Evidence map›Paper›PMID 36380755›Full record

ArticlebioRxiv : the preprint server for biology2022

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance.

Ryan Connor, David A Yarmosh, Wolfgang Maier, Migun Shakya, Ross Martin, Rebecca Bradford, J Rodney Brister, Patrick Sg Chain, Courtney A Copeland, Julia di Iulio and 15 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors.

Ryan ConnorNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
David A YarmoshAmerican Type Culture Collection, 10807 University Blvd, Manassas, VA 20110, USA.
Wolfgang MaierGalaxy Europe Team, University of Freiburg, Freiburg, Germany.
Migun ShakyaBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA.
Ross MartinClinical Virology Department, Gilead Sciences, 333 Lakeside Dr, Foster City, CA 94404, USA.
Rebecca BradfordAmerican Type Culture Collection, 10807 University Blvd, Manassas, VA 20110, USA.
J Rodney BristerNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Patrick Sg ChainBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA.
Courtney A CopelandDeloitte Consulting LLP, 1919 North Lynn St, Suite 1500, Rosslyn, VA 22209 USA.
Julia di IulioVir Biotechnology Inc., San Francisco, CA, USA.
Bin HuBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA.
Philip EbertEli Lilly and Company, Indianapolis, IN.
Jonathan GuntiNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Yumi JinNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Kenneth S KatzNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Andrey KocherginNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Tré LaRosaDeloitte Consulting LLP, 1919 North Lynn St, Suite 1500, Rosslyn, VA 22209 USA.
Jiani LiClinical Virology Department, Gilead Sciences, 333 Lakeside Dr, Foster City, CA 94404, USA.
Po-E LiBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA.
Chien-Chi LoBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA.
Sujatha RashidAmerican Type Culture Collection, 10807 University Blvd, Manassas, VA 20110, USA.
Evguenia S MaiorovaClinical Virology Department, Gilead Sciences, 333 Lakeside Dr, Foster City, CA 94404, USA.
Chunlin XiaoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Vadim ZaluninNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Kim D PruittNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Funding

NIAID NIH HHS HHSN272201600013C
6 · The paper itself

Abstract

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

Identifiers

PMID36380755
PMCPMC9645426

What OpenQuestion holds

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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.