scholarly journals SNP and Phylogenetic Characterization of Low Viral Load SARS-CoV-2 Specimens by Target Enrichment

2021 ◽  
Vol 1 ◽  
Author(s):  
Gregory S. Orf ◽  
Kenn Forberg ◽  
Todd V. Meyer ◽  
Illya Mowerman ◽  
Aurash Mohaimani ◽  
...  
Keyword(s):  
Viral Load ◽  
The United States ◽  
Diagnostic Tools ◽  
Snp Analysis ◽  
Metagenomic Sequencing ◽  
Target Enrichment ◽  
Public Health Response ◽  
Genome Coverage ◽  
The Public ◽  
Viral Loads

Background: Surveillance of SARS-CoV-2 across the globe has enabled detection of new variants and informed the public health response. With highly sensitive methods like qPCR widely adopted for diagnosis, the ability to sequence and characterize specimens with low titers needs to keep pace.Methods: Nucleic acids extracted from nasopharyngeal swabs collected from four sites in the United States in early 2020 were converted to NGS libraries to sequence SARS-CoV-2 genomes using metagenomic and xGen target enrichment approaches. Single nucleotide polymorphism (SNP) analysis and phylogeny were used to determine clade assignments and geographic origins of strains.Results: SARS-CoV-2-specific xGen enrichment enabled full genome coverage for 87 specimens with Ct values <29, corresponding to viral loads of >10,000 cp/ml. For samples with viral loads between 103 and 106 cp/ml, the median genome coverage for xGen was 99.1%, sequence depth was 605X, and the “on-target” rate was 57 ± 21%, compared to 13%, 2X and 0.001 ± 0.016%, respectively, for metagenomic sequencing alone. Phylogenetic analysis revealed the presence of most clades that existed at the time of the study, though clade GH dominated in the Midwest.Conclusions: Even as vaccines are being widely distributed, a high case load of SARS-CoV-2 infection persists around the world. Viral genetic surveillance has succeeded in warning the public of new variants in circulation and ensured that diagnostic tools remain resilient to a steadily increasing number of mutations. Target capture offers a means of characterizing low viral load samples which would normally pose a challenge for metagenomic sequencing.

scholarly journals United States response to the COVID-19 pandemic, January–November 2020

2021 ◽  
pp. 1-14
Author(s):  
Mathew Alexander ◽  
Lynn Unruh ◽  
Andriy Koval ◽  
William Belanger
Keyword(s):  
United States ◽  
The United States ◽  
Contact Tracing ◽  
Public Health Response ◽  
The Public ◽  
The Past ◽  
Health Response ◽  
Physical Infrastructure ◽  
Key Policy ◽  
United States Healthcare

Abstract As of November 2020, the United States leads the world in confirmed coronavirus disease 2019 (COVID-19) cases and deaths. Over the past 10 months, the United States has experienced three peaks in new cases, with the most recent spike in November setting new records. Inaction and the lack of a scientifically informed, unified response have contributed to the sustained spread of COVID-19 in the United States. This paper describes major events and findings from the domestic response to COVID-19 from January to November 2020, including on preventing transmission, COVID-19 testing and contact tracing, ensuring sufficient physical infrastructure and healthcare workforce, paying for services, and governance. We further reflect on the public health response to-date and analyse the link between key policy decisions (e.g. closing, reopening) and COVID-19 cases in three states that are representative of the broader regions that have experienced spikes in cases. Finally, as we approach the winter months and undergo a change in national leadership, we highlight some considerations for the ongoing COVID-19 response and the broader United States healthcare system. These findings describe why the United States has failed to contain COVID-19 effectively to-date and can serve as a reference in the continued response to COVID-19 and future pandemics.

Journalists and Public Health Professionals: Challenges of a Symbiotic Relationship

2014 ◽  
Vol 9 (1) ◽  
pp. 59-63 ◽  
Author(s):  
Pauline Lubens
Keyword(s):  
Public Health ◽  
Health Professionals ◽  
Health Care Professionals ◽  
The United States ◽  
Accurate Information ◽  
Symbiotic Relationship ◽  
Public Health Response ◽  
Policy Makers ◽  
The Public ◽  
Health Goals

AbstractJournalists and health professionals share a symbiotic relationship during a disease outbreak as both professions play an important role in informing the public’s perceptions and the decisions of policy makers. Although critics in the United States have focused on US reporters and media outlets whose coverage has been sensationalist and alarmist, the discussion in this article is based on the ideal—gold standard—for US journalists. Journalists perform three primary functions during times of health crises: disseminating accurate information to the public, medical professionals, and policy makers; acting as the go-between for the public and decision makers and health and science experts; and monitoring the performance of institutions responsible for the public health response. A journalist’s goal is to responsibly inform the public in order to optimize the public health goals of prevention while minimizing panic. The struggle to strike a balance between humanizing a story and protecting the dignity of patients while also capturing the severity of an epidemic is harder in the era of the 24-7 news cycle. Journalists grapple with dueling pressures: confirming that their information is correct while meeting the demand for rapid updates. Just as health care professionals triage patients, journalists triage information. The challenge going forward will be how to get ahead of the story from the onset, racing against the pace of digital dissemination of misinformation by continuing to refine the media-science relationship. (Disaster Med Public Health Preparedness. 2014;0:1-5)

Building a Public-Private Partnership to Enhance Laboratory Preparedness and Response in the United States

2020 ◽  
pp. 1-4 ◽  
Author(s):  
Reynolds M. Salerno ◽  
Jasmine Chaitram ◽  
Joanne D. Andreadis
Keyword(s):  
Public Health ◽  
Clinical Laboratory ◽  
Diagnostic Testing ◽  
Health Sector ◽  
High Volume ◽  
The United States ◽  
Public Health Emergency ◽  
Public Health Response ◽  
The Public ◽  
Communication And Coordination

ABSTRACT The public health community has recognized that it cannot handle responses to all possible public health emergencies on its own. The public health sector has deep scientific expertise and excels at initial identification, complex characterization, and test development. The private sector has many resources and capabilities that can complement and augment the public health response. This is especially true in the clinical laboratory sector. Many commercial laboratories are designed for high-volume, high-throughput diagnostic testing in a way that public health laboratories are not. Significant steps have been taken since 2017 to improve the communication and coordination between public health and the private clinical laboratory community, especially during a response to a public health emergency. This paper describes the strong foundation that has been built for an improved clinical and public health laboratory response to the next public health emergency.

scholarly journals High prevalence of Lynx rufus gammaherpesvirus 1 in wild Vermont bobcats

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4982 ◽  
Author(s):  
Dagan A. Loisel ◽  
Ryan M. Troyer ◽  
Sue VandeWoude
Keyword(s):  
United States ◽  
Viral Load ◽  
Horizontal Transmission ◽  
Mammalian Species ◽  
The United States ◽  
Lynx Rufus ◽  
Pcr Analysis ◽  
Dna Viruses ◽  
Viral Loads ◽  
High Prevalence

Gammaherpesviruses (GHVs) are host specific DNA viruses that infect a large range of mammalian species. These viruses preferentially target host lymphocyte cell populations and infection may lead to morbidity or mortality in immunocompromised, co-infected, or non-adapted hosts. In this study, we tested for the presence of Lynx rufus gammaherpesvirus 1 (LruGHV1) in a northeastern United States population of wild bobcats (L. rufus). We estimated prevalence of infection and viral load in infected individuals using quantitative real-time PCR analysis of spleen DNA from 64 Vermont bobcats. We observed an overall prevalence of 64% using this methodology. Bobcat age was significantly positively associated with GHV infection status, and we noted a trend for higher viral loads in young animals, but prevalence and viral load were similar in male and female bobcats. A single LruGHV1 variant was identified from the sequencing of the viral glycoprotein B gene of Vermont bobcats. This gene sequence was 100% similar to that reported in Florida bobcats and slightly variant from other isolates identified in the Western USA. Our work suggests broad geographic distribution and high prevalence of LruGHV1 in bobcat populations across the United States with infection attributes that suggest horizontal transmission of the agent. Geographic differences in viral genotype may reflect historical migration and expansion events among bobcat populations.

scholarly journals Vaccinated and unvaccinated individuals have similar viral loads in communities with a high prevalence of the SARS-CoV-2 delta variant

2021 ◽  
Author(s):  
Kasen K Riemersma ◽  
Brittany E Grogan ◽  
Amanda Kita-Yarbro ◽  
Gunnar E Jeppson ◽  
David H O'Connor ◽  
...  
Keyword(s):  
Viral Load ◽  
Vaccine Coverage ◽  
High Volume ◽  
The United States ◽  
Quantitative Information ◽  
Self Report ◽  
Local Health ◽  
Viral Loads ◽  
Viral Load Data ◽  
Single Standard

SARS-CoV-2 variant B.1.617.2 (delta) is associated with higher viral loads [1] and increased transmissibility relative to other variants, as well as partial escape from polyclonal and monoclonal antibodies [2]. The emergence of the delta variant has been associated with increasing case counts and test-positivity rates, indicative of rapid community spread. Since early July 2021, SARS-CoV-2 cases in the United States have increased coincident with delta SARS-CoV-2 becoming the predominant lineage nationwide [3]. Understanding how and why the virus is spreading in settings where there is high vaccine coverage has important public health implications. It is particularly important to assess whether vaccinated individuals who become infected can transmit SARS-CoV-2 to others. In Wisconsin, a large local contract laboratory provides SARS-CoV-2 testing for multiple local health departments, providing a single standard source of data using the same assay to measure virus burdens in test-positive cases. This includes providing high-volume testing in Dane County, a county with extremely high vaccine coverage. These PCR-based tests provide semi-quantitative information about the viral load, or amount of SARS-CoV-2 RNA, in respiratory specimens. Here we use this viral load data to compare the amount of SARS-CoV-2 present in test-positive specimens from people who self-report their vaccine status and date of final immunization, during a period in which the delta variant became the predominant circulating variant in Wisconsin. We find no difference in viral loads when comparing unvaccinated individuals to those who have vaccine "breakthrough" infections. Furthermore, individuals with vaccine breakthrough infections frequently test positive with viral loads consistent with the ability to shed infectious viruses. Our results, while preliminary, suggest that if vaccinated individuals become infected with the delta variant, they may be sources of SARS-CoV-2 transmission to others.

scholarly journals Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

Science ◽  
2019 ◽  
Vol 363 (6422) ◽  
pp. 74-77 ◽  
Author(s):  
L. E. Kafetzopoulou ◽  
S. T. Pullan ◽  
P. Lemey ◽  
M. A. Suchard ◽  
D. U. Ehichioya ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Lassa Fever ◽  
World Health ◽  
Metagenomic Sequencing ◽  
Public Health Response ◽  
The Public ◽  
Real Time Analysis ◽  
Health Response ◽  
Health Organization ◽  
First Time

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

scholarly journals Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Caroline Charre ◽  
Christophe Ginevra ◽  
Marina Sabatier ◽  
Hadrien Regue ◽  
Grégory Destras ◽  
...  
Keyword(s):  
Consensus Sequence ◽  
Amplicon Sequencing ◽  
Reference Sequence ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Genome Coverage ◽  
Viral Loads ◽  
A Genome ◽  
Complete Genomes ◽  
Enrichment Methods

Abstract Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.

Thank You for Not Smoking: The Public Health Response to Tobacco-Related Mortality in the United States

2006 ◽  
pp. 423-436
Author(s):  
Michael P. Eriksen ◽  
Lawrence W. Green ◽  
Corinne G. Husten ◽  
Linda L. Pederson ◽  
Terry F. Pechacek
Keyword(s):  
Public Health ◽  
United States ◽  
The United States ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
Related Mortality

scholarly journals How to Provide Sexual Education: Lessons from a Pandemic on Masculinity, Individualism, and the Neoliberal Agenda

2021 ◽  
Vol 18 (8) ◽  
pp. 4144
Author(s):  
Sharon Lamb ◽  
Marta Pagán-Ortiz ◽  
Sara Bonilla
Keyword(s):  
Public Health ◽  
Sex Education ◽  
Personal Responsibility ◽  
The United States ◽  
Sexual Education ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
National Values ◽  
The Individual

Sex education in the United States is often approached through an individual lens that focuses on personal protection, safety, and rights. This focus on personal responsibility and care-for-self reflects national values and permeates governmental systems and actions, including generalized public health approaches. This issue has been most recently highlighted in the individual and systemic attitudes, beliefs, and responses towards the recent, ongoing crisis following the global surge of COVID-19. In this paper, we provide examples and discuss lessons gleaned from the public health response to this crisis, particularly in the areas and intersections of gender, individualism, and neoliberalism, and the parallels of these issues in sex education. We make an appeal for a collectivist and community-oriented approach to sex education, which would focus not only on prevention and protection, but on inequities, ethics, and care for others.

scholarly journals Public health response to two incidents of confirmed MERS-CoV cases travelling on flights through London Heathrow Airport in 2014 – lessons learnt

2015 ◽  
Vol 20 (18) ◽  
Author(s):  
F Parry-Ford ◽  
N Boddington ◽  
R Pebody ◽  
N Phin ◽  
Collective on behalf of the Incident Management Team
Keyword(s):  
Public Health ◽  
International Health ◽  
The United States ◽  
World Health ◽  
Contact Tracing ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
Health Organization

In May 2014, Public Health England was alerted to two separate laboratory-confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection who transited through London Heathrow Airport while symptomatic on flights from Saudi Arabia to the United States of America. We present the rationale for the public health response to both incidents, and report results of contact tracing. Following a risk assessment, passengers seated two seats around the cases were prioritised for contact tracing and a proactive media approach was used to alert all passengers on the planes of their possible exposure in both incidents. In total, 64 United Kingdom (UK) residents were successfully contacted, 14 of whom were sat in the priority area two seats all around the case(s). Five passengers reported respiratory symptoms within 14 days of the flight, but all tested were negative for MERS-CoV. Details of non-UK residents were passed on to relevant World Health Organization International Health Regulation focal points for follow-up, and no further cases were reported back. Different approaches were used to manage contact tracing for each flight due to variations in the quality and timeliness of the passenger contact information provided by the airlines involved. No evidence of symptomatic onward transmission was found.

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