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1.
Adv Ther (Weinh) ; 4(10): 2100179, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1567924

ABSTRACT

[This corrects the article DOI: 10.1002/adtp.202100055.].

2.
Clin Infect Dis ; 73(11): e4154-e4165, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1559099

ABSTRACT

BACKGROUND: Children and older adults with coronavirus disease 2019 (COVID-19) display a distinct spectrum of disease severity yet the risk factors aren't well understood. We sought to examine the expression pattern of angiotensin-converting enzyme 2 (ACE2), the cell-entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the role of lung progenitor cells in children and older patients. METHODS: We retrospectively analyzed clinical features in a cohort of 299 patients with COVID-19. The expression and distribution of ACE2 and lung progenitor cells were systematically examined using a combination of public single-cell RNA-seq data sets, lung biopsies, and ex vivo infection of lung tissues with SARS-CoV-2 pseudovirus in children and older adults. We also followed up patients who had recovered from COVID-19. RESULTS: Compared with children, older patients (>50 years.) were more likely to develop into serious pneumonia with reduced lymphocytes and aberrant inflammatory response (P = .001). The expression level of ACE2 and lung progenitor cell markers were generally decreased in older patients. Notably, ACE2 positive cells were mainly distributed in the alveolar region, including SFTPC positive cells, but rarely in airway regions in the older adults (P < .01). The follow-up of discharged patients revealed a prolonged recovery from pneumonia in the older (P < .025). CONCLUSIONS: Compared to children, ACE2 positive cells are generally decreased in older adults and mainly presented in the lower pulmonary tract. The lung progenitor cells are also decreased. These risk factors may impact disease severity and recovery from pneumonia caused by SARS-Cov-2 infection in older patients.

3.
Preprint in English | Other preprints | ID: ppcovidwho-296081

ABSTRACT

Background Relation extraction is a fundamental task for extracting gene-disease associations from biomedical text. Existing tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts. Results In this work, we propose RENET2, a deep learning-based relation extraction method, which implements section filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles. We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles. In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22%, 30.30% and 29.24% higher than the best existing tools BeFree, DTMiner and BioBERT, respectively. We applied RENET2 to (1) ~1.89M full-text articles from PMC and found ~3.72M gene-disease associations;and (2) the LitCovid articles set and ranked the top 15 proteins associated with COVID-19, supported by recent articles. Conclusion RENET2 is an efficient and accurate method for full-text gene-disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at https://github.com/sujunhao/RENET2 .

4.
NAR Genom Bioinform ; 3(3): lqab062, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1301371

ABSTRACT

Relation extraction (RE) is a fundamental task for extracting gene-disease associations from biomedical text. Many state-of-the-art tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts. A few studies have explored extracting gene-disease associations from full-text articles, but there exists a large room for improvements. In this work, we propose RENET2, a deep learning-based RE method, which implements Section Filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles. We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles. In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22, 30.30, 29.24 and 23.87% higher than BeFree, DTMiner, BioBERT and RENET, respectively. We applied RENET2 to (i) ∼1.89M full-text articles from PubMed Central and found ∼3.72M gene-disease associations; and (ii) the LitCovid articles and ranked the top 15 proteins associated with COVID-19, supported by recent articles. RENET2 is an efficient and accurate method for full-text gene-disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at GitHub.

5.
Adv Ther (Weinh) ; : 2100055, 2021 May 20.
Article in English | MEDLINE | ID: covidwho-1242700

ABSTRACT

Identifying effective drug treatments for COVID-19 is essential to reduce morbidity and mortality. Although a number of existing drugs have been proposed as potential COVID-19 treatments, effective data platforms and algorithms to prioritize drug candidates for evaluation and application of knowledge graph for drug repurposing have not been adequately explored. A COVID-19 knowledge graph by integrating 14 public bioinformatic databases containing information on drugs, genes, proteins, viruses, diseases, symptoms and their linkages is developed. An algorithm is developed to extract hidden linkages connecting drugs and COVID-19 from the knowledge graph, to generate and rank proposed drug candidates for repurposing as treatments for COVID-19 by integrating three scores for each drug: motif scores, knowledge graph PageRank scores, and knowledge graph embedding scores. The knowledge graph contains over 48 000 nodes and 13 37 000 edges, including 13 563 molecules in the DrugBank database. From the 5624 molecules identified by the motif-discovery algorithms, ranking results show that 112 drug molecules had the top 2% scores, of which 50 existing drugs with other indications approved by health administrations reported. The proposed drug candidates serve to generate hypotheses for future evaluation in clinical trials and observational studies.

6.
Environ Microbiol ; 23(5): 2339-2363, 2021 05.
Article in English | MEDLINE | ID: covidwho-1153385

ABSTRACT

The global propagation of SARS-CoV-2 and the detection of a large number of variants, some of which have replaced the original clade to become dominant, underscores the fact that the virus is actively exploring its evolutionary space. The longer high levels of viral multiplication occur - permitted by high levels of transmission -, the more the virus can adapt to the human host and find ways to success. The third wave of the COVID-19 pandemic is starting in different parts of the world, emphasizing that transmission containment measures that are being imposed are not adequate. Part of the consideration in determining containment measures is the rationale that vaccination will soon stop transmission and allow a return to normality. However, vaccines themselves represent a selection pressure for evolution of vaccine-resistant variants, so the coupling of a policy of permitting high levels of transmission/virus multiplication during vaccine roll-out with the expectation that vaccines will deal with the pandemic, is unrealistic. In the absence of effective antivirals, it is not improbable that SARS-CoV-2 infection prophylaxis will involve an annual vaccination campaign against 'dominant' viral variants, similar to influenza prophylaxis. Living with COVID-19 will be an issue of SARS-CoV-2 variants and evolution. It is therefore crucial to understand how SARS-CoV-2 evolves and what constrains its evolution, in order to anticipate the variants that will emerge. Thus far, the focus has been on the receptor-binding spike protein, but the virus is complex, encoding 26 proteins which interact with a large number of host factors, so the possibilities for evolution are manifold and not predictable a priori. However, if we are to mount the best defence against COVID-19, we must mount it against the variants, and to do this, we must have knowledge about the evolutionary possibilities of the virus. In addition to the generic cellular interactions of the virus, there are extensive polymorphisms in humans (e.g. Lewis, HLA, etc.), some distributed within most or all populations, some restricted to specific ethnic populations and these variations pose additional opportunities for/constraints on viral evolution. We now have the wherewithal - viral genome sequencing, protein structure determination/modelling, protein interaction analysis - to functionally characterize viral variants, but access to comprehensive genome data is extremely uneven. Yet, to develop an understanding of the impacts of such evolution on transmission and disease, we must link it to transmission (viral epidemiology) and disease data (patient clinical data), and the population granularities of these. In this editorial, we explore key facets of viral biology and the influence of relevant aspects of human polymorphisms, human behaviour, geography and climate and, based on this, derive a series of recommendations to monitor viral evolution and predict the types of variants that are likely to arise.


Subject(s)
Biological Evolution , COVID-19/prevention & control , COVID-19/virology , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/genetics , Disease Transmission, Infectious/prevention & control , Genetic Variation , Host-Pathogen Interactions , Humans , SARS-CoV-2/physiology , Virus Replication
7.
Theranostics ; 11(5): 2170-2181, 2021.
Article in English | MEDLINE | ID: covidwho-1016389

ABSTRACT

Introduction: An increasing number of children with severe coronavirus disease 2019 (COVID-19) is being reported, yet the spectrum of disease severity and expression patterns of angiotensin-converting enzyme 2 (ACE2) in children at different developmental stages are largely unknow. Methods: We analysed clinical features in a cohort of 173 children with COVID-19 (0-15 yrs.-old) between January 22, 2020 and March 15, 2020. We systematically examined the expression and distribution of ACE2 in different developmental stages of children by using a combination of children's lung biopsies, pluripotent stem cell-derived lung cells, RNA-sequencing profiles, and ex vivo SARS-CoV-2 pseudoviral infections. Results: It revealed that infants (< 1yrs.-old), with a weaker potency of immune response, are more vulnerable to develop pneumonia whereas older children (> 1 yrs.-old) are more resistant to lung injury. The expression levels of ACE2 however do not vary by age in children's lung. ACE2 is notably expressed not only in Alveolar Type II (AT II) cells, but also in SOX9 positive lung progenitor cells detected in both pluripotent stem cell derivatives and infants' lungs. The ACE2+SOX9+ cells are readily infected by SARS-CoV-2 pseudovirus and the numbers of the double positive cells are significantly decreased in older children. Conclusions: Infants (< 1 yrs.-old) with SARS-CoV-2 infection are more vulnerable to lung injuries. ACE2 expression in multiple types of lung cells including SOX9 positive progenitor cells, in cooperation with an unestablished immune system, could be risk factors contributing to vulnerability of infants with COVID-19. There is a need to continue monitoring lung development in young children who have recovered from SARS-CoV-2 infection.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19/pathology , Lung/cytology , Stem Cells/metabolism , Adolescent , Biopsy , Child , Child, Preschool , Female , Humans , Immune System , Infant , Infant, Newborn , Lung/virology , Male , RNA-Seq , Risk Factors , SARS-CoV-2 , SOX9 Transcription Factor/metabolism , Single-Cell Analysis , Stem Cells/virology
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