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Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology.

ABSTRACT: We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic tree, differed among the Nordic countries of Norway, Sweden, Denmark, Finland, and Iceland. Our results suggest that although geographical connectivity, population density, and openness influence the spread and the size of SARS-CoV-2 transmission clusters, the different country-specific intervention strategies had the largest impact. We also found a significant positive association between the size and duration of transmission clusters in the Nordic countries, suggesting that the rapid deployment of contact tracing is a key response measure in reducing virus transmission.

SUBMITTER: Duchene S

PROVIDER: S-EPMC8755353 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology.

Duchene Sebastian S Featherstone Leo L Freiesleben de Blasio Birgitte B Holmes Edward C EC Bohlin Jon J Pettersson John H O JHO

Open forum infectious diseases 20220103 3

We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic tree, differed among the Nordic countries of Norway, Sweden, Denmark, Finland, and Iceland. Our results suggest that although geographical connectivity, population density, and openness influence the spread and the size of SARS-CoV-2 transmission clusters, the different country-specific interv ...[more]

PMID: 35229003

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Project description:BackgroundIn late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.MethodsWe did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.FindingsThe ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.Interpretation2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.FundingNational Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.

Project description:Background/purposeWe aimed to describe the epidemiology of trauma activations and variations in injury patterns, injury severity, and hospital length-of-stay for injured children in Los Angeles (LA) County during the coronavirus-disease-19 (COVID-19) pandemic.MethodsWe conducted a retrospective cross-sectional study of children aged < 18-years evaluated in 15 trauma centers from 2019 to 2020 and entered in the LA County trauma registry. We defined 01/01/2019-03/18/2020 as pre-pandemic and 03/19/2020-12/31/2020 as the pandemic period. Our primary outcome was pediatric trauma activations. We analyzed demographic and clinical data, including types and severity of injuries sustained. We conducted unadjusted bivariate analyzes of injury patterns between periods. Segmented linear regression models were used to test rates (per 100,000 LA County children) of trauma activations pre-pandemic versus the pandemic period.ResultsWe studied 4399 children with trauma activations, 2695 of which occurred pre-pandemic and 1701 in the pandemic period. Motor vehicle collisions, gunshot wounds, and burns increased during the pandemic (all p-values< 0.05), while sports injuries decreased (p < 0.001). Median injury severity scores (p = 0.323) and Glasgow Coma Scales (p = 0.558) did not differ between periods, however mortality (p = 0.023) decreased during the pandemic. Segmented linear regression estimates demonstrated that rates of trauma activations pre-pandemic were similar to the pandemic period (p = 0.384).ConclusionPediatric trauma activations in LA County did not significantly differ during the COVID-19 pandemic, but types and severity of injuries varied between pre-pandemic and pandemic periods. With lockdown restrictions being lifted and novel SARS-CoV-2 variants circulating, our investigation describes this recent epidemiologic phenomenon to aid future preparation for healthcare systems.Level of evidenceLevel III TYPE OF STUDY: Retrospective cross-sectional study.

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Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology.

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Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology.

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