Igor Siveroni
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View article: Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions Open
Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out …
View article: thednainus/sarscov2simulations: version 1.0.0 of R package sarscov2simulations
thednainus/sarscov2simulations: version 1.0.0 of R package sarscov2simulations Open
Functions to simulate coalescent trees based on structured coalescent models. This package also contains functions to simulate sequence data based on phylogenetic trees.
View article: Genomic epidemiology of a densely sampled COVID-19 outbreak in China
Genomic epidemiology of a densely sampled COVID-19 outbreak in China Open
Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographicall…
View article: State-level tracking of COVID-19 in the United States
State-level tracking of COVID-19 in the United States Open
As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted coun…
View article: State-level tracking of COVID-19 in the United States
State-level tracking of COVID-19 in the United States Open
As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted coun…
View article: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment
Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment Open
Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in t…
View article: Report 33: Modelling the allocation and impact of a COVID-19 vaccine
Report 33: Modelling the allocation and impact of a COVID-19 vaccine Open
Several SARS-CoV-2 vaccine candidates are now in late-stage trials, with efficacy and safety results expected by the end of 2020. Even under optimistic scenarios for manufacture and delivery, the doses available in 2021 are likely to be li…
View article: COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions
COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions Open
Background Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. Inte…
View article: Report 32: Targeting interventions to age groups that sustain COVID-19 transmission in the United States
Report 32: Targeting interventions to age groups that sustain COVID-19 transmission in the United States Open
Following inial declines, in mid 2020, a resurgence in transmission of novel coronavirus disease (COVID-19) has occurred in the United States and parts of Europe. Despite the wide implementaon of non-pharmaceucal inter-venons, it is s…
View article: Report 31: Estimating the burden of COVID-19 in Damascus, Syria: an analysis of novel data sources to infer mortality under-ascertainment
Report 31: Estimating the burden of COVID-19 in Damascus, Syria: an analysis of novel data sources to infer mortality under-ascertainment Open
The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported substantially lower mortality rates than in Europe and the Americas. One hypothesis is that thes…
View article: Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity
Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity Open
Summary Global dispersal and increasing frequency of the SARS-CoV-2 Spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of…
View article: Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies Open
Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at …
View article: State-level tracking of COVID-19 in the United States
State-level tracking of COVID-19 in the United States Open
As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted coun…
View article: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment
Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment Open
Background : The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in…
View article: Genomic epidemiology of a densely sampled COVID-19 outbreak in China
Genomic epidemiology of a densely sampled COVID-19 outbreak in China Open
Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographicall…
View article: BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis Open
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary q…
View article: BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis
BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis Open
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary q…
View article: Bayesian phylodynamic inference with complex models
Bayesian phylodynamic inference with complex models Open
Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry. The parameters of a population genetic model may also have intrinsic…
View article: Bayesian phylodynamic inference with complex models
Bayesian phylodynamic inference with complex models Open
Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry.The parameters of a population genetic model may also have intrinsic …