scholarly journals Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

2021 ◽  
Author(s):  
Sarah A. Nadeau ◽  
Timothy G. Vaughan ◽  
Christiane Beckmann ◽  
Ivan Topolsky ◽  
Chaoran Chen ◽  
...  
Keyword(s):  
Transmission Dynamics ◽  
Added Value ◽  
Outbreak Detection ◽  
Contact Tracing ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Health Measures ◽  
Genome Data ◽  
Transmission Chain ◽  
Local Transmission

Genome sequences allow quantification of changes in case introductions from abroad and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using these data, we estimated introductions and their persistence throughout 2020. By contrasting estimates with null models, we estimate at least 83% of introductions were adverted during Switzerland's border closures. Further, transmission chain persistence roughly doubled after the partial lockdown was lifted. Then, using a novel phylodynamic method, we suggest transmission in newly introduced outbreaks slowed 36 - 64% upon outbreak detection in summer 2020, but not in fall. This could indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

scholarly journals Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama.

2020 ◽  
Author(s):  
Danilo Franco ◽  
Claudia Gonzalez ◽  
Leyda E Abrego ◽  
Jean P Carrera ◽  
Yamilka Diaz ◽  
...  
Keyword(s):  
Doubling Time ◽  
Mitigation Strategies ◽  
Transmission Dynamics ◽  
Mitigation Measures ◽  
Epidemiological Surveillance ◽  
Contact Tracing ◽  
Reproductive Number ◽  
Surveillance Systems ◽  
Whole Genomes ◽  
Local Transmission

Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease control strategies. We investigated the early transmission patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number (Rt) using date of symptom onset in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission clusters is crucial to interrupt local transmission of SARS-CoV-2 in a region.

scholarly journals Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

2020 ◽  
Author(s):  
Yatish Turakhia ◽  
Bryan Thornlow ◽  
Angie S. Hinrichs ◽  
Nicola De Maio ◽  
Landen Gozashti ◽  
...  
Keyword(s):  
Real Time ◽  
Viral Genome ◽  
Genome Browser ◽  
Contact Tracing ◽  
Human Populations ◽  
Genome Sequences ◽  
New Era ◽  
Link Type ◽  
History Of ◽  
Local Transmission

AbstractAs the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering a new era of “genomic contact tracing” – that is, using viral genome sequences to trace local transmission dynamics. However, because the viral phylogeny is already so large – and will undoubtedly grow many fold – placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient, tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach improves the speed of phylogenetic placement of new samples and data visualization by orders of magnitude, making it possible to complete the placements under real-time constraints. Our method also provides the key ingredient for maintaining a fully-updated reference phylogeny. We make these tools available to the research community through the UCSC SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for laboratories worldwide.Software AvailabilityUSHER is available to users through the UCSC Genome Browser at https://genome.ucsc.edu/cgi-bin/hgPhyloPlace. The source code and detailed instructions on how to compile and run UShER are available from https://github.com/yatisht/usher.

scholarly journals Accounting for imported cases in estimating the time-varying reproductive number of COVID-19

2021 ◽  
Author(s):  
Tim K. Tsang ◽  
Peng Wu ◽  
Eric H. Y. Lau ◽  
Benjamin J. Cowling
Keyword(s):  
Public Health ◽  
Control Measures ◽  
Transmission Dynamics ◽  
Reproductive Number ◽  
Considerable Proportion ◽  
Time Varying ◽  
Health Measures ◽  
Imported Cases ◽  
The Impact ◽  
Local Transmission

ABSTRACTBackgroundEstimating the time-varying reproductive number, Rt, is critical for monitoring transmissibility of an emerging infectious disease during outbreaks. When local transmission is effectively suppressed, imported cases could substantially impact transmission dynamics.MethodsWe developed methodology to estimate separately the Rt for local cases and imported cases, since certain public health measures aim only to reduce onwards transmission from imported cases. We applied the framework to data on COVID-19 outbreaks in Hong Kong.ResultsWe estimated that the Rt for local cases decreased from above one in the early phase of outbreak to below one after tightening of public health measures. Assuming the same infectiousness of local and imported cases underestimated Rt for local cases due to control measures targeting travelers.ConclusionsWhen a considerable proportion of all cases are imported, the impact of imported cases in estimating Rt is critical. The methodology described here can allow for differential infectiousness of local imported cases.

scholarly journals Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Early Phase ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Local Spread ◽  
Control And Prevention ◽  
Local Transmission

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals Elucidating the Local Transmission Dynamics of Highly Pathogenic Avian Influenza H5N6 in the Republic of Korea by Integrating Phylogenetic Information

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 691
Author(s):  
Dae-Sung Yoo ◽  
Byungchul Chun ◽  
Kyung-Duk Min ◽  
Jun-Sik Lim ◽  
Oun-Kyoung Moon ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Highly Pathogenic Avian Influenza ◽  
Transmission Dynamics ◽  
Republic Of Korea ◽  
Transmission Risk ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
The Republic ◽  
The Impact ◽  
Local Transmission

Highly pathogenic avian influenza (HPAI) virus is one of the most virulent and infectious pathogens of poultry. As a response to HPAI epidemics, veterinary authorities implement preemptive depopulation as a controlling strategy. However, mass culling within a uniform radius of the infection site can result in unnecessary depopulation. Therefore, it is useful to quantify the transmission distance from infected premises (IPs) before determining the optimal area for preemptive depopulation. Accordingly, we analyzed the transmission risk within spatiotemporal clusters of IPs using transmission kernel estimates derived from phylogenetic clustering information on 311 HPAI H5N6 IPs identified during the 2016–2017 epidemic, Republic of Korea. Subsequently, we explored the impact of varying the culling radius on the local transmission of HPAI given the transmission risk estimates. The domestic duck farm density was positively associated with higher transmissibility. Ring culling over a radius of 3 km may be effective for areas with high dense duck holdings, but this approach does not appear to significantly reduce the risk for local transmission in areas with chicken farms. This study provides the first estimation of the local transmission dynamics of HPAI in the Republic of Korea as well as insight into determining an effective ring culling radius.

scholarly journals Complete Genome Sequences of Six Listeria monocytogenes Sequence Type 9 Isolates from Meat Processing Plants in Norway

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Annette Fagerlund ◽  
Solveig Langsrud ◽  
Birgitte Moen ◽  
Even Heir ◽  
Trond Møretrø
Keyword(s):  
Listeria Monocytogenes ◽  
Complete Genome ◽  
Foodborne Pathogen ◽  
Sequence Type ◽  
Nanopore Sequencing ◽  
Meat Processing ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Fatal Disease ◽  
Processing Plants

ABSTRACT Listeria monocytogenes is a foodborne pathogen that causes the often-fatal disease listeriosis. We present here the complete genome sequences of six L. monocytogenes isolates of sequence type 9 (ST9) collected from two different meat processing facilities in Norway. The genomes were assembled using Illumina and Nanopore sequencing data.

scholarly journals Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

scholarly journals Transmission dynamics of the delta variant of SARS-CoV-2 infections in Daejeon, South Korea

2021 ◽  
Author(s):  
Hari Hwang ◽  
Jun-Sik Lim ◽  
Sun-Ah Song ◽  
Chiara Achangwa ◽  
Woobeom Sim ◽  
...  
Keyword(s):  
South Korea ◽  
Symptom Onset ◽  
Credible Interval ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Strict Adherence ◽  
Virus Shedding ◽  
Viral Shedding ◽  
Asymptomatic Patients

Abstract Background The delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear. Methods We analyzed all case patients in local clusters and temporal patterns of viral shedding using contact tracing data from 405 cases associated with the delta variant of SARS-CoV-2 between 22 June and 31 July 2021 in Daejeon, South Korea. Results Overall, half of the cases were aged under 19 years, and 20% were asymptomatic at the time of epidemiological investigation. We estimated the mean serial interval as 3.26 days (95% credible interval 2.92, 3.60), and 12% of the transmission occurred before symptom onset of the infector. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63% (52/82). We estimated that 15% (95% confidence interval, 13–18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from asymptomatic patients, and the highest viral load was observed two days after symptom onset. The temporal pattern of viral shedding did not differ between children and adults (P = 0.48). Conclusions Our findings suggest that the delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, and strict adherence to public health measures are needed to mitigate the community transmission of the delta variant.

scholarly journals Transmission dynamics and the effects of non-pharmaceutical interventions in the COVID-19 outbreak resurged in Beijing, China: a descriptive and modelling study

BMJ Open ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. e047227
Author(s):  
Xiaoming Cui ◽  
Lin Zhao ◽  
Yuhao Zhou ◽  
Xin Lin ◽  
Runze Ye ◽  
...  
Keyword(s):  
Close Contact ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Population Mobility ◽  
Wholesale Market ◽  
The People ◽  
Spatiotemporal Analyses ◽  
Epidemiological Characteristics ◽  
Pharmaceutical Interventions ◽  
Modelling Study

ObjectiveTo evaluate epidemiological characteristics and transmission dynamics of COVID-19 outbreak resurged in Beijing and to assess the effects of three non-pharmaceutical interventions.DesignDescriptive and modelling study based on surveillance data of COVID-19 in Beijing.SettingOutbreak in Beijing.ParticipantsThe database included 335 confirmed cases of COVID-19.MethodsTo conduct spatiotemporal analyses of the outbreak, we collected individual records on laboratory-confirmed cases of COVID-19 from 11 June 2020 to 5 July 2020 in Beijing, and visitor flow and products transportation data of Xinfadi Wholesale Market. We also built a modified susceptible-exposed-infected-removed model to investigate the effect of interventions deployed in Beijing.ResultsWe found that the staff working in the market (52.2%) and the people around 10 km to this epicentre (72.5%) were most affected, and the population mobility entering-exiting Xinfadi Wholesale Market significantly contributed to the spread of COVID-19 (p=0.021), but goods flow of the market had little impact on the virus spread (p=0.184). The prompt identification of Xinfadi Wholesale Market as the infection source could have avoided a total of 25 708 (95% CI 13 657 to 40 625) cases if unnoticed transmission lasted for a month. Based on the model, we found that active screening on targeted population by nucleic acid testing alone had the most significant effect.ConclusionsThe non-pharmaceutical interventions deployed in Beijing, including localised lockdown, close-contact tracing and community-based testing, were proved to be effective enough to contain the outbreak. Beijing has achieved an optimal balance between epidemic containment and economic protection.

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