Pilot genome-wide association study of antibody response to inactivated SARS-CoV-2 vaccines.

Vaccines are a key weapon against the COVID-19 pandemic caused by SARS-CoV-2. However, there are inter-individual differences in immune response to SARS-CoV-2 vaccines and genetic contributions to these differences have barely been investigated. Here, we performed genome-wide association study (GWAS) of antibody levels in 168 inactivated SARS-CoV-2 vaccine recipients. A total of 177 SNPs, corresponding to 41 independent loci, were identified to be associated with IgG, total antibodies or neutral antibodies. Specifically, the rs4543780, the intronic variant of FAM89A gene, was associated with total antibodies level and was annotated as a potential regulatory variant affecting gene expression of FAM89A, a biomarker differentiating bacterial from viral infections in febrile children. These findings might advance our knowledge of the molecular mechanisms driving immunity to SARS-CoV-2 vaccine.

Targeted screening of genetic associations with COVID-19 susceptibility and severity.

The COVID-19 pandemic has resulted in great morbidity and mortality worldwide and human genetic factors have been implicated in the susceptibility and severity of COVID-19. However, few replicate researches have been performed, and studies on associated genes mainly focused on genic regions while regulatory regions were a lack of in-depth dissection. Here, based on previously reported associated variants and genes, we designed a capture panel covering 1,238 candidate variants and 25 regulatory regions of 19 candidate genes and targeted-sequenced 96 mild and 145 severe COVID-19 patients. Genetic association analysis was conducted between mild and severe COVID-19 patients, between all COVID-19 patients and general population, or between severe COVID-19 patients and general population. A total of 49 variants were confirmed to be associated with susceptibility or severity of COVID-19 (p < 0.05), corresponding to 18 independent loci. Specifically, rs1799964 in the promoter of inflammation-related gene TNF, rs9975538 in the intron of interferon receptor gene IFNAR2, rs429358 in the exon of APOE, rs1886814 in the intron of FOXP4-AS1 and a list of variants in the widely reported 3p21.31 and ABO gene were confirmed. It is worth noting that, for the confirmed variants, the phenotypes of the cases and controls were highly consistent between our study and previous reports, and the confirmed variants identified between mild and severe patients were quite different from those identified between patients and general population, suggesting the genetic basis of susceptibility and severity of SARS-CoV-2 infection might be quite different. Moreover, we newly identified 67 significant associated variants in the 12 regulatory regions of 11 candidate genes (p < 0.05). Further annotation by RegulomeDB database and GTEx eQTL data filtered out two variants (rs11246060 and rs28655829) in the enhancer of broad-spectrum antiviral gene IFITM3 that might affect disease severity by regulating the gene expression. Collectively, we confirmed a list of previously reported variants and identified novel regulatory variants associated with susceptibility and severity of COVID-19, which might provide biological and clinical insights into COVID-19 pathogenesis and treatment.

Pilot genome-wide association study of antibody response to inactivated SARS-CoV-2 vaccines

Vaccines are a key weapon against the COVID-19 pandemic caused by SARS-CoV-2. However, there are inter-individual differences in immune response to SARS-CoV-2 vaccines and genetic contributions to these differences have barely been investigated. Here, we performed genome-wide association study (GWAS) of antibody levels in 168 inactivated SARS-CoV-2 vaccine recipients. A total of 177 SNPs, corresponding to 41 independent loci, were identified to be associated with IgG, total antibodies or neutral antibodies. Specifically, the rs4543780, the intronic variant of FAM89A gene, was associated with total antibodies level and was annotated as a potential regulatory variant affecting gene expression of FAM89A, a biomarker differentiating bacterial from viral infections in febrile children. These findings might advance our knowledge of the molecular mechanisms driving immunity to SARS-CoV-2 vaccine.

Knowledge domain and emerging trends in Takotsubo cardiomyopathy: a scientometric review based on CiteSpace analysis.

Takotsubo cardiomyopathy (TTC) is often acute with a high mortality rate and is subject to relapse. Meanwhile, its complex pathogenesis has attracted increasing attention. To learn more about TTC, CiteSpace V.5.7 R5W was used in this study to analyze the research status, hot spots, and trends in TTC before 2020. The keywords, co-citation references, as well as country and institution distribution were explored. A total of 2,349 papers were reviewed. The United States, Italy, and Germany were the main countries studying TTC and had good cooperation relationships. The Mayo Clinic topped the institution list, but the rate of inter-institutional cooperation was not high. Research hotspots include disease features, auxiliary diagnostic methods, epidemiology, and pathophysiological mechanisms, and the latest ones are complications related to prognosis, such as cardiovascular abnormalities caused by myocardial infarction and normal or non-obstructive coronary arteries (MINOCA), atrial fibrillation, stroke, cancer, and COVID-19. In conclusion, the research of TTC is in a hot development period. Our research will help clinicians and researchers to better understand TTC and its research status by providing a foundation for research objectives. In doing this, our research will help to provide better scientific management, diagnosis, and treatment for patients with TTC, which will in turn improve the prognosis of this condition.

dbGSRV: A manually curated database of genetic susceptibility to respiratory virus.

Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyperlinks to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a convenient resource for researchers to browse and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights in our understanding and treatment of respiratory virus infection. Database URL: http://www.ehbio.com/dbGSRV/front/.

In vivo structure and dynamics of the SARS-CoV-2 RNA genome.

The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5'-UTR and 3'-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

[Analysis of traditional Chinese medicine from patent information sharing platform of coronavirus disease 2019 (COVID-19)].

Coronavirus disease 2019(COVID-19) is a newly emerged and highly contagious respiratory disease. Traditional Chinese medicine(TCM) has both systematism theory knowledge and clinical practical value in the prevention and treatment of COVID-19. Therefore, it was particularly important to examine the effect of TCM in the prevention and treatment of COVID-19. The patents of TCM might reflect the latest progression of scientific research. We aimed to provide reference for the prevention and treatment of COVID-19 by extracting and analyzing the TCM patents from the Patent Information Sharing Platform of COVID-19. The antiviral TCM patents were screened and exported from the Patent Information Sharing Platform. VOSviewer 1.6.14 was used to visualize and analyze the network of TCM in these patents. There were total 292 TCM patents, including 52 patents for etiological treatment and 240 patents for symptomatic treatment. Thirty-two provinces and 1 076 inventors were involved, mainly from Beijing, Guangdong and Jiangsu. Overall, there were 356 TCMs, 71 single prescriptions, and 221 compound prescriptions. The patents for treatment of coronavirus mainly focused on the treatment of coronavirus, while the patents for symptomatic treatment mainly focuses on the improvement of respiratory symptoms, such as fever and cough. There were 14 highly frequently used TCMs, including Glycyrrhizae Radix et Rhizoma, Scutellariae Radix, Lonicerae Japonicae Flos, Forsythiae Fructus, Isatidis Radix, Astragali Radix, Menthae Haplocalycis Herba, Gypsum Fibrosum, Houttuyniae Herba, Isatidis Folium, Rhei Radix et Rhizoma, Gardeniae Fructus, Platycodonis Radix, Armeniacae Semen Amarum. The analyzed results of the TCM patents from the patent information sharing platform of COVID-19 were consistent with the Guideline of Diagnosis and Treatment of COVID-19(7th edition), and the combination of TCM in each cluster may also provide future directions for drug compatibility.