Publications
| Title | Journal | Date |
Driver Project | Abstract |
|---|---|---|---|---|
| Developing a prototype for federated analysis to enhance privacy and enable trustworthy access to COVID-19 research data | International Journal of Medical Informatics | Dec-24 | DP2-iPOP | To set out the methodology used by ICODA in developing a rapid prototype to support secure, federated methods for the access and analysis of sensitive health data. |
| Data challenges for international health emergencies: lessons learned from ten international COVID-19 driver projects | The Lancet Digital Health | May-24 | This Health Policy paper focuses on the challenges and lessons learned from ten of the ICODA driver projects, involving researchers from 19 countries and a range of health-related datasets. | |
| Using electronic medical records to understand the impact of SARS-CoV-2 lockdown measures on maternal and neonatal outcomes in Kampala, Uganda | PLOS Global Public Health | Dec-23 | DP-IROC | The DP-IROC team investigated the use of EHR to assess risk factors for adverse pregnancy and infant outcomes that can be incorporated into a data visualization dashboard for real time decision making during pandemics. This study analysed data from the UgandaEMR collected at pre-, during- and post-lockdown timepoints of the COVID-19 pandemic to determine its use in monitoring risk factors for adverse pregnancy and neonatal outcomes. |
| Public Involvement & Engagement in health inequalities research on COVID-19 pandemic: a case study of CIDACS/FIOCRUZ BAHIA | International Journal of Population Data Science | Jun-23 | DP-IDS-COVID19 | A multidisciplinary team from Cidacs/Fiocruz Bahia developed a Social Disparities Index for Covid-19 (IDS-COVID-19) to support the evaluation of effects of health inequalities on the pandemic in Brazil. Public Involvement and Engagement were the pillars of this research because they allowed us to access first hand experiences about the social context in our country. |
| What we talk about when we talk about COVID-19 vaccination campaign impact: a narrative review | Frontiers in Public Health | May-23 | DP-EFFECT | The present work presents a narrative review, describing and discussing COVID-19 vaccination impact studies, mapping their relevant characteristics, such as study design, approaches and outcome variables, while analyzing their similarities, distinctions, and main insights. |
| Quality of routine health data at the onset of the COVID-19 pandemic in Ethiopia, Haiti, Laos, Nepal, and South Africa | Population Health Metrics | May-23 | DP-REHCORD | During the COVID-19 pandemic, governments and researchers have used routine health data to estimate potential declines in the delivery and uptake of essential health services. This research relies on the data being high quality and, crucially, on the data quality not changing because of the pandemic. In this paper, we investigated those assumptions and assessed data quality before and during COVID-19. |
| Changes in preterm birth and stillbirth during COVID-19 lockdowns in 26 countries | Nature Human Behaviour | Feb-23 | DP2-iPOP | Preterm birth (PTB) is the leading cause of infant mortality worldwide. Changes in PTB rates, ranging from −90% to +30%, were reported in many countries following early COVID-19 pandemic response measures (‘lockdowns’)… |
| Maré cohort-profile: a prospective cohort study based in a socially vulnerable community during the COVID-19 pandemic in Rio de Janeiro, Brazil | Gates Open Research | Feb-23 | DP-EFFECT | Here, we present the protocol for a community-based prospective cohort study in the largest complex of favelas (slums) in Rio de Janeiro, Brazil (Complexo da Maré). The study participants are residents initially recruited during a massive vaccination campaign in the community. |
| Tracking health system performance in times of crisis using routine health data: lessons learned from a multi-country consortium | Health Research Policy and Systems | Jan-23 | DP-REHCORD | COVID-19 has prompted the use of readily available administrative data to track health system performance in times of crisis and to monitor disruptions in essential healthcare services. In this commentary we describe our experience working with these data and lessons learned across countries. Since April 2020, the Quality Evidence for Health System Transformation (QuEST) network has used administrative data and routine health information systems (RHIS) to assess health system performance during COVID-19 in Chile, Ethiopia, Ghana, Haiti, Lao People’s Democratic Republic, Mexico, Nepal, South Africa, Republic of Korea and Thailand. |
| Profile of COVID-19 in Brazil—risk factors and socioeconomic vulnerability associated with disease outcome: retrospective analysis of population-based registers | BMJ Global Health | Dec-22 | DP-RASUP | To classify the most up-to-date factors associated with COVID-19 disease outcomes in Brazil… |
| LMIC-PRIEST: Derivation and validation of a clinical severity score for acutely ill adults with suspected COVID-19 in a middle-income setting | PLOS ONE | Nov-22 | DP-PRIEST | Uneven vaccination and less resilient health care systems mean hospitals in LMICs are at risk of being overwhelmed during periods of increased COVID-19 infection. Risk-scores proposed for rapid triage of need for admission from the emergency department (ED) have been developed in higher-income settings during initial waves of the pandemic… |
| Seroepidemiology of SARS-CoV-2 on a partially vaccinated island in Brazil: determinants of infection and vaccine response | Frontiers in Public Health | Nov-22 | DP-EFFECT | A vaccination campaign targeted adults in response to the pandemic in the City of Rio de Janeiro.We aimed to evaluate the seroprevalence of SARS-CoV-2 antibodies and identify factors associated with seropositivity on vaccinated and unvaccinated residents. We performed a seroepidemiologic survey in all residents of Paquetá Island, a neighborhood of Rio de Janeiro city, during the COVID-19 vaccine roll-out. |
| The effect of lifting COVID-19 restrictions on utilization of primary care services in Nepal: a difference-in-differences analysis | BMJ Global Health | Nov-22 | DP-REHCORD | An increasing number of studies have reported disruptions in health service utilisation due to the COVID-19 pandemic and its associated restrictions. However, little is known about the effect of lifting COVID-19 restrictions on health service utilisation. The objective of this study was to estimate the effect of lifting COVID-19 restrictions on primary care service utilisation in Nepal. |
| Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa | International Journal of Infectious Diseases | Nov-22 | DP-ACCORD | We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection… |
| Prediction of upcoming global infection burden of influenza seasons after relaxation of public health and social measures during the COVID-19 pandemic: a modelling study | Lancet Global Health | Oct-22 | DP-CHAIN | The transmission dynamics of influenza were affected by public health and social measures (PHSMs) implemented globally since early 2020 to mitigate the COVID-19 pandemic. We aimed to assess the effect of COVID-19 PHSMs on the transmissibility of influenza viruses and to predict upcoming influenza epidemics… |
| Data capture and sharing in the COVID-19 pandemic: a cause for concern | Lancet Digital Health | Sep-22 | DP1-EFCT | Routine health care and research have been profoundly influenced by digital-health technologies. These technologies range from primary data collection in electronic health records (EHRs) and administrative claims to web-based artificial-intelligence-driven analyses… |
| Effect of the COVID-19 pandemic on health service utilization across regions of Ethiopia: An interrupted time series analysis of health information system data from 2019–2020 | PLOS Global Public Health | Sep-22 | DP-REHCORD | The spread of COVID-19 and associated deaths have remained low in Ethiopia. However, the pandemic could pose a public health crisis indirectly through disruptions in essential health services… |
| Epidemiologic information discovery from open-access COVID-19 case reports via pretrained language model | iScience | Sep-22 | DP-CHAIN | Although open-access data are increasingly common and useful to epidemiological research, the curation of such datasets is resource-intensive and time-consuming. Despite the existence of a major source of COVID-19 data, the regularly disclosed case reports were often written in natural language with an unstructured format |
| Primary healthcare protects vulnerable populations from inequity in COVID-19 vaccination: An ecological analysis of nationwide data from Brazil | The Lancet Regional Health Americas | Aug-22 | DP-EFFECT | There is limited information on the inequity of access to vaccination in low-and-middle-income countries during the COVID-19 pandemic. Here, we described the progression of the Brazilian immunisation program for COVID-19, and the association of socioeconomic development with vaccination rates, considering the potential protective effect of primary health care coverage… |
| Prognostic accuracy of triage tools for adults with suspected COVID-19 in a middle-income setting: an observational cohort study | BMJ Emergency Medicine Journal | Aug-22 | DP-PRIEST | Tools proposed to triage acuity in suspected COVID-19 in the ED have been derived and validated in higher-income settings during early waves of the pandemic. We estimated the accuracy of seven risk-stratification tools recommended to predict severe illness in the Western Cape, South Africa… |
| ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19 | Nature Scientific Data | Jul-22 | DP-ISARIC | The International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) COVID-19 dataset is one of the largest international databases of prospectively collected clinical data on people hospitalized with COVID-19… |
| Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa | International Journal of Infectious Diseases | Jul-22 | DP – ACCORD | We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection… |
| Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa | Tropical Medicine and International Health | Jun-22 | DP-ACCORD | The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained… |
| Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis | International Journal of Infectious Diseases | May-22 | DP-ACCORD | At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity… |
| Assessing the spread risk of COVID-19 associated with multi-mode transportation networks in China | Fundamental Research | Apr-22 | DP-CHAIN | The spatial spread of COVID-19 during early 2020 in China was primarily driven by outbound travelers leaving the epicenter, Wuhan, Hubei province… |
| The resilient intensive care unit | Springer Open | Apr-22 | DP-EFFECT | The COVID-19 pandemic tested the capacity of intensive care units (ICU) to respond to a crisis and demonstrated their fragility. Unsurprisingly, higher than usual mortality rates, lengths of stay (LOS), and ICU-acquired complications occurred during the pandemic. However, worse outcomes were not universal nor constant across ICUs and significant variation in outcomes was reported, demonstrating that some ICUs could adequately manage the surge of COVID-19… |
| Overcoming disruptions in essential health services during the COVID-19 pandemic in Mexico | BMJ Global Health | Mar-22 | DP-REHCORD | Significant disruptions in health services during the first year of the COVID-19 pandemic prompted the Mexican Institute of Social Security (IMSS) to implement the National Strategy for Health Services Recovery (NHSR strategy) to ensure resumption of essential health services provided to almost 68 million IMSS affiliates… |
| Vaccine effectiveness of ChAdOx1 nCoV-19 against COVID-19 in a socially vulnerable community in Rio de Janeiro, Brazil: a test-negative design study | Clinical Microbiology and Infection | Mar-22 | DP-EFFECT | To estimate the vaccine effectiveness after first and second dose of ChAdOx1 nCoV-19 against symptomatic COVID-19 and infection in a socially vulnerable community in Brazil when Gamma and Delta were the predominant variants circulating… |
| COVID-19 and resilience of healthcare systems in ten countries | Nature Medicine | Mar-22 | DP-REHCORD | Declines in health service use during the Coronavirus Disease 2019 (COVID-19) pandemic could have important effects on population health. In this study, we used an interrupted time series design to assess the immediate effect of the pandemic on 31 health services… |
| Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India | Nature Medicine | Feb-22 | DP-CHAIN | Given global Coronavirus Disease 2019 (COVID-19) vaccine shortages and inequity of vaccine distributions, fractionation of vaccine doses might be an effective strategy for reducing public health and economic burden, notwithstanding the emergence of new variants of concern… |
| Reproduction Numbers of SARS-CoV-2 Variants: A Systematic Review and Meta-analysis | Clinical Infectious Diseases | Feb-22 | DP-CHAIN | The COVID-19 pandemic continues to pose substantial risks to public health, worsened by the emergence of SARS-CoV-2 variants which may have a higher transmissibility and reduce vaccine effectiveness… |
| Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests | Journal of Virological Methods | Jan-22 | DP-ACCORD | Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant… |
| Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa | Tropical Medicine and International Health | Jan-22 | DP-ACCORD | We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained. |
| Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis | International Journal of Infectious Diseases | Jan-22 | DP-ACCORD | Emerging data suggest that SARS-CoV-2 Omicron variant of concern (VOC)is associated with reduced risk of severe disease. The extent to which this reflects a difference in the inherent virulence of Omicron, or just higher levels of population immunity, is currently not clear. |
| Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. | Gates Open Research | Oct-21 | DP-ACCORD | A novel proxy for the Delta variant, RNA-dependent RNA polymerase target delay in the Seegene Allplex™ 2019-nCoV PCR assay, was associated with higher mortality (adjusted Odds Ratio 1.45 [95%CI 1.13-1.86]), compared to presumptive Beta infection, in the Western Cape, South Africa (April-July 2021). Prior diagnosed infection and vaccination were protective |
| Disruption in essential health services in Mexico during COVID-19: an interrupted time series analysis of health information system data | BMJ Global Health | Aug-21 | DP-REHCORD | The COVID-19 pandemic has disrupted health systems around the world. The objectives of this study are to estimate the overall effect of the pandemic on essential health service use and outcomes in Mexico, describe observed and predicted trends in services over 24 months, and to estimate the number of visits lost through December 2020 |
| The international Perinatal Outcomes in the Pandemic (iPOP) study: protocol | Wellcome Open Research | Feb-21 | DP2-iPOP | Preterm birth is the leading cause of infant death worldwide, but the causes of preterm birth are largely unknown… |
| Open Science to Address COVID-19: Sharing Data to Make Our Research Investment Go Further | Springer Link | Dec-20 | DP1-EFCT | Over 1000 randomized clinical trials (RCTs) for the treatment and prevention of COVID-19 have been initiated. With access to the data from RCTs, researchers can integrate and summarize findings, evaluate new hypotheses, design future trials, and prioritize the next research questions to be addressed… |
| Enabling a healthy start for vulnerable newborns | The Lancet | Oct-20 | DP2-iPOP | As co leads of the new international Perinatal Outcomes in the Pandemic (iPOP) Consortium, we are delighted that the Lancet Small Vulnerable Newborn Series1 will focus crosssector attention on the high burden of baby deaths (encompassing miscarriage, stillbirth, and neonatal mortality) and disability (following preterm birth and low birthweight), which remain largely intractable with current siloed approaches |
Further research outputs and resources
| Title | Journal | Date |
Driver Project | Abstract |
|---|---|---|---|---|
| Funding and undertaking research during the first year of the COVID-19 pandemic: COVID CIRCLE lessons for funders |
UK Collaborative on Development Research (UKCDR) | ICODA | As part of the report we have developed seven case studies involving research projects and programmes which have demonstrated innovative best practice in research in epidemics. Each case study highlights factors of success in applying one or more of the Seven Funder Principles for supporting high quality research for the most pressing global needs in epidemics and pandemics, to inform future funding and research practice. |
|
| Grand Challenges ICODA Data Science Initiative – Blog 3 | Aridhia | May-22 | DP-RASUP | One of several driver projects from Brazil-based Oswaldo Cruz Foundation (Fiocruz), this one is led by a team of four: lead PI Juliane Oliveira, a mathematician and researcher at Fiocruz and at the Universidade do Porto (Portugal)… |
| Grand Challenges ICODA Data Science Initiative – Blog 2 | Aridhia | Mar-22 | DP-PIH CovCo | This driver project from Partners In Health and Harvard Medical School looks to examine how the pandemic has impacted the care received by chronic care patients in four countries: Haiti, Malawi, Mexico and Rwanda… |
| Grand Challenges ICODA Data Science Initiative – Blog 1 | Aridhia | Nov-21 | DP-CHAIN | A few months ago, we reported on the launch of the Grand Challenges ICODA Data Science initiative by the Bill & Melinda Gates Foundation. These 10 projects will use the ICODA Workbench (powered by Aridhia’s DRE) to explore the answers to critical research questions relating to COVID-19. Over the coming weeks, we will take a look at some of these projects and what they aim to achieve… |
| Data and Analytics – Put your expertise to work to address the COVID-19 pandemic | Biopharmaceutical report | Sep-21 | DP1-EFCT | The worldwide toll of the COVID-19 pandemic is substantial, so is the response of the many professionals in healthcare. Be it in the patient care, research or government sectors, many talented experts have joined together to advance the development of treatments to address infections from the virus |
| Pandemic upheaval offers a huge natural experiment | Nature | Aug-21 | DP2-iPOP | The disruption that the coronavirus has caused to daily life has created unique research opportunities for scientists |
| Team Science: Defining and Achieving Success | Clinical and Investigative Medicine | Jun-21 | DP2-iPOP | Meghan Azad and Nathalie Rodriguez share share their Top 10 Tips for defining and achieving success in Team Science |
| Pacifying A Pandemic With Numbers | Invivo – Informa Pharma Intelligence | Jun-21 | DP1-EFCT | Powered by prominent global health philanthropies and the UK’s world-class collaborative capabilities in disease surveillance, the new International COVID-19 Data Alliance (ICODA) is gearing up to address a crucial – and yet unanswered – policy question for public health: can sharing data curated from a diversity of sources provide the hard evidence needed to improve patient outcomes against the virus – not just for today’s pandemic, but for future ones as well? Much will depend on a robust response from big pharma… |
| The urgent need for better coordination across the global data sharing landscape | ICODA | Jun-21 | ICODA | Mapping of the landscape of COVID-19 data-related activities |
Pre-prints
| Title | Journal | Date |
Driver Project | Abstract |
|---|---|---|---|---|
| COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting | medRXiv | Oct-22 | DP-ACCORD | Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age… |
| What did you do to stay ‘sane’ during the pandemic? A qualitative study to identify self-care mental health strategies utilized in a vulnerable population | Gates Open Research | Jul-22 | DP-EFFECT | Mental health has deteriorated during the COVID-19 pandemic. These impacts are likely to be more severe in socially vulnerable communities. During March and April 2021, we conducted open-ended interviews with 317 community members in Complexo de Favelas da Maré, Rio de Janeiro, Brazil, one of the largest slum areas in South America… |
| Profile of COVID-19 in Brazil: Risk Factors and Socioeconomic Vulnerability Associated with Disease Outcome | The Lancet | Apr-22 | DP-RASUP | Background: COVID-19 spread at different rates across the globe, and severe outcomes of the disease are influenced by clinical and socioeconomic elements… |
Generic governance processes for re-use
These process documents were created as part of the ICODA programme. They are open, free to use and amend as needed by your organisation, we just request you attribute us following our Attribution Policy.
Generic data controllership agreements for re-use
These agreements were created as part of the ICODA programme. They are open, free to use and amend as needed in support of establishing your organisation as a data controller, we just request you attribute us following our Attribution Policy. You can find background to this capability and the agreements used as part of the ICODA programme and generic versions provided for re-use on our data controllership page.
Digital Object Identifiers (DOIs)
Digital Object Identifiers (DOIs) were created for assets as part of the ICODA programme, ensuring they are always findable.
Datasets
Details of the datasets used by researchers as part of the ICODA programme can be found on the Health Data Research Gateway
ICODA project teams were provided with instructions and support to prepare and publish the metadata for their research data.