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Barmania F, Mellet J, Ryder MA, Ford G, Herd CL, Tamuhla T, Hendricks C, Giles R, Kalua T, Joubert F, Tiffin N, Pepper MS. Coronavirus Host Genetics South Africa (COHG-SA) database-a variant database for gene regions associated with SARS-CoV-2 outcomes. Eur J Hum Genet 2022; 30:880-888. [PMID: 35351987 PMCID: PMC8960680 DOI: 10.1038/s41431-022-01089-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 12/28/2022] Open
Abstract
The SARS-CoV-2 virus is responsible for the COVID-19 global public health emergency, and the disease it causes is highly variable in its clinical presentation. Clinical phenotypes are heterogeneous both in terms of presentation of symptoms in the host and response to therapy. Several studies and initiatives have been established to analyse and review host genetic epidemiology associated with COVID-19. Our research group curated these articles into a web-based database using the python application-server framework Django. The database provides a searchable research tool describing current literature surrounding COVID-19 host genetic factors associated with disease outcome. This paper describes the COHG-SA database and provides an overview of the analyses that can be derived from these data.
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Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Ryder
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Graeme Ford
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Candice L Herd
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Tsaone Tamuhla
- Computational Biology Division, Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Hendricks
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Rachel Giles
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Thumbiko Kalua
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nicki Tiffin
- Computational Biology Division, Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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Schonhaut L, Costa-Roldan I, Oppenheimer I, Pizarro V, Han D, Díaz F. Scientific publication speed and retractions of COVID-19 pandemic original articles. Rev Panam Salud Publica 2022; 46:e25. [PMID: 35432503 PMCID: PMC9004690 DOI: 10.26633/rpsp.2022.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022] Open
Abstract
Objective. To describe the editorial processing time of published COVID-19 research articles and compare this with a similar topic, human influenza, and analyze the number of publications, withdrawals, and retractions. Methods. A descriptive-analytical study using PubMed on research articles with the MeSH terms human influenza and COVID-19. Time to acceptance (from submission to acceptance) and time to publication (from acceptance to publication) were compared. Retractions and withdrawals were reviewed both qualitatively and quantitatively. Results. There were 31 319 research articles on COVID-19 and 4 287 on human influenza published during 2020. The median time to acceptance for COVID-19 was lower than that for human influenza (8 vs. 92 days). The median time to publication for COVID-19 articles was shorter than those on human influenza (12 vs. 16 days); 47.0% of COVID-19 research articles were accepted within the first week of submission, and 19.5% within one day. There were 82 retractions and withdrawals for COVID-19 articles, 1 for human influenza, and 5 for articles that contain both terms; these were mainly related to ethical misconduct, and 27 (31.0%) were published by the same group of authors in one highest-quartile journal. Conclusions. The conundrum between fast publishing and adequate standards is shown in this analysis of COVID-19 research articles. The speed of acceptance for COVID-19 manuscripts was 11.5 times faster than for human influenza. The high number of acceptances within a day or week of submission and the number of retractions and withdrawals of COVID-19 papers might be a warning sign about the possible lack of a quality control process in scientific publishing and the peer review process.
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Affiliation(s)
| | | | | | | | | | - Franco Díaz
- Universidad Finis Terrae Escuela de Medicina, Santiago, Chile
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Leaning in the publishing of articles in scientific journals during the COVID-19 pandemic. JOURNAL OF RESEARCH IN APPLIED AND BASIC MEDICAL SCIENCES 2021. [DOI: 10.52547/rabms.7.2.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Affiliation(s)
- Kenneth E Remy
- Department of Pediatrics, Division of Critical Care Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
- Department of Internal Medicine, Division of Pulmonary Critical Care Medicine, Washington University School of Medicine, St. Louis, MO
| | - Niranjan Kissoon
- Department of Pediatrics, The University of British Columbia, The Child and Family Research Institute, and BC Children's Hospital, Vancouver, BC, Canada
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