Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020.
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ABSTRACT:
SUBMITTER: Kwon JH
PROVIDER: S-EPMC8574293 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIn the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data.AimWe applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata.MethodsWe investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission.ResultsWe identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions.ConclusionsEarly spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.
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Project description:This study presents a framework for determining the prioritization of vaccine introduction in the National Immunization Program (NIP) of the Republic of Korea, with a focus on case examples assessed in 2021 and 2023. We describe the predefined criteria for evaluating the prioritization of vaccines in the NIP and the established process in the Republic of Korea. These criteria included disease characteristics, vaccine characteristics, rationality and efficiency of resource allocation, and the acceptance of immunization. The process of prioritizing NIP introduction involved several sequential steps: a demand survey, evidence collection, preliminary evaluation, priority evaluation, and decision making. In 2021 and 2023, 14 and 25 committee members participated in evaluating the prioritization of vaccines in the NIP, respectively. Overall, 13 and 19 NIP vaccine candidates were included in the 2021 and 2023 evaluations, respectively. Through the Delphi survey and consensus processes, the priority order was determined: vaccination against Rotavirus infection was the top priority in 2021, while Influenza 4v (for chronic disease patients) took precedence in 2023. This study demonstrates an evidence-based decision-making process within the healthcare field. The outlined approach may provide valuable guidance for policymakers in other countries seeking to prioritize the inclusion of new vaccines in their NIP.
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Project description:Background:The recent COVID-19 pandemic has emerged as a threat to global health. Though current evidence on the epidemiology of the disease is emerging, very little is known about the predictors of recovery. Objectives:To describe the epidemiology of confirmed COVID-19 patients in the Republic of Korea and identify predictors of recovery. Materials and Methods:Using publicly available data for confirmed COVID-19 cases from the Korea Centers for Disease Control and Prevention from January 20, 2020, to April 30, 2020, we undertook descriptive analyses of cases stratified by sex, age group, place of exposure, date of confirmation, and province. Correlation was tested among all predictors (sex, age group, place of exposure, and province) with Pearson's correlation coefficient. Associations between recovery from COVID-19 and predictors were estimated using a multivariable logistic regression model. Results:Majority of the confirmed cases were females (56%), 20-29 age group (24.3%), and primarily from three provinces-Gyeongsangbuk-do (36.9%), Gyeonggi-do (20.5%), and Seoul (17.1%). The case fatality ratio was 2.1%, and 41.6% cases recovered. Older patients, patients from provinces such as Daegu, Gyeonggi-do, Gyeongsangbuk-do, Jeju-do, Jeollabuk-do, and Jeollanam-do, and those contracting the disease from healthcare settings had lower recovery. Conclusions:Our study adds to the very limited evidence base on potential predictors of recovery among confirmed COVID-19 cases. We call additional research to explore the predictors of recovery and support development of policies to protect the vulnerable patient groups.
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Project description:UNLABELLED:For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. IMPORTANCE:In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.
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Project description:Corona virus disease 2019 (COVID-19) has been declared a global pandemic and is a major public health concern worldwide. In this study, we aimed to determine the role of environmental factors, such as climate and air pollutants, in the transmission of COVID-19 in the Republic of Korea. We collected epidemiological and environmental data from two regions of the Republic of Korea, namely Seoul metropolitan region (SMR) and Daegu-Gyeongbuk region (DGR) from February 2020 to July 2020. The data was then analyzed to identify correlations between each environmental factor with confirmed daily COVID-19 cases. Among the various environmental parameters, the duration of sunshine and ozone level were found to positively correlate with COVID-19 cases in both regions. However, the association of temperature variables with COVID-19 transmission revealed contradictory results when comparing the data from SMR and DGR. Moreover, statistical bias may have arisen due to an extensive epidemiological investigation and altered socio-behaviors that occurred in response to a COVID-19 outbreak. Nevertheless, our results suggest that various environmental factors may play a role in COVID-19 transmission.
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