Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis DOI Creative Commons
Karen O’Connor, Davy Weissenbacher, Amir Elyaderani

et al.

JMIR Research Protocols, Journal Year: 2025, Volume and Issue: 14, P. e58567 - e58567

Published: April 22, 2025

Background There has been an unprecedented effort to sequence the SARS-CoV-2 virus and examine its molecular evolution. This facilitated by availability of publicly accessible databases, such as GISAID (Global Initiative on Sharing All Influenza Data) GenBank, which collectively hold millions records. Genomic epidemiology, however, seeks go beyond phylogenetic (the study evolutionary relationships among biological entities) analysis linking genetic information patient characteristics disease outcomes, enabling a comprehensive understanding transmission dynamics impact. While these repositories include fields reflecting patient-related metadata for given sequence, inclusion demographic clinical details is scarce. The current in published sequencing studies quality remains unexplored. Objective Our review aims quantitatively assess extent patient-reported papers reporting original whole genome analyze publication patterns using bibliometric analysis. Finally, we will evaluate efficacy reliability machine learning classifier accurately identifying relevant scoping review. Methods National Institutes Health’s LitCovid collection be used automated classification having deposited sequences public repositories, while independent search conducted MEDLINE PubMed Central validation. Data extraction Covidence (Veritas Health Innovation Ltd). extracted data synthesized summarized quantify literature studies. For analysis, points, author affiliations, citation metrics, keywords, Medical Subject Headings terms extracted. Results expected completed early 2025. model developed have classified publications through February 2023. As September 2024, August 2024 are being prepared processing. Screening underway validated from classifier. Direct searches screening results began October 2024. We summarize narratively describe our findings tables, graphs, charts where applicable. Conclusions report types reported genomic viral SARS-CoV-2, identify gaps metadata, make recommendations improving consistency this area. uncover trends including differences based or geographic regions. insights gained may help improve enhancing utility facilitating future research infectious diseases. Trial Registration OSF Registries osf.io/wrh95; https://doi.org/10.17605/OSF.IO/WRH95 International Registered Report Identifier (IRRID) DERR1-10.2196/58567

Language: Английский

Mental health outcomes of quarantine and isolation for infection prevention: A systematic umbrella review of the global evidence DOI Creative Commons
Md Mahbub Hossain, Abida Sultana, Neetu Purohit

et al.

Epidemiology and Health, Journal Year: 2020, Volume and Issue: unknown, P. e2020038 - e2020038

Published: June 2, 2020

Transmission of infectious diseases is often prevented by quarantine and isolation the populations at risk. These approaches restrict mobility, social interactions, daily activities affected individuals. In recent coronavirus disease 2019 (COVID-19) pandemic, are being adopted in many contexts, which necessitates an evaluation global evidence on how such measures impact mental health outcomes among populations. This umbrella review aimed to synthesize available for preventing diseases.We searched nine major databases additional sources included articles if they were systematically conducted reviews, published as peer-reviewed journal articles, reported or any population.Among 1,364 citations, only eight reviews met our criteria. Most primary studies those high-income nations hospital settings. a high burden problems patients, informal caregivers, healthcare providers who experienced isolation. Prevalent individuals include depression, anxiety, mood disorders, psychological distress, posttraumatic stress disorder, insomnia, fear, stigmatization, low self-esteem, lack self-control, other adverse outcomes.This found severe have undergone different contexts. multipronged interventions including policy strengthening services globally promoting psychosocial wellbeing high-risk

Language: Английский

Citations

534

COVID-19 PANDEMIA AND PUBLIC AND GLOBAL MENTAL HEALTH FROM THE PERSPECTIVE OF GLOBAL HEALTH SECURITY DOI Open Access

Miro Jakovljević,

Sarah Bjedov,

Nenad Jakšić

et al.

Psychiatria Danubina, Journal Year: 2020, Volume and Issue: 32(1), P. 6 - 14

Published: April 15, 2020

The Coronavirus disease 2019 pandemic emerged in Wuhan, China and has spread all over the world caused huge threats to health lives.It affected different frontiers of lives induced many psychiatric individual collective problems such as panic, anxiety, depression, post-traumatic stress disorders, suspiciousness, infodemia, cacophony, xenophobia, racisms, etc.The COVID-19 outbreak public global mental crisis well a psychosocial experiment.Psychiatry other sciences can play very useful role supporting well-being patients their families, healthcare personnel society.For successful fighting with present future pandemics we have learn more about psychological aspects from perspectives health.

Language: Английский

Citations

304

Mental health outcomes of quarantine and isolation for infection prevention: A systematic umbrella review of the global evidence DOI
Md Mahbub Hossain, Abida Sultana, Neetu Purohit

et al.

Published: March 13, 2020

Background: Transmission of infectious diseases is often prevented by quarantine and isolation the populations at risk. These approaches restrict mobility, social interactions, daily activities affected individuals. In recent novel coronavirus disease (COVID-19) pandemic, are being adopted in many contexts, which necessitates an evaluation global evidence on how such measures impact mental health outcomes among populations. This umbrella review aimed to synthesize available for preventing diseases.Materials methods: We searched nine major databases additional sources included articles if they were systematically conducted reviews, published as peer-reviewed journal articles, reported or any population.Results: Among 1364 citations, only eight reviews met our criteria. Most primary studies those high-income nations hospital settings. a high burden problems patients, informal caregivers, healthcare providers who experienced isolation. Prevalent individuals include depression, anxiety, mood disorders, psychological distress, posttraumatic stress disorder, insomnia, fear, stigmatization, low self-esteem, lack self-control, other adverse outcomes.Conclusion: found severe have undergone different contexts. multipronged interventions including policy strengthening services globally promoting psychosocial wellbeing high-risk

Language: Английский

Citations

144

Scientific globalism during a global crisis: research collaboration and open access publications on COVID-19 DOI Creative Commons
Jenny J. Lee, John P. Haupt

Higher Education, Journal Year: 2020, Volume and Issue: 81(5), P. 949 - 966

Published: July 24, 2020

This study sought to understand the nature of scientific globalism during a global crisis, particularly COVID-19. Findings show that occurs differently when comparing COVID-19 publications with non-COVID-19 as well before pandemic. Despite tense geopolitical climate, countries increased their proportion international collaboration and open-access However, not all engaged more globally. Countries have been impacted by crisis those relatively lower GDPs tended participate in than counterparts.

Language: Английский

Citations

139

A Bibliometric Analysis of COVID-19 across Science and Social Science Research Landscape DOI Open Access
Aleksander Aristovnik, Dejan Ravšelj, Lan Umek

et al.

Sustainability, Journal Year: 2020, Volume and Issue: 12(21), P. 9132 - 9132

Published: Nov. 3, 2020

The lack of knowledge about the COVID-19 pandemic has encouraged extensive research in academic sphere, reflected exponentially growing scientific literature. While state reveals it is currently an early stage developing knowledge, a comprehensive and in-depth overview still missing. Accordingly, paper’s main aim to provide bibliometric analysis across science social landscape, using innovative approaches (e.g., Venn diagram, Biblioshiny descriptive statistics, VOSviewer co-occurrence network analysis, Jaccard distance cluster text mining based on binary logistic regression). considers Scopus database, including all relevant information related publications (n = 16,866) available first half 2020. empirical results indicate domination health sciences terms number total citations, while physical humanities lag behind significantly. Nevertheless, there evidence collaboration within between different subject area classifications with gradual increase importance non-health disciplines. findings emphasize great need for approach that various disciplines so as benefit not only community but evidence-based policymaking part efforts properly respond pandemic.

Language: Английский

Citations

136

Characteristics of academic publications, preprints, and registered clinical trials on the COVID-19 pandemic DOI Creative Commons
Silvia Gianola, Tiago S. Jesus, Silvia Bargeri

et al.

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(10), P. e0240123 - e0240123

Published: Oct. 6, 2020

The COVID-19 pandemic has unleashed a deluge of publications. For this cross-sectional study we compared the amount and reporting characteristics COVID-19-related academic articles preprints number ongoing clinical trials systematic reviews. To do this, searched PubMed database citations abstracts for published life science journals by using appropriate combinations medical subject headings (MeSH terms), section MedRxiv BioRxiv archives up to 20 May 2020 (21 weeks). In addition, Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Trials Register, 15 other trial registers, as well PROSPERO, international prospective register each publication were extracted. Regression analyses Z tests used detect trends their relative proportions. A total 3635 publications 3805 retrieved. Only 8.6% (n = 329) already in indexed journals. preprint increased significantly over time (p<0.001). Case reports (6% vs 0.9% preprints; p<0.001) letters (17.4% 0.5% accounted greater share Differently, randomized controlled (0.22% 0.63%; reviews (0.08% 5%) made preprints. proportion studies registered at Clinicaltrials.gov, Register was 57.9%, 49.5%, 98.9%, respectively, most which still "recruiting". PROSPERO listed 962 review protocols. Preprints slightly more prevalent than but both increasing number. void left lack primary filled an outpour immediate opinions (i.e., editor) PubMed-indexed Summarizing, have gained traction publishing response demand prompt access empirical, albeit not peer-reviewed, findings during present pandemic.

Language: Английский

Citations

124

Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic DOI Creative Commons
Hyokyoung G. Hong, Yi Li

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(7), P. e0236464 - e0236464

Published: July 21, 2020

The coronavirus pandemic has rapidly evolved into an unprecedented crisis. susceptible-infectious-removed (SIR) model and its variants have been used for modeling the pandemic. However, time-independent parameters in classical models may not capture dynamic transmission removal processes, governed by virus containment strategies taken at various phases of epidemic. Moreover, few account possible inaccuracies reported cases. We propose a Poisson with time-dependent rates to random errors reporting estimate disease reproduction number, which reflect effectiveness control strategies. apply our method study several severely impacted countries, analyze forecast evolving spread coronavirus. developed interactive web application facilitate readers' use method.

Language: Английский

Citations

103

Ritmo de crecimiento diario de la producción científica sobre Covid-19. Análisis en bases de datos y repositorios en acceso abierto DOI Creative Commons
Daniel Torres‐Salinas

El Profesional de la Informacion, Journal Year: 2020, Volume and Issue: 29(2)

Published: April 14, 2020

The scientific community is facing one of its greatest challenges in solving a global health problem: COVID-19 pandemic. This situation has generated an unprecedented volume publications. What the volume, terms publications, research on COVID-19? general objective this work to obtain vision daily growth production different databases (Dimensions, Web Science Core Collection, Scopus-Elsevier, Pubmed and eight repositories). In relation results obtained, Dimensions indexes total 9435 publications (69% with peer review 2677 preprints) well above Scopus (1568) WoS (718). classic biliometric phenomenon exponential (R2 = 0.92). rate 500 doubles every 15 days. case weekly around 1000 Of repositories analysed, Central, Medrxiv SSRN are leaders. Despite their enormous contribution, journals continue be core communication. Finally, it been established that three out four available open access. information explosion demands serious coordinated response from professionals, which places us at centre

Language: Английский

Citations

98

Global trends in coronavirus research at the time of Covid-19: A general bibliometric approach and content analysis using SciMAT DOI Open Access
Enrique Herrera‐Viedma,

José-Ricardo López-Robles,

Javier Guallar

et al.

El Profesional de la Informacion, Journal Year: 2020, Volume and Issue: 29(3)

Published: June 3, 2020

Covid-19 represents the greatest challenge facing mankind today. In December 2019, several cases of pneumonia unknown etiology were reported from China. This coronavirus infection subsequently identified as aroused worldwide concern. As a result, scientific community has focused attention on Covid-19, revealed by recent research in literature based holistic approach. this regard, study conducts bibliometric analysis with an emphasis disease, using reference publications Web Science Core Collection 1970 to 2020. analyzes 12,571 (April 18) 2020 applying advanced techniques SciMAT software. The current therefore provides complete conceptual main types and strains quantifying performance indicators, identifying authors, organizations, countries, sources, areas, evaluating development field. Furthermore, science map is constructed understand corresponding intellectual structure lines (themes). thereby offers approach field evaluates indicators related coronavirus, focus Covid-19. Finally, serves framework strengthen existing develop new ones, establishing synergistic relationships that not visible without maps generated herein.

Language: Английский

Citations

97

Analysis of the scientific production of the effect of COVID-19 on the environment: A bibliometric study DOI Open Access
Luis‐Alberto Casado‐Aranda, Juan Sánchez‐Fernández,

María I. Viedma-del-Jesús

et al.

Environmental Research, Journal Year: 2020, Volume and Issue: 193, P. 110416 - 110416

Published: Nov. 3, 2020

Language: Английский

Citations

97