scholarly journals FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 892 ◽  
Author(s):  
Adriano de Bernadi Schneider ◽  
Denis Jacob Machado ◽  
Sayal Guirales ◽  
Daniel A. Janies
Keyword(s):  
Public Health ◽  
Phylogenetic Analysis ◽  
Hepatitis C ◽  
Data Partitioning ◽  
Annotation Pipeline ◽  
Viral Genomes ◽  
Content Variation ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Public Health Threat

Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus, named “Fast Loci Annotation of Viruses” (FLAVi; http://flavi-web.com/), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.

scholarly journals The Elimination of Hepatitis C as a Public Health Threat

2019 ◽  
Vol 10 (4) ◽  
pp. a036939
Author(s):  
Margaret Hellard ◽  
Sophia E. Schroeder ◽  
Alisa Pedrana ◽  
Joseph Doyle ◽  
Campbell Aitken
Keyword(s):  
Public Health ◽  
Hepatitis C ◽  
Health Threat ◽  
Public Health Threat

scholarly journals Hepatitis C Virus Treatment: Simplifying the Simple and Optimizing the Difficult

2020 ◽  
Vol 222 (Supplement_9) ◽  
pp. S745-S757
Author(s):  
Oluwaseun Falade-Nwulia ◽  
Mark S Sulkowski
Keyword(s):  
Public Health ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Population Level ◽  
Direct Acting Antivirals ◽  
Hepatitis C Treatment ◽  
New Era ◽  
Wide Range ◽  
Public Health Threat ◽  
Direct Acting

Abstract The availability of safe, efficacious, oral direct-acting antivirals (DAAs) have ushered in a new era of hepatitis C treatment with potential to eliminate hepatitis C as a public health threat. To achieve population-level effectiveness of these oral DAAs, hepatitis C treatment by a wide range of providers in different settings will be essential to increase the number of persons treated. We provide a clinical review of hepatitis C treatment with a focus on practical tools for management of hepatitis C in majority of currently infected individuals who can be easily cured and optimization of treatment for those in whom treatment may not be as simple.

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

2020 ◽  
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.

CHILDREN OF HOMOSEXUALS AND TRANSSEXUALS MORE APT TO BE HOMOSEXUAL: A REPLY TO CAMERON

2006 ◽  
Vol 39 (1) ◽  
pp. 153-154 ◽  
Author(s):  
TODD G. MORRISON
Keyword(s):  
Public Health ◽  
Scientific Journals ◽  
Family Research ◽  
Health Threat ◽  
Traditional Family ◽  
Moral Framework ◽  
The Family ◽  
Public Health Threat ◽  
Clear And Present Danger ◽  
Research Institute

Paul Cameron, author of ‘Children of Homosexuals and Transsexuals More Apt to be Homosexual’ (Cameron, 2006) is chairman of the Family Research Institute (FRI), a conservative organization whose mandate is to preserve ‘America’s historic moral framework and the traditional family’ (http://www.familyresearchinst.org/; accessed 18th June 2006). The FRI states that research in scientific journals is needed to prove that ‘homosexuality is a public health threat and a clear and present danger to our civilization’ (http://www.familyresearchinst.org/Default.aspx?tabid = 145; accessed 18th June 2006).

An opt-out approach to hepatitis C virus testing in English prisons: the literature underpinning the policy

2021 ◽  
Vol 30 (20) ◽  
pp. 1158-1164
Author(s):  
Kathryn Jack
Keyword(s):  
Public Health ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Public Health Policy ◽  
World Health ◽  
Opt Out ◽  
The World ◽  
Public Health Threat ◽  
Hcv Testing ◽  
Virus Testing

Background: The World Health Organization's aim to eliminate hepatitis C virus (HCV) infection as a public health threat by 2030 is dependent on testing people. HCV prevalence is higher in prisons, so to increase test uptake an ‘opt-out’ approach to blood-borne virus testing in English and Welsh prisons was introduced. Aims: This literature review examines the evidence behind the introduction of this public health policy. Methods: Four healthcare databases were searched for publications between January 2000 and February 2020 on the opt-out approach to blood-borne virus testing in prisons. Findings: Sixteen studies published between 2009 and 2019 were included. Analysis of their findings showed that an increase in HCV test uptake in prisons occurs when an opt-out approach is used in combination with additional interventions. Contextual differences between UK and US prisons may affect HCV test uptake. Conclusion: An opt-out approach to HCV testing in prisons can increase test uptake as part of a complex of interventions.

scholarly journals Measuring hepatitis C virus elimination as a public health threat: Beyond global targets

2020 ◽  
Vol 27 (8) ◽  
pp. 770-773
Author(s):  
Daniela K. van Santen ◽  
Rachel Sacks‐Davis ◽  
Joseph S. Doyle ◽  
Nick Scott ◽  
Maria Prins ◽  
...  
Keyword(s):  
Public Health ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Virus Elimination ◽  
Health Threat ◽  
Public Health Threat

Modelling the elimination of hepatitis C as a public health threat in Iceland: A goal attainable by 2020

2018 ◽  
Vol 68 (5) ◽  
pp. 932-939 ◽  
Author(s):  
Nick Scott ◽  
Sigurður Ólafsson ◽  
Magnús Gottfreðsson ◽  
Thorarinn Tyrfingsson ◽  
Valgerdur Rúnarsdóttir ◽  
...  
Keyword(s):  
Public Health ◽  
Hepatitis C ◽  
Health Threat ◽  
Public Health Threat
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