Dataset Information

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.

ABSTRACT: Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12^th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.

SUBMITTER: Moreno GK

PROVIDER: S-EPMC7609670 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.

Moreno Gage K GK Braun Katarina M KM Riemersma Kasen K KK Martin Michael A MA Halfmann Peter J PJ Crooks Chelsea M CM Prall Trent T Baker David D Baczenas John J JJ Heffron Anna S AS Ramuta Mitchell M Khubbar Manjeet M Weiler Andrea M AM Accola Molly A MA Rehrauer William M WM O'Connor Shelby L SL Safdar Nasia N Pepperell Caitlin S CS Dasu Trivikram T Bhattacharyya Sanjib S Kawaoka Yoshihiro Y Koelle Katia K O'Connor David H DH Friedrich Thomas C TC

Nature communications 20201103 1

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12<sup>th</sup> known introduction of SARS-CoV-2 in the United States, but this did not lead to descend ...[more]

PMID: 33144575

Similar Datasets

Project description:Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

Project description:Health and care technologies often succeed on a small scale but fail to achieve widespread use (scale-up) or become routine practice in other settings (spread). One reason for this is under-theorization of the process of scale-up and spread, for which a potentially fruitful theoretical approach is to consider the adoption and use of technologies as social practices.This study aimed to use an in-depth case study of assisted living to explore the feasibility and usefulness of a social practice approach to explaining the scale-up of an assisted-living technology across a local system of health and social care.This was an individual case study of the implementation of a Global Positioning System (GPS) "geo-fence" for a person living with dementia, nested in a much wider program of ethnographic research and organizational case study of technology implementation across health and social care (Studies in Co-creating Assisted Living Solutions [SCALS] in the United Kingdom). A layered sociological analysis included micro-level data on the index case, meso-level data on the organization, and macro-level data on the wider social, technological, economic, and political context. Data (interviews, ethnographic notes, and documents) were analyzed and synthesized using structuration theory.A social practice lens enabled the uptake of the GPS technology to be studied in the context of what human actors found salient, meaningful, ethical, legal, materially possible, and professionally or culturally appropriate in particular social situations. Data extracts were used to illustrate three exemplar findings. First, professional practice is (and probably always will be) oriented not to "implementing technologies" but to providing excellent, ethical care to sick and vulnerable individuals. Second, in order to "work," health and care technologies rely heavily on human relationships and situated knowledge. Third, such technologies do not just need to be adopted by individuals; they need to be incorporated into personal habits and collaborative routines (both lay and professional).Health and care technologies need to be embedded within sociotechnical networks and made to work through situated knowledge, personal habits, and collaborative routines. A technology that "works" for one individual in a particular set of circumstances is unlikely to work in the same way for another in a different set of circumstances. We recommend the further study of social practices and the application of co-design principles. However, our findings suggest that even if this occurs, the scale-up and spread of many health and care technologies will be neither rapid nor smooth.

Dataset Information

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.

Publications

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets