Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols

Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with this approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, as well as the reads derived from the viral sub-genomic RNAs and/or human and bacterial contamination.

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Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols

PLoS ONE ◽

10.1371/journal.pone.0259277 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0259277

Author(s):

Broňa Brejová ◽

Kristína Boršová ◽

Viktória Hodorová ◽

Viktória Čabanová ◽

Askar Gafurov ◽

...

Keyword(s):

Viral Genome ◽

Bacterial Contamination ◽

Policy Decision ◽

Nanopore Sequencing ◽

Genome Sequences ◽

Genomic Rnas ◽

Long Pcr ◽

Health Policy Decision ◽

Sequences Analysis ◽

Policy Decision Making

Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.

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Measuring the health of populations: explaining composite indicators

Journal of Public Health Research ◽

10.4081/jphr.2012.e35 ◽

2012 ◽

Vol 1 (3) ◽

pp. 35 ◽

Cited By ~ 19

Author(s):

Adnan A. Hyder ◽

Prasanthi Puvanachandra ◽

Richard H. Morrow

Keyword(s):

Disease Burden ◽

Policy Decision ◽

Main Approach ◽

Mortality And Morbidity ◽

Alternative Interventions ◽

Composite Measures ◽

Value Choices ◽

The World ◽

Health Policy Decision ◽

Policy Decision Making

Indicators that summarise the health status of a population and that provide comparable measures of a population disease burden are increasingly vital tools for health policy decision making. Decisions concerning health systems across the world are greatly affected by changes in disease profiles and population dynamics, and must develop the capacity to respond to such changes effectively within the resources of each nation. Decisions must be based on evidence of the patterns of diseases, their risk factors and the effectiveness of alternative interventions. This paper focuses on the main approaches used for developing summary measures that include mortality and morbidity occurring in a population. It discusses the rationale for composite measures and reviews the origins of each main approach. The paper also examines methodological differences among these approaches making explicit the value choices that each entails, outlines the advantages and limitations of each measure, and shows how they relate to one another.

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The State of Cancer Care in America: Impact of State Policy on Access to High-Quality Cancer Care

Journal of the National Comprehensive Cancer Network ◽

10.6004/jnccn.2020.7541 ◽

2020 ◽

Vol 18 (4) ◽

pp. 400-404

Author(s):

Terrell Johnson ◽

Lindsey A.M. Bandini ◽

Kara Martin ◽

Lee Jones ◽

Jennifer Carlson ◽

...

Keyword(s):

Health Policy ◽

Cancer Care ◽

Policy Decision ◽

The State ◽

Washington Dc ◽

Patients With Cancer ◽

Quality Cancer Care ◽

Challenges And Opportunities ◽

Health Policy Decision ◽

Policy Decision Making

Health policy in America has shifted rapidly over the last decade, and states are increasingly exercising greater authority over health policy decision-making. This localization and regionalization of healthcare policy poses significant challenges for patients with cancer, providers, advocates, and policymakers. To identify the challenges and opportunities that lay ahead of stakeholders, NCCN hosted the 2019 Policy Summit: The State of Cancer Care in America on June 27, 2019, in Washington, DC. The summit featured multidisciplinary panel discussions to explore the implications for access to quality cancer care within a shifting health policy landscape from a patient, provider, and lawmaker perspective. This article encapsulates the discussion from this NCCN Policy Summit.

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