Evidence map›Paper›PMID 33113345›Full record

ArticleCell reports2020

High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.

Ryan P McNamara, Carolina Caro-Vegas, Justin T Landis, Razia Moorad, Linda J Pluta, Anthony B Eason, Cecilia Thompson, Aubrey Bailey, Femi Cleola S Villamor, Philip T Lange and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.

0numbers the graph read from it
0cells of the map it votes in
31citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

31 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023
    Review
  8. Article
  9. Review
  10. Scaling Biosafety Up During and Down After the COVID-19 Pandemic.Applied biosafety : journal of the American Biological Safety Association · 2022
    Review
  11. Article
  12. Article
  13. Article
  14. Article
  15. Evolution and Epidemiology of SARS-CoV-2 Virus.Methods in molecular biology (Clifton, N.J.) · 2022
    Article
  16. Review
  17. Article
  18. Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases · 2021
    Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Ryan P McNamaraDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Carolina Caro-VegasDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Justin T LandisDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Razia MooradDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Linda J PlutaDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Anthony B EasonDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Cecilia ThompsonDepartment of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA.
Aubrey BaileyKuopio Center for Gene and Cell Therapy, Kuopio, Finland.
Femi Cleola S VillamorDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Philip T LangeDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Jason P WongDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Tischan SeltzerDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Jedediah SeltzerDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Yijun ZhouDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Wolfgang VahrsonBasel, Switzerland.
Angelica JuarezDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
James O MeyoDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA.
Tiphaine CalabreÉcole supérieure de Chimie Physique Électronique (CPE), Lyon, France.
Grant BroussardDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA.
Ricardo Rivera-SotoDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA.
Danielle L ChappellDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Ralph S BaricLineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA; Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Blossom DamaniaDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
Melissa B MillerDepartment of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA. Electronic address: melissa.miller@unchealth.unc.edu.
Dirk P DittmerDepartment of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA. Electronic address: dirkdittmer@me.com.

Funding

Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5M
Vironomics and Biostatistics CoreP01CA019014 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BLOSSOM A DAMANIA, NANCY JOAN RAAB-TRAUB · 1985 to 2026
$43.8M
Mechanisms of KSHV TransmissionR01CA239583 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DAMANIA, BLOSSOM A, DITTMER, DIRK P · 2019 to 2023
$2.8M
NCI NIH HHS P01 CA019014NCI NIH HHS P30 CA016086NCI NIH HHS R01 CA239583
6 · The paper itself

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. Four strains carry a deletion in a predicted stem loop of the 3' UTR. The data are consistent with community spread within local populations and the larger continental United States. The data instill confidence in current testing sensitivity and validate "testing by sequencing" as an option to uncover cases, particularly nonstandard coronavirus disease 2019 (COVID-19) clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States.

Indexed as

BetacoronavirusCoronavirus InfectionsCOVID-19High-Throughput Nucleotide SequencingHumansPandemicsPhylogenyPneumonia, ViralSARS-CoV-2Spike Glycoprotein, CoronavirusUnited StatesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2coronavirusCOVID-19mutational landscapenext-generation sequencingSARS-CoV-2single-nucleotide variationstesting by sequencing

Identifiers

PMID33113345
PMCPMC7574689

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.