatty acid profile in growing-finishing pigs.

Two 125-day experiments of the same design were conducted to evaluate the effects of a heterotrophically grown microalgae (AURA) containing docosahexaenoic acid (DHA) on pig performance, carcass traits and the fatty acid composition of lean and adipose tissue. In each experiment, 144 Hypor pigs were blocked by sex, allocated to three treatment groups, and fed 0, 0.25% or 0.50% AURA in isonutritive, isocaloric diets. Pigs were weighed on days 0, 28, 56, 84 and 112. Feed and water intakes were measured every 28 days. Pigs were slaughtered on day 125. Data from the two studies were analysed as a single data set. Performance and carcass traits did not differ between treatments. Both microalgae treatment levels enriched (p < .05) Longissimus lumborum (LL) and backfat in DHA and improved (p < .05) their ratios of n-6 to n-3 fatty acids.

Reducing catheter-related thrombosis using a risk reduction tool centered on catheter to vessel ratio.

In vascular access practices, the internal vessel size is considered important, and a catheter to vessel ratio (CVR) is recommended to assist clinicians in selecting the most appropriate-sized device for the vessel. In 2016, new practice recommendations stated that the CVR can increase from 33 to 45% of the vessels diameter. There has been evidence on larger diameter catheters and increased thrombosis risk in recent literature, while insufficient information established on what relationship to vessel size is appropriate for any intra-vascular device. Earlier references to clinical standards and guidelines did not clearly address vessel size in relation to the area consumed or external catheter diameter. The aim of this manuscript is to present catheter-related thrombosis evidence and develop a standardized process of ultrasound-guided vessel assessment, integrating CVR, Virchow's triad phenomenon and vessel health and preservation strategies, empowering an evidence-based approach to device placement. Through review, calculation and assessment on the areas of the 33 and 45% rule, a preliminary clinical tool was developed to assist clinicians make cognizant decisions when placing intravascular devices relating to target vessel size, focusing on potential reduction in catheter-related thrombosis. Increasing the understanding and utilization of CVRs will lead to a safer, more consistent approach to device placement, with potential thrombosis reduction strategies. The future of evidence-based data relies on the clinician to capture accurate vessel measurements and device-related outcomes. This will lead to a more dependable data pool, driving the relationship of catheter-related thrombosis and vascular assessment.

High-throughput and sensitive analysis of urinary heterocyclic aromatic amines using isotope-dilution liquid chromatography-tandem mass spectrometry and robotic sample preparation system.

Heterocyclic aromatic amines (HCAA) are listed by the US Food and Drug Administration (FDA) as harmful or potentially harmful constituents of tobacco smoke. However, quantifying HCAA exposure is challenging. In this study, we developed a sensitive, precise, and accurate isotope dilution, liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify urinary HCAAs in smokers and nonsmokers. The high-throughput robotic sample preparation system could handle a throughput of over 300 samples per day, while maintaining intra-day and inter-day imprecision and bias ≤10 %. The limits of detection of carcinogenic HCAAs ranged from 0.31 to 0.83 pg/mL. The validated method was applied to measure HCAAs in urine collected from smokers and non-smokers. This sensitive and efficient analytical method is ideal to support large-scale biomonitoring studies of HCAA exposure. Graphical Abstract LC/MS/MS and robotic sample preparation system for urinary HCAA analysis.

Use Alkalinity Monitoring to Optimize Bioreactor Performance.

In recent years, the agricultural community has reduced flow of nitrogen from farmed landscapes to stream networks through the use of woodchip denitrification bioreactors. Although deployment of this practice is becoming more common to treat high-nitrate water from agricultural drainage pipes, information about bioreactor management strategies is sparse. This study focuses on the use of water monitoring, and especially the use of alkalinity monitoring, in five Iowa woodchip bioreactors to provide insights into and to help manage bioreactor chemistry in ways that will produce desirable outcomes. Results reported here for the five bioreactors show average annual nitrate load reductions between 50 and 80%, which is acceptable according to established practice standards. Alkalinity data, however, imply that nitrous oxide formation may have regularly occurred in at least three of the bioreactors that are considered to be closed systems. Nitrous oxide measurements of influent and effluent water provide evidence that alkalinity may be an important indicator of bioreactor performance. Bioreactor chemistry can be managed by manipulation of water throughput in ways that produce adequate nitrate removal while preventing undesirable side effects. We conclude that (i) water should be retained for longer periods of time in bioreactors where nitrous oxide formation is indicated, (ii) measuring only nitrate and sulfate concentrations is insufficient for proper bioreactor operation, and (iii) alkalinity monitoring should be implemented into protocols for bioreactor management.

Acute ethanol preexposure promotes liver regeneration after partial hepatectomy in mice by activating ALDH2.

It is known that chronic ethanol significantly impairs liver regeneration. However, the effect of acute ethanol exposure on liver regeneration remains largely unknown. To address this question, C57Bl6/J mice were exposed to acute ethanol (6 g/kg intragastrically) for 3 days, and partial hepatectomy (PHx) was performed 24 h after the last dose. Surprisingly, acute ethanol preexposure promoted liver regeneration. This effect of ethanol did not correlate with changes in expression of cell cycle regulatory genes (e.g., cyclin D1, p21, and p27) but did correlate with protection against the effect of PHx on indices of impaired lipid and carbohydrate metabolism. Ethanol preexposure protected against inhibition of the oxidant-sensitive mitochondrial enzyme, aconitase. The activity of aldehyde dehydrogenase 2 (ALDH2) was significantly increased by ethanol preexposure. The effect of ethanol was blocked by inhibiting (Daidzin) and was mimicked by activating (Alda-1) ALDH2. Lipid peroxides are also substrates for ALDH2; indeed, alcohol preexposure blunted the increase in lipid peroxidation (4OH-nonenal adducts) caused by PHx. Taken together, these data suggest that acute preoperative ethanol exposure "preconditions" the liver to respond more rapidly to regenerate after PHx by activating mitochondrial ALDH2, which prevents oxidative stress in this compartment.

Quantitative analysis of five tobacco-specific N-nitrosamines in urine by liquid chromatography-atmospheric pressure ionization tandem mass spectrometry.

A liquid chromatography tandem mass spectrometry (LC/MS/MS) method was developed and validated for the determination of five total tobacco-specific N-nitrosamines (TSNA), including free and conjugated forms in urine. The limits of detection for 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, N'-nitrosonornicotine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, N'-nitrosoanatabine and N'-nitrosoanabasine were 0.6, 0.6, 10.0, 0.4 and 0.4 pg/mL, respectively, with a linear calibration range of up to 20,000 pg/mL. Intra- and inter-day precision for TSNA measurements ranged from 0.82 to 3.67% and from 2.04 to 7.73% respectively. For total TSNAs, the ß-glucuronidase amount was optimized for hydrolysis time and yield. Different liquid chromatography columns and mobile phases with different pH conditions were evaluated. The validated method was then applied to 50 smoker and 30 nonsmoker urine samples. Our results suggest that this sensitive and relatively simple analytical method is suitable for application to epidemiological investigations of health risks associated with the exposure to tobacco smoke or secondhand smoke in both smokers and nonsmokers.

A comparison of Toxocara canis embryonation under controlled conditions in soil and hair.

Toxocara spp. eggs require a period of time under appropriate environmental conditions to become infective to definitive and paratenic hosts. Temperature and humidity are important factors known to affect the levels of development in soil. We aimed to investigate whether the eggs of T. canis could embryonate in dog hair under controlled conditions of temperature and humidity and, if so, to what degree. No previous work had been carried out on embryonation in hair under controlled conditions. Soil samples exposed to the same conditions as the hair samples were considered a suitable comparison in order to investigate differing levels of development. Development at two temperatures (10°C and 20°C) and the addition of water to samples was investigated over a period of 8 weeks. Importantly, we demonstrated that unembryonated T. canis eggs are capable of development in hair under controlled conditions. The rate of development is lower than that observed in soil, but remains biologically significant in terms of the overall numbers of potentially infective embryonated eggs present. Temperature is responsible for the rate of embryonation while moisture is essential for encouraging development and maintaining egg viability in general. In light of these findings the transmission of Toxocara spp. as a result of direct contact with well-cared-for owned dogs seems unlikely, but should not be ignored.

Safe Insertion of Arterial Catheters (SIA): An ultrasound-guided protocol to minimize complications for arterial cannulation.

Direct puncture and cannulation of peripheral arteries is frequently performed in critical care and in emergency settings, mainly for hemodynamic monitoring and blood sampling. While there is abundant literature on peripheral arterial cannulation in children and adults, there is still scope for clinical improvements which may impact on patient safety. Although the radial artery is the most frequently utilized access site today, due to its superficial proximity, ease of access, and low risk of adverse events, other sites are sometimes chosen. The authors propose the Safe Insertion of Arterial Catheters (SIA) protocol, an ultrasound-guided insertion bundle applying a systematic approach to arterial cannulation, with a focus on improving insertion practices, reducing procedural complications, increasing the patient safety profile, and improving device performance.

The prevalence and distribution of Alaria alata, a potential zoonotic parasite, in foxes in Ireland.

The digenean trematode Alaria alata, an intestinal parasite of wild canids is widely distributed in Europe. The recent finding of the mesocercarial life cycle stage in the paratenic wild boar host suggests that it may potentially infect humans Mohl et al. (Parasitol Res 105:1-15, 2009). Over 500 foxes were examined during a wildlife survey for zoonotic diseases in 2009 and 2010. The prevalence of A. alata ranged from 21% to 26% in 2009 and 2010, and the intensity of infection varied, with the majority of foxes having between one and ten trematodes, but a small number of animals had parasitic burdens greater than 500. The location of foxes was geo-referenced and mapped using a geographic information system. The results of the spatial analysis suggest that A. alata may have a limited distribution being confined mainly to areas of pasture especially in the central plain and north Munster. Hot spot analysis indicated a clustering and that the level of parasitism was greatest in foxes from those areas where the prevalence of infection was highest.

Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites.

SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to compliment whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60% and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20%, 96.40%, 99.60%, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from December 7-22, 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. Importance: SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our real-time RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between VOCs and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.

Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites.

SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.

SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva.

BACKGROUND: Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. METHODS AND FINDINGS: In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72-28.51), followed by Alpha (23.93, 18.36-28.49), Gamma (24.74, 18.84-30.64), and the more historic clade 20G (25.21, 20.50-29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n=1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n=167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. CONCLUSIONS: COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.