Comparative analysis of clinical and immunological profiles across Omicron BA.5.2 subvariants using next-generation sequencing in a Chinese cohort.

Objective: The Omicron BA.5.2 variant of SARS-CoV-2 has undergone several evolutionary adaptations, leading to multiple subvariants. Rapid and accurate characterization of these subvariants is essential for effective treatment, particularly in critically ill patients. This study leverages Next-Generation Sequencing (NGS) to elucidate the clinical and immunological features across different Omicron BA.5.2 subvariants. Methods: We enrolled 28 patients infected with the Omicron variant, hospitalized in Zhangjiajie People's Hospital, Hunan, China, between January 20, 2023, and March 31, 2023. Throat swabs were collected upon admission for NGS-based identification of Omicron subvariants. Clinical data, including qSOFA scores and key laboratory tests, were collated. A detailed analysis of lymphocyte subsets was conducted to ascertain the extent of immune cell damage and disease severity. Results: Patients were infected with various Omicron subvariants, including BA.5.2.48, BA.5.2.49, BA.5.2.6, BF.7.14, DY.1, DY.2, DY.3, and DY.4. Despite having 43 identical mutation sites, each subvariant exhibited unique marker mutations. Critically ill patients demonstrated significant depletion in total lymphocyte count, T cells, CD4, CD8, B cells, and NK cells (P < 0.05). However, there were no significant differences in clinical and immunological markers across the subvariants. Conclusion: This study reveals that critically ill patients infected with different Omicron BA.5.2 subvariants experience similar levels of cellular immune dysfunction and inflammatory response. Four mutations - ORF1a:K3353R, ORF1a:L3667F, ORF1b:S997P, S:T883I showed correlation with immunological responses although this conclusion suffers from the small sample size. Our findings underscore the utility of NGS in the comprehensive assessment of infectious diseases, contributing to more effective clinical decision-making.

Six-month follow-up after recovery of COVID-19 Delta variant survivors via CT-based deep learning.

Purpose: Using computer-aided diagnosis (CAD) methods to analyze the discharge and 6-month follow-up data of COVID-19 Delta variant survivors, evaluate and summarize the recovery and prognosis, and improve people's awareness of this disease. Methods: This study collected clinical data, SGRQ questionnaire results, and lung CT scans (at both discharge and 6-month follow-up) from 41 COVID-19 Delta variant survivors. Two senior radiologists evaluated the CT scans before in-depth analysis. Deep lung parenchyma enhancing (DLPE) method was used to accurately segment conventional lesions and sub-visual lesions in CT images, and then quantitatively analyze lung injury and recovery. Patient recovery was also measured using the SGRQ questionnaire. The follow-up examination results from this study were combined with those of the original COVID-19 for further comparison. Results: The participants include 13 males (31.7%) and 28 females (68.3%), with an average age of 42.2 ± 17.7 years and an average BMI of 25.2 ± 4.4 kg/m2. Compared discharged CT and follow-up CT, 48.8% of survivors had pulmonary fibrosis, mainly including irregular lines (34.1%), punctuate calcification (12.2%) and nodules (12.2%). Compared with discharged CT, the ground-glass opacity basically dissipates at follow-up. The mean SGRQ score was 0.041 (0-0.104). The sequelae of survivors mainly included impaired sleep quality (17.1%), memory decline (26.8%), and anxiety (21.9%). After DLPE process, the lesion volume ratio decreased from 0.0018 (0.0003, 0.0353) at discharge to 0.0004 (0, 0.0032) at follow-up, p < 0.05, and the absorption ratio of lesion was 0.7147 (-1.0303, 0.9945). Conclusion: The ground-glass opacity of survivors had dissipated when they were discharged from hospital, and a little fibrosis was seen in CT after 6-month, mainly manifested as irregular lines, punctuate calcification and nodules. After DLPE and quantitative calculations, we found that the degree of fibrosis in the lungs of most survivors was mild, which basically did not affect lung function. However, there are a small number of patients with unabsorbed or increased fibrosis. Survivors mainly had non-pulmonary sequelae such as impaired sleep quality and memory decline. Pulmonary prognosis of Delta variant patients was better than original COVID-19, with fewer and milder sequelae.

Exploring New Characteristics: Using Deep Learning and 3D Reconstruction to Compare the Original COVID-19 and Its Delta Variant Based on Chest CT.

Purpose: Computer-aided diagnostic methods were used to compare the characteristics of the Original COVID-19 and its Delta Variant. Methods: This was a retrospective study. A deep learning segmentation model was applied to segment lungs and infections in CT. Three-dimensional (3D) reconstruction was used to create 3D models of the patient's lungs and infections. A stereoscopic segmentation method was proposed, which can subdivide the 3D lung into five lobes and 18 segments. An expert-based CT scoring system was improved and artificial intelligence was used to automatically score instead of visual score. Non-linear regression and quantitative analysis were used to analyze the dynamic changes in the percentages of infection (POI). Results: The POI in the five lung lobes of all patients were calculated and converted into CT scores. The CT scores of Original COVID-19 patients and Delta Variant patients since the onset of initial symptoms were fitted over time, respectively. The peak was found to occur on day 11 in Original COVID-19 patients and on day 15 in Delta Variant patients. The time course of lung changes in CT of Delta Variant patients was redetermined as early stage (0-3 days), progressive and peak stage (4-16 days), and absorption stage (17-42 days). The first RT-PCR negative time in Original COVID-19 patients appeared earlier than in Delta Variant patients (22 [17-30] vs. 39 [31-44], p < 0.001). Delta Variant patients had more re-detectable positive RT-PCR test results than Original COVID-19 patients after the first negative RT-PCR time (30.5% vs. 17.1%). In the early stage, CT scores in the right lower lobe were significantly different (Delta Variant vs. Original COVID-19, 0.8 ± 0.6 vs. 1.3 ± 0.6, p = 0.039). In the absorption stage, CT scores of the right middle lobes were significantly different (Delta Variant vs. Original COVID-19, 0.6 ± 0.7 vs. 0.3 ± 0.4, p = 0.012). The left and the right lower lobes contributed most to lung involvement at any given time. Conclusion: Compared with the Original COVID-19, the Delta Variant has a longer lung change duration, more re-detectable positive RT-PCR test results, different locations of pneumonia, and more lesions in the early stage, and the peak of infection occurred later.

Optimization of biotransformation from phytosterol to androstenedione by a mutant Mycobacterium neoaurum ZJUVN-08.

Biotransformation of phytosterol (PS) by a newly isolated mutant Mycobacterium neoaurum ZJUVN-08 to produce androstenedione has been investigated in this paper. The parameters of the biotransformation process were optimized using fractional factorial design and response surface methodology. Androstenedione was the sole product in the fermentation broth catalyzed by the mutant M. neoaurum ZJUVN-08 strain. Results showed that molar ratio of hydroxypropyl-ß-cyclodextrin (HP-ß-CD) to PS and substrate concentrations were the two most significant factors affecting androstenedione production. By analyzing the statistical model of three-dimensional surface plot, the optimal process conditions were observed at 0.1 g/L inducer, pH 7.0, molar ratio of HP-ß-CD to PS 1.92:1, 8.98 g/L PS, and at 120 h of incubation time. Under these conditions, the maximum androstenedione yield was 5.96 g/L and nearly the same with the non-optimized (5.99 g/L), while the maximum PS conversion rate was 94.69% which increased by 10.66% compared with the non-optimized (84.03%). The predicted optimum conditions from the mathematical model were in agreement with the verification experimental results. It is considered that response surface methodology was a powerful and efficient method to optimize the parameters of PS biotransformation process.