Transmission of SARS-CoV-2 Omicron Variant under a Dynamic Clearance Strategy in Shandong, China.

SARS-CoV-2 Omicron caused a large wave of COVID-19 cases in China in spring 2022. Shandong was one of the most affected regions during this epidemic yet was also among those areas that were able to quickly contain the transmission. We aimed to investigate the origin, genetic diversity, and transmission patterns of the Omicron epidemic in Shandong under a dynamic clearance strategy. We generated 1,149 Omicron sequences, performed phylogenetic analysis, and interpreted results in the context of available epidemiological information. We observed that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to majority of local cases. We found evidence suggesting that some local clusters were potentially associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. We identified a BA.1.1 genome with the R493Q reversion mutation in the spike receptor binding domain, potentially associated with an escape from vaccine and Omicron infection elicited neutralizing immunity. Our findings illustrated how the dynamic clearance strategy constrained this epidemic's size, duration, and geographical distribution. IMPORTANCE Starting in March 2022, the Omicron epidemic caused a large wave of COVID-19 cases in China. Shandong was one of the most affected regions during this epidemic but was also among those areas that were able to quickly contain the transmission. We investigated the origin, genetic diversity, and transmission patterns of Omicron epidemic in Shandong under a dynamic clearance strategy. We found that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to most local cases. We found evidence suggesting that some local clusters were associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. Our study illustrated the transmission patterns of Omicron epidemic in Shandong and provided a looking glass onto this epidemic in China.

Traditional Chinese Medicine for COVID-19: A Network Meta-Analysis and Systematic Review.

To compare the efficacy of different traditional Chinese medicine (TCM) therapies for the treatment of coronavirus disease 2019 (COVID-19) and provide a higher level of evidence in the form of network meta-analysis (NMA) and systematic review. We searched the studies from the following databases: CNKI, VIP, WanFang, SinoMed, PubMed, Embase, and Web of Science from the establishment of the respective database until December 2021. Relevant studies were screened according to the pre-established inclusion criteria. The quality of the included randomized controlled trials (RCTs) and controlled clinical trials (CCTs) were assessed using the risk of bias (ROB) tool and the Methodological Index for Non-Randomized Studies (MINORS), respectively. R software 4.1.1 and Stata 13.1 were used for data analysis and mapping. A total of 34 studies were included in this network meta-analysis that tested 24 TCM interventions and included 3443 patients. Using cluster analysis of time to negative SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR), the length of hospital stay and composite events, we found that Jinyinhua oral liquid (JYH, 120 mL) + conventional Western medicine (CWM) has the highest SUCRA value at 88.64%, 85.61% and 84.24%. The traditional meta-analysis results revealed that Qingfei Paidu decoction + CWM were significantly different compared with CWM alone for the score of clinical symptoms (MD =-0.75, 95% CI [-1.04, -0.47]). Nine studies reported 57 adverse reactions (ADRs) and 3 adverse events (ADEs) in TCM + CWM groups, and eight studies reported 33 ADRs and 8 ADEs in CWM groups. In conclusion, the combination of TCM and CWM approaches may enhance the efficacy of CWM in COVID-19 patients. Based on the NMA result, JYH (120 mL) + CWM may be a more effective treatment and deserves further investigation. However, the differences in many comparisons between TCM interventions did not reach statistical significance; therefore, further high-quality studies are required to validate these findings.

On-Site Viral Inactivation and RNA Preservation of Gargle and Saliva Samples Combined with Direct Analysis of SARS-CoV-2 RNA on Magnetic Beads.

Samples of nasopharyngeal swabs (NPS) are commonly used for the detection of SARS-CoV-2 and diagnosis of COVID-19. As an alternative, self-collection of saliva and gargle samples minimizes transmission to healthcare workers and relieves the pressure of resources and healthcare personnel during the pandemic. This study aimed to develop an enhanced method enabling simultaneous viral inactivation and RNA preservation during on-site self-collection of saliva and gargle samples. Our method involves the addition of saliva or gargle samples to a newly formulated viral inactivation and RNA preservation (VIP) buffer, concentration of the viral RNA on magnetic beads, and detection of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction directly from the magnetic beads. This method has a limit of detection of 25 RNA copies per 200 µL of gargle or saliva sample and 9-111 times higher sensitivity than the viral RNA preparation kit recommended by the United States Centers for Disease Control and Prevention. The integrated method was successfully used to analyze more than 200 gargle and saliva samples, including the detection of SARS-CoV-2 in 123 gargle and saliva samples collected daily from two NPS-confirmed positive SARS-CoV-2 patients throughout the course of their infection and recovery. The VIP buffer is stable at room temperature for at least 6 months. SARS-CoV-2 RNA (65 copies/200 µL sample) is stable in the VIP buffer at room temperature for at least 3 weeks. The on-site inactivation of SARS-CoV-2 and preservation of the viral RNA enables self-collection of samples, reduces risks associated with SARS-CoV-2 transmission, and maintains the stability of the target analyte.

Humoral immunity and transcriptome differences of COVID-19 inactivated vacciane and protein subunit vaccine as third booster dose in human.

Under the background of the severe human health and world economic burden caused by COVID-19, the attenuation of vaccine protection efficacy, and the prevalence and immune escape of emerging variants of concern (VOCs), the third dose of booster immunization has been put on the agenda. Systems biology approaches can help us gain new perspectives on the characterization of immune responses and the identification of factors underlying vaccine-induced immune efficacy. We analyzed the antibody signature and transcriptional responses of participants vaccinated with COVID-19 inactivated vaccine and protein subunit vaccine as a third booster dose. The results from the antibody indicated that the third booster dose was effective, and that heterologous vaccination with the protein subunit vaccine as a booster dose induced stronger humoral immune responses than the homologous vaccination with inactivated vaccine, and might be more effective against VOCs. In transcriptomic analysis, protein subunit vaccine induced more differentially expressed genes that were significantly associated with many important innate immune pathways. Both the homologous and heterologous boosters could increase the effectiveness against COVID-19, and compared with the inactivated vaccine, the protein subunit vaccine, mediated a stronger humoral immune response and had a more significant correlation with the innate immune function module, which provided certain data support for the third booster immunization strategy.

Comorbidities and complications of COVID-19 associated with disease severity, progression, and mortality in China with centralized isolation and hospitalization: A systematic review and meta-analysis.

Background: Coronavirus disease 2019 (COVID-19) causes life-threatening with the high-fatality rates and spreads with high-infectious disease worldwide. We aimed to systematically review the comorbidities and complications of COVID-19 that are associated with various disease severity, progression, and mortality in China, to provide contemporary and reliable estimates in settings with centralized isolation and hospitalization. Methods: In this systematic review and meta-analysis, we searched four main English language databases, and four main Chinese language databases for observational studies published from inception to January 2022, to identify all the related comorbidities and complications of COVID-19, in the China region with centralized isolation and hospitalization, with disease severity, progression, and mortality. Literature search, data extraction, and quality assessment were independently conducted by two reviewers. We used the generalized linear mixed model to estimate pooled effect sizes for any comorbidities and complications, and subgroup in gender ratio was done to further address the potential heterogeneity. Results: Overall, 187 studies describing 77,013 patients, namely, 54 different comorbidities and 46 various complications of COVID-19, were identified who met our inclusion criteria. The most prevalent comorbidities were hypertension [20.37% 95% CI (15.28-26.63), 19.29% (16.17-22.85), 34.72% (31.48-38.10), and 43.94% (38.94-49.06)] and diabetes [7.84% (5.78-10.54), 8.59% (7.25-10.16), 17.99% (16.29-19.84), and 22.68% (19.93-25.69)] in mild, moderate, severe, and critical cases. The most prevalent complications were liver injury [10.00% (1.39-46.72), 23.04% (14.20-35.13), and 43.48% (39.88-47.15)] in mild, moderate, and severe cases, and acute respiratory distress syndrome [ARDS; 94.17% (20.78-99.90)] and respiratory failure [90.69% (28.08-99.59)] in critical cases. Renal insufficiency [odds ratio (OR) 17.43 (6.69-45.43)] in comorbidities and respiratory failure [OR 105.12 (49.48-223.33)] in complications were strongly associated in severe/critical than in mild/moderate cases. The highest estimated risk in intensive care unit (ICU) admission, progression, and mortality was an autoimmune disease, nervous system disease, and stroke in comorbidities, shock, and ARDS in complications. Conclusion: Comorbidities and complications in inpatients with COVID-19 were positively associated with increased risk in severe and critical cases, ICU admission, exacerbation, and death during centralized isolation and hospitalization. Prompt identification of comorbidities and complications in inpatients with COVID-19 can enhance the prevention of disease progression and death and improve the precision of risk predictions.

TCM2COVID: A resource of anti-COVID-19 traditional Chinese medicine with effects and mechanisms.

In China, traditional Chinese medicine (TCM) has been widely used for coronavirus infectious disease 2019 (COVID-19) prevention, treatment, and recovery and has played a part in the battle against the disease. A variety of TCM treatments have been recommended for different stages of COVID-19. But, to the best of our knowledge, a comprehensive database for storing and organizing anti-COVID TCM treatments is still lacking. Herein, we developed TCM2COVID, a manually curated resource of anti-COVID TCM formulas, natural products (NPs), and herbs. The current version of TCM2COVID (1) documents over 280 TCM formulas (including over 300 herbs) with detailed clinical evidence and therapeutic mechanism information; (2) records over 80 NPs with detailed potential therapeutic mechanisms; and (3) launches a useful web server for querying, analyzing and visualizing documented formulas similar to those supplied by the user (formula similarity analysis). In summary, TCM2COVD provides a user-friendly and practical platform for documenting, querying, and browsing anti-COVID TCM treatments, and will help in the development and elucidation of the mechanisms of action of new anti-COVID TCM therapies to support the fight against the COVID-19 epidemic. TCM2COVID is freely available at http://zhangy-lab.cn/tcm2covid/.

[Clinical observation of Xuanfei Baidu Decoction in treatment of severe coronavirus disease 2019 (COVID-19)].

The present study evaluated the effectiveness and safety of Xuanfei Baidu Decoction(XFBD) for severe cases with coronavirus disease 2019(COVID-19).Forty-one patients(diagnosed as severe or critical type) admitted to Hubei Provincial Hospital of Integrated Chinese and Western Medicine and Wuhan Hospital of Traditional Chinese Medicine from February 1 to March 1, 2020, were included.All patients were treated with XFBD based on conventional therapies.Clinical outcomes, length of hospital stay, and lung CT images of patients were observed.Laboratory indicators were compared between admission and the 14 th day of treatment.Traditional Chinese medicine(TCM) symptoms and signs on the 7 th and 14 th days of treatment were also compared with baseline.The differences in clinical characteristics and clinical outcomes between XFBD and western medicine or conventional therapies were analyzed with the published trials on severe COVID-19 cases during the same period as external controls.According to the results, among the 41 cases, 40 were cured and discharged, and 1 died; the median length of hospital stay was 22 days, and the improvement rate of lung CT was 87.2%(34/39).Compared with the conditions on admission, the levels of white blood cells(WBC), C-reactive protein(CRP), fibrinogen(FIB), and lactate dehydrogenase(LDH) were reduced(P<0.05, P<0.01), and levels of procalcitonin(PCT), prothrombin time(PT), creatine kinase(CK), alanine aminotransferase(AST), total bilirubin(TBiL), and other indicators showed a downward trend.Moreover, symptoms like fever, cough, chest tightness/shortness of breath, dyspnea, head and body pain, anorexia, and greasy tongue coating were significantly improved on the 7 th and 14 th days of treatment(P<0.05, P<0.01), and fatigue was improved on the 14 th day of treatment(P<0.01).The mortality, adverse reactions, and major events of the XFBD group were significantly lower than those of the western medicine and conventional treatment groups in the same period, and the usage of antibiotics, hormones, vasopressin, and invasive mechanical ventilation during treatment were generally less than other groups.In conclusion, XFBD has good efficacy and safety in the treatment of severe COVID-19 cases by improving inflammation and clinical symptoms, promoting the absorption of lung inflammation, and reducing mortality.

Transcriptome Analysis of Peripheral Blood Mononuclear Cells in SARS-CoV-2 Naïve and Recovered Individuals Vaccinated With Inactivated Vaccine.

The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the host's molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.

On-Site Viral Inactivation and RNA Preservation of Gargle and Saliva Samples Combined with Direct Analysis of SARS-CoV-2 RNA on Magnetic Beads

Samples of nasopharyngeal swabs (NPS) are commonly used for the detection of SARS-CoV-2 and diagnosis of COVID-19. As an alternative, self-collection of saliva and gargle samples minimizes transmission to healthcare workers and relieves the pressure of resources and healthcare personnel during the pandemic. This study aimed to develop an enhanced method enabling simultaneous viral inactivation and RNA preservation during on-site self-collection of saliva and gargle samples. Our method involves the addition of saliva or gargle samples to a newly formulated viral inactivation and RNA preservation (VIP) buffer, concentration of the viral RNA on magnetic beads, and detection of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction directly from the magnetic beads. This method has a limit of detection of 25 RNA copies per 200 μL of gargle or saliva sample and 9–111 times higher sensitivity than the viral RNA preparation kit recommended by the United States Centers for Disease Control and Prevention. The integrated method was successfully used to analyze more than 200 gargle and saliva samples, including the detection of SARS-CoV-2 in 123 gargle and saliva samples collected daily from two NPS-confirmed positive SARS-CoV-2 patients throughout the course of their infection and recovery. The VIP buffer is stable at room temperature for at least 6 months. SARS-CoV-2 RNA (65 copies/200 μL sample) is stable in the VIP buffer at room temperature for at least 3 weeks. The on-site inactivation of SARS-CoV-2 and preservation of the viral RNA enables self-collection of samples, reduces risks associated with SARS-CoV-2 transmission, and maintains the stability of the target analyte.

Design of a Digital Game Intervention to Promote Socio-Emotional Skills and Prosocial Behavior in Children

In emergency contexts such as the COVID-19 pandemic, mental health risk factors affect children and may affect behavioral and emotional problems including anxiety, self-blame, emotional disturbance, and stress. Preventive measures are crucial to address these health risks. Research highlights strength-based factors, such as socio-emotional skills and prosocial behaviors, as important for childhood development and socio-emotional wellbeing. Yet, the initial evidence base shows mixed effectiveness and insufficient behavior change theory application into socio-emotional and prosocial digital game interventions. Additionally, few interventions are designed with a clear process to convert theory into practical game solutions and very limited guidance on the digital game development process exists. This study describes the Intervention Mapping Protocol (IMP) and theory application in the design of a digital game intervention which aims to strengthen social-emotional skills development and promote prosocial behavior in 8–11-year-old children. The method systematically describes the steps of the IMP process in detail to guide future theory-based game design. The results explain the final digital game prototype that was co-designed with continuous input and insights provided by stakeholders and feedback from children. This paper contributes to our understanding of theory application in the design of digital game interventions focused on health and behavior change and provides much needed guidance on how theory and stakeholder input can be incorporated into a final game design.

CRISPR/Cas12a-mediated gold nanoparticle aggregation for colorimetric detection of SARS-CoV-2.

The trans-cleavage activity of the target-activated CRISPR/Cas12a liberated an RNA crosslinker from a molecular transducer, which facilitated the assembly of gold nanoparticles. Integration of the molecular transducer with isothermal amplification and CRISPR/Cas12a resulted in visual detection of the N gene and E gene of SARS-CoV-2 in 45 min.

CRISPR technology incorporating amplification strategies: molecular assays for nucleic acids, proteins, and small molecules.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) protein systems have transformed the field of genome editing and transcriptional modulation. Progress in CRISPR-Cas technology has also advanced molecular detection of diverse targets, ranging from nucleic acids to proteins. Incorporating CRISPR-Cas systems with various nucleic acid amplification strategies enables the generation of amplified detection signals, enrichment of low-abundance molecular targets, improvements in analytical specificity and sensitivity, and development of point-of-care (POC) diagnostic techniques. These systems take advantage of various Cas proteins for their particular features, including RNA-guided endonuclease activity, sequence-specific recognition, multiple turnover trans-cleavage activity of Cas12 and Cas13, and unwinding and nicking ability of Cas9. Integrating a CRISPR-Cas system after nucleic acid amplification improves detection specificity due to RNA-guided recognition of specific sequences of amplicons. Incorporating CRISPR-Cas before nucleic acid amplification enables enrichment of rare and low-abundance nucleic acid targets and depletion of unwanted abundant nucleic acids. Unwinding of dsDNA to ssDNA using CRISPR-Cas9 at a moderate temperature facilitates techniques for achieving isothermal exponential amplification of nucleic acids. A combination of CRISPR-Cas systems with functional nucleic acids (FNAs) and molecular translators enables the detection of non-nucleic acid targets, such as proteins, metal ions, and small molecules. Successful integrations of CRISPR technology with nucleic acid amplification techniques result in highly sensitive and rapid detection of SARS-CoV-2, the virus that causes the COVID-19 pandemic.

Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR Technology.

We have developed a single-tube assay for SARS-CoV-2 in patient samples. This assay combined advantages of reverse transcription (RT) loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated (Cas) enzyme Cas12a. Our assay is able to detect SARS-CoV-2 in a single tube within 40 min, requiring only a single temperature control (62 °C). The RT-LAMP reagents were added to the sample vial, while CRISPR Cas12a reagents were deposited onto the lid of the vial. After a half-hour RT-LAMP amplification, the tube was inverted and flicked to mix the detection reagents with the amplicon. The sequence-specific recognition of the amplicon by the CRISPR guide RNA and Cas12a enzyme improved specificity. Visible green fluorescence generated by the CRISPR Cas12a system was recorded using a smartphone camera. Analysis of 100 human respiratory swab samples for the N and/or E gene of SARS-CoV-2 produced 100% clinical specificity and no false positive. Analysis of 50 samples that were detected positive using reverse transcription quantitative polymerase chain reaction (RT-qPCR) resulted in an overall clinical sensitivity of 94%. Importantly, this included 20 samples that required 30-39 threshold cycles of RT-qPCR to achieve a positive detection. Integration of the exponential amplification ability of RT-LAMP and the sequence-specific processing by the CRISPR-Cas system into a molecular assay resulted in improvements in both analytical sensitivity and specificity. The single-tube assay is beneficial for future point-of-care applications.

Evidence for the medicinal value of Squama Manitis (pangolin scale): A systematic review.

BACKGROUND: Squama Manitis (pangolin scale) has been used in traditional Chinese medicine for thousands of years. However, its efficacy has not been systematically reviewed. This review aims to fill the gap. METHODS: We searched six electronic databases including PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure Database (CNKI), WanFang Database and SinoMed from inception to May 1, 2020. Search terms included "pangolin", "Squama Manitis", "Manis crassicaudata", "Manis javanica", "Malayan pangolins", "Manis pentadactyla", "Ling Li", "Chuan Shan Jia", "Shan Jia", "Pao Jia Zhu", "Jia Pian" and "Pao Shan Jia". The Cochrane Risk of Bias (RoB) assessment tool and Newcastle-Ottawa Scale (NOS) were used to evaluate the risk of bias of the included randomized controlled trials (RCTs) and case control studies (CCSs). RESULTS: After screening, 15 articles that met the inclusion criteria were finally included. There were 4 randomized controlled trials, 1 case control study, 3 case series and 7 case reports. A total of 15 different diseases were reported in these studies, thus the data could not be merged to generate powerful results. Two RCTs suggested that Squama Manitis combined with herbal decoction or antibiotics could bring additional benifit for treating postpartum hypogalactia and mesenteric lymphadenitis. However, this result was not reliable due to low methodological quality and irrational outcomes. The other two RCTs generated negative results. All the non-RCTs did not add any valuable evidence to the efficacy of Squama Manitis beacause of small samples, incomplete records, non-standardized outcome detection. In general, currently available evidence cannot support the clinical use of Squama Manitis. CONCLUSION: There is no reliable evidence that Squama Manitis has special medicinal value. The removal of Squama Manitis from Pharmacopoeia is rational.

Chinese medical drugs for coronavirus disease 2019: A systematic review and meta-analysis.

BACKGROUND: Integration of Chinese medical drugs (CMD) and western medicine (WM) has been widely used in the treatment of Coronavirus Disease 2019 (COVID-19). This systematic review aimed to evaluate the efficacy and safety of CMD for COVID-19. METHOD: A literature search was performed in six databases from injection to June 2020. Both randomized controlled trials (RCTs) and quasi-RCTs were considered as eligible. The quality of included RCTs were assessed by Cochrane Risk of Bias Tool, and Review Manager 5.3 software was used to do meta-analysis. RESULT: Eleven studies with 1259 patients were included in this study. CMD included herbal decoction and Chinese patent medicine. The methodological quality was evaluated as generally unclear. The results of meta-analysis showed that the integration of CMD and WM had better efficacy than WM in number of patients turned to severe and critical type (RR = 0.47, 95% CI=[0.32, 0.69], P < 0.0001), length of hospital stay (MD= -7.95, 95% CI=[-14.66, -1.24], P = 0.02), defervescence time (MD= -1.20, 95% CI=[-2.03, -0.38], P = 0.004), cough resolution rate (RR = 1.37, 95% CI=[1.15, 1.64], P = 0.0004), fatigue resolution rate (RR = 1.37, 95% CI=[1.02, 1.83], P = 0.04), and tachypnea resolution rate (RR = 2.20, 95% CI=[1.11, 4.39], P = 0.02). As for safety, there was no significant difference between two groups. CONCLUSION: CMD may bring potential benefit to patients suffered from COVID-19. However, the quality of included trials is not good enough. High quality study with core outcome set are still required.

Tongue features of patients with coronavirus disease 2019: a retrospective cross-sectional study.

BACKGROUND: Traditional Chinese medicine (TCM) has been widely used in the treatment of coronavirus disease 2019 (COVID-19). Tongue features should be referred for diagnosis and treatment of diseases in TCM. Therefore, it is necessary to analyze the tongue features of the patients suffered from COVID-19. METHODS: COVID-19 Symptom Database (established by Evidence-based Medicine Center of Tianjin University of TCM) was searched for eligible tongue pictures. The tongue pictures were assessed by TCM experts to extract the data of tongue color, coating color, tongue body shape and coating proper feature. The relationship between tongue features and patient's condition was analyzed. RESULTS: Patients diagnosed as mild and moderate COVID-19 commonly had light red tongue and white coating. Severe patients had purple tongue and yellow coating. The proportion of critical patients with tender tongue increased to 75%. Greasy coating was a significant characteristic of patients with COVID-19. The proportions of greasy coating were 53.33%, 73.30%, 83.67 and 87.5% in disease category of mild, moderate, severe and critical. In addition, the thick coating proportion increased from mild (24.89%) to critical (50.00%). CONCLUSIONS: Tongue features have certain relationship with the category of COVID-19. Tongue features can serve as potential indicators for the evaluation of patient's condition and prognosis. Further studies are needed to enhance the quantification of tongue features and develop standards.