Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

Abstract The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data was available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.

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Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

10.1101/2020.09.21.300913 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ales Varabyou ◽

Christopher Pockrandt ◽

Steven L. Salzberg ◽

Mihaela Pertea

Keyword(s):

Public Health ◽

Phylogenetic Analysis ◽

Efficient Method ◽

Rapid Detection ◽

Health Policies ◽

Large Collection ◽

Sequencing Data ◽

Public Health Policies ◽

Viral Genomes ◽

Rule Out

AbstractThe ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, previous methods for detecting recombination and reassortment events cannot handle the computational requirements of analyzing tens of thousands of genomes, a scenario that has now emerged in the effort to track the spread of the SARS-CoV-2 virus. Furthermore, the low divergence of near-identical genomes sequenced in short periods of time presents a statistical challenge not addressed by available methods. In this work we present Bolotie, an efficient method designed to detect recombination and reassortment events between clades of viral genomes. We applied our method to a large collection of SARS-CoV-2 genomes and discovered hundreds of isolates that are likely of a recombinant origin. In cases where raw sequencing data was available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. Our findings further show that several recombinants appear to have persisted in the population.

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Side-Effects of Public Health Policies Against COVID-19: The Story of an Over-Reaction

10.20944/preprints202102.0269.v1 ◽

2021 ◽

Author(s):

Edouard Lansiaux ◽

Noe Tchagaspanian ◽

Juliette Arnaud ◽

Pierre Durand ◽

Mark Changizi ◽

...

Keyword(s):

Public Health ◽

Side Effects ◽

Health Policies ◽

Moral Principle ◽

Western World ◽

Global Response ◽

Public Health Policies ◽

One Dimensional ◽

Short Period ◽

The World

Let us all take a moment to talk, once again, about this new coronavirus pandemic that the world has been facing since November 2019 and about its global response. After a short period marked by the pandemic underestimation risk by most governments, the Western world went nuts and overreacted, most probably so as not to be accused of inaction. In many cases, the overall benefits of the chosen policies were not sufficiently questioned, which resulted in many side effects on global health .The medical motto “primum non nocere”, a moral principle everyone should at least consider following, was evidently not taken into account. It has been overlooked, and the virus has become an obsession, to the extent that nearly everything else, even the most valuable things in life, is still now under appreciated if not simply ignored. This review highlighted facts against this simplistic, one-dimensional view.

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Person, Place, and Time: Monitoring the Geographical and Temporal Context of Public Health Policies

PsycEXTRA Dataset ◽

10.1037/e507502013-086 ◽

2012 ◽

Author(s):

Michael Chaiton

Keyword(s):

Public Health ◽

Health Policies ◽

Temporal Context ◽

Public Health Policies

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Population simulations of COVID-19 outbreaks provide tools for risk assessment and continuity planning

JAMIA Open ◽

10.1093/jamiaopen/ooaa074 ◽

2021 ◽

Author(s):

Bo Peng ◽

Rowland W Pettit ◽

Christopher I Amos

Keyword(s):

Public Health ◽

Risk Assessment ◽

Emergency Response ◽

Robustness Analysis ◽

Health Policies ◽

Command Line ◽

Public Health Policies ◽

Continuity Planning ◽

Quantitative Estimates ◽

Community Infection

Abstract Objectives We developed COVID-19 Outbreak Simulator (https://ictr.github.io/covid19-outbreak-simulator/) to quantitatively estimate the effectiveness of preventative and interventive measures to prevent and battle COVID-19 outbreaks for specific populations. Materials and methods Our simulator simulates the entire course of infection and transmission of the virus among individuals in heterogeneous populations, subject to operations and influences, such as quarantine, testing, social distancing, and community infection. It provides command-line and Jupyter notebook interfaces and a plugin system for user-defined operations. Results The simulator provides quantitative estimates for COVID-19 outbreaks in a variety of scenarios and assists the development of public health policies, risk-reduction operations, and emergency response plans. Discussion Our simulator is powerful, flexible, and customizable, although successful applications require realistic estimation and robustness analysis of population-specific parameters. Conclusion Risk assessment and continuity planning for COVID-19 outbreaks are crucial for the continued operation of many organizations. Our simulator will be continuously expanded to meet this need.

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Results from the European Union MAPEC_LIFE cohort study on air pollution and chromosomal damage in children: are public health policies sufficiently protective?

Environmental Sciences Europe ◽

10.1186/s12302-020-00352-3 ◽

2020 ◽

Vol 32 (1) ◽

Cited By ~ 1

Author(s):

Elisabetta Ceretti ◽

◽

Francesco Donato ◽

Claudia Zani ◽

Milena Villarini ◽

...

Keyword(s):

Public Health ◽

Air Pollution ◽

European Union ◽

Cohort Study ◽

Health Policies ◽

The European Union ◽

Chromosomal Damage ◽

Public Health Policies

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Characterization of death from colorectal cancer in Mato Grosso State/Legal Amazon/Brazil, 2000-2016

European Journal of Public Health ◽

10.1093/eurpub/ckaa166.1130 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

R S Caló ◽

B S N Souza ◽

N D Galvão ◽

R A G Souza ◽

J C S Oliveira ◽

...

Keyword(s):

Public Health ◽

Colorectal Cancer ◽

International Classification Of Diseases ◽

Health Policies ◽

Rectosigmoid Junction ◽

Mato Grosso ◽

Public Health Policies ◽

Goods And Services ◽

Classification Of Diseases ◽

Using Data

Abstract Background Colorectal cancer has been one of the cancers that most contributed to mortality, in both sexes in the world. In Brazil, cancer is among the top five causes of death and colorectal cancer is ranked on the fifth position. Of the Federative Units belonging to the Legal Amazon, Mato Grosso stands out for the higher adjusted incidence of colorectal cancer for both sexes. Thus, the objective is to characterize deaths from colorectal cancer, according to sociodemographic variables in Mato Grosso from 2000 to 2016. Methods A descriptive study was carried out, using data from the Mortality Information System, made available by the Department of Health of the Mato Grosso State. Deaths of all ages were selected, whose basic cause was identified by the codes from the International Classification of Diseases: (C.18) colon cancer, (C.19) rectosigmoid junction cancer, (C.20) rectal cancer or (C.21) anus cancer. Results Between 2000 and 2016, 31,607 deaths from cancer were registered. Of these, 1,750 (5.6%) were due to colorectal cancer. An increased number of deaths was observed at the end of the period, with a variation from 46 deaths in 2000 from 173 in 2016. Highest frequency was verified in men (51.3%), people aged 60 years or older (59.7%), black (54.6%), married (52.3%) and those with primary education (55.2%). According to Brazilian occupation classification options or those answers filled out on the death certificate, highest frequency were for “Retired” (26.2%), “Housewife” (23.1%), Agricultural/Forestry and Fisheries” (11.3%) and “Production of Industrial Goods and Services” (10.3%). Conclusions This study evidenced the increased number of deaths due to colorectal cancer in Mato Grosso State, and identified priority groups for interventions through public health policies which should include screening and early diagnosis to cope with the disease. Key messages Evidenced the increased number of deaths due to colorectal cancer in Mato Grosso State. Identified priority groups for interventions through public health policies.

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Epidemiological surveillance and performance assessment: the two roles of health indicators during the COVID-19 pandemic

International Journal of Law in Context ◽

10.1017/s1744552321000276 ◽

2021 ◽

Vol 17 (2) ◽

pp. 186-203

Author(s):

Nathan Genicot

Keyword(s):

Public Health ◽

Performance Assessment ◽

Health Indicators ◽

Health Policies ◽

Epidemiological Surveillance ◽

Public Health Policies ◽

History Of ◽

And Performance ◽

The One ◽

Massive Development

AbstractThe COVID-19 pandemic has given rise to the massive development and use of health indicators. Drawing on the history of international public health and of the management of infectious disease, this paper attempts to show that the normative power acquired by metrics during the pandemic can be understood in light of two rationales: epidemiological surveillance and performance assessment. On the one hand, indicators are established to evaluate and rank countries’ responses to the outbreak; on the other, the evolution of indicators has a direct influence on the content of public health policies. Although quantitative data are an absolute necessity for coping with such disasters, it is critical to bear in mind the inherent partiality and precarity of the information provided by health indicators. Given the growing importance of normative quantitative devices during the pandemic, and assuming that their influence is unlikely to decrease in the future, they call for close scrutiny.

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