Mean CT Values Research Articles

Deep Learning Reconstruction Improves the Image Quality of CT Angiography Derived From 80-kVp Cerebral CT Perfusion Data

To investigate the impact of the deep learning reconstruction (DLR) technique on the image quality of CT angiography (CTA) derived from 80-kVp cerebral CT perfusion (CTP) data and compare it with hybrid-iterative reconstruction (HIR). Thirty-three patients underwent CTP at 80 kVp were prospectively enrolled. CTP data were reconstructed with HIR and DLR. Four image datasets were reconstructed: HIRpeak and DLRpeak were single arterial phase images derived from the time point showing the peak value, HIRtMIP and HIRtAve were time-resolved maximum intensity projection image and time-resolved average image derived from three time points with the greatest enhancement of HIR. The mean CT values, standard deviation, signal-to-noise ratio, and contrast-to-noise ratio of the internal carotid artery and basilar artery were compared among the four image dataset. Image quality was performed using a five-point rating scale. Arterial stenosis was evaluated. DLRpeak had the highest CT value and contrast-to-noise ratio in the internal carotid artery and basilar artery (all p < 0.001). DLRpeak showed the best subjective image quality and had the highest score (4.93 ± 0.4) compared to the other three HIR CTA images (all p < 0.001). The degree of vascular stenosis was consistent among the four evaluated sequences (HIRtAve, HIRpeak, and HIRtMIP DLRpeak). For CTA derived from 80-kVp cerebral CTP data, images reconstructed with deep learning showed better image quality and improved intracranial artery visualization than those processed with HIR and other currently used techniques.

Low-Dose CT Screening of Persistent Subsolid Lung Nodules: First-Order Features in Radiomics.

Nondisappearing subsolid nodules requiring follow-up are often detected during lung cancer screening, but changes in their invasiveness can be overlooked owing to slow growth. We aimed to develop a method for automatic identification of invasive tumors among subsolid nodules during multiple health checkups using radiomics technology based on low-dose computed tomography (LD-CT) and examine its effectiveness. We examined patients who underwent LD-CT screening from 2014 to 2019 and had lung adenocarcinomas resected after 5-year follow-ups. They were categorized into the invasive or less-invasive group; the annual growth/change rate (Δ) of the nodule voxel histogram using three-dimensional CT (e.g., tumor volume, solid volume percentage, mean CT value, variance, kurtosis, skewness, and entropy) was assessed. A discriminant model was designed through multivariate regression analysis with internal validation to compare its efficacy with that of a volume doubling time of < 400 days. The study included 47 tumors (23 invasive, 24 less invasive), with no significant difference in the initial tumor volumes. Δskewness was identified as an independent predictor of invasiveness (adjusted odds ratio, 0.021; p = 0.043), and when combined with Δvariance, it yielded high accuracy in detecting invasive lesions (88% true-positive, 80% false-positive). The detection model indicated surgery 2 years earlier than the volume doubling time, maintaining accuracy (median 3 years vs.1 year before actual surgery, p = 0.011). LD-CT radiomics showed promising potential in ensuring timely detection and monitoring of subsolid nodules that warrant follow-up over time.

Comparison of L452R mutation variant diagnosis in SARS-COV-2 PCR positive samples with two different qPCR kits

Objectives: Quantitative reverse transcription‐polymerase chain reaction (qPCR) is used as the gold standard method to diagnose COVID-19 infection caused by SARS-CoV-2 which is the cause of the most important epidemic in world history. It was aimed to compare the results of two of the most commonly used commercial kits for the diagnosis of SARS-CoV-2 mutation in our laboratory during the pandemic. Methods: Our study included 5000 SARS-CoV-2 PCR positive nasopharyngeal swab samples (2500 L452R mutation positive samples, 2500 L452R mutation negative samples). PCR positivity and negativity of the L452R mutation of the positive SARS-CoV-2 positive samples were identified with the Diagnovital® (DIAGNO5plex NS SARS-CoV-2 Real Time PCR Kit [A1 Life Sciences Istanbul]) kit. The mentioned samples were also studied with a different commercial PCR kit, Bio-Speedy® (SARS-CoV-2 Emerging Plus Real Time PCR Kit [Bioeksen R&amp;amp;D Technologies Istanbul]). Results: A total of 5000 samples included in the study were concluded as SARS-CoV-2 positive with both tests. One hundred and fifty of 2500 samples that were found positive for SARS-CoV-2 but negative for L452R mutations with the Diagnovital® kit were found positive with the Bio-Speedy® kit for SARS-CoV-2. The compatability between the two kits was found to be high (Kappa= 0.940). The mean Ct values of the samples found positive with the Diagnovital® kit and Bio-Speedy® kit were 24.15 ± 6.75 and 20.72 ± 7.17, respectively and the difference was statistically significant. Conclusions: It was determined the two commercial kits included in the study were extremely compatible based on their analysis. Therefore both kits can be used safely for COVID-19 symptomatic patients.

Development of a high-resolution melt-based assay to rapidly detect the azole-resistant Candida auris isolates.

Candida auris is a multidrug-resistant yeast that rapidly spreads, making it the leading Candidate for the next pandemic. One main leading cause of emerging resistant C. auris isolates is nonsynonymous mutations. This study aimed to detect the Y132F mutation, one of the most important azole resistance-associated mutations in the ERG-11 gene of C. auris, by developing a reliable high-resolution melt (HRM)-based method. Five C. auris isolates from Iran, plus three control isolates from other Clades were used in the study. The antifungal susceptibility testing through micro broth dilution was performed to recheck their susceptibility to three azole antifungals, including fluconazole, itraconazole, and voriconazole. Moreover, the polymerase chain reaction (PCR) sequencing of the ERG-11 gene was performed. Following the bioinformatic analysis and HRM-specific primer design, an HRM-based assay was developed and evaluated to detect ERG-11 mutations. The minimum inhibitory concentrations of fluconazole among Iranian C. auris isolates ranged from 8 to 64 μg/mL. The PCR-sequencing of the ERG-11 gene and bioinformatic analyses revealed the mutation of Y132F, a substitution consequence of A to T on codon 395 in one fluconazole-resistant isolate (IFRC4050). The developed HRM assay successfully differentiated the targeted single nucleotide polymorphism between mutant and wild types (temperature [Tm]: 81.79 ℃ - cycle threshold [CT]: 20.06 for suspected isolate). For both mutant and non-mutant isolates, the mean Tm range was 81.79-82.39 °C and the mean CT value was 20.06-22.93. These results were completely in accordance with the findings of DNA sequencing. The fast-track HRM-based method successfully detected one of the most common mechanisms of resistance in the ERG-11 gene of C. auris within 3 h. Finally, the development of more panels of HRM assays for the detection of all azole resistance mutations in C. auris ERG-11 is recommended to expand the scope of the field and facilitate the elaboration of rapid and accurate methods of antifungal resistance assessment.

Epidemiology of COVID-19 and the Utility of Cycle Threshold (Ct) Values in Predicting the Severity of Disease.

Advanced molecular diagnostic methods like real-time polymerase chain reaction (PCR) play a vital role in the early recognition of viral infections, including the coronavirus disease 2019 (COVID-19). Therefore, in the context of the recent COVID-19 pandemic, this study aimed to determine the correlation of cycle threshold (Ct) values with symptoms in COVID-19-positive patients. A retrospective study was conducted in a virus research diagnostic laboratory (VRDL) at a COVID-19-dedicated tertiary care hospital in South India. A total of 5563 COVID-19-positive patients were analyzed for symptom spectrum and duration of illness with Ct values of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Around 80% (n= 4401) of the patients were symptomatic and the rest were asymptomatic. Among the symptomatic patients, fever (66%) was the most common symptom. About 44% of symptomatic patients had a low Ct value (Ct ≤ 24). There was a significant difference in symptoms among patients with low, medium, and high Ct values. In the subpopulation of symptomatic patients analyzed for the association of Ct value and duration of illness, the mean duration of illness was three days and almost 88% of the patients were tested within five days of onset of symptoms. It has been observed that a shorter duration of illness lowers the Ct values. A significant association was seen between the mean Ct value and days since symptom onset (p-value = 0.016). Most of the symptomatic patients had lower Ct values in comparison to the asymptomatic patients. A significant association between low Ct values and the duration of symptoms observed in our study explains the viral dynamics, i.e., higher viral shedding at the onset of symptoms and declinesthereafter.

Preoperative CT findings and prognosis of pulmonary sarcomatoid carcinoma: comparison with conventional NSCLC of similar tumor size

BackgroundPulmonary sarcomatoid carcinoma (PSC) is a rare subtype of non-small cell lung cancer (NSCLC) but differs in terms of treatment strategies compared with conventional-NSCLC (c-NSCLC). However, preoperative CT differentiation between PSC and c-NSCLC remains a challenge. This study aimed to explore the CT findings and prognosis of PSC compared with c-NSCLC of similar tumor size.MethodsClinical data and CT findings of 31 patients with PSC and 87 patients with c-NSCLC were retrospectively analyzed. Clinical data included sex, age, and smoking history. CT findings included tumor size, tumor location, calcification, vacuole/cavity, pleural invasion, mean CT value, and low-attenuation area (LAA) ratio. Kaplan‒Meier curves and log-rank tests were used for survival analysis. A Cox regression model was constructed to evaluate prognostic risk factors associated with overall survival (OS). The Spearman correlation among clinicoradiological outcomes were analyzed.ResultsThe mean tumor size of PSC and c-NSCLC were both 5.1 cm. The median survival times of PSC and c-NSCLC were 8 months and 34 months, respectively (P < 0.001). Calcification and vacuoles/cavities were rarely present in PSC. Pleural invasion occurred in both PSC and c-NSCLC (P = 0.285). The mean CT values of PSC and c-NSCLC on plain scan (PS), arterial phase (AP), and venous phase (VP) were 30.48 ± 1.59 vs. 36.25 ± 0.64 Hu (P = 0.002), 43.26 ± 2.96 vs. 58.71 ± 1.65 Hu (P < 0.001) and 50.26 ± 3.28 vs. 64.24 ± 1.86 Hu (P < 0.001), the AUCs were 0.685, 0.757 and 0.710, respectively. Compared to c-NSCLC, PSC had a larger LAA ratio, and the AUC was 0.802, with an optimal cutoff value of 20.6%, and the sensitivity and specificity were 0.645 and 0.862, respectively. Combined with the mean CT value and LAA ratio, AP + VP + LAA yielded the largest AUC of 0.826. The LAA ratio were not independent risk factors for PSC in this study. LAA ratio was negatively correlated with PS (r = -0.29), AP (r = -0.58), and VP (r = -0.66). LAA showed a weak positive correlation with tumor size(r = 0.27).ConclusionsPSC has a poorer prognosis than c-NSCLC of similar tumor size. The mean CT value and LAA ratio contributes to preoperative CT differentiation of PSC and c-NSCLC.

Comparing SARS-CoV-2 Viral Load in Human Saliva to Oropharyngeal Swabs, Nasopharyngeal Swabs, and Sputum: A Systematic Review and Meta-Analysis.

A systematic review and meta-analysis were conducted to investigate the SARS-CoV-2 viral load in human saliva and compared it with the loads in oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, the salivary viral loads of symptomatic and asymptomatic COVID-19 patients were compared. Searches were conducted using four electronic databases: PubMed, Embase, Scopus, and Web of Science, for studies published on SARS-CoV-2 loads expressed by CT values or copies/mL RNA. Three reviewers evaluated the included studies to confirm eligibility and assessed the risk of bias. A total of 37 studies were included. Mean CT values in saliva ranged from 21.5 to 39.6 and mean copies/mL RNA ranged from 1.91 × 101 to 6.98 × 1011. Meta-analysis revealed no significant differences in SARS-CoV-2 load in saliva compared to oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, no significant differences were observed in the salivary viral load of symptomatic and asymptomatic COVID-19 patients. We conclude that saliva specimen can be used as an alternative for SARS-CoV-2 detection in oropharyngeal swabs, nasopharyngeal swabs, and sputum.

Viral etiologies of lower respiratory tract infections in children < 5 years of age in Addis Ababa, Ethiopia: a prospective case–control study

BackgroundLower respiratory tract infections (LRTIs) are a major cause of morbidity and mortality in children worldwide and disproportionally affect Sub-Saharan Africa. Despite the heaviest burden of LRIs in Ethiopia, to date, no published studies have reported a comprehensive viral etiology of LRTIs among children in Ethiopia. The objective of this study was to determine and estimate the etiological contribution of respiratory viruses to LRTIs in < 5 years children in Ethiopia.MethodsA prospective case–control study was conducted from September 2019 to May 2022 in two major governmental hospitals, St. Paul Hospital Millennium Medical College and ALERT Hospital in Addis Ababa, Ethiopia. Nasopharyngeal/oropharyngeal samples and socio-demographic and clinical information were collected from children under 5 years. A one-step Multiplex real-time PCR (Allplex™ Respiratory Panel Assays 1–3) was done to detect respiratory viruses. STATA software version 17 was used for the data analysis. We computed the odds ratio (OR), the attributable fraction among exposed (AFE) and the population attributable fraction (PAF) to measure the association of the detected viruses with LRTIs.ResultsOverall, 210 LRTIs cases and 210 non-LRTI controls were included in the study. The likelihood of detecting one or more viruses from NP/OP was higher among cases than controls (83.8% vs. 50.3%, p = 0.004). The multivariate logistic regression showed a significantly higher detection rate for RSV A (OR: 14.6, 95% CI 4.1–52.3), RSV B (OR: 8.1, 95% CI 2.3–29.1), influenza A virus (OR: 5.8, 95% CI 1.5–22.9), and PIV 1 (OR: 4.3, 95% CI 1.1–16.4), among cases when compared with controls. The overall AFE and PAF for RSV A were (93.2% and 17.3%), RSV B (87.7% and 10.4%) and Influenza A virus (82.8% and 6.3%), respectively. The mean CT values were significantly lower for only RSV B detected in the case groups as compared with the mean CT values of RSV B detected in the control group (p = 0.01).ConclusionsRSV, Influenza A and PIV 1 viruses were significantly associated with LRTIs in < 5 years children in Addis Ababa, Ethiopia. Therefore, we underscore the importance of developing prevention strategies for these viruses in Ethiopia and support the importance of developing and introducing an effective vaccine against these viruses.

Viral and antibody dynamics of acute infection with SARS-CoV-2 omicron variant (B.1.1.529): a prospective cohort study from Shenzhen, China

Elucidating viral dynamics within the host is important for designing public health measures against SARS-CoV-2, particularly during the early stages of infection when transmission potential rapidly increases. We aimed to analyse the viral and antibody dynamics of the omicron variant in relation to symptom onset or laboratory confirmation and replication dynamics throughout the infection course. In this prospective cohort study, patients with laboratory-confirmed SARS-CoV-2 infection who were admitted to Shenzhen Third People's Hospital (Shenzhen, China) between Jan 11, 2020, and April 24, 2022, were screened for eligibility. We included immunocompetent individuals with acute SARS-CoV-2 infection without antiviral agents targeting SARS-CoV-2. Serial nasopharyngeal swabs and plasma samples were analysed for viral RNAs and specific IgG antibodies of SARS-CoV-2. The comparative viral and antibody kinetics in association with symptom onset or laboratory confirmation and replication dynamics throughout the infection course were calculated by the locally estimated scatterplot smoothing curve fitting polynomial regression. The associations between viral and antibody dynamics and vaccination, age, sex, disease severity, and underlying health conditions were analysed using the Mann-Whitney U test and the Gehan-Breslow-Wilcoxon method. 15 406 serial nasopharyngeal swabs and 2324 plasma samples were taken from 2043 individuals with acute SARS-CoV-2 infection (n=217 prototype [A.1] and D614G [B.1] variant [wild-type]; n=105 delta variant [B.1.617.2]; n=1721 omicron variant [B.1.1.529]) and were included for the analyses. The mean Ct value of omicron variant on the first day post symptom onset (dpo; defined as the first day post laboratory confirmation in asymptomatic participants) was 22·65 (95% CI 22·05-23·26). Peak viral load was reached with a mean Ct value of 17·63 (17·47-17·79) at a mean of 3·19 dpo (95% CI 3·09-3·28), and viral clearance (Ct values ≥35) was reached at a mean of 13·50 dpo (95% CI 13·32-13·67). Omicron variant showed faster viral replication and clearance than wild-type SARS-CoV-2 and delta variant, and the viral load at the first dpo and the peak viral load was lower than delta variant but higher than wild-type SARS-CoV-2. Age, sex, disease severity, and underlying health conditions were associated with the viral dynamics of omicron variant, with faster viral clearance found in young (aged 0-14 years), male, and asymptomatic participants, and those without underlying health conditions. Replication dynamics thoughout the infection course showed that peak viral load was reached at a mean of 5·06 dpo (4·76-5·36) and viral clearance took a mean of 14·27 days (13·6-14·93) for omicron variant. SARS-CoV-2-specific IgG increased earlier and faster to significantly higher concentrations in breakthrough infection than naive infection with omicron variant, despite long intervals (≥7 months) between the last dose of vaccination and infection. Our data provide a comprehensive overview of the longitudinal viral and antibody dynamics of omicron variant in people with acute SARS-CoV-2 infection, with important implications for public health strategies, including population screening, antiviral treatment, isolation periods, and vaccination. National Natural Science Foundation of China and Emergency Key Program of Guangzhou Laboratory. For the Chinese translation of the abstract see Supplementary Materials section.

A Hypertonic Seawater Nasal Irrigation Solution Containing Algal and Herbal Natural Ingredients Reduces Viral Load and SARS-CoV-2 Detection Time in the Nasal Cavity.

Nasal irrigation is thought to decrease the viral load present in the nasal cavity. Our aim was to assess the effect of a hypertonic seawater solution [with algal and herbal natural ingredients (Sinomarin®)] on the viral load of nasopharynx in patients hospitalized with severe COVID-19 pneumonia. We conducted a prospective, randomized, controlled trial from June 2022 to December 2022. We allocated 56 patients with COVID-19 pneumonia into two groups (28 in each group)-the hypertonic seawater group [nasal irrigations with a hypertonic seawater solution (Sinomarin®) every 4 h for 16 h per day, for two consecutive days] and the control group (no nasal irrigations). A second nasopharyngeal swab was collected 48 h after the baseline nasopharyngeal swab (8 h after the last wash in the hypertonic seawater group) to estimate the SARS-CoV-2 viral load as determined by cycle threshold (Ct) values. In the hypertonic seawater group, the mean Ct values significantly increased two days after the initial measurement [ΔCt 48-0 h = 3.86 ± 3.03 cycles, p < 0.001 (95%CI: 2.69 to 5.04)]. No significant differences in the Ct values were observed in the control group [ΔCt 48-0 h = -0.14 ± 4.29, p = 0.866 (95%CI: -1.80 to -1.52)]. At follow-up, 17 patients from the hypertonic seawater group had negative test results compared to only 9 patients from the control group (p = 0.03). Nasal irrigations with a hypertonic seawater solution containing algal and herbal natural ingredients significantly decreased nasopharyngeal viral load and the detection time of SARS-CoV-2 in the nasal cavity.

Photodynamic therapy (pdt) in early stages of acute adult covid-19 patients: effects on viral load measured by qpcr

Background: The Covid-19 pandemic has negatively impacted Global Health and the world’s economy dramatically since early 2020. Although the development of vaccines has made fast progress, there are currently only a few effective medications and treatment options available for infected patients available. Objectives: The objective of this study was to evaluate the efficacy and safety of Photodynamic Therapy (PDT) with Riboflavin and a specially designed light treatment kit with blue and UVA light as a treatment tool for reducing viral load and clinical symptoms in patients with early stage Covid-19 infection. Methods: This interventional, non-randomized study involved 140 adult subjects. Participants were allocated to receive either PDT plus daily testing for 5 days or to receive conventional care plus testing. The viral load in the oral and nasal cavity and clinical symptoms were measured at the start of the study and after 24,48,72,96,120 and 168 hours. Results: The mean CT value in the treatment group was 29.63 at day 1 and 36.3 at day 5, for a difference of 6.68 threshold cycles and a confidence interval of [5.2;8.72]. Based on Welch’s t-test for two samples, this difference was significant (p&lt;0.01). The same test showed no difference in the means of the control group. Further analysis showed a significant difference between the treatment and control group in the clinical symptoms after 5 days as well, when controlled for the differences at the beginning. Conclusion: PDT decreases viral load and improves clinical symptoms in patients in early stages of Covid-19 significantly. It could be a promising tool for treatment of acutely infected patients in early stages to prevent progression of disease.

Imaging biomarkers on Angio-CT for predicting the efficacy of transarterial chemoembolization in hepatocellular carcinoma.

This study aimed to evaluate whether the lipiodol deposition pattern on intraprocedural Angio-CT could predict tumor treatment response in hepatocellular carcinoma (HCC) patients treated with conventional transarterial chemoembolization (c-TACE). This retrospective study enrolled intermediated and advanced HCC nodules treated with c-TACE and Angio-CT from June 2021 to June 2022. The therapeutic efficacy was evaluated according to the mRECIST standards. First, Angio-CT was used to determine lipiodol deposition at the end of c-TACE, redefined as complete, partial-complete, and incomplete groups. Second, the mean CT value of lipiodol deposition and its association with therapeutic efficacy were calculated in the complete model. Finally, the relationship between imaging biomarkers and efficacy was evaluated. A total of 45 patients with 72 HCC nodules were enrolled with 28 nodules in the complete group, 31 nodules in the partial-complete group, and 13 nodules in the incomplete group. The complete response (CR) proportion was significantly higher in patients with good lipiodol deposition compared with patients with poor lipiodol deposition (P<0.0001). There was no significantly different CR rate between CT value ≥800 and <800 HU (P=0.119) in the complete group. Meanwhile, the non-CR rate in cases with hepatic vein development was significantly higher than that in cases with no hepatic vein development in the arterial phase (P<0.0001). Complete lipiodol deposition on Angio-CT during c-TACE was a predictive factor for therapeutic response to TACE. For HCC nodules with well-deposited lipiodol, hepatic vein development on Angio-CT in the arterial phase was strongly associated with poor efficacy of TACE.

Differentiation Between Heterogeneous GGN and Part-Solid Nodule Using 2 D Grayscale Histogram Analysis of Thin-Section CT Image

Introduction/BackgroundTo evaluate cases of surgically resected pulmonary adenocarcinoma (Ad) with heterogenous ground-glass nodules (HGGNs) or part-solid nodules (PSNs) and to clarify the differences between them, and between invasive adenocarcinoma (IVA) and minimally invasive adenocarcinoma (MIA) + adenocarcinoma in situ (AIS) using grayscale histogram analysis of thin-section computed tomography (TSCT). Materials and Methods241 patients with pulmonary Ad were retrospectively classified into HGGNs and PSNs on TSCT by three thoracic radiologists. Sixty HGGNs were classified into 17 IVAs, 26 MIAs, and 17 AISs. 181 PSNs were classified into 114 IVAs, 55 MIAs, and 12 AISs. ResultsWe found significant differences in area (P = 0.0024), relative size of solid component (P <0.0001), circumference (P <0.0001), mean CT value (P <0.0001), standard deviation of the CT value (P <0.0001), maximum CT value (P <0.0001), skewness (P <0.0001), kurtosis (P <0.0001), and entropy (P <0.0001) between HGGNs and PSNs. In HGGNs, we found significant differences in relative size of solid component (P <0.0001), mean CT value (P = 0.0005), standard deviation of CT value (P = 0.0071), maximum CT value (P = 0.0237), and skewness (P = 0.0027) between IVAs and MIA+AIS lesions. In PSNs, we found significant differences in area (P = 0.0029), relative size of solid component (P = 0.0003), circumference (P = 0.0004), mean CT value (P = 0.0011), skewness (P = 0.0009), and entropy (P = 0.0002) between IVAs and the MIA+AIS lesions. ConclusionQuantitative evaluations using grayscale histogram analysis can clearly distinguish between HGGNs and PSNs, and may be useful for estimating the pathology of such lesions.

Correlating symptoms to infectivity among vaccinated healthcare workers with COVID-19

Background: Directing COVID-19 diagnostic testing to healthcare workers (HCWs) who are likely to be infected has potential to reduce staffing shortages and decrease opportunity for in-hospital transmission; however, HCWs with COVID-19 may exhibit a range of symptoms. We assessed the burden of symptoms in relation to cycle threshold (Ct) values as a surrogate for viral shedding in vaccinated healthcare workers. Methods: We retrospectively reviewed employee health records of COVID-19–vaccinated employees who tested positive for SARS-CoV-2 between December 2020 and January 2022 at 2 academic hospital systems. We reviewed demographic data, reasons for testing including symptoms, exposure history, medical history, vaccination dates, Ct values, and genotypes when available. We compared mean Ct values between symptomatic and minimally symptomatic cases using independent sample t tests. Patients were defined as minimally symptomatic if they had no symptoms or a single symptom that is not cough, fever, or anosmia at the time of testing. Patients were defined as more symptomatic if they reported &gt;1 symptom or cough, fever, or anosmia. Results: In total, 298 HCWs tested positive for COVID-19. Most positive cases were female (73%), white (78%), and had patient-facing roles (77%). Genotypic testing (n = 109) revealed that most genotypes belonged to the SARS-CoV-2 delta variant (AY lineages, B1.617.2). More cases were minimally symptomatic (62%) than were more symptomatic (38%). None required hospitalization during the study period. Mean Ct values (n = 141) showed no significant difference between more symptomatic and minimally symptomatic cases (19.8 vs 20.6; P = .40) (Fig. 1). Also, there was no significant difference in mean Ct value, comparing those with vaccination 90 days prior to positive (20.52 vs 19.88; P = .537). Conclusions: Our study shows no significant difference in cycle threshold values between minimally symptomatic and more symptomatic infections in vaccinated HCWs. In addition, HCWs exhibit high viral load even when infected within 90 days after vaccination. When considering whether to attend work, HCWs should be aware that mild symptoms and recent vaccination do not necessarily reflect low transmissibility and that they should follow CDC guidance regarding when to return to work.Disclosures: None

Establishment and Verification of Benign and Malignant Prediction Model of Subcentimeter Pulmonary Ground Glass Nodules Based on HRCT

Pre-operative accuracy of subcentimeter ground glass nodules (SGGNs) is a difficult problem in clinical practice, but there are few clinical studies on the benign and malignant prediction model of SGGNs. The aim of this study was to help identify benign and malignant lesions of SGGNs based on the imaging features of high resolution computed tomography (HRCT) and the general clinical data of patients, and to build a risk prediction model. This study retrospectively analyzed the clinical data of 483 patients with SGGNs who underwent surgical resection and were confirmed by histology from the First Affiliated Hospital of University of Science and Technology of China from August 2020 to December 2021. The patients were divided into the training set (n=338) and the validation set (n=145) according to 7:3 random assignment. According to the postoperative histology, they were divided into adenocarcinoma group and benign lesion group. The independent risk factors and models were analyzed by univariate analysis and multivariate Logistic regression. The receiver operator characteristic (ROC) curve was constructed to evaluate the model differentiation, and the calibration curve was used to evaluate the model consistency. The clinical application value of the decision curve analysis (DCA) evaluation model was drawn, and the validation set data was substituted for external verification. Multivariate Logistic analysis screened out patients' age, vascular sign, lobular sign, nodule volume and mean-CT value as independent risk factors for SGGNs. Based on the results of multivariate analysis, Nomogram prediction model was constructed, and the area under ROC curve was 0.836 (95%CI: 0.794-0.879). The critical value corresponding to the maximum approximate entry index was 0.483. The sensitivity was 76.6%, and the specificity was 80.1%. The positive predictive value was 86.5%, and the negative predictive value was 68.7%. The benign and malignant risk of SGGNs predicted by the calibration curve was highly consistent with the actual occurrence risk after sampling 1,000 times using Bootstrap method. DCA showed that patients showed a positive net benefit when the predictive probability of the predicted model probability was 0.2 to 0.9. Based on preoperative medical history and preoperative HRCT examination indicators, the benign and malignant risk prediction model of SGGNs was established to have good predictive efficacy and clinical application value. The visualization of Nomogram can help to screen out high-risk groups of SGGNs, providing support for clinical decision-making.

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture.

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/μl to 0.1 pg/μl (10-1 to 10-4). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10-1 (mean Ct value: 20.3) and 10-2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

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.

Thin-slice computed tomography enables to classify pulmonary subsolid nodules into pre-invasive lesion/minimally invasive adenocarcinoma and invasive adenocarcinoma: a retrospective study

The aim was to investigate the ability of thin-slice computed tomography (TSCT) to differentiate invasive pulmonary adenocarcinomas (IACs) from pre-invasive/minimally invasive adenocarcinoma (AAH-MIAs), manifesting as subsolid nodules (SSNs) of diameter less than 30 mm. The CT findings of 810 patients with single subsolid nodules diagnosed by pathology of resection specimens were analyzed (atypical adenomatous hyperplasia, n = 13; adenocarcinoma in situ, n = 175; minimally invasive adenocarcinoma, n = 285; and invasive adenocarcinoma, n = 337). According to the classification of lung adenocarcinoma published by WHO classification of thoracic tumors in 2015, TSCT features of 368 pure ground-glass nodules (pGGN) and 442 part-solid nodules (PSNs) were compared AAH-MIAs with IACs. Logistic regression and receiver operating characteristic (ROC) curve analyses were performed. In pGGNs, multivariate analysis of factors found to be significant by univariate analysis revealed that higher mean-CT values (p = 0.006, OR 1.006, 95% CI 1.002–1.010), larger tumor size (p < 0.001, OR 1.483, 95% CI 1.304–1.688) with air bronchogram and non-smooth margins were significantly associated with IACs. The optimal cut-off tumor diameter for AAH-MIAs lesions was less than 10.75 mm (sensitivity, 82.8%; specificity, 80.6%) and optimal cut-off mean-CT value − 629HU (sensitivity, 78.1%; specificity, 50.7%). In PSNs, multivariate analysis of factors found to be significant by univariate analysis revealed that smaller tumor diameter (p < 0.001, OR 0.647, 95% CI 0.481–0.871), smaller size of solid component (p = 0.001, OR 83.175, 95% CI 16.748–413.079),and lower mean-CT value of solid component (p < 0.001, OR 1.009, 95% CI 1.004–1.014) were significantly associated with AAH-MIAs (p < 0.05). The optimal cut-off tumor diameter, size of solid component, and mean-CT value of solid component for AAH-MIAs lesions were less than 14.595 mm (sensitivity, 71.1%; specificity, 83.4%), 4.995 mm (sensitivity, 97.8%; specificity, 92.3%) and − 227HU (sensitivity, 65.6%; specificity, 76.3%), respectively. In subsolid nodules, whether pGGN or PSNs, the characteristics of TSCT can help in distinguishing IACs from AAH-MIAs.

Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation

Although infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) does not appear to be as serious a threat to public health as it was in 2020–2021, the increased transmissibility of multiple Omicron descendants may constitute a continuous challenge for health care systems, and reliable detection of new variants is still imperative. This study evaluates the performance of three SARS-CoV-2 diagnostic tests: Novel Coronavirus (2019-nCoV) Real Time Multiplex RT-PCR Kit (Liferiver); Vitassay qPCR SARS-CoV-2 (Vitaassay) and TaqPath COVID‑19 CE-IVD RT-PCR Kit (Thermo Fisher Scientific). The analytical sensitivity of the assays as well as their specificity were determined with the use of synthetic nucleic acid standards and clinical samples. All assays appeared to be 100% specific for SARS-CoV-2 RNA in general and the Omicron variant in particular. The LOD determined during this validation was 10 viral RNA copies/reaction for Liferiver and TaqPath and 100 viral RNA copies for Vitassay. We cannot exclude that the LOD for the Vitassay might be lower and close to the manufacturer's declared value of ≥ 20 genome copies/reaction, as we obtained 90% positive results for 10 viral RNA copies/reaction. Mean Ct values at the concentration of 10 viral RNA copies/reaction for the Liferiver, Vitassay and TaqPath kits (35, 37 and 33, respectively) were significantly lower than the cutoff values declared by the manufacturers (≤ 41, ≤ 40 and ≤ 37, respectively). We suggest reporting outcomes based on LOD and cutoff Ct values determined during internal validation rather than those declared by the assays’ producers.

Community SARS-CoV-2 Dynamics and Cycle Threshold Use to Enhance Public Health Surveillance in the Dominican Republic

To propose appropriate containment measures and optimize surveillance strategies, it is of utmost importance to understand the dynamics of SARS-CoV-2 transmission within different age groups and its symptomatic and asymptomatic presentations. This study aimed to understand the cycle-threshold (Ct) of SARS-CoV-2 within individuals attending hospital-based facilities in the Dominican Republic. A total of 3,309 saliva samples were analysed from 14 provinces, which yielded a positivity rate of 18.01% (n=596) across 24 sites. Saliva specimens and levels of viral RNA were quantified by RT-qPCR. Overall mean Ct values were 29.3 cycles and significantly correlated with community positivity rate (r=-0.034, p=0.04). There was no significant difference in mean Ct values between studied age groups [F (19, 30) = 0.65, p = 0.5] and no significant correlation between mean Ct by age groups and community positivity. When comparing asymptomatic and symptomatic patients by age groups, the patients between 5 and 17 years old demonstrated a statistically significant mean difference in Ct values with 27.5 and 32.4 cycles, respectively (t (14) = -2.3, p = 0.03). Results identified in this study demonstrate how understanding community viral load is crucial for optimal SARS-CoV-2 surveillance and should be evaluated in the context of transmissibility dynamics.