Pub Date : 2024-09-16DOI: 10.1101/2024.09.16.24313707
Shan Qiao, Xingyu Fang, Camryn Garrett, Ran Zhang, Xiaoming Li, Yuhao Kang
Study Objectives: In-depth interviews are one of the most widely used approaches for qualitative studies in public health. The coding of transcripts is a critical step for information extraction and preliminary analysis. However, manual coding is often labor-intensive and time-consuming. The emergence of generative artificial intelligence (GenAI), supported by Large Language Models (LLMs), presents new opportunities to understand human languages, which may significantly facilitate the coding process. This study aims to build a computational coding framework that uses GenAI to automatically detect and extract themes from in-depth interview transcripts. Methods: We conducted an experiment using transcripts of in-depth interviews with maternity care providers in South Carolina. We leveraged ChatGPT to perform two tasks automatically: (1) deductive coding, which involves applying a predefined set of codes to dialogues; and (2) inductive coding, which can generate codes from dialogues without any preconceptions or assumptions. We fine-tuned ChatGPT to understand the content of the interview transcripts, enabling it to detect and summarize codes. We then evaluated the performance of the proposed approach by comparing the codes generated by ChatGPT with those generated manually by human coders, involving human-in-the-loop evaluation. Results: The results demonstrated the potential of GenAI in detecting and summarizing codes from in-depth interview transcripts. ChatGPT could be utilized for both deductive and inductive coding processes. The overall accuracy of GenAI is higher than 80% and the codes it generated showed high positive associations with those generated manually. More impressively, GenAI reduced the time required for coding by 81%, demonstrating its efficiency compared to traditional methods. Discussion: GenAI models like ChatGPT show high generalizability, scalability and efficiency in handling large datasets, and are proficient in multi-level semantic structure identification. They demonstrate promising results in qualitative coding, making it a valuable tool for supporting people in public health research. However, challenges such as inaccuracy, systematic biases, and privacy concerns must be addressed when using them in practice. GenAI-based coding results should be handled with caution and reviewed by human coders to ensure accuracy and reliability.
{"title":"Generative AI for Qualitative Analysis in a Maternal Health Study: Coding In-depth Interviews using Large Language Models (LLMs)","authors":"Shan Qiao, Xingyu Fang, Camryn Garrett, Ran Zhang, Xiaoming Li, Yuhao Kang","doi":"10.1101/2024.09.16.24313707","DOIUrl":"https://doi.org/10.1101/2024.09.16.24313707","url":null,"abstract":"Study Objectives: In-depth interviews are one of the most widely used approaches for qualitative studies in public health. The coding of transcripts is a critical step for information extraction and preliminary analysis. However, manual coding is often labor-intensive and time-consuming. The emergence of generative artificial intelligence (GenAI), supported by Large Language Models (LLMs), presents new opportunities to understand human languages, which may significantly facilitate the coding process. This study aims to build a computational coding framework that uses GenAI to automatically detect and extract themes from in-depth interview transcripts.\u0000Methods: We conducted an experiment using transcripts of in-depth interviews with maternity care providers in South Carolina. We leveraged ChatGPT to perform two tasks automatically: (1) deductive coding, which involves applying a predefined set of codes to dialogues; and (2) inductive coding, which can generate codes from dialogues without any preconceptions or assumptions. We fine-tuned ChatGPT to understand the content of the interview transcripts, enabling it to detect and summarize codes. We then evaluated the performance of the proposed approach by comparing the codes generated by ChatGPT with those generated manually by human coders, involving human-in-the-loop evaluation. Results: The results demonstrated the potential of GenAI in detecting and summarizing codes from in-depth interview transcripts. ChatGPT could be utilized for both deductive and inductive coding processes. The overall accuracy of GenAI is higher than 80% and the codes it generated showed high positive associations with those generated manually. More impressively, GenAI reduced the time required for coding by 81%, demonstrating its efficiency compared to traditional methods.\u0000Discussion: GenAI models like ChatGPT show high generalizability, scalability and efficiency in handling large datasets, and are proficient in multi-level semantic structure identification. They demonstrate promising results in qualitative coding, making it a valuable tool for supporting people in public health research. However, challenges such as inaccuracy, systematic biases, and privacy concerns must be addressed when using them in practice. GenAI-based coding results should be handled with caution and reviewed by human coders to ensure accuracy and reliability.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-15DOI: 10.1101/2024.09.13.24313660
John Ioannidis, Thomas A. Collins, Eran Bendavid, Jeroen Baas
We examined the growth trajectory and impact of COVID-19-related papers in the scientific literature until August 1, 2024 and how the scientific workforce was engaged in this work. Scopus indexed 718,660 COVID-19-related publications. As proportion of all indexed scientific publications, COVID-19-related publications peaked in September 2021 (4.7%) remained at 4.3-4.6% for another year and then gradually declined, but was still 1.9% in July 2024). COVID-19-related publications included 1,978,612 unique authors: 1,127,215 authors had ≥5 full papers in their career and 53,418 authors were in the top-2% of their scientific subfield based on a career-long composite citation indicator. Authors with >10%, >30% and >50% of their total career citations be to COVID-19-related publications were 376,942, 201,702, and 125,523, respectively. As of August 1, 2024, 65 of the top-100 most-cited papers published in 2020 were COVID-19-related, declining to 24/100, 19/100, 7/100, and 5/100 for the most-cited papers published in 2021, 2022, 2023, and 2024, respectively. Across 174 scientific subfields, 132 had ≥10% of their active influential (top-2% by composite citation indicator) authors publish something on COVID-19 during 2020-2024. Among the 300 authors with highest composite citation indicator specifically for their COVID-19-related publications, 41 were editors or journalists/columnists and another 23 had most of their COVID-19 citations to published items other than full papers (opinion pieces/letters/notes). COVID-19 massively engaged the scientific workforce in unprecedented ways. As the pandemic ended, there has been a sharp decline in the overall volume and high impact of newly published COVID-19-related publications.
{"title":"Covidization and decovidization of the scientific literature and scientific workforce","authors":"John Ioannidis, Thomas A. Collins, Eran Bendavid, Jeroen Baas","doi":"10.1101/2024.09.13.24313660","DOIUrl":"https://doi.org/10.1101/2024.09.13.24313660","url":null,"abstract":"We examined the growth trajectory and impact of COVID-19-related papers in the scientific literature until August 1, 2024 and how the scientific workforce was engaged in this work. Scopus indexed 718,660 COVID-19-related publications. As proportion of all indexed scientific publications, COVID-19-related publications peaked in September 2021 (4.7%) remained at 4.3-4.6% for another year and then gradually declined, but was still 1.9% in July 2024). COVID-19-related publications included 1,978,612 unique authors: 1,127,215 authors had ≥5 full papers in their career and 53,418 authors were in the top-2% of their scientific subfield based on a career-long composite citation indicator. Authors with >10%, >30% and >50% of their total career citations be to COVID-19-related publications were 376,942, 201,702, and 125,523, respectively. As of August 1, 2024, 65 of the top-100 most-cited papers published in 2020 were COVID-19-related, declining to 24/100, 19/100, 7/100, and 5/100 for the most-cited papers published in 2021, 2022, 2023, and 2024, respectively. Across 174 scientific subfields, 132 had ≥10% of their active influential (top-2% by composite citation indicator) authors publish something on COVID-19 during 2020-2024. Among the 300 authors with highest composite citation indicator specifically for their COVID-19-related publications, 41 were editors or journalists/columnists and another 23 had most of their COVID-19 citations to published items other than full papers (opinion pieces/letters/notes). COVID-19 massively engaged the scientific workforce in unprecedented ways. As the pandemic ended, there has been a sharp decline in the overall volume and high impact of newly published COVID-19-related publications.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.13.24312550
Azarreia Paulos, Leul Mulu, Kalab Metiku
Background- Postpartum cardiomyopathy (PPCM) is a condition that is characterized by the weakening of heart muscles which is known as left ventricular dysfunction and occurs during the later stages of pregnancy or during the early stages of postpartum. Objective- To evaluate the role of abnormal immune responses and risk factors such as advanced age, high parity, and presence of gestational diabetes in the pathogenesis of PPCM in Ethiopia. Method- A cross-sectional hospital-based study was conducted at Saint Paul Millennium Medical College (SPMCC) between January 2021 and January 2023. All female pregnant patients who were attending the Maternal Care Fetal Unit, Antenatal Unit, and High-Risk Unit at SPMMC were included in this study. However, among those patients, those mothers younger than 20 years old and older than 40 years old were excluded from the study. The total sample size collected from this facility was 250 patients. Results- Oxidative stress and inflammation were primarily correlated with pre-eclampsia and gestational diabetes. These risk factors were particularly prevalent within patients diagnosed with PPCM, 52.8% and 40% respectively. Prolactin Cleavage and Microvascular Dysfunction was associated with higher BMI and advanced age. With a general increasing trend observed in PPCM incidence and advancing age. As well as a high prevalence rate of PPCM in patients with Obesity Class I (at 33.0%). Another notable risk factor was high parity ( 45.0% with 4+ prior pregnancies). The most common symptom presented was dyspnea at 35.0%. The mortality rate was 14% whilst recurrence and the fully recovered ratio were at 13.1% and 34.0%, respectively. Conclusion- Results aligned with those conducted in other African countries (e.g. Zambia and South Africa) however mitigating high mortality as well as low full recovery rate will need to be done by earlier diagnosis, effective treatment, and intervention mechanisms. A different study design will need to be conducted (over a longer time period) to support and make findings more holistic.
{"title":"Cross-Sectional Analysis of the Association Between Abnormal Immune Responses in the Pathogenesis of Postpartum Cardiomyopathy in Ethiopian Women: A Hospital-based Study at Saint Paul Hospital","authors":"Azarreia Paulos, Leul Mulu, Kalab Metiku","doi":"10.1101/2024.09.13.24312550","DOIUrl":"https://doi.org/10.1101/2024.09.13.24312550","url":null,"abstract":"Background- Postpartum cardiomyopathy (PPCM) is a condition that is characterized by the weakening of heart muscles which is known as left ventricular dysfunction and occurs during the later stages of pregnancy or during the early stages of postpartum. Objective- To evaluate the role of abnormal immune responses and risk factors such as advanced age, high parity, and presence of gestational diabetes in the pathogenesis of PPCM in Ethiopia. Method- A cross-sectional hospital-based study was conducted at Saint Paul Millennium Medical College (SPMCC) between January 2021 and January 2023. All female pregnant patients who were attending the Maternal Care Fetal Unit, Antenatal Unit, and High-Risk Unit at SPMMC were included in this study. However, among those patients, those mothers younger than 20 years old and older than 40 years old were excluded from the study. The total sample size collected from this facility was 250 patients. Results- Oxidative stress and inflammation were primarily correlated with pre-eclampsia and gestational diabetes. These risk factors were particularly prevalent within patients diagnosed with PPCM, 52.8% and 40% respectively. Prolactin Cleavage and Microvascular Dysfunction was associated with higher BMI and advanced age. With a general increasing trend observed in PPCM incidence and advancing age. As well as a high prevalence rate of PPCM in patients with Obesity Class I (at 33.0%). Another notable risk factor was high parity ( 45.0% with 4+ prior pregnancies). The most common symptom presented was dyspnea at 35.0%. The mortality rate was 14% whilst recurrence and the fully recovered ratio were at 13.1% and 34.0%, respectively. Conclusion- Results aligned with those conducted in other African countries (e.g. Zambia and South Africa) however mitigating high mortality as well as low full recovery rate will need to be done by earlier diagnosis, effective treatment, and intervention mechanisms. A different study design will need to be conducted (over a longer time period) to support and make findings more holistic.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.12.24313566
Brianna M White, Whitney S Brakefield, Olufunto A Olusanya, Rameshwari Prasad, Fekede A Kumsa, Soheil Hashtarkhani, Arash Shaban-Nejad
Introduction/Background: The COVID-19 pandemic has disrupted major aspects of daily life since its emergence in late 2019, impacting health and well-being worldwide. Aside from genetic predisposition, numerous external factors play key roles in determining levels of disease susceptibility and overall health status. Aim/Objectives: This review and policy analysis sought to examine literature focused on the impact of neighborhood environments on population health and well-being during the COVID-19 pandemic period. Examined studies explore the impacts of various aspects of the neighborhood environment (i.e., walkability, transportation, access to healthcare/vaccination, etc.) during the COVID-19 era on population health and well-being. Methods: Databases were searched for studies published from March 2020 to August 2022. Selected studies examine the impacts of various aspects of the neighborhood environment (i.e., walkability, transportation, access to healthcare/vaccination, climate, crime rates, persistent poverty, the social spread of misinformation, etc.) during the COVID-19 era on population health and well-being. Results: Findings from our review suggest that those living in less-than-favorable environments were faced with significant challenges, making vulnerable populations more prone to the severity of COVID-19 infection. Conclusion: We argue these results establish cause for the consideration of the effects of neighborhood environments in developing intelligent intervention strategies for both pandemic recovery and preparation for future public health emergencies, especially among vulnerable populations.
{"title":"The Impacts of Neighborhood Disparities on US Population Health During the COVID-19 Pandemic: A Literature Review and Policy Analysis for Future Response","authors":"Brianna M White, Whitney S Brakefield, Olufunto A Olusanya, Rameshwari Prasad, Fekede A Kumsa, Soheil Hashtarkhani, Arash Shaban-Nejad","doi":"10.1101/2024.09.12.24313566","DOIUrl":"https://doi.org/10.1101/2024.09.12.24313566","url":null,"abstract":"Introduction/Background: The COVID-19 pandemic has disrupted major aspects of daily life since its emergence in late 2019, impacting health and well-being worldwide. Aside from genetic predisposition, numerous external factors play key roles in determining levels of disease susceptibility and overall health status.\u0000Aim/Objectives: This review and policy analysis sought to examine literature focused on the impact of neighborhood environments on population health and well-being during the COVID-19 pandemic period. Examined studies explore the impacts of various aspects of the neighborhood environment (i.e., walkability, transportation, access to healthcare/vaccination, etc.) during the COVID-19 era on population health and well-being.\u0000Methods: Databases were searched for studies published from March 2020 to August 2022. Selected studies examine the impacts of various aspects of the neighborhood environment (i.e., walkability, transportation, access to healthcare/vaccination, climate, crime rates, persistent poverty, the social spread of misinformation, etc.) during the COVID-19 era on population health and well-being. Results: Findings from our review suggest that those living in less-than-favorable environments were faced with significant challenges, making vulnerable populations more prone to the severity of COVID-19 infection. Conclusion: We argue these results establish cause for the consideration of the effects of neighborhood environments in developing intelligent intervention strategies for both pandemic recovery and preparation for future public health emergencies, especially among vulnerable populations.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.12.24313529
Skyler Finucane, Alexandria Renault, Mary Hayden, Kacey Ernst, Sarah Yeo
Vector-borne diseases are an increasing threat to human health and well-being in the United States. Understanding public perception and practices taken to reduce vector abundance and vector-human contact can guide effective interventions that can mitigate health risks. Nevertheless, vector-borne disease surveys, which are widely used in the field to understand public perception and practices, are often inconsistent in terms of structure and implementation. This protocol is designed to provide guidance for public health professionals and researchers in the development of future KAP studies by ensuring uniformity in design and structure. This manuscript describes a rigorous three-phase protocol for the development of standardized vector-borne disease survey modules that can be used throughout the United States to generate data that are comparable across diverse regions. During phase one, a workshop with subject matter experts and a comprehensive literature review will be conducted to identify survey domains and generate items of interest. Survey items will also be mapped based on two theoretical frameworks, the Health Belief Model and the Risks, Attitudes, Norms, Abilities and Self-Regulation framework, to help gauge individual perceptions of risk severity and self-efficacy. During phase two, a group of expert judges will evaluate survey items based on content relevance, representativeness, and technical quality. During the final phase, cognitive interviews and surveys with target audience groups will be conducted to ensure the face validity of the modules. Participants will be drawn from a diverse range of educational and geographic locations, and computer-assisted personal interviewing will be implemented. The surveys developed through this protocol will be available to researchers aiming to gain deeper insights into the public's knowledge, attitudes, and practices concerning vector-borne diseases, facilitating the collection of more comparable data across various regions in the United States.
在美国，病媒传播的疾病对人类健康和福祉的威胁与日俱增。了解公众的看法以及为减少病媒数量和病媒与人类接触而采取的做法，可以指导采取有效的干预措施，从而降低健康风险。然而，被广泛用于实地了解公众看法和做法的病媒传播疾病调查在结构和实施方面往往并不一致。本协议旨在通过确保设计和结构的统一性，为公共卫生专业人员和研究人员今后开展 KAP 研究提供指导。本手稿描述了制定标准化病媒传染疾病调查模块的严格的三阶段方案，该模块可在全美范围内使用，以生成不同地区之间可比的数据。在第一阶段，将召开主题专家研讨会并进行全面的文献综述，以确定调查领域并生成感兴趣的项目。调查项目还将根据健康信念模型和风险、态度、规范、能力和自我调节框架这两个理论框架进行映射，以帮助衡量个人对风险严重性和自我效能的看法。在第二阶段，一组专家评委将根据内容相关性、代表性和技术质量对调查项目进行评估。在最后阶段，将对目标受众群体进行认知访谈和调查，以确保模块的表面有效性。参与者将来自不同的教育和地理位置，并将采用计算机辅助个人访谈。研究人员可利用通过本方案开发的调查，深入了解公众对病媒传播疾病的认识、态度和做法，从而有助于收集美国各地区更具可比性的数据。
{"title":"Developing and validating modular surveys for vector-borne diseases: a study protocol","authors":"Skyler Finucane, Alexandria Renault, Mary Hayden, Kacey Ernst, Sarah Yeo","doi":"10.1101/2024.09.12.24313529","DOIUrl":"https://doi.org/10.1101/2024.09.12.24313529","url":null,"abstract":"Vector-borne diseases are an increasing threat to human health and well-being in the United States. Understanding public perception and practices taken to reduce vector abundance and vector-human contact can guide effective interventions that can mitigate health risks. Nevertheless, vector-borne disease surveys, which are widely used in the field to understand public perception and practices, are often inconsistent in terms of structure and implementation.\u0000This protocol is designed to provide guidance for public health professionals and researchers in the development of future KAP studies by ensuring uniformity in design and structure. This manuscript describes a rigorous three-phase protocol for the development of standardized vector-borne disease survey modules that can be used throughout the United States to generate data that are comparable across diverse regions. During phase one, a workshop with subject matter experts and a comprehensive literature review will be conducted to identify survey domains and generate items of interest. Survey items will also be mapped based on two theoretical frameworks, the Health Belief Model and the Risks, Attitudes, Norms, Abilities and Self-Regulation framework, to help gauge individual perceptions of risk severity and self-efficacy. During phase two, a group of expert judges will evaluate survey items based on content relevance, representativeness, and technical quality. During the final phase, cognitive interviews and surveys with target audience groups will be conducted to ensure the face validity of the modules. Participants will be drawn from a diverse range of educational and geographic locations, and computer-assisted personal interviewing will be implemented. The surveys developed through this protocol will be available to researchers aiming to gain deeper insights into the public's knowledge, attitudes, and practices concerning vector-borne diseases, facilitating the collection of more comparable data across various regions in the United States.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.10.24313441
Adrian Muwonge, Paul R Bessell, Barend Mark de Clare Bronsvoort, Ibrahim Mugerwa, Erisa Mwaka, Emmanuel Ssebaggala, Wee Aidan Bryan, Aggelos Kiayias, Christine Mbabazi Mpyangu, Moses Lutakome Joloba
Abstract Background: Haulage truck drivers can quickly connect distant communities, with risks of potential disease introduction. However, interventions to limit such risk must balance public health protection, economic continuity, and individual rights. Here distinguishing between their role in disease introduction and its onward spread is crucial for achieving this balance. Methods: To investigate the role of haulage during the Delta wave of COVID-19 in Uganda. We fit a susceptible-infectious-recovered (SIR) model to the 625,422 records in the national surveillance dataset to assess the notion of a “core-risk group” by examining the incidence and impact of haulage-targeted interventions in border districts associated with heavy haulage traffic compared to the districts in the central region of Uganda. Results: Although haulage drivers accounted for only 0.036% of the cases, the border districts associated with them registered 12.02% more cases than inland districts, suggesting a role in disease introduction. This risk was particularly higher in Tororo, compared to Amuru and Kyotera, which border Kenya, South Sudan, and Tanzania, respectively. Some interventions even increased the risk in Tororo by as much as 6%. However, in general, the haulage targeted interventions reduced the case load in border districts but registered limited impact on inland districts. This suggests a limited role in secondary within country spread. We note that combining such interventions with vaccination achieved greater reduction in case load. Conclusions: Our findings suggest that truck drivers were a core risk group, though this risk was transient and in some cases exacerbated by some interventions. Pandemic preparedness strategies should characterize risks posed by core groups to ensure interventions balance public safety with individual rights in key sectors like supply chains.
{"title":"Assessing the Impact of Haulage drivers in Uganda's COVID-19 Delta Wave","authors":"Adrian Muwonge, Paul R Bessell, Barend Mark de Clare Bronsvoort, Ibrahim Mugerwa, Erisa Mwaka, Emmanuel Ssebaggala, Wee Aidan Bryan, Aggelos Kiayias, Christine Mbabazi Mpyangu, Moses Lutakome Joloba","doi":"10.1101/2024.09.10.24313441","DOIUrl":"https://doi.org/10.1101/2024.09.10.24313441","url":null,"abstract":"Abstract Background: Haulage truck drivers can quickly connect distant communities, with risks of potential disease introduction. However, interventions to limit such risk must balance public health protection, economic continuity, and individual rights. Here distinguishing between their role in disease introduction and its onward spread is crucial for achieving this balance. Methods: To investigate the role of haulage during the Delta wave of COVID-19 in Uganda. We fit a susceptible-infectious-recovered (SIR) model to the 625,422 records in the national surveillance dataset to assess the notion of a “core-risk group” by examining the incidence and impact of haulage-targeted interventions in border districts associated with heavy haulage traffic compared to the districts in the central region of Uganda. Results: Although haulage drivers accounted for only 0.036% of the cases, the border districts associated with them registered 12.02% more cases than inland districts, suggesting a role in disease introduction. This risk was particularly higher in Tororo, compared to Amuru and Kyotera, which border Kenya, South Sudan, and Tanzania, respectively. Some interventions even increased the risk in Tororo by as much as 6%. However, in general, the haulage targeted interventions reduced the case load in border districts but registered limited impact on inland districts. This suggests a limited role in secondary within country spread. We note that combining such interventions with vaccination achieved greater reduction in case load. Conclusions: Our findings suggest that truck drivers were a core risk group, though this risk was transient and in some cases exacerbated by some interventions. Pandemic preparedness strategies should characterize risks posed by core groups to ensure interventions balance public safety with individual rights in key sectors like supply chains.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Background Dengue and Chikungunya are Aedes-borne diseases that are predominantly prevalent in tropical and subtropical regions, affecting public health globally. Dengue is caused by multiple antigenically different Dengue virus (DENV) serotypes (DENV-1 to DENV-4) in the Flaviviridae family and Chikungunya (CHIKV) in the Togaviridae family. Both viral diseases can produce similar clinical manifestations, especially in the early stages of infection which poses a significant challenge for timely diagnosis and improper disease management. Currently in India, diagnosis of Dengue and Chikungunya relies on ELISA-based tests, which often lead to false negatives and under estimation of the actual disease burden. The city of Bengaluru, in the state of Karnataka, in Southern India, witnesses spike in Dengue infection, and hence it is important to diagnose these arboviral infections early as well as accurately, to estimate the disease burden for precise epidemiological assessments. Methods A multiplex, quantitative, real-time PCR assay, DENCHIK was developed that can detect and differentiate between all four DENV serotypes and CHIKV infections simultaneously. Using DENCHIK assay, a total of 903 sera samples from suspected febrile patients were screened. The blood samples were collected across 161 public health centers, maternity homes and referral hospitals, in urban Bengaluru, between July 2022 - December 2022. The sensitivity and specificity of DENCHIK assay was compared with ELISA (NS1 antigen and Immunoglobulin M (IgM) antibodies) and two commercially available q RT-PCR assays for DENV and CHIKV. Findings Using DENCHIK assay, out of 903 samples, 36% infections were DENV, 17% CHIKV infections and 8% were coinfections with DENV-CHIKV. In contrast, ELISA detected 29.90% of DENV and 22.92% of CHIKV infections. We observed 9% prevalence of DENV infections using NS1 ELISA as compared to 24% as detected by IgM ELISA. DENV-1 was the predominant serotype followed by DENV-2, DENV-3 and DENV-4. There was an increase in the prevalence of DENV and CHIKV infections from June 2022 to September 2022, coinciding with the monsoon season. However, there was no significant difference observed in the prevalence of DENV and CHIKV infections across genders and age groups. The sensitivity and specificity of DENCHIK assay in DENV detection as compared to NS1 ELISA assay was observed to be 62.82% and 66.45%, respectively. In comparison to commercially available q RT-PCR assays for DENV detection, DENCHIK assay exhibited 99% and 98% sensitivity and specificity, respectively. Similarly, in case of CHIKV 26% sensitivity, 86% specificity and 98% sensitivity and specificity were observed, as compared to the IgM ELISA and commercial RT-PCR assays, respectively. Conclusion DENCHIK assay successfully enabled, simultaneous amplification of all four DENV serotypes and Chikungunya, in a single tube from clinical samples with high sensitivity and specificity. DENCHIK assay detected
{"title":"Development of a cost-effective multiplex quantitative RT-PCR assay for early detection and surveillance of Dengue, Chikungunya, and co-infections from clinical samples in low-resource settings","authors":"Shruthi Uppoor, Samruddhi Walaskar, Ritika Majji, Deepanraj SP, Thrilok Chandra K.V, Madhusudan H.N, Balasundar A.S, Rakesh kumar Mishra, Farah Ishtiaq, Mansi Rajendra Malik","doi":"10.1101/2024.09.10.24313257","DOIUrl":"https://doi.org/10.1101/2024.09.10.24313257","url":null,"abstract":"Abstract\u0000Background\u0000Dengue and Chikungunya are Aedes-borne diseases that are predominantly prevalent in tropical and subtropical regions, affecting public health globally. Dengue is caused by multiple antigenically different Dengue virus (DENV) serotypes (DENV-1 to DENV-4) in the Flaviviridae family and Chikungunya (CHIKV) in the Togaviridae family. Both viral diseases can produce similar clinical manifestations, especially in the early stages of infection which poses a significant challenge for timely diagnosis and improper disease management. Currently in India, diagnosis of Dengue and Chikungunya relies on ELISA-based tests, which often lead to false negatives and under estimation of the actual disease burden. The city of Bengaluru, in the state of Karnataka, in Southern India, witnesses spike in Dengue infection, and hence it is important to diagnose these arboviral infections early as well as accurately, to estimate the disease burden for precise epidemiological assessments. Methods\u0000A multiplex, quantitative, real-time PCR assay, DENCHIK was developed that can detect and differentiate between all four DENV serotypes and CHIKV infections simultaneously. Using DENCHIK assay, a total of 903 sera samples from suspected febrile patients were screened. The blood samples were collected across 161 public health centers, maternity homes and referral hospitals, in urban Bengaluru, between July 2022 - December 2022. The sensitivity and specificity of DENCHIK assay was compared with ELISA (NS1 antigen and Immunoglobulin M (IgM) antibodies) and two commercially available q RT-PCR assays for DENV and CHIKV. Findings\u0000Using DENCHIK assay, out of 903 samples, 36% infections were DENV, 17% CHIKV infections and 8% were coinfections with DENV-CHIKV. In contrast, ELISA detected 29.90% of DENV and 22.92% of CHIKV infections. We observed 9% prevalence of DENV infections using NS1 ELISA as compared to 24% as detected by IgM ELISA. DENV-1 was the predominant serotype followed by DENV-2, DENV-3 and DENV-4. There was an increase in the prevalence of DENV and CHIKV infections from June 2022 to September 2022, coinciding with the monsoon season. However, there was no significant difference observed in the prevalence of DENV and CHIKV infections across genders and age groups.\u0000The sensitivity and specificity of DENCHIK assay in DENV detection as compared to NS1 ELISA assay was observed to be 62.82% and 66.45%, respectively. In comparison to commercially available q RT-PCR assays for DENV detection, DENCHIK assay exhibited 99% and 98% sensitivity and specificity, respectively. Similarly, in case of CHIKV 26% sensitivity, 86% specificity and 98% sensitivity and specificity were observed, as compared to the IgM ELISA and commercial RT-PCR assays, respectively. Conclusion\u0000DENCHIK assay successfully enabled, simultaneous amplification of all four DENV serotypes and Chikungunya, in a single tube from clinical samples with high sensitivity and specificity. DENCHIK assay detected","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.10.24313420
Charls Erik Halder
Background: The health system is required to be safe, equitable, and accessible to all ages, gender, and vulnerable groups, including older persons and persons with disability, and address their specific needs and concerns. However, limited evidence is available on the effectiveness and practicality of gender and protection mainstreaming interventions in health response in humanitarian crises. Objective: The overall objective of the research was to explore practices, gaps, and challenges and generate recommendations regarding gender and protection mainstreaming in health response to the Rohingya refugee crisis in Cox’s Bazar, Bangladesh. Methodology: The research employed a qualitative case study design to explore the practice of gender and protection mainstreaming in health response in Cox’s Bazar. Data collection methods include an extensive literature review and in-depth interviews with professionals. Result: The study found a range of good practices on gender and protection mainstreaming in health response, e.g. placement of a gender action plan, monitoring system for gender and disability inclusion, emergency preparedness and response system, availability of sex-segregated toilets and waiting spaces, availability of gender-based violence service and engagement of female community health workers. The study also revealed some best practices which have the potential to scale up, e,g. psycho-social spaces at health facilities for children, palliative care for terminally ill patients, integrated medical and protection services, and facilitation of community health facility support groups. Critical gaps were found in the areas of women’s leadership, coordination, capacity building, targeted interventions for vulnerable groups, infrastructural adaptation and consultation with the community on their concerns. Conclusion: We urge policymakers, sector coordinators, health program management, healthcare workers, and global stakeholders to address the gaps and challenges, learn and scale up the best practices, and take action to implement the study's recommendations to maximise gender and protection mainstreaming in health response.
{"title":"The Practice of Gender and Protection Mainstreaming in Health Response in Humanitarian Crisis - A Case Study from the Refugee Camps in Cox’s Bazar, Bangladesh","authors":"Charls Erik Halder","doi":"10.1101/2024.09.10.24313420","DOIUrl":"https://doi.org/10.1101/2024.09.10.24313420","url":null,"abstract":"Background: The health system is required to be safe, equitable, and accessible to all ages, gender, and vulnerable groups, including older persons and persons with disability, and address their specific needs and concerns. However, limited evidence is available on the effectiveness and practicality of gender and protection mainstreaming interventions in health response in humanitarian crises.\u0000Objective: The overall objective of the research was to explore practices, gaps, and challenges and generate recommendations regarding gender and protection mainstreaming in health response to the Rohingya refugee crisis in Cox’s Bazar, Bangladesh. Methodology: The research employed a qualitative case study design to explore the practice of gender and protection mainstreaming in health response in Cox’s Bazar. Data collection methods include an extensive literature review and in-depth interviews with professionals.\u0000Result: The study found a range of good practices on gender and protection mainstreaming in health response, e.g. placement of a gender action plan, monitoring system for gender and disability inclusion, emergency preparedness and response system, availability of sex-segregated toilets and waiting spaces, availability of gender-based violence service and engagement of female community health workers. The study also revealed some best practices which have the potential to scale up, e,g. psycho-social spaces at health facilities for children, palliative care for terminally ill patients, integrated medical and protection services, and facilitation of community health facility support groups. Critical gaps were found in the areas of women’s leadership, coordination, capacity building, targeted interventions for vulnerable groups, infrastructural adaptation and consultation with the community on their concerns.\u0000Conclusion: We urge policymakers, sector coordinators, health program management, healthcare workers, and global stakeholders to address the gaps and challenges, learn and scale up the best practices, and take action to implement the study's recommendations to maximise gender and protection mainstreaming in health response.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"61 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.10.24312933
Maarten de Jong, Jolinda de Korne-Elenbaas, Ewout Fanoy, Gertjan Medema, Miranda de Graaf, Amrish Y Baidjoe, Maria Prins, Maarten F. Schim van der Loeff, Joost Daams, Ana Maria de Roda Husman, Janneke Heijne
Background Infectious disease surveillance and outbreak investigations have significantly benefited from sewage monitoring as an indicator for pathogen circulation in human populations. The use of sewage surveillance accelerated during the COVID-19 pandemic with the quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in sewage providing predictions of SARS-CoV-2 infections and hospital admissions. A comprehensive overview how sewage monitoring can further inform local and regional public health actions proactively is needed to optimize its future use. By conducting a scoping review, we aim to provide an overview of reported public health actions as a response to sewage monitoring for pathogens. Methods This scoping review will include peer-reviewed published literature from the databases MEDLINE, EMBASE and Web of Science. Literature describing public health actions as a response to sewage monitoring in the field of human infectious diseases will be considered for inclusion. Literature not written in English, published prior to 1 January 2014, systematic reviews, editorials and letters to the editor will be excluded. Screening of literature against the inclusion criteria and the subsequent data extraction will be performed by two reviewers. The described public health actions, and corresponding sewage sampling methods and microbiological analytic tools and techniques that can be applied on sewage samples for detecting pathogens will also be extracted. The extracted data from included literature will be combined into a narrative synthesis.
背景传染病监测和疫情调查从污水监测中获益匪浅，因为污水是病原体在人群中传播的指标。在 COVID-19 大流行期间，污水监测的使用速度加快，污水中严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）的定量提供了对 SARS-CoV-2 感染和入院人数的预测。为了优化污水监测的未来应用，我们需要全面了解污水监测如何进一步为地方和区域公共卫生行动提供前瞻性信息。通过开展范围审查，我们旨在概述已报告的公共卫生行动，作为对污水病原体监测的回应。方法本次范围界定审查将包括 MEDLINE、EMBASE 和 Web of Science 等数据库中经同行评审发表的文献。在人类传染病领域中，描述公共卫生行动作为对污水监测的回应的文献将被考虑纳入。非英文文献、2014 年 1 月 1 日之前发表的文献、系统综述、社论和致编辑的信将被排除在外。根据纳入标准筛选文献以及随后的数据提取工作将由两名审稿人完成。此外，还将提取所描述的公共卫生行动、相应的污水采样方法以及可用于污水样本检测病原体的微生物分析工具和技术。从收录的文献中提取的数据将合并成叙述性综述。
{"title":"Public health actions in response to pathogen detection in sewage: a scoping review protocol","authors":"Maarten de Jong, Jolinda de Korne-Elenbaas, Ewout Fanoy, Gertjan Medema, Miranda de Graaf, Amrish Y Baidjoe, Maria Prins, Maarten F. Schim van der Loeff, Joost Daams, Ana Maria de Roda Husman, Janneke Heijne","doi":"10.1101/2024.09.10.24312933","DOIUrl":"https://doi.org/10.1101/2024.09.10.24312933","url":null,"abstract":"Background\u0000Infectious disease surveillance and outbreak investigations have significantly benefited from sewage monitoring as an indicator for pathogen circulation in human populations. The use of sewage surveillance accelerated during the COVID-19 pandemic with the quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in sewage providing predictions of SARS-CoV-2 infections and hospital admissions. A comprehensive overview how sewage monitoring can further inform local and regional public health actions proactively is needed to optimize its future use. By conducting a scoping review, we aim to provide an overview of reported public health actions as a response to sewage monitoring for pathogens. Methods\u0000This scoping review will include peer-reviewed published literature from the databases MEDLINE, EMBASE and Web of Science. Literature describing public health actions as a response to sewage monitoring in the field of human infectious diseases will be considered for inclusion. Literature not written in English, published prior to 1 January 2014, systematic reviews, editorials and letters to the editor will be excluded. Screening of literature against the inclusion criteria and the subsequent data extraction will be performed by two reviewers. The described public health actions, and corresponding sewage sampling methods and microbiological analytic tools and techniques that can be applied on sewage samples for detecting pathogens will also be extracted. The extracted data from included literature will be combined into a narrative synthesis.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142225040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.09.24313359
Isabel Meciar, Coral E Gartner, Ariel McLay, Cheneal Puljevic
Introduction: There are concerns that progressively stringent tobacco control policies will result in increased illicit tobacco trade (ITT). We reviewed the international evidence base to identify studies examining the impact of tobacco control polices on ITT. Methods: Guided by JBI scoping review methodology, we searched six databases (PubMed, CINAHL, EMBASE, PsycINFO, Scopus, and Web of Science) in 2022 and 2024 for original research published in English since 2000. One reviewer screened titles and abstracts, and two reviewers screened full-text articles against inclusion criteria. We report the results according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews Checklist. Results: We identified 60 articles examining the impact of eight tobacco control policies or combination of policies on the ITT, including tobacco tax increases or decreases (n=43); menthol bans (n=5); decreasing allowable cigarette filter ventilation levels (n=1); standardised packaging (n=5); tobacco sales bans (n=1); a substantial reduction in the number of tobacco retailers (n=1); a very low nicotine content mandate (VLNC; n=2); and multicomponent policy interventions (n=4). Conclusions: The available evidence is predominantly focused on the impact of tobacco tax increases on the ITT, with equal numbers of studies describing an increase in the ITT or no impact on the ITT, countering claims that tobacco tax increases are the primary driver of increased ITT. Evidence on the impact of other tobacco control policies on the ITT is limited. Collaborative efforts to develop accurate and consistent methods to assess the ITT are needed.
导言：有人担心逐步严格的烟草控制政策会导致非法烟草贸易（ITT）的增加。我们对国际证据库进行了审查，以确定有关烟草控制政策对 ITT 影响的研究：在 JBI 范围综述方法的指导下，我们在 2022 年和 2024 年检索了六个数据库（PubMed、CINAHL、EMBASE、PsycINFO、Scopus 和 Web of Science）中自 2000 年以来用英语发表的原创研究。一位审稿人筛选了标题和摘要，两位审稿人根据纳入标准筛选了全文。我们根据《系统综述和元分析首选报告项目扩展范围综述核对表》报告结果：我们发现了60篇文章，研究了8种烟草控制政策或政策组合对ITT的影响，包括烟草税的增加或减少（43篇）；薄荷醇禁令（5篇）；降低卷烟过滤嘴允许通风量（1篇）；标准化包装（5篇）；烟草销售禁令（1篇）；烟草零售商数量的大幅减少（1篇）；尼古丁含量极低的规定（VLNC；2篇）；以及多成分政策干预（4篇）：现有证据主要集中于烟草税增加对 ITT 的影响，同样数量的研究描述了 ITT 的增加或对 ITT 没有影响，反驳了烟草税增加是 ITT 增加的主要驱动力的说法。其他烟草控制政策对 ITT 影响的证据有限。我们需要共同努力制定准确一致的方法来评估 ITT。
{"title":"The impact of tobacco control policies on illicit tobacco trade: A scoping review","authors":"Isabel Meciar, Coral E Gartner, Ariel McLay, Cheneal Puljevic","doi":"10.1101/2024.09.09.24313359","DOIUrl":"https://doi.org/10.1101/2024.09.09.24313359","url":null,"abstract":"Introduction: There are concerns that progressively stringent tobacco control policies will result in increased illicit tobacco trade (ITT). We reviewed the international evidence base to identify studies examining the impact of tobacco control polices on ITT.\u0000Methods: Guided by JBI scoping review methodology, we searched six databases (PubMed, CINAHL, EMBASE, PsycINFO, Scopus, and Web of Science) in 2022 and 2024 for original research published in English since 2000. One reviewer screened titles and abstracts, and two reviewers screened full-text articles against inclusion criteria. We report the results according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews Checklist.\u0000Results: We identified 60 articles examining the impact of eight tobacco control policies or combination of policies on the ITT, including tobacco tax increases or decreases (n=43); menthol bans (n=5); decreasing allowable cigarette filter ventilation levels (n=1); standardised packaging (n=5); tobacco sales bans (n=1); a substantial reduction in the number of tobacco retailers (n=1); a very low nicotine content mandate (VLNC; n=2); and multicomponent policy interventions (n=4).\u0000Conclusions: The available evidence is predominantly focused on the impact of tobacco tax increases on the ITT, with equal numbers of studies describing an increase in the ITT or no impact on the ITT, countering claims that tobacco tax increases are the primary driver of increased ITT. Evidence on the impact of other tobacco control policies on the ITT is limited. Collaborative efforts to develop accurate and consistent methods to assess the ITT are needed.","PeriodicalId":501276,"journal":{"name":"medRxiv - Public and Global Health","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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