Lower Ct Values Research Articles

Evaluation of CLINITEST® Rapid Covid-19 + Influenza antigen test in a cohort of symptomatic patients in an emergency department.

Rapid management of patients with respiratory tract infections in hospital emergency departments is one of the main objectives since the concurrent circulation of respiratory viruses following the SARS-CoV-2 pandemic. The use of new combined point-of-care antigen tests for detecting influenza A/B and SARS-CoV-2 represents an advantage in response time over the molecular tests. The objective was to evaluate the suitability of the CLINITEST® Rapid Covid-19 + Influenza Antigen test (Siemens Healthineers, Germany) (RCIA test) by measuring the sensitivity, specificity, Cohen's kappa, and cut-off values. Nasopharyngeal samples were collected from a randomised group of symptomatic patients of all ages at emergency department during January-February 2023. In parallel, these patients were screened for influenza A/B, and SARS-CoV-2 using RT-PCR. The Ct (cycle threshold) values were collected for positive [RT-PCR (+) /RCIA test (+)] and false negative [(RT-PCR (+) /RCIA test (-)] samples. A subanalysis was performed in the paediatric population (< 16 years-old). We included 545 patients (55.8% females) with a median age of 7 years-old (IQR: 1-66.5). The RCIA test showed a sensitivity of 59.7% [95%CI: 46.9-67.33] for influenza A, 65.6% [95%CI: 49.5-80.3] for influenza B, and 76.9% [95%CI: 45.8-84.8] for SARS-CoV-2. The specificity was between 90.7%-99.7% with a moderate/high level of agreement with RT-PCR (kappa score: 0.6-0.8) for the three respiratory viruses included in the RCIA test. The sensitivity of the RCIA test is insufficient for screening of patients, including patients with low Ct values (Ct > 20). Despite its good specificity and Cohen's kappa value, its use as a screening test is not comparable to RT-PCR systems in the ED environment with a high number of false negative results.

Laboratory Results and Clinical Characteristics of Probable Omicron Patients at Dr. Wahidin Sudirohusodo Hospital

Since the Omicron variant was first detected on November 24, 2021, in Southern Africa, it has now been detected in more than 110 countries and is estimated to continue to spread. Given the rapid spread and serious dangers of COVID-19, it is urgent to continuously improve and expand research on its clinical diagnosis and treatment. The analysis of this study identifies the laboratory results and clinical characteristics of probable Omicron. This study aimed to determine the laboratory results and clinical characteristics of probable Omicron patients at Dr. Wahidin Sudirohusodo Hospital. This descriptive study used a cross-sectional approach with medical record data of probable Omicron patients at Dr. Wahidin Sudirohusodo Hospital from January to July 2022 with a total of 241 research subjects. The results of the analysis showed that probable Omicron patients at Dr. Wahidin Sudirohusodo Hospital who were hospitalized consisted of 124 (51.5%) males and 117 (48.5%) females, 66 (22.8%) subjects with age range &gt;60 years, 88 (30.4%) subjects with age range of 40-60 years, 45 (15.6%) subjects with age range 19-40 years and 42 (14.5%) subjects with age &lt;18. Most subjects, which consisted of 79 (27.3%) patients reside in Makassar. The mean WBC count, NLR value, LMR value, and CT value found in this study were 10.8; 5.6; 0.5; and 33.94, respectively. The Omicron variant infects more males than females mainly at the age of 40-60 years, with a relatively low average CT value of 33.94 and a slight increase of NLR, MLR, and WBC count.

Evaluation of Mortality Risk Factors of COVID-19 in Jakarta Tertiary Hospital During Peak of Second Wave and Predictive Utility of Community RT-PCR Low CT Values

Background: The Delta variant of SARS-CoV-2 led to a surge in COVID-19 cases in Indonesia. This study aimed to assess the demographic profile and mortality rates of hospitalized COVID-19 patients in YARSI referral hospital, Jakarta, comparing pre-Delta and Delta wave periods. The study also investigated whether low CT values in RT-PCR tests indicated heightened viral transmission before the Delta wave surge. Method: A retrospective analysis was conducted on 1,457 COVID-19 patients hospitalized at YARSI (January-August 2021) and 25,279 RT-PCR test results from walk-in patients (April-August 17, 2021). Differences were evaluated using Chi-square or Fisher’s Exact Tests while binary logistic regression was used to assess mortality risk factors. Results: There were increased proportions of pregnant women, patients aged 20-29 and those with coronary artery disease during the Delta wave. This period also showed a significant increase in mortality rates, with the highest seen in patients &gt;60 years old or those with multiple comorbidities. Notably, most of the deceased patients (131 of 139) were unvaccinated. Analysis of RT-PCR data showed rising percentages of positive results with low CT values (below 21 or 15) from April to June. Conclusion: The Delta wave saw a higher risk of hospitalization among young individuals and pregnant women, despite their low mortality risk. The unvaccinated and those with multiple comorbidities faced higher mortality risks. Increases in RT-PCR positivity with low CT values preceded the July COVID-19 case surge.

Validating Radiosensitivity with Pre-Exposure Differential Gene Expression in Peripheral Blood Predicting Survival and Non-Survival in a Second Irradiated Rhesus Macaque Cohort.

Radiosensitivity differs in humans and possibly in closely related nonhuman primates. The reasons for variation in radiosensitivity are not well known. In an earlier study, we examined gene expression (GE) pre-radiation in peripheral blood among male (n = 62) and female (n = 60) rhesus macaques (n = 122), which did or did not survive (up to 60 days) after whole-body exposure of 7.0 Gy (LD66/60). Eight genes (CHD5, CHI3L1, DYSF, EPX, IGF2BP1, LCN2, MBOAT4, SLC22A4) revealed significant associations with survival. Access to a second rhesus macaque cohort (males = 40, females = 23, total n = 63) irradiated with 5.8-7.2 Gy (LD29-50/60) and some treated with gamma-tocotrienol (GT3, a radiation countermeasure) allowed us to validate these gene expression changes independently. Total RNA was isolated from whole blood samples and examined by quantitative RT-PCR on a 96-well format. cycle threshold (Ct)-values normalized to 18S rRNA were analyzed for their association with survival. Regardless of the species-specific TaqMan assay, similar results were obtained. Two genes (CHD5 and CHI3L1) out of eight revealed a significant association with survival in the second cohort, while only CHD5 (involved in DNA damage response and proliferation control) showed mean gene expression changes in the same direction for both cohorts. No expected association of CHD5 GE with dose, treatment, or sex could be established. Instead, we observed significant associations for those comparisons comprising pre-exposure samples with CHD5 Ct values ≤ 11 (total n = 17). CHD5 Ct values ≤ 11 in these comparisons were mainly associated with increased frequencies (61-100%) of non-survivors, a trend which depending on the sample numbers, reached significance (P = 0.03) in males and, accordingly, in females. This was also reflected by a logistic regression model including all available samples from both cohorts comprising CHD5 measurements (n = 104, odds ratio 1.38, 95% CI 1.07-1.79, P = 0.01). However, this association was driven by males (odds ratio 1.62, 95% CI 1.10-2.38, P = 0.01) and CHD5 Ct values ≤ 11 since removing low CHD5 Ct values from this model, converted to insignificance (P = 0.19). A second male subcohort comprising high CHD5 Ct values ≥ 14.4 in both cohorts (n = 5) appeared associated with survival. Removing these high CHD5 Ct values converted the model borderline significant (P = 0.051). Based on the probability function of the receiver operating characteristics (ROC) curves, 8 (12.3%) and 5 (7.7%) from 65 pre-exposure RNA measurements in males, death and survival could be predicted with a negative and positive predictive value ranging between 85-100%. An associated odds ratio reflected a 62% elevated risk for dying or surviving per unit change (Ct-value) in gene expression, considering the before-mentioned CHD5 thresholds in RNA copy numbers. In conclusion, we identified two subsets of male animals characterized by increased (Ct values ≤ 11) and decreased (Ct values ≥ 14.4) CHD5 GE copy numbers before radiation exposure, which independently of the cohort, radiation exposure or treatment appeared to predict the death or survival in males.

Semi-quantitative assessment of gastrointestinal viruses in stool samples with Seegene Allplex gastrointestinal panel assays: a solution to the interpretation problem of multiple pathogen detection?

The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections. The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined. After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting. By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.

Efficacy and viral dynamics of tecovirimat in patients with MPOX: A multicenter open-label, double-arm trial in Japan

IntroductionTecovirimat's application in treating mpox remains under-researched, leaving gaps in clinical and virological understanding. MethodsThe Tecopox study in Japan evaluated the efficacy and safety of tecovirimat in patients with smallpox or mpox, who were divided into oral tecovirimat and control groups. Patients with mpox enrolled between June 28, 2022, and April 30, 2023, were included. Demographic and clinical details along with blood, urine, pharyngeal swab, and skin lesion samples were gathered for viral analysis. A multivariable Tobit regression model was employed to identify factors influencing prolonged viral detection. ResultsNineteen patients were allocated to the tecovirimat group, and no patients were allocated to the control group. The median age was 38.5 years, and all patients were males. Ten patients (52.6%) were infected with human immunodeficiency virus (HIV). Sixteen patients (84.2%) had severe disease. Nine of the 15 patients (60.0%) (four patients withdrew before day 14) had negative PCR results for skin lesion specimens 14 days after inclusion. The mortality rates were 0% on days 14 and 30. No severe adverse events were reported. HIV status and the number of days from symptom onset to tecovirimat administration were associated with lower Ct values (p = 0.027 and p < 0.001, respectively). The median number of days when PCR testing did not detect the mpox virus in each patient was 19.5 days. ConclusionEarly tecovirimat administration might reduce viral shedding duration, thereby mitigating infection spread. Moreover, patients infected with HIV showed prolonged viral shedding, increasing the transmission risk compared to those without HIV.

Comparison of a novel rapid sampling method to serum and tonsil scraping to detect PRRSV in acutely infected sows

Few practical methods are available to monitor the PRRSV status of the sows. Common sampling methods for sows like serum sampling, and tonsil scraping involve restraining individual sows and are labor-intensive, time-consuming, relatively invasive, and therefore, have limited use in large-scale production settings. Thus, a practical and rapid method of sampling large numbers of sows is needed. This study aimed to develop a new sampling method, named tonsil-oral scraping (TOSc) and compare TOSc to serum and tonsil scraping in terms of PRRSV qPCR detection rate and Ct values in thirty matched sows, thirty days after PRRSV outbreak. TOSc recovered a mixture of oral fluids and tonsil exudates from the sow oral cavity within seconds without restraining the animals. Results showed that, numerically, the TOSc samples had higher PRRSV qPCR detection rate (100 %) compared to serum (16.8 %) and tonsil scraping (73.1 %). Moreover, TOSc samples had lower average Ct values (29.7) than tonsil scraping (30.7) and serum (35.2). There was no significant difference in the detection rate between TOSc and tonsil scraping (Tukey test, p = 0.992), while there was a significant difference between serum and tonsil scraping (Tukey test, p < 0.001), as well as between serum and TOSc (Tukey test, p < 0.001). In terms of Ct values, there was no statistically significant difference between TOSc and tonsil scrapings (Dunn Test, p > 0.05), while there was a significant difference between tonsil scraping with serum (Dunn Test, p < 0.01), and TOSc with serum (Dunn Test, p < 0.01). Our results suggest great potential of the TOSc as a novel, practical, and rapid tool for PRRSV RNA detection in sows to assess sow herd status.

Multisite Mpox Infection and Viral Dynamics Among Persons With HIV in Metro Atlanta.

The 2022 mpox outbreak primarily involved sexual transmission among men who have sex with men and disproportionately affected persons with human immunodeficiency virus (HIV). We examined viral dynamics and clinical features in a cohort evaluated for mpox infection at a comprehensive HIV clinic in Atlanta, Georgia. Viral DNA was found in 8 oropharyngeal and 5 anorectal specimens among 10 mpox cases confirmed by lesion swab polymerase chain reaction. Within-participant anatomic site of lowest cycle threshold (Ct) value varied, and lower Ct values were found in oropharyngeal and anorectal swabs when corresponding symptoms were present. This provides insight into mpox infection across multiple anatomic sites among people with HIV.

A single-center experience on long-term clinical performance of a rapid SARS-CoV-2 Antigen Detection Test, STANDARD Q COVID-19 Ag Test

The COVID-19 pandemic in Korea has dynamically changed with the occurrence of more easily transmissible variants. A rapid and reliable diagnostic tool for detection of SARS-CoV-2 is needed. While RT-PCR is currently the gold standard for detecting SARS-CoV-2, the procedure is time-consuming and requires expert technicians. The rapid antigen detection test (RADT) was approved as a confirmatory test on 14 March 2022 due to rapid dissemination of the Omicron variant. The benefits of the RADT are speed, simplicity, and point-of-care feasibility. The aim of our study was to evaluate the clinical performance of RADT compared to RT-PCR in a single center over 15 months, fully covering the SARS-CoV-2 ‘Variants of Concern (VOC).’ A total of 14,194 cases was simultaneously tested by RT-PCR and RADT from January 2021 to March 2022 in Gangnam Severance Hospital and were retrospectively reviewed. PowerChek SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit, and STANDARD Q COVID-19 Ag Test were used. Positive rates, sensitivities, specificities, positive predictive values (PPV), and negative predictive values (NPV) were estimated for five periods (3 months/period). Receiver operator characteristic curve (ROC) analysis was performed, and Spearman’s rank test assessed the correlation between RT-PCR Ct values and semi-quantitative RADT results. The overall positive rate of RT-PCR was 4.64%. The overall sensitivity and specificity were 0.577 [95% confidence interval (CI) 0.539–0.614] and 0.991 [95% CI 0.989–0.993], respectively. ROC analysis resulted in an area under the curve of 0.786 (P < 0.0001, Yuden’s index = 0.568). The PCR positive rates were estimated as 0.11%, 0.71%, 4.51%, 2.02%, and 13.72%, and PPV was estimated as 0.045, 0.421, 0.951, 0.720, and 0.798 in Periods 1, 2, 3, 4, and 5, respectively. A significant and moderate negative correlation between PCR Ct values and semi-quantitative RADT results was observed (Spearman’s ρ = − 0.646, P < 0.0001). The RADT exhibited good performance in specimens with low Ct values (Ct ≤ 25.00) by RT-PCR. The PPV was significantly higher in Periods 3 and 5, which corresponds to rapid dissemination of the Delta and Omicron variants. The high PPV implies that individuals with a positive RADT result are very likely infected with SARS-CoV-2 and would require prompt quarantine rather than additional RT-PCR testing. The sensitivity of 0.577 indicates that RADT should not replace RT-PCR. Nonetheless, given the high PPV and the ability to track infected persons through rapid results, our findings suggest that RADT could play a significant role in control strategies for further SARS-CoV-2 variants.

Ozone micron bubble pretreatment for antibiotic resistance genes reduction in hospital wastewater treatment

Ozone micron bubble (OMB) treatment offers a promising approach to effectively eliminate Antibiotic Resistance Genes (ARGs) from infectious medical wastewater and mitigate the threat of drug resistance transmission. This study evaluated the effectiveness of OMB treatment for reducing ARGs from infectious medical wastewater in laboratory and on-site pilot treatment setups. In part, the presence of antibiotic residues in a hospital wastewater treatment plant (WWTP) and the impact of hospital wastewater on the distribution of ARGs in a wastewater collection system were also investigated. The results of wastewater collection system survey revealed a high prevalence of ARGs in the system, particularly mcr-1, largely originating from medical wastewater discharges. Furthermore, analysis of antibiotic residues in the hospital wastewater treatment system showed significant accumulation, particularly of quinolone antibiotics, in the biomass of the biological oxidation tank, suggesting a potential risk of ARG proliferation within the system. Comparison of wastewater samples from domestic and hospital WWTPs revealed a relatively higher abundance of ARGs in the latter, with differences ranging from 2.2 to sixfold between corresponding locations in the treatment plants. Notably, the biological oxidation unit of both WWTPs exhibited a greater proportion of ARGs among all sampled points, indicating the potential proliferation of ARGs within the biomass of the treatment units. ARG degradation experiments showed that OMB treatment resulted in a significantly lower CT value (9.3 mg O3 L−1 min) compared to ozone coarse bubble treatment (102 mg O3 L−1 min) under identical test conditions. Moreover, the use of OMB on site significantly reduced the accumulation of ARGs in hospital wastewater, underscoring its potential as an effective solution for mitigating ARG spread.

Performance Evaluation of Rapid Antigen Test for COVID-19 with SARS-CoV-2 RT-PCR using Nasopharyngeal Swab with Special Reference to RNA Dependent RNA Polymerase (RdRp) Cycle Threshold Values

SARS-CoV-2 is highly contagious, which spreads even by patients having no clinical symptoms or also from people suffering with only mild symptoms. The gold standard test for its diagnosis is reverse-transcription PCR (RT-PCR) but at times of pandemic, Rapid antigen tests (RAT) are required, which has a very less turn-around time. Evaluation of the performance of COVID-19 Rapid antigen test in comparison to SARS-CoV-2 RT-PCR using nasopharyngeal swab, in relation to RNA dependent RNA polymerase (RdRp) Cycle threshold (Ct) values. This observational and cross-sectional study was done on patients coming with features of Influenza-like illness (ILI) or for any aerosol generating procedure or on high-risk patients seeking hospitalization. Both RT-PCR and RAT for COVID-19 were done on samples collected from each patient and results were compared. Altogether, 5314 samples were tested, out of which 104 (01.95 %) &amp; 229 (04.31 %) samples were found positive by the RAT &amp; RT PCR test, respectively. Sensitivity, specificity, PPV and NPV of RAT were found to be 44.54%, 99.96%, 98.08% and 97.56%, respectively. 98.9 % of samples with Ct value ≤ 20 were positive by RAT, whereas only 2.2% samples having Ct value ≥ 26 were found to be positive. Cases having lower Ct values were found to be more symptomatic and vice-versa. RAT are not efficient in detecting the virus in samples showing high Ct values (Ct ≥ 26) by RT-PCR test. Patients with samples showing low Ct values (Ct ≤ 20) had more severe symptoms and vice-versa.

Differential Viral Dynamics by Sex and Body Mass Index During Acute SARS-CoV-2 Infection: Results From a Longitudinal Cohort Study.

There is evidence of an association of severe coroanavirus disease (COVID-19) outcomes with increased body mass index (BMI) and male sex. However, few studies have examined the interaction between sex and BMI on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral dynamics. Participants conducted RT-PCR testing every 24-48 hours over a 15-day period. Sex and BMI were self-reported, and Ct values from E-gene were used to quantify viral load. Three distinct outcomes were examined using mixed-effects generalized linear models, linear models, and logistic models, respectively: all Ct values (model 1), nadir Ct value (model 2), and strongly detectable infection (at least 1 Ct value ≤28 during their infection) (model 3). An interaction term between BMI and sex was included, and inverse logit transformations were applied to quantify the differences by BMI and sex using marginal predictions. In total, 7988 participants enrolled in this study and 439 participants (model 1) and 309 (models 2 and 3) were eligible for these analyses. Among males, increasing BMI was associated with lower Ct values in a dose-response fashion. For participants with BMIs greater than 29 kg/m2, males had significantly lower Ct values and nadir Ct values than females. In total, 67.8% of males and 55.3% of females recorded a strongly detectable infection; increasing proportions of men had Ct values <28 with BMIs of 35 and 40 kg/m2. We observed sex-based dimorphism in relation to BMI and COVID-19 viral load. Further investigation is needed to determine the cause, clinical impact, and transmission implications of this sex-differential effect of BMI on viral load.

Cycle Threshold Values Predict COVID-19 Severity and Mortality but are not Correlated with Laboratory Markers

Many studies have evaluated the possible utility of cycle threshold (Ct) values as a predictor of Coronavirus disease 2019 (COVID-19) severity and patient outcome. Given the inconsistent results, we aimed to evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Ct values and disease severity, inflammatory markers, and outcomes in Iranian patients with COVID-19.&#x0D; A retrospective study of 528 patients with COVID-19 hospitalized from September 2020 to October 2021 was conducted. Demographic, clinical, and laboratory data of patients were retrieved from electronic medical records. Ct values were analyzed as a continuous variable after subcategorizing into 3 groups: low (Ct values&lt;20), medium (Ct values 20 to 30), and high (Ct values&gt;30).&#x0D; Of the 528 patients (45.1% female) aged 13 to 97 years, 109 patients had low Ct values, 312 patients had medium, and 107 patients had high Ct values. Patients with low Ct values were more likely to present with critical COVID-19, require invasive mechanical ventilation and develop complications such as acute respiratory distress syndrome and pneumonia. Furthermore, patients with low or medium Ct values were more likely to die compared to patients with high Ct values.Multivariate analysis showed that patients with low or medium Ct values were more likely to have severe COVID-19 compared with patients with high Ct values. The multivariate analysis also showed a higher risk of mortality in patients with low Ct values compared to patients with high Ct values, although this was not statistically significant.&#x0D; Our findings revealed that Ct values were an independent predictor of COVID-19 severity. The risk of mortality was higher in patients with low Ct values. However, further investigation is needed to address the correlation between Ct values and inflammatory factors.

Assessment of Salivary Glands as Reservoirs of SARS-CoV-2 and the Contagiousness of Saliva in Asymptomatic COVID-19 Patients: Is Delta Variant More Contagious?

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection transmits when aerosols or droplets containing the virus are inhaled or come directly into contact, mainly in close contact with an infected person. Objectives: This study aimed to evaluate the role of the salivary glands in the secretion of SARS-CoV-2-infected saliva and determine the contagiousness of saliva in asymptomatic coronavirus disease 2019 (COVID-19) patients. Methods: In this cross-sectional analytical study between March 2021 and March 2022, 85 asymptomatic COVID-19 individuals with positive nasopharyngeal/oropharyngeal swabs were recruited. The SARS-CoV-2 cycle threshold (Ct) value was investigated in concomitant nasopharyngeal swabs (NPS), saliva, and pure saliva (collected directly from the salivary duct opening) using Real Time-PCR assay. Statistical analysis was performed using SPSS software (version 23), and a p-value of &lt; 0.05 was considered significant. Results: The saliva Ct-value was the lowest (the highest viral load) for Delta (29.82 ± 4.66), Omicron (32.75 ± 4.82), and Alpha (36.83 ± 4.8) variants, respectively. Delta-infected saliva and pure saliva revealed the strongest correlation (correlation coefficient = 0.971, P &lt; 0.001). Saliva Ct-value was significantly lower in Delta- (P &lt; 0.001) and Omicron- (P = 0.012) infected patients than in Alpha-infected patients. The pure saliva Ct-value was significantly lower (P = 0.014) in Delta samples (30.13 ± 4.51). Asymptomatic Alpha- and Omicron-infected patients revealed significantly lower NPS Ct-value (30.52 ± 4.02 and 29.44 ± 3.34) than the saliva (36.83 ± 4.8 and 32.75 ± 4.82). Conclusions: The major salivary glands secrete SARS-CoV-2-infected saliva in nearly all Delta-infected and most Omicron-infected asymptomatic individuals. Although the transmission process is complex, saliva droplets and aerosols seem to have a higher contagiousness potential in individuals infected with the Delta variant.

Identification and characterization of porcine Rotavirus A in Chilean swine population.

Rotavirus A (RVA) is a common cause of diarrhea in newborn pigs, leading to significant economic losses. RVA is considered a major public health concern due to genetic evolution, high prevalence, and pathogenicity in humans and animals. The objective of this study was to identify and characterize RVA in swine farms in Chile. A total of 154 samples (86 oral fluids and 68 fecal samples) were collected, from 22 swine farms. 58 (38%) samples belonging to 14 farms were found positive for RVA by real-time RT-PCR. The samples with low Ct values (21) and the two isolates were selected for whole genome sequencing. Nearly complete genomes were assembled from both isolates and partial genomes were assembled from five clinical samples. BLAST analysis confirmed that these sequences are related to human and swine-origin RVA. The genomic constellation was G5/G3-P[7]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Phylogenetic analysis showed that VP4, VP1, VP2, NSP2, NSP3, NSP4, and NSP5 sequences were grouped in monophyletic clusters, suggesting a single introduction. The phylogenies for VP7, VP6, VP3, and NSP1 indicated two different origins of the Chilean sequences. The phylogenetic trees showed that most of the Chilean RVA sequences are closely related to human and swine-origin RVA detected across the world. The results highlight the potential zoonotic nature of RVA circulating in Chilean swine farms. Therefore, it is important to continue RVA whole genome sequencing globally to fully understand its complex epidemiology and early detection and characterization of zoonotic strains.

Related factors of viral nucleic acid change in critically ill patients with SARS-CoV-2 infection after treatment with Nirmatrelvir/Ritonavir: a single center retrospective cohort study

To describe negative conversion and rebound of patients with severe and critical acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection after treatment with Nirmatrelvir/Ritonavir, and to analyze related factors associating with failure of SARS-CoV-2 negative conversion and relapse and prognosis. A single center retrospective cohort study was conducted. Patients aged ≥ 16 years old who were diagnosed with severe or critical SARS-CoV-2 infection and took Nirmatrelvir/Ritonavir for 5 days in Peking University First Hospital from December 7, 2022 to January 27, 2023, were included. General characteristics and clinical data were collected from electronic medical record system. The Kaplan-Meier curve of SARS-CoV-2 negative conversion was drawn. Factors with P < 0.10 were incorporated into multivariate Logistic regression model to analyze the relationship between the factors and persistent nucleic acid positive and rebound. A total of 31 severe and 37 critical SARS-CoV-2 infection patients were included. The median duration from initiation of Nirmatrelvir/Ritonavir to negative conversion of SARS-CoV-2 for both was 6.0 days, and the negative conversion rate on day 15 was 93.5% and 86.5%, respectively. SARS-CoV-2 rebound was observed in 7 patients (11.3%), among whom were 1 severe patient and 6 critical patients. The above 7 patients with SARS-CoV-2 rebound and 6 patients with failure of SARS-CoV-2 negative conversion were compared with 55 patients with persistent negative conversion. Factors with P < 0.10, including the lowest lymphocyte count (LYM), the highest D-dimer, the highest procalcitonin (PCT), the lowest Ct value, cardiovascular diseases other than hypertension and coronary heart disease, were incorporated into multivariate Logistic regression analysis. The decreased LYM [odds ratio (OR) = 0.146, 95% confidence interval (95%CI) was 0.031-0.689, P = 0.015] and the increased PCT (OR = 2.008, 95%CI was 1.042-3.868, P = 0.037) were revealed to be independent risk factors of the failure of SARS-CoV-2 negative conversion or rebound. The proportion of mechanical ventilation and invasive ventilation were significantly higher in patients with persistent SARS-CoV-2 infection or rebound than those in patients with SARS-CoV-2 negative conversion (84.6% vs. 38.2%, 69.2% vs. 25.5%, both P < 0.01), but no significant difference in mechanical ventilation and invasive ventilation duration was observed. Compared with the patients with SARS-CoV-2 negative conversion, more patients with persistent SARS-CoV-2 infection or rebound were admitted to intensive care unit (ICU, 76.9% vs. 50.9%), and length of ICU stay in patients with persistent SARS-CoV-2 infection or rebound tended to be longer [days: 13.0 (10.3, 24.3) vs. 11.0 (5.3, 23.0), P > 0.05]. The decreased LYM and increased PCT are independent risk factors for the failure of SARS-CoV-2 negative conversion or rebound in patients with severe and critical SARS-CoV-2 infection. Attention should be paid to these patients for their poor prognosis.

Diagnostic Performance Between Chest CT Severity Score and Initial Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Cycle Values in COVID-19 Patients and Their Relation With the Clinical Status of Patients.

Reverse transcription-polymerase chain reaction (RT-PCR) is used as a standard test for the diagnosis of SARS-CoV-2 viral RNA from nasopharyngeal aspirates. However, this method lacks sensitivity and cannot assess disease severity. A CT scan of the thorax provides a CT severity score (CT-SS), which depicts lung involvement and disease severity. This study aims to investigate the diagnostic value of chest CT compared with RT-PCR cycle threshold (Ct) values in COVID-19 and relate it clinically with the disease severity of patients. This retrospective observational study was conducted in a tertiary center from April 2021 to March 2022. We included 511 patients who had tested RT-PCR positive for COVID-19, were hospitalized, and had undergone high-resolution CT (HRCT) thorax. Data was collected from patient records regarding name, age, sex, admission data, baseline investigations including Ct value, management, and outcome. HRCT was reviewed to assess lung involvement and calculate CT-SS. Data was analyzed using SPSS Statistics version 25 (IBM Corp. Released 2017. IBM SPSS Statistics for Windows, Version 25.0. Armonk, NY: IBM Corp.). The mean age of patients was 50.4 ± 13.7 years, and the majority (67.5%) were male. Gender-wise, there was no difference in RT-PCR cycle threshold (Ct) values; however, CT-SS was significantly higher in males (17.5 ± 4.8 vs.10.5 ± 6.6, t=-13.6, p<0.0001). ICU admission was needed for 34.8% of patients, and they had a significantly lower Ct value (21.7 ± 3.3 vs. 22.8 ± 3.7, t=21.10, p<0.0001) and higher CT-SS (16.3 ± 4.5 vs. 6.7 ± 5.1, t=-3.32, p=0.001). Ct values could not differentiate between moderate and severe patients. CT-SS was not related to the viral load at admission. Patients who succumbed had significantly lower Ct values and higher CT-SS.

Development of highly sensitive one-step reverse transcription-quantitative PCR for SARS-CoV-2 detection in wastewater

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is a major public health concern that has highlighted the need to monitor circulating strains to better understand the coronavirus disease 2019 (COVID-19) pandemic. This study was carried out to monitor SARS-CoV-2 RNA and its variant-specific mutations in wastewater using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). One-step RT-qPCR using the SARS-CoV-2 Detection RT-qPCR Kit for Wastewater (Takara Bio), which amplified two N-gene regions simultaneously using CDC N1 and N2 assays with a single fluorescence dye, demonstrated better performance in detecting SARS-CoV-2 RNA (positive ratio, 66 %) compared to two-step RT-qPCR using CDC N1 or N2 assay (40 % each, and 52 % when combined), with significantly lower Ct values. The one-step RT-qPCR assay detected SARS-CoV-2 RNA in 59 % (38/64) of influent samples collected from a wastewater treatment plant in Japan between January 2021 and March 2022. The correlation between the concentration of SARS-CoV-2 RNA in the wastewater and the number of COVID-19 cases reported each day for 7 days pre- and post-sampling was significant (p < 0.05, r = 0.76 ± 0.03). Thirty-one influent samples which showed two-well positive for SARS-CoV-2 RNA were further tested by six mutations site-specific one-step RT-qPCR (E484K, L452R, N501Y, T478K, G339D, and E484A mutations). The N501Y mutation was detected between March and June 2021 but was replaced by the L452R and T478K mutations between July and October 2021, reflecting the shift from Alpha to Delta variants in the study region. The G339D and E484A mutations were identified in January 2022 and later when the incidence of the Omicron variant peaked. These findings indicate that wastewater-based epidemiology has the epidemiological potential to complement clinical tests to track the spread of COVID-19 and monitor variants circulating in communities.

Comparison of Positive/Inconclusive Xpert Xpress SARS-CoV-2 with the Standard M nCoV Real-Time Detection.

COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can be diagnosed using rapid real-time PCR, real-time reverse transcription PCR (rRT-PCR), or rapid antigen testing. Among these, rRT-PCR is considered the gold standard assay. The Xpert Xpress SARS-CoV-2 assay is a rapid real-time PCR test, approved by the Korean Disease Control and Prevention Agency in 2020. The overall concordance and positive concordance rates of the Xpert assay with the STANDARD M nCoV Real-Time Detection kit were determined. All samples with positive or inconclusive Xpert test results from July 2021 to February 2023 that underwent confirmatory testing using the reference rRT-PCR assay were included in the analysis. Samples from 224 patients (93 men and 131 women) with a median age of 59 years (range 15 - 90 years) were included. Of 212 samples that tested positive using Xpert, 112 (52.8%) were true positves and 100 (47.2%) were false positives on rRT-PCR testing. The overall concordance and positive concordance rates were 52.8% (112/212) and 54.5% (112/224), respectively. In the Xpert positive group, the samples had a lower Ct value for the E gene than the N2 gene. The Ct values for the E and N2 genes were significantly lower in the positive group than in the inconclusive group. Positive or inconclusive Xpert results should be confirmed by the gold standard rRT-PCR for early control of this disease. Furthermore, Korea's policy should be reconsidered given the high false-positive rate of the rapid real-time PCR Xpert Xpress SARS-CoV-2 assay.

Clinical, epidemiological, and virological features of Mpox in Beijing, China – May 31–June 21, 2023

ABSTRACT The first locally acquired case in the Chinese mainland was reported on May 31, 2023, lagging behind other countries. In this study, we aimed to examine the early clinical and epidemiological characteristics of the earliest cases of Mpox in Beijing, China. Additionally, we investigated the sequence and transmission patterns of the Mpox virus (MPXV). We analyzed 37 reported cases of Mpox in Beijing from May 31, 2023 to June 21, 2023. The age range of the subjects was 24–51 years. Thirty-six cases (97.3%) were identified in men who have sex with men (MSM), and 19 cases (51.4%) tested positive for the human immunodeficiency virus. Thirty-three cases were symptomatic, while four were asymptomatic. Skin lesions were observed in 32 cases (97.0%), fever in 26 (78.8%), and swollen lymph nodes in 17 (51.5%). Rash typically appeared in the genital or perianal area 1–3 days before fever onset, with a minimum incubation period of 2 days. For individuals with skin rashes, the skin lesion samples showed 100% positivity and low Ct values. There were high oropharyngeal swab (75.8%) and blood (84.6%) positivity rates. All MPXV strains belonged to the B.1.3 branch of the West African lineage. These strains carried 76–86 nucleotide substitutions compared with the reference human MPXV genome, and genetic diversity was observed. Our findings provide the first insights into the landscape of early transmission of Mpox in Beijing and help inform policy formulation in the Chinese mainland.