Predicting unseen antibodies’ neutralizability via adaptive graph neural networks

The effects of novel antibodies are hard to predict owing to the complex interactions between antibodies and antigens. Zhang and colleagues use a graph-based method to learn a dynamic representation that allows for predictions of neutralization activity and demonstrate the method by recommending probable antibodies for human immunodeficiency virus, severe acute respiratory syndrome coronavirus 2, influenza and dengue. Most natural and synthetic antibodies are 'unseen'. That is, the demonstration of their neutralization effects with any antigen requires laborious and costly wet-lab experiments. The existing methods that learn antibody representations from known antibody-antigen interactions are unsuitable for unseen antibodies owing to the absence of interaction instances. The DeepAAI method proposed herein learns unseen antibody representations by constructing two adaptive relation graphs among antibodies and antigens and applying Laplacian smoothing between unseen and seen antibodies' representations. Rather than using static protein descriptors, DeepAAI learns representations and relation graphs 'dynamically', optimized towards the downstream tasks of neutralization prediction and 50% inhibition concentration estimation. The performance of DeepAAI is demonstrated on human immunodeficiency virus, severe acute respiratory syndrome coronavirus 2, influenza and dengue. Moreover, the relation graphs have rich interpretability. The antibody relation graph implies similarity in antibody neutralization reactions, and the antigen relation graph indicates the relation among a virus's different variants. We accordingly recommend probable broad-spectrum antibodies against new variants of these viruses.

Efficacy and safety of Reyanning mixture combined with conventional Western medicine for treating COVID-19: A protocol for systematic review and meta-analysis.

BACKGROUND: Since its first report in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly emerged as a pandemic affecting nearly all countries worldwide. So far, there is no specific anti-coronavirus therapy approved for the treatment of COVID-19. In China, some traditional Chinese medicines (TCM) have been successfully applied to the treatment of SARS-CoV-2 and have achieved good clinical results, including the Reyanning mixture, but there is no systematic review about it. This study will systematically evaluate its efficacy and safety in the treatment of COVID-19. METHODS: The following electronic bibliographic databases will be searched to identify relevant studies: PubMed, MEDLINE, EMBASE, CNKI, CBM, and Wanfang databases. We will use the Cochrane Handbook for Systematic Reviews of Interventions to assess the risk of bias. The protocol will be conducted according to the approach and Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). Manager 5.3 software and STATA 16.0 software were used to perform the meta-analysis. RESULTS: The systematic review and meta-analysis aims to review and pool current clinical outcomes of Reyanning mixture for the treatment of COVID-19. CONCLUSION: The conclusion of this review will provide evidence to judge whether Reyanning mixture combined with Conventional Western Medicine is an effective and safe intervention for COVID-19. INPLASY REGISTRATION NUMBER: INPLASY2020120044.

Traditional Chinese medicine Lianhua Qingwen for treating COVID-19: A protocol for a meta-analysis and systematic review of randomized controlled trials.

BACKGROUND: Since the outbreak of coronavirus disease 2019 (COVID-19) in 2019, it has swept the world with rapid development and is one of the infectious diseases that seriously threatened global public health. Because of the complex pathogenesis, high infectivity, and high fatality rate of COVID-19, there are no effective treatments for this epidemic at present. Traditional Chinese Medicine (TCM) has a long clinical history in the prevention and treatment of such acute infectious diseases. The therapeutic effect of Lianhua Qingwen (LHQW) on this new coronary pneumonia has attracted the attention of all walks of life, and relevant research reports continue to appear. Here, we intend to conduct a systematic review and meta-analysis of randomized controlled trials (RCT) to evaluate the efficacy of LHQW in COVID-19 patients. METHODS: We will search each database from the built-in until Dec 2020. The English literature mainly search the Cochrane Library, EMBASE, PubMed, and Web of Science, while the Chinese literature come from CNKI, VIP, Chinese Biomedical Database (CBM), Chinese Science Citation Database (CSCD), and Wan Fang database. Simultaneously, we will retrieve clinical registration tests. This study only screens the RCT of LHQW against COVID-19 and evaluates its efficacy and safety. We will use the Cochrane Handbook to systematically review interventions to assess the risk of bias. The protocol will be reported according to the approach and preferred report items for systematic review and meta-analysis protocols (PRISMA - P). Finally, RevMan software version 5.3 will be used for meta-analysis. RESULTS: The systematic review and meta-analysis aim to review and pool current clinical outcomes of LHQW for treating COVID-19. CONCLUSION: This study will provide further evidence for the efficacy and safety of LHQW in the treatment of COVID-19. INPLASY REGISTRATION NUMBER: INPLASY2020120043.

The therapeutic efficacy of Xuanfei Baidu Formula combined with conventional drug in the treatment of coronavirus disease 2019: A protocol for systematic review and meta-analysis.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a new acute espiratory infectious disease that has been in a public health emergency of international concern. In China, the combination of Xuanfei Baidu Formula (XBF) and conventional drug is used in the clinical treatment of patients with new coronary pneumonia, However, there is no comprehensive and systematic evidence on the effectiveness and safety of XBF. MATERIALS AND METHODS: We search for research in PubMed, China National Knowledge Infrastructure, Wan-fang Database, China Biomedical Database, and Chinese Science Citation Database. For "Xuanfei Baidu Formula" and "COVID-19," we screened suitable articles without language restrictions on keywords, Review Manager 5.3 and STATA 14.2 software was used for the data analysis. RESULTS: The systematic review and meta-analysis will evaluate the efficacy and safety of XBF combined with conventional drug in the treatment of COVID-19. CONCLUSION: We will provide evidence of XBF for the treatment on COVID-19 patients. INPLASY REGISTRATION NUMBER: INPLASY2020120011.

The therapeutic efficacy of Chinese patent medicine combined with routine western medicine in the treatment of coronavirus disease 2019 (COVID-19): A protocol for systematic review and meta-analysis.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a potentially fatal disease. clinical practice shows that Chinese Patent Medicine (CPM) has played an important role in the outbreak, Among them, Jinhua Qinggan granules, Lianhua Qingwen capsule, and Xuebiqing injection have an effect in treating COVID-19 patients, but it has not been systematically evaluated for efficacy and safety. We provide a protocol for systematic review and meta-analysis. MATERIALS AND METHODS: Retrieved the database, including the China National Knowledge Infrastructure, Chinese Biomedical Database, Wan Fang database, and PubMed. The quality of each study is assessed according to the criteria of the Cochrane Handbook for Systematic Reviews of Interventions. Using Manager 5.3 software and STATA 16.0 software were used to perform the meta-analysis. RESULTS: The systematic review and meta-analysis aims to review and pool current clinical outcomes of CPM combined with routine western medicine (RWM) for the treatment of COVID-19. CONCLUSION: This study will provide evidence of CPM (including Jinhua Qinggan granule, Lianhua Qingwen capsule, and Xuebiqing injection) for the treatment on COVID-19 patients.INPLASY Registration number: INPLASY202050050.

Dynamic changes of peripheral blood T lymphocytes in COVID-19 patients

Objective: To analyze the dynamic changes of T lymphocytes in patients with COVID-19. Methods: Blood samples were collected from 40 COVID-19 cases and 40 healthy controls in Beihai People's Hospital from January to February, 2020. The counts of CD4 +T and CD8 +T lymphocytes were detected by flow cytometry. Moreover, the T lymphocyte counts in 24 convalescent patients with two consecutive negative nucleic acid test results were also detected. Results: The leukocytes and lymphocytes in the patients with acute COVID-19 were significantly lower than those in the healthy controls [(4.71±1.54)×10 9cell/L vs (6.26±1.44)×10 9cell/L, (1.13±0.41)×10 9cell/L vs (1.51±0.39)×10 9cell/L;both P<0.05]. The counts of CD4 +T and CD8 +T lymphocytes in the patients with acute COVID-19 were significantly lower than those in the healthy controls [(447.15±144.42) cell/μl vs (592.83±146.76) cell/μl, (309.35±173.05) cell/μl vs (397.20±136.94) cell/μl;both P<0.05], while no significant difference was observed in the CD4 +/CD8 +T cell ratio (P>0.05). In the 24 convalescent COVID-19 patients, the counts of CD4 +T and CD8 +T lymphocytes were higher during convalescence than in the acute phase [(598.08±138.71) cell/μl vs (420.67±147.38) cell/μl, (439.08±166.94) cell/μl vs (296.67±151.06) cell/μl;both P<0.05], but there was no significant difference in the T lymphocyte counts between the convalescent patients and the healthy controls (P>0.05). Conclusions: A transient immune deficiency occurred in patients with acute COVID-19, but the impaired immune function could restore to normal level during recovery.