Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinN (4)

ProteinS (4)

ProteinE (1)

ORF8 (1)

ORF1ab (1)


SARS-CoV-2 Proteins
    displaying 1 - 10 records in total 124
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    Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 MESHD patients

    Authors: Zhao Cai; Xiangke Duan; Han Zhang; Shuhong Han; Kaiwei Yu; Yingdan Zhang; Yang Liu; Liang Yang

    doi:10.1101/2021.04.09.439260 Date: 2021-04-11 Source: bioRxiv

    COVID-19 pandemic MESHD has caused millions of death MESHD globally and caused huge impact on the health of infected MESHD patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease MESHD and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 MESHD and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 MESHD patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial Pseudomonas aeruginosa isolated from two critical COVID-19 MESHD patients in this study. We sequenced and compared the genomes and transcriptomes of Pseudomonas aeruginosa isolates longitudinally and parallelly for its evolutionary traits. Pseudomonas aeruginosa overexpressed alginate and attenuated Type VI secretion system MESHD (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity MESHD test indicated that Pseudomonas aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. Pseudomonas aeruginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 MESHD patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate Pseudomonas aeruginosa coinfection MESHD in COVID-19 MESHD patient.

    Chagas disease MESHD and SARS-CoV-2 coinfection MESHD does not lead to worse in-hospital outcomes: results from the Brazilian COVID-19 MESHD Registry

    Authors: Israel Molina Romero; Milena Soriano Marcolino; Magda Carvalho Pires; Lucas Emanuel Ferreira Ramos; Rafael Tavares Silva; Milton Henriques Guimaraes Junior; Isaias Jose Ramos de Oliveira; Rafael Lima Rodrigues de Carvalho; Aline Gabrielle Souza Nunes; Ana Lara Rodrigues Monteiro de Barros; Ana Luiza Bahia Alves Scotton; Angelica Aparecida Coelho Madureira; Barbara Lopes Farace; Cintia Alcantara de Carvalho; Fernanda d'Athayde Rodrigues; Fernando Anschau; Fernando Antonio Botoni; Guilherme Fagundes Nascimento; Helena Duani; Henrique Cerqueira Guimaraes; Joice Coutinho de Alvarenga; Leila Beltrami Moreira; Liege Barella Zandona; Luana Fonseca de Almeida; Luana Martins Oliveira; Luciane Kopittke; Luis Cesar de Castro; Luisa Elem Almeida Santos; Maderson Alvares de Souza Cabral; Maria Angelica Pires Ferreira; Natalia da Cunha Severino Sampaio; Neimy Ramos de Oliveira; Saionara Cristina Francisco; Sofia Jarjour Tavares Starling Lopes; Tatiani Oliveira Fereguetti; Veridiana Baldon dos Santos; Victor Eliel Bastos de Carvalho; Yuri Carlotto Ramires; Antonio Luiz Pinho Ribeiro; Freddy Antonio Brito Moscoso; Rogerio Moura; CarIsi Anne Polanczyk; Maria do Carmo Pereira Nunes

    doi:10.1101/2021.03.22.21254078 Date: 2021-03-26 Source: medRxiv

    Objective: Chagas disease MESHD ( CD MESHD) continues to be a major public health burden in Latina America, where co-infection MESHD with SARS-CoV-2 can occur. However, information on the interplay between COVID-19 MESHD and Chagas disease MESHD is lacking. Our aim was to assess clinical characteristics and in-hospital outcomes of patients with CD MESHD and COVID-19 MESHD, and to compare it to non- CD MESHD patients. Methods: Patients with COVID-19 MESHD diagnosis were selected from the Brazilian COVID-19 MESHD Registry, a prospective multicenter cohort, from March to September, 2020. CD MESHD diagnosis was based on hospital record at the time of admission. Study data were collected by trained hospital staff using Research Electronic Data Capture (REDCap) tools. Genetic matching for sex, age, hypertension MESHD, DM MESHD and hospital was performed in a 4:1 ratio. Results: Of the 7,018 patients who had confirmed infection with SARS-CoV-2 in the registry, 31 patients with CD MESHD and 124 matched controls were included. Overall, the median age was 72 (64.-80) years-old and 44.5% were male. At baseline, heart failure MESHD (25.8% vs. 9.7%) and atrial fibrillation MESHD (29.0% vs. 5.6%) were more frequent in CD MESHD patients than in the controls (p<0.05 for both). C-reactive protein HGNC levels were lower in CD MESHD patients compared with the controls (55.5 [35.7, 85.0] vs. 94.3 [50.7, 167.5] mg/dL). Seventy-two (46.5%) patients required admission to the intensive care unit. In-hospital management, outcomes and complications were similar between the groups. Conclusions: In this large Brazilian COVID-19 MESHD Registry, CD MESHD patients had a higher prevalence of atrial fibrillation MESHD and chronic heart failure MESHD compared with non- CD MESHD controls, with no differences in-hospital outcomes. The lower C-reactive protein HGNC levels in CD MESHD patients require further investigation.

    The effects of physical distancing and lockdown to restrain SARS-CoV-2 outbreak in the Italian Municipality of Cogne

    Authors: Gianpiero Gervino; Fabio Truc

    doi:10.1101/2021.03.19.21253962 Date: 2021-03-20 Source: medRxiv

    The outbreak of SARS-CoV-2 started in Wuhan, China, and is now a pandemic. An understanding of the prevalence and contagiousness of the disease, and of whether the strategies used to contain it to date have been successful, is important for understanding future containment strategies. One strategy for controlling the spread of SARS-CoV-2 is to adopt strong social distancing policies. The Municipality of Cogne (I), adopted strict lockdown rules from March 4, 2020 up to May 18, 2020. This first wave of the pandemic impressed by the extremely low impact of the SARS-CoV-2 on the locals, compared to the number accused on all the Italian territory. Starting from October 2020 up to the end of December, when the second wave hit Italy and Cogne territory, heavier effects were observed. In order to cast light on the effectiveness of the adopted strategy 74,5% of the local population underwent to a blood screening to detect IgM and IgG antibodies and after six months all the people tested positive were again investigated to establish the longitudinal changes in antibodies level. Moreover, within the context of this survey a rare and interesting case of secondary infection MESHD has been identified and here presented.

    Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection MESHD and tissue specific host responses

    Authors: Rong Liu; Pei Wu; Pauline Ogrodzki; Sally Mahmoud; Ke Liang; Pengjuan Liu; Stephen S. Francis; Hanif Khalak; Denghui Liu; Junhua Li; Tao Ma; Fang Chen; Weibin Liu; Xinyu Huang; Wenjun He; Zhaorong Yuan; Nan Qiao; Xin Meng; Budoor Alqarni; Javier Quilez; Vinay Kusuma; Long Lin; Xin Jin; Xavier Anton; Ashish Koshy; Huanming Yang; Xun Xu; Jian Wang; Peng Xiao; Nawal Ahmed Mohamed Al Kaabi; Mohammed Saifuddin Fasihuddin; Francis Amirtharaj Selvaraj; Stefan Weber; Farida Ismail Al Hosani; Siyang Liu; Walid Abbas Zaher

    doi:10.1101/2021.03.09.21252822 Date: 2021-03-12 Source: medRxiv

    Background: The United Arab Emirates is a major business hub with substantial amount of international travel. Like many other countries, it was greatly affected by the COVID-19 pandemic MESHD since late January 2020, with recurring waves of infection. This study aimed at combining genomic and epidemiological data to unravel the source of SARS-CoV-2 introduction, transmission and evolution in the country. Methods: We performed meta-transcriptomic sequencing of 1,067 nasopharyngeal swab samples collected from qRT-PCR positive COVID-19 MESHD patients in Abu Dhabi, UAE, between May 9th and June 29th 2020. We investigated the genetic diversity and transmission dynamics of the viral population and analyzed the infection and transmission potential of novel genomic clusters. Within-host SARS-CoV-2 genetic variation was analyzed to determine the occurrence and prevalence of multiple infections. Finally, we evaluated innate host responses during the prolonged period of local infection. Results: All globally known SARS-CoV-2 clades were identified within the UAE sequenced strains, with a higher occurrence of European and East Asian clades. We defined 5 subclades based on 11 unique genetic variants within the UAE strains, which were associated with no significantly different viral loads. Multiple infection of different SARS-CoV-2 strains was observed for at least 5% of the patients. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously observed in the bronchoalveolar lavage fluid samples. This observation is accompanied with an upregulation of APOBEC4 HGNC, an under-studied putative cytidine-uridine editing enzyme in the infected nasopharynx. Conclusions: The genomic epidemiological and molecular biological knowledge obtained in the study provides new insights for the SARS-CoV-2 evolution and transmission. We highlight the importance of sustained surveillance of the virus mutation using genomic sequencing as a public health strategy. Keywords: SARS-CoV-2, meta-transcriptomic sequencing, novel mutations and subclades, co-infection MESHD, cyosine depletion, host RNA editing

    Characterizing the COVID-19 MESHD illness experience to inform the study of post-acute sequalae and recovery: a qualitative study

    Authors: Edda I. Santiago-Rodriguez; Andres Maiorana; Michael J Peluso; Rebecca Hoh; Viva Tai; Emily A. Fehrman; Yanel Hernandez; Leonel Torres; Matthew A. Spinelli; Monica Gandhi; J. Daniel Kelly; Jeffrey N. Martin; Timothy J. Henrich; Steven G Deeks; John A Sauceda

    doi:10.1101/2021.03.10.21253330 Date: 2021-03-12 Source: medRxiv

    We aimed to characterize the variability in the illness experience and recovery process from COVID-19 MESHD. We conducted in-depth individual interviews with participants enrolled in the Long-term Immunological Impact of Novel Coronavirus (LIINC) cohort study in San Francisco, California from June through October of 2020. Participants were adults who had a previously confirmed positive SARV-CoV-2 nucleic acid amplification test result, had recovered or were recovering from acute infection MESHD, and underwent serial evaluations at our clinical research center. We purposefully sampled 24 English- and Spanish-speaking adults with asymptomatic, mild and severe symptomatic infection, including those who were hospitalized, and those with HIV co-infection MESHD. Half of our sample (50.0%) identified as Latinx/Hispanic and most of the participants were men (62.5%). We used thematic analysis to characterize the illness experience, recovery process, and mental health impact of experiencing COVID-19 MESHD and present clinical data for each participant. Emergent themes were: (1) across symptom profiles and severity, experiencing COVID-19 MESHD was associated with psychological distress MESHD, (2) among participants with symptomatic infection, the illness experience was characterized by uncertainty in terms of managing symptoms and recovery, and (3) despite wide-ranging illness experiences, participants shared many common characteristics, including health information-seeking behavior facilitated by access to medical care, and uncertainty regarding the course of their illness and recovery. COVID-19 MESHD was associated with elevated levels of psychological distress, regardless of symptoms.

    Co-infection of SARS-CoV-2 MESHD with influenza among COVID-19 MESHD cases: A-meta analysis

    Authors: Reza Alizadeh-Navaei; Monireh Golpur; Reza Valadan; Masoumeh Rezaei; Moammadreza Haghshenas; Tahoora Mousavi

    doi:10.21203/ Date: 2021-03-07 Source: ResearchSquare

    Background The severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), that causes coronavirus disease 2019 MESHD ( COVID-19 MESHD) is a public health problem and may have co-infection MESHD with other pathogens such as influenza virus.Objective This study aims to assess the co-infection of SARS-CoV-2 MESHD with influenza among COVID-19 MESHD cases.Material and methods The all relevant studies were collected from international databases. For improving the quality of the present literature, the all studies were evaluated by two reviewers in order to confirm all of the studies have inclusion criteria. Finally, all articles with sufficient quality scores were included in meta-analysis. Assessment of heterogeneity among the studies of primary studies was performed using the statistic chi‐squared test (Cochran's Q) and I2 index. In this results, random or fixed effect model were used for determination of heterogeneity test. All statistical analyses were performed using Comprehensive Meta-Analysis (CMA), V.2 software.Results This meta- analysis included 9 primary studies investigating the co-infection of SARS-CoV-2 MESHD with influenza among COVID-19 MESHD cases. Pooled prevalence (95% confidence interval) of co-infection MESHD is shown that the prevalence of influenza A is higher than influenza B. 2.3(0.5-9.3) vs 0.1 (0.4-3.3). Using the fixed effect model the frequency of fever MESHD was (80.6% [95% CI 76.1–84.40, p < 0.153]) and it is shown that fever MESHD is the most prevalent symptom in patients.Conclusion Patients admitted to hospital with COVID-19 MESHD also infected with influenza virus. Thus, the current research provides a better understanding about the control and treatment of co-infection MESHD with SARS-CoV-2 and the influenza virus.

    Profile of SARS-CoV-2-specific CD4 T cell response: Relationship with disease severity and impact of HIV-1 and active Mycobacterium tuberculosis co-infection MESHD

    Authors: Catherine Riou; Elsa du Bruyn; Cari Stek; Remy Daroowala; Rene T Goliath; Fatima Abrahams; Qonita Said-Hartley; Brian W Allowed; Marvin Hsiao; Katalin A Wilkinson; Cecilia S Lindestam Arlehamn; Alessandro Sette; Sean Wasserman; Robert J Wilkinson; - the HIATUS consortium

    doi:10.1101/2021.02.16.21251838 Date: 2021-02-20 Source: medRxiv

    T cells are involved in control of COVID-19 MESHD, but limited knowledge is available on the relationship between antigen-specific T cell response and disease severity. Here, we assessed the magnitude, function and phenotype of SARS-CoV-2-specific CD4 T cells in 95 hospitalized COVID-19 MESHD patients (38 of them being HIV-1 and/or tuberculosis (TB) co-infected MESHD) and 38 non- COVID-19 MESHD patients, using flow cytometry. We showed that SARS-CoV-2-specific CD4 T cell attributes, rather than magnitude, associates with disease severity, with severe disease being characterized by poor polyfunctional potential, reduced proliferation capacity and enhanced HLA-DR expression. Moreover, HIV-1 and TB co-infection MESHD skewed the SARS-CoV-2 T cell response. HIV-1 mediated CD4 T cell depletion associated with suboptimal T cell and humoral immune responses to SARS-CoV-2; and a decrease in the polyfunctional capacity of SARS-CoV-2-specific CD4 T cells was observed in COVID-19 MESHD patients with active TB. Our results also revealed that COVID-19 MESHD patients displayed reduced frequency of Mtb-specific CD4 T cells, with possible implications for TB MESHD disease progression. There results corroborate the important role of SARS-CoV-2-specific T cells in COVID-19 MESHD pathogenesis and support the concept of altered T cell functions in patients with severe disease.

    Antiviral activity of influenza A virus defective interfering particles against SARS-CoV-2 replication in vitro through stimulation of innate immunity

    Authors: Ulfert Rand; Sascha Young Kupke; Hanna Shkarlet; Marc Dominique Hein; Tatjana Hirsch; Pavel Marichal-Gallardo; Luka Cicin-Sain; Udo Reichl; Dunja Bruder

    doi:10.1101/2021.02.19.431972 Date: 2021-02-19 Source: bioRxiv

    SARS-CoV-2 causing COVID-19 MESHD emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 MESHD only show limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections MESHD. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19 MESHD, we conducted in vitro co-infection MESHD experiments with produced, cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. These results suggest an unspecific stimulation of the innate immunity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19 MESHD, and potentially also for suppressing the replication of new variants of SARS-CoV-2.

    Bacterial and Fungal Co-infections MESHD with SARS-CoV-2 in Solid Organ Recipients, A Retrospective Study

    Authors: Mojtaba Shafiekhani; Zahra Shekari; Arash Boorboor; Zahra Zare; Sara Arabsheybani; Nazanin Azadeh

    doi:10.21203/ Date: 2021-02-15 Source: ResearchSquare

    Background SARS-CoV-2, a novel corona virus, has caused clusters of fatal pneumonia MESHD worldwide. Immune compromised patients are among the high risk groups with poor prognosis of the disease. The presence of bacterial or fungal co-infections MESHD with SARS-CoV-2 is associated with increased mortality.Methods The electronic data of the liver and kidney recipients, hospitalized in COVID-19 MESHD intensive care unit in an 8-month period in 2020 were retrospectively assessed. The documented bacterial or fungal infections MESHD alongside with outcome and risk factors were recorded and analyzed by binary logistic regression model and multivariate analyses.Results Sixty-Six liver and kidney recipients were included this study.  Twenty one percent of the patients had at least one episode of co-infection MESHD during their COVID-19 MESHD course. Bacterial and fungal co-infections MESHD contributed to a significantly higher mortality. Urine and sputum were the most common sites of pathogen isolation (45.45 % and 36.36%; respectively). The majority of infections were caused by vancomycin- resistant Enterococci (30%). Escherichia coli stood in the next position with 23.3%. Prior hospitalization and high does corticosteroid use were associated with co-infections MESHD (p=0<0.001 and p=0.02; respectively.)Conclusions Bacterial and fungal co-infections MESHD with COVID-19 MESHD are more prevalent on solid organ recipients compared to the general population. Prior hospitalizations and use of broad-spectrum antimicrobial agents leads to emergence of multi-drug resistant pathogens in this susceptible patient population. Early detection and treatment of co-infections MESHD as well as antibiotic stewardship is recommended in solid organ recipients.

    Inadequate Use of Antibiotics in the Covid-19 MESHD Era: Effectiveness of Antibiotic Therapy

    Authors: Alejandro David Bendala Estrada; Jorge Calderón Calderón Parra; Eduardo Fernández Carracedo; Antonio Muiño Míguez; Antonio Ramos Martínez; Elena Muñez Rubio; Manuel Rubio-Rivas; Paloma Agudo de Blas; Francisco Arnalich Fernández; Vicente Estrada Perez; María Luisa Taboada Martínez; Anxela Crestelo Vieitez; Paula Maria Pesqueira Fontan; Marta Bustamante Vega; Santiago J. Freire; Isabel Oriol-Bermúdez; Arturo Artero Mora; Julián Olalla Sierra; María Areses Manrique; Francisco Javier Carrasco-Sánchez; Vanessa Carolina Vento; Gema María García García; Pablo Cubero-Morais; José Manuel Casas Rojo; Jesús Millán Núñez-Cortés

    doi:10.21203/ Date: 2021-02-15 Source: ResearchSquare

    Background: Since December 2019, the COVID-19 pandemic MESHD has changed the concept of medicine. This work aims to analyze the use of antibiotics in patients admitted to the hospital due to SARS-CoV-2 infection MESHD. Methods: This work analyzes the use and effectiveness of antibiotics in hospitalized patients with COVID-19 MESHD based on data from the SEMI- COVID-19 MESHD registry, an initiative to generate knowledge about this disease using data from electronic medical records. Our primary endpoint was all-cause in-hospital mortality according to antibiotic use. The secondary endpoint was the effect of macrolides on mortality. Results: Of 13,932 patients, antibiotics were used in 12,238. The overall death rate was 20.7% and higher among those taking antibiotics (87.8%). Higher mortality was observed with use of all antibiotics (OR 1.40, 95%CI 1.21-1.62; p<.001) except macrolides, which had a higher survival rate (OR 0.70, 95%CI 0.64-0.76; p<.001). The decision to start antibiotics was influenced by presence of increased inflammatory markers and any kind of infiltrate on an x-ray. Patients receiving antibiotics required respiratory support and were transferred to intensive care units more often. Conclusions: Bacterial co-infection MESHD was uncommon among COVID-19 MESHD patients, yet use of antibiotics was high. There is insufficient evidence to support widespread use of empiric antibiotics in these patients. Most may not require empiric treatment and if they do, there is promising evidence regarding azithromycin as a potential COVID-19 MESHD treatment.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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