Evidence map›Paper›PMID 35155489›Full record

ArticleFrontiers in medicine2021

Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel.

Darci R Smith, Christopher Singh, Jennetta Green, Matthew R Lueder, Catherine E Arnold, Logan J Voegtly, Kyle A Long, Gregory K Rice, Andrea E Luquette, Haven L Miner and 6 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.5field-weighted citation impact, top 37% of its field
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

5 citing papers in PubMed, 5 citations in OpenAlex.

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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

16 authors at 3 institutions in 1 country.

Darci R SmithBiological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States.
Christopher SinghBiological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States.
Jennetta GreenBiological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States.
Matthew R LuederBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Catherine E ArnoldBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Logan J VoegtlyBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Kyle A LongBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Gregory K RiceBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Andrea E LuquetteBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Haven L MinerBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Lindsay GlangBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Andrew J BennettBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Robin H MillerBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Francisco MalagonBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Regina Z CerBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Kimberly A Bishop-LillyBiological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States.
Naval Medical Research Command · USLeidos (United States) · USParsons (United States) · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.

Indexed as

emerging SARS-CoV-2 variantsnasal swabssequencingvaccine breakthrough infectionviable virus

Identifiers

PMID35155489
PMCPMC8829001
OpenAlexW4225602988

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.