Mean Threshold Values Research Articles

Associations between genetic mutations in different SARS-CoV-2 strains and negative conversion time of viral RNA among imported cases in Hangzhou: A cross-sectional study

PurposePrevious studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have focused on factors that influence the achievement of negative conversion of viral RNA. This study aimed to investigate the effects of the genetic mutations in different SARS-CoV-2 strains on the negative conversion time (NCT) among imported cases in Hangzhou, Zhejiang Province, China, in order to provide valuable insights for developing targeted epidemic prevention guidelines. MethodsThis retrospective study involved 146 imported SARS-CoV-2 cases in Hangzhou from 8 April 2021 to 11 June 2022. We compared the SARS-CoV-2-specific indicators, clinical indexes, and NCT among the wild-type (WT), Delta, and Omicron groups. Spearman correlation analysis was used to identify the correlations of NCT with mutation types/frequencies. ResultsThe mean age of the imported cases was 35.3 (SD: 12.3) years, with 71.92 % males and 28.08 % females. The mean cycle threshold (Ct) values of open reading frame 1ab (ORF1ab) and nucleocapsid (N) RNA were 25.17 (SD: 6.44) and 23.4 (SD: 6.76), respectively. The mutations of SARS-CoV-2 strains were mainly located in N, membrane (M), spike (S), ORF1a, ORF1b, ORF3a, ORF6, and ORF9b genes among the WT, Delta, and Omicron groups. NCT was significantly prolonged in the WT and Delta groups compared to the Omicron group. T lymphocyte, white blood cell, eosinophil, and basophil counts were dramatically higher in the WT group than the Delta group. White blood cell, red blood cell, and basophil counts were significantly lower in the Delta group than the Omicron group. Spearman correlation analysis revealed a significant correlation between the NCT of viral RNA and mutation types of viral genes of WT and Omicron strains. Additionally, NCT was markedly negatively correlated with the frequencies of five mutations in Omicron strains (ORF1b:P1223L, ORF1b:R1315C, ORF1b:T2163I, ORF3a:T223I, and ORF6:D61L). ConclusionsThis study indicates that five mutations in Omicron strains (ORF1b:P1223L/R1315C/T2163I, ORF3a:T223I and ORF6:D61L) shortened NCT in imported SARS-CoV-2 cases.

Prognostic value of near-infrared spectroscopy regional oxygen saturation and cerebrovascular reactivity index in acute traumatic neural injury: a CAnadian High-Resolution Traumatic Brain Injury (CAHR-TBI) Cohort Study

BackgroundNear-infrared spectroscopy regional cerebral oxygen saturation (rSO2) has gained interest as a raw parameter and as a basis for measuring cerebrovascular reactivity (CVR) due to its noninvasive nature and high spatial resolution. However, the prognostic utility of these parameters has not yet been determined. This study aimed to identify threshold values of rSO2 and rSO2-based CVR at which outcomes worsened following traumatic brain injury (TBI).MethodsA retrospective multi-institutional cohort study was performed. The cohort included TBI patients treated in four adult intensive care units (ICU). The cerebral oxygen indices, COx (using rSO2 and cerebral perfusion pressure) as well as COx_a (using rSO2 and arterial blood pressure) were calculated for each patient. Grand mean thresholds along with exposure-based thresholds were determined utilizing sequential chi-squared analysis and univariate logistic regression, respectively.ResultsIn the cohort of 129 patients, there was no identifiable threshold for raw rSO2 at which outcomes were found to worsen. For both COx and COx_a, an optimal grand mean threshold value of 0.2 was identified for both survival and favorable outcomes, while percent time above − 0.05 was uniformly found to have the best discriminative value.ConclusionsIn this multi-institutional cohort study, raw rSO2was found to contain no significant prognostic information. However, rSO2-based indices of CVR, COx and COx_a, were found to have a uniform grand mean threshold of 0.2 and exposure-based threshold of − 0.05, above which clinical outcomes markedly worsened. This study lays the groundwork to transition to less invasive means of continuously measuring CVR.

Convalescent Plasma Therapy for The Management of Covid‐19: A Single Center Experience of Chhattisgarh State of Central India

The recent outbreak of the coronavirus disease 2019 (COVID19) pandemic has caused a rethinking of the efficacy of previous convalescent plasma transfusions. In hospitalized patients with COVID-19, convalescent plasma (CP) is being used as a treatment along with other supportive therapy. There is a contradictory data on the effectiveness of CP in reducing COVID-19-related mortality to date. To evaluate the efficacy and safety of CP on mortality reduction in patients with COVID-19 admitted in intensive care unit. This retrospective observational study was carried out on patients treated in our institute at Nava Raipur, Chhattisgarh, from 1st April-2020 till 31st December 2020. A total of 138 adult patients with moderate and severe COVID-19 requiring oxygen, were reviewed. Of these, 119 patients were admitted to the intensive care unit. Out of these, 44 moderate to severely symptomatic patients received CP as well as the best supportive treatment, while the remaining 75 received only the best supportive care as either they did not consent for CP therapy or could not arranged CP donors. The data was collected from the Hospital Management Information System and analyzed to assess the effectiveness and safety of CP as well as the demographic information of the patients encountered. In the overall group of 119 patients who were admitted to the ICU, 44 received CP along with best supportive care of which 9 patients could not survived (20.45%) and 75 received only the best supportive care of which 32 patients were died (42.60%). Mortality was significantly lower in plasma group (20.45% vs 42.60%; P=0.0159; OR=0.3455 95% CI: 0.1457 to 0.8196). Mean age of the patient population was 56 years in the plasma group and 61 years in the other group. 34 patients (28.6%) had comorbidities in the form of Diabetes and Thyroid disorders and 7 patients had malignancy. Average duration of ICU stay in the CCP group was 9.1 days while in the Non CCP arm it was 7.7 days. The mean threshold value of oxygen requirement at which the CCP tx was requested - 6.6 lit/min. The mean signal cut off value (SCO) by Vitros-ECi for COVID IgG antibodies in CCP eligible donors was 9.1 (manufacturers cut off value >1.0). In the survival group of CCP recipient, the average SCO value was 8.8 while in the other group it was 9.4. Mild allergic reactions noted in two patients during the CCP transfusion, which were managed conservatively with transfusion halt and anti-histaminic. Our study concluded that the use of COVID convalescent plasma was associated with the reduced mortality in moderately symptomatic COVID-19 patients who needed O2 support. The beneficial effect was associated with multiple factors including both patient as well as plasma donor related factors. Further research into the mechanism of actions of CP in COVID-19 may help predict the good responders.

Performance of Mucorales spp. qPCR in bronchoalveolar lavage fluid for the diagnosis of pulmonary mucormycosis.

To estimate the diagnostic performance of Mucorales polymerase chain reaction (PCR) in Bronchoalveolar lavage fluid (BALF) in routine practice. This was a single-center retrospective study including all consecutive patients>18 years who underwent Mucorales PCR assay in BALF between January 2021 and May 2022. Index testing was prospectively performed using the MycoGENIE Aspergillus spp.-Mucorales spp. PCR. The reference was the diagnosis of pulmonary mucormycosis by the Adjudication Committee. Mucorales PCR in BALF was performed for 938 patients and was positive for 21 of 938 (2.2%). Eleven pulmonary mucormycosis (including one disseminated) were diagnosed. Among them, one (9.1%) was classified as proven mucormycosis, three (27.3%) as probable, and seven (63.6%) as possible according to the EORTC/MSGERC 2019 criteria. The main host factor was hematological malignancy (10 of 11, 90.9%). Mucorales PCR was positive in serum for eight patients (72.7%). Three patients had positive PCR in BALF, but negative in serum. The mean cycle threshold value was significantly lower in mucormycosis than false-positive cases. Sensitivity was 72.7% (95% confidence interval [CI], 43.4-90.3%), and specificity was 98.6% (95% CI, 97.6-99.2%). The positive and negative predictive values were 38.1% (95% CI, 20.8-59.1%) and 99.7% (95% CI, 99.1-99.9%), respectively. Mucorales PCR in BALF showed good diagnostic performance for mucormycosis, particularly in combination with serum PCR. A positive result should be interpreted with caution, given the possibility of carriage in the airway. However, its high negative predictive value and specificity suggest the utility of Mucorales PCR in BALF in the diagnosis of pulmonary mucormycosis.

Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection.

In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative. Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved. Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN. TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.

A pilot study on salivary HPV DNA detection to monitor active disease from patients with recurrent respiratory papillomatosis

PurposeRecurrent respiratory papillomatosis (RRP) is a human papillomavirus (HPV)-related disease affecting the upper airway and saliva could be an important non-invasive sampling source for viral screening and clinical monitoring. We investigated whether HPV DNA could be detected in saliva (cellular pellets and supernatant) from RRP patients and influence on clinical manifestation of the disease. Materials and methodsIn this pilot study, saliva samples from 14 RRP patients were obtained in preoperative condition (n = 7) and in disease-free interval (DFI; n = 7). Healthy donors (n = 14) were also included. HPV DNA was investigated by polymerase chain reaction (PCR)-based assays. ResultsFrom cellular pellets, HPV-positive saliva was only detected from preoperative collections (5/7; 71.4 %) and showed a mean cycle threshold (Ct) value of 24.33 (±1.25), whereas all patients in DFI were HPV-negative (Ct ≥ 32.16), revealing significant difference between these two clinical moments (p = 0.021). Patients in DFI and healthy donors showed similar Ct values. From saliva supernatant, detectable HPV cell-free DNA (cfDNA) occurred in 42.9 % (3/7) and 57.1 % (4/7) of preoperative collections using the commercial cfDNA kits from Norgen and Qiagen, respectively. Salivary cfDNA size distribution obtained by TapeStation analysis showed a predominant size range of 150 to 400 bp in both patients and healthy controls, corresponding to mononucleosomal and dinucleosomal fragments. ConclusionsIn conclusion, HPV DNA screening in saliva (both cellular pellets and cfDNA) may have clinical utility to monitor active disease of RRP patients.

Diagnostic utility of intranodular saline lavage in TaqMan probe-based real-time PCR diagnosis of lumpy skin disease

Lumpy skin disease (LSD), caused by the poxvirus lumpy skin disease virus has entered India, causing serious economic consequences for the Indian dairy sector. To evaluate the diagnostic value of intranodular saline lavage in the identification of LSD-infected animals, skin nodule tissue biopsy, intranodular saline lavage, whole blood, and nasal swab specimens were collected simultaneously from LSD-symptomatic animals. TaqMan probe-based real-time PCR was performed targeting the EEV glycoprotein gene (LSDV126) and the results were compared. qPCR analysis could detect LSDV in all the skin nodule tissue biopsy and intranodular saline lavage. The mean cycle threshold (Cq) values of skin nodule tissue biopsy samples (23.94 ± 2.97) were also comparable with intranodular saline lavage (25.23 ± 2.41) samples. Whole blood and nasal swabs have an extremely poor detection rate for PCR-based viral detection.Our findings demonstrate that intranodular saline lavage is an excellent alternative specimen for the detection of LSDV. Taking into consideration, the simplicity of specimen collection, intranodular saline lavage could be adopted in field conditions for accurate LSDV surveillance testing.

Utility of Central 10 Degrees Visual Field Test With Size V Stimulus in End-Stage Glaucoma.

In end-stage glaucoma, the central 10-degree visual field test with a size V stimulus provided useful information, including the number of points with detectable retinal sensitivity threshold values and retinal sensitivity threshold values. The purpose of this study was to evaluate the clinical utility of the central 10-degree visual field test with a size V stimulus in end-stage glaucoma. A total of 73 eyes with end-stage glaucoma (visual field limited to a radius of <10 degrees from fixation) were included. Central 10 degrees visual field tests were performed using both size III and V stimuli. Reliability indices, test duration, number of points with detectable retinal sensitivity threshold values, and retinal sensitivity threshold values at 4 central points, 4 quadrants, and 3 clusters (papillomacular area, superior half, and inferior half) were compared between the test results using size III and V stimuli. When the size V stimulus was used, the mean test duration increased from 7.8 to 13.3 minutes ( P < 0.001), the mean number of test points with detectable retinal sensitivity threshold values in total area increased from 19.0 to 37.3 ( P < 0.001), and the mean retinal sensitivity threshold values in total area increased from 3.9 to 9.3 dB ( P < 0.001) compared with the test results with the size III stimulus. Significant increase in the visual field parameters was found in all quadrants and clusters ( P < 0.001), and a greater increase was associated with better visual acuity and greater mean deviation of the visual field ( P < 0.05). The central 10-degree visual field test with a size V stimulus provided more information than the test with a size III stimulus in end-stage glaucoma.

Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing.

Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014-2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.

Changes in the cochlear and retrocochlear parts of the auditory system in 19-39 and 40-60 years old patients with type 1 diabetes mellitus.

Pathophysiological alterations in the cochlea and functional tests of the auditory pathway support that in diabetes both vasculopathy and neural changes could be present. The aim of our research was to study the differential effect of type 1 diabetes mellitus (T1DM) on two different age groups. Audiological investigation was carried out in 42 patients and 25 controls at the same age groups. Investigation of the conductive and sensorineural part of the hearing system by pure tone audiometry, distortion product otoacoustic emission measurement and acoustically evoked brainstem response registration were evaluated. Among the 19-39-year-old people the incidence of hearing impairment was not different in the diabetes and control groups. Among the 40-60-year-old people hearing impairment was more common in the diabetes group (75%) than in the control group (15,4%). Among patients with type 1 diabetes, the mean threshold values were higher in both age groups at all frequencies although significant difference was in 19-39 years old group: 500-4000Hz right ear, 4000Hz left ear, in 40-60 years old group: 4000-8000 Hz both ears. In the 19-39 years old diabetes group only at 8000 Hertz on the left side was a significant (p<0,05) difference in otoacoustic emissions. In the 40-60 years old diabetes group significantly less otoacoustic emissions at 8000 Hz on the right side (p<0,01) and at 4000-6000-8000 Hertz on the left side, (p<0,05, p<0,01, p<0,05 respectively) was present compared to the control group. According to ABR (auditory brainstem response) latencies and wave morphologies, a possible retrocochlear lesion arose in 15% of the 19-39 years old and 25% of the 40-60 years old diabetes group. According to our results, T1DM affects negatively the cochlear function and the neural part of the hearing system. The alterations are more and more detectable with aging.

Infectivity of Maize Chlorotic Mottle Virus from Contaminated Maize Seeds

Seeds have been identified as major sources of introduction and spread of pathogens, with viruses being detected in the seed and also on the seed coat. In this study, the infectivity of Maize chlorotic mottle virus (MCMV) through seeds was investigated. Maize seeds that had tested positive for MCMV previously using double antibody enzyme-linked immunosorbent assay (DAS-ELISA) and real-time reverse transcription polymerase chain reaction (real time RT-PCR) were obtained from various sources. The seeds were soaked in phosphate buffer overnight and the solution used to inoculate maize seedlings. The whole seed was also ground and mixed with the buffer and used for inoculation of seedlings by hand rubbing. Visible MCMV symptoms were observed on less than 2% of the 547 seedlings inoculated with the seed soak and seed extract from contaminated seed 28 days after inoculation and this was confirmed using DAS-ELISA. Use of real time reverse transcription polymerase chain reaction revealed infectivity of MCMV from one of the seed sources used. The mean cycle threshold (Ct) values of samples that showed infectivity ranged from 28.21 to 29.40 cycles. The means were significantly different (P&lt;0.001) from the other samples tested, the healthy and negative controls. When compared to seedlings inoculated with MCMV-infected leaf sap, there was visible development of symptoms associated with MCMV infection, with a severity score of three and Ct values as low as 11.53. The results show evidence of infection of MCMV on maize seedlings caused by virus present in seed extract. Despite rare occurrence of infectivity, the presence of viable virus may cause spread of the virus in the field, leading to development of maize lethal necrosis disease where a cereal potyvirus is present.

COVID-19 PCR: frequency of internal control inhibition in clinical practice.

Diagnosis of COVID-19 (coronavirus disease 2019) is best performed with real-time (quantitative) PCR (qPCR), the most sensitive method for detection and quantification of viral RNA. Using the Centers for Disease Control and Prevention (CDC) protocol, for each sample tested for the virus, three qPCR tests are performed, targeting the viral genes N1 and N2, in addition to the internal control gene RNase P. Samples in which internal control fails to amplify should be labelled 'invalid'. This study aims to determine the frequency of inhibition of the RNase P gene used as an internal control in qPCR tests for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in a reference hospital in Southern Brazil during the COVID-19 pandemic (1 February 2021 to 31 March 2021). A total 10, 311 samples were available for analysis. The mean cycle threshold (Ct) value for the RNAse P gene was 26.65 and the standard deviation was 3.18. A total of 252 samples were inhibited (2.4%) during the study period: amongst these, 77 (30.5%) showed late amplifications (beyond 2 standard deviations from the mean Ct value), and 175 (69.4%) revealed no fluorescence at all for the RNase P gene. This study showed a low percentage of inhibition using RNase P as an internal control in COVID-19 PCRs using the CDC protocol, thus proving the effectiveness of this protocol for identification of SARS-CoV-2 in clinical samples. Re-extraction was efficacious for samples that showed little or no fluorescence for the RNase P gene.

A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris.

Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.

Evaluating oral swab samples for PRRSV surveillance in weaning-age pigs under field conditions.

The use of serum and family oral fluids for porcine reproductive and respiratory syndrome virus (PRRSV) surveillance in weaning-age pigs has been previously characterized. Characterizing more sample types similarly offers veterinarians and producers additional validated sample options for PRRSV surveillance in this subpopulation of pigs. Oral swab sampling is relatively easy and convenient; however, there is sparse information on how it compares to the reference sample type for PRRSV surveillance under field conditions. Therefore, this study's objective was to compare the PRRSV reverse-transcription real-time polymerase chain reaction (RT-rtPCR) test outcomes of oral swabs (OS) and sera samples obtained from weaning-age pig litters. At an eligible breeding herd, six hundred twenty-three weaning-age piglets from 51 litters were each sampled for serum and OS and tested for PRRSV RNA by RT-rtPCR. PRRSV RT-rtPCR positivity rate was higher in serum samples (24 of 51 litters, 83 of 623 pigs, with a mean cycle threshold (Ct) value of RT-rtPCR-positive samples per litter ranging from 18.9 to 32.0) compared to OS samples (15 of 51 litters, 33 of 623 pigs, with a mean Ct of RT-rtPCR positive samples per litter ranging from 28.2 to 36.9); this highlights the importance of interpreting negative RT-rtPCR results from OS samples with caution. Every litter with a positive PRRSV RT-rtPCR OS had at least one viremic piglet, highlighting the authenticity of positive PRRSV RT-rtPCR tests using OS; in other words, there was no evidence of environmental PRRSV RNA being detected in OS. Cohen's kappa analysis (Ck = 0.638) indicated a substantial agreement between both sample types for identifying the true PRRSV status of weaning-age pigs.

SARS-CoV-2 and the ocular surface: test accuracy and viral load.

This study aimed to evaluate the pre-sence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the ocular surface of individuals clinically suspected of coronavirus disease 2019 (COVID-19) and determine the accuracy of different approaches of molecular testing on the ocular surface based on the nasopharyngeal positivity status for COVID-19. A total of 152 individuals with suspected COVID-19 symptoms who simultaneously underwent nasopharyngeal and two different tear film collection techniques for quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) were included. Tears were collected and randomized: one eye had the filter strip for the Schirmer test and the contralateral eye had conjunctival swab/cytology in the inferior fornix. All patients underwent slit lamp biomicroscopy. The accuracy of various ocular surface collection techniques used for the detection of SARS-CoV-2 RNA was determined. Of the 152 patients enrolled in the study, 86 (56.6%) had COVID-19 confirmed by nasopharyngeal PCR. Both tear film collection techniques detected viral particles: the Schirmer test was positive in 16.3% (14/86) and the conjunctival swab/cytology in 17.4% (15/86), with no statistically significant differences. No positive ocular tests were found among those with negative nasopharyngeal PCR tests. The overall agreement of the ocular tests was 92.7%, and in combination, the sensitivity would increase to 23.2%. The mean cycle threshold values in the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests were 18.2 ± 5.3, 35.6 ± 1.4, and 36.4 ± 3.9, respectively. Compared with the nasopharyngeal test, the Schirmer (p=0.001) and conjunctival swab/cytology (p<0.001) tests had significantly different Ct values. The Schirmer (16.3%) and conjunctival swab (17.4%) tests were comparably capable of detecting SARS-CoV-2 RNA in the ocular surface by RT-PCR accurately based on nasopharyngeal status and demonstrated indistinct sensitivity and specificity. Simultaneous specimen sampling and processing from the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests demonstrated significantly lower viral load in both ocular surface approaches than in the nasopharyngeal test. Ocular manifestations detected by slit lamp biomicroscopy were not associated with ocular RT-PCR positivity.

Anosmia/hyposmia differences between severe acute respiratory syndrome coronavirus 2 variants; objective olfactory function evaluation

Objectives: This study aimed to investigate whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants cause more or less loss of smell than the wild type variant as a clinical finding that may guide physicians in addition to the increased mortality feature. Patients and Methods: In the prospective study, Connecticut Chemosensory Clinical Research Center (CCCRC) odor testing was performed on patients hospitalized for coronavirus disease 2019 (COVID-19) between May 2021 and December 2021, and variants of SARS-CoV-2 isolated from patients were analyzed. A total of 51 patients (30 males and 21 females; mean age 59.3±14.2 years; range, 29 to 88 years) were included in the study. Age, sex, and COVID-19 vaccine status of the patients were recorded. The patients were asked whether they had new-onset odor or taste complaints and whether they differently perceived smells they knew. Results: The delta variant was detected in 14 patients, the alpha variant was detected in 20 patients, and no variant of concern was detected in 17 patients. Odor disorders were present in 79.4% of all patients (13.73% anosmia, 15.69% severe hyposmia, 13.7% moderate hyposmia, and 37.2% mild hyposmia). There was no statistically significant difference between sex, age, smoking habits, presence of parosmia, degree of smell disorder, and Vicks definition results according to the variants (p&gt;0.05). A statistically significant difference was found between alpha and delta variants in terms of patients' complaints of decreased smell and taste, mean olfactory threshold value, and mean olfactory score variables (p&lt;0.05). There was no difference in terms of age and identification score. The complaints of smell and taste disorders, the mean threshold value of odor, and the mean odor score were found to be significantly lower in the delta variant than in the alpha variant. Conclusion: SARS-CoV-2 variants differ significantly in olfactory dysfunction. Future clinical and laboratory studies may show the diagnostic, clinical, and prognostic significance of olfactory nerve injury.

Clinical Feasibility of a Saliva-Based Antigen Qualitative Test for Severe Acute Respiratory Syndrome Coronavirus 2.

Nasopharyngeal swabs (NPS) are generally used as specimen samples for antigen qualitative tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The principle of the reaction to the antigen protein is the same when saliva is used, and saliva samples were reported to be as accurate as NPS for real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) testing to identify SARS-CoV-2. Unlike NPS collection, self-collected saliva does not expose healthcare workers to the risk of infection. In this study, we evaluated the feasibility of using saliva samples for a SARS-CoV-2 antigen qualitative test (TA2107SA) under development. Saliva samples were collected from patients with confirmed or suspected COVID-19 infection and analyzed. The sensitivity, specificity, and concordance index of the antigen qualitative test were calculated using an RT-qPCR test as reference. Saliva samples were collected from 105 patients. The mean interval from onset to specimen collection was 5.7 days. The mean cycle threshold (Ct) value of RT-qPCR was 31.3. The sensitivity, specificity, and concordance index were 70.7%, 100%, and 0.85, respectively. In 33 patients with Ct values <30, the results of both the RT-qPCR and antigen tests were positive. The sensitivity of the saliva-based TA2107SA SARS-CoV-2 antigen qualitative test was slightly lower than that of the conventional antigen qualitative test using NPS samples from the same patient. Saliva-based antigen qualitative tests for SARS-CoV-2 are an alternative option during a pandemic.

Diagnostic accuracy of a novel SARS CoV-2 rapid antigen test and usefulness of specimens collected from the anterior nasal cavity

ObjectivesWe aimed to validate a newly developed antigen-detecting rapid diagnostic test (Ag-RDT) for SARS-CoV-2 using anterior nasal specimens. MethodsBetween February 12 and September 30, 2021, 16 patients (age range, <1 month-76 years) were enrolled, and samples were collected simultaneously from anterior nasal and nasopharyngeal sites continuously during hospitalization. The primary end points were the diagnostic accuracy of the Ag-RDT and utility of anterior nasal specimens. ResultsIn total, 226 sets of paired samples were obtained. In 88.2% of specimens, the viral load was high at the nasopharyngeal site. The mean cycle threshold values for the anterior nasal and nasopharyngeal sites were 32.4 and 29.9, respectively. Using the real-time polymerase chain reaction results as a reference, the Ag-RDT showed a 100% sensitivity up to day 6 of the illness, using specimens with moderate or high viral load (cycle threshold <30) from either site. From day 7, the sensitivity was 70.4-90.6% and 83.9-84.6% for the anterior nasal and nasopharyngeal sites, respectively. The specificity remained at 100%. ConclusionOur novel Ag-RDT meets the World Health Organization criteria and provides stable sensitivity and specificity and accurate results with anterior nasal specimens.

Agreement Between SARS-CoV-2 PCR Test Results Using Nasopharyngeal and Mid-Turbinate Specimens Among Asymptomatic Working-Age Adults.

The aim of this study was to determine whether mid-turbinate specimens reliably detect active infection in asymptomatic adults undergoing regular COVID-19 PCR testing. Qualitative agreement between 2481 paired nasopharyngeal and mid-turbinate PCR results was assessed. Mean cycle threshold values for each positive result were evaluated as an indicator of active infection. Overall agreement between nasopharyngeal and mid-turbinate tests was 98.4%. Positive percent agreement was 37.2%, and negative percent agreement was ~100%. Test pairs with lower cycle thresholds (≤30 and ≤25) reached 67% and 100% positive percent agreement, respectively. SARS-CoV-2 infections with high viral loads were detected regardless of specimen type. Mid-turbinate swabs reduced staff discomfort and may decrease repeated positive test results weeks or months after initial infection. Discordant pairs generally had high cycle threshold values (>30) indicating low viral load and little risk of transmitting COVID-19.

Use of Self-Collected Saliva Samples for the Detection of SARS-CoV-2.

ObjectiveUsing a US Food and Drug Administration (FDA) emergency use authorization (EUA) reverse transcription polymerase chain reaction (RT-PCR) method, we examined the analytic performance accuracy of saliva specimens as compared to nasopharyngeal (NP) specimens in symptomatic patients. Correlation between test results and symptoms was also evaluated.MethodsOver a 5-week period in 2020, 89 matched saliva and nasopharyngeal swabs were collected from individuals exhibiting symptoms consistent with SARS-CoV-2. Specimens were tested with an FDA EUA-approved RT-PCR method, and performance characteristics were compared.ResultsThe concordance rate between saliva and nasopharyngeal testing was 93.26%. The mean cycle threshold value of saliva when compared to the NP specimen was 3.56 cycles higher. As compared to NP swab, saliva testing demonstrates acceptable agreement but lower sensitivity.ConclusionWhen compared to a reference method using NP swabs, the use of saliva testing proved to be a reliable method. Self-collected saliva testing for SARS-CoV-2 allows for a viable option when trained staff or collection materials are in short supply.