Evidence map›Paper›PMID 37004335›Full record

ArticleEBioMedicine2023

SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and convalescent immunity.

Lauren J Beesley, Kelly R Moran, Kshitij Wagh, Lauren A Castro, James Theiler, Hyejin Yoon, Will Fischer, Nick W Hengartner, Bette Korber, Sara Y Del Valle

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in EBioMedicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

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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

10 authors.

Lauren J BeesleyStatistical Sciences, Los Alamos National Laboratory, Los Alamos, NM, USA. Electronic address: lvandervort@lanl.gov.
Kelly R MoranStatistical Sciences, Los Alamos National Laboratory, Los Alamos, NM, USA.
Kshitij WaghTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
Lauren A CastroInformation Systems and Modeling, Los Alamos National Laboratory, Los Alamos, NM, USA.
James TheilerSpace Data Science and Systems, Los Alamos National Laboratory, Los Alamos, NM, USA.
Hyejin YoonTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
Will FischerTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
Nick W HengartnerCenter for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.
Bette KorberTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA; The New Mexico Consortium, Los Alamos, NM, USA.
Sara Y Del ValleInformation Systems and Modeling, Los Alamos National Laboratory, Los Alamos, NM, USA.

Funding

Optimizing glycan shield coverage, germline B cell receptor binding and epitope diversity of V2-apex targeted HIV-1 Env immunogensR37AI150590 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Beatrice H Hahn · 2019 to 2026
$6.9M
NIAID NIH HHS R37 AI150590
6 · The paper itself

Abstract

backgroundThroughout the COVID-19 pandemic, the SARS-CoV-2 virus has continued to evolve, with new variants outcompeting existing variants and often leading to different dynamics of disease spread.

methodsIn this paper, we performed a retrospective analysis using longitudinal sequencing data to characterize differences in the speed, calendar timing, and magnitude of 16 SARS-CoV-2 variant waves/transitions for 230 countries and sub-country regions, between October 2020 and January 2023. We then clustered geographic locations in terms of their variant behavior across several Omicron variants, allowing us to identify groups of locations exhibiting similar variant transitions. Finally, we explored relationships between heterogeneity in these variant waves and time-varying factors, including vaccination status of the population, governmental policy, and the number of variants in simultaneous competition.

findingsThis work demonstrates associations between the behavior of an emerging variant and the number of co-circulating variants as well as the demographic context of the population. We also observed an association between high vaccination rates and variant transition dynamics prior to the Mu and Delta variant transitions.

interpretationThese results suggest the behavior of an emergent variant may be sensitive to the immunologic and demographic context of its location. Additionally, this work represents the most comprehensive characterization of variant transitions globally to date.

fundingLaboratory Directed Research and Development (LDRD), Los Alamos National Laboratory.

Indexed as

COVID-19SARS-CoV-2HumansPandemicsRetrospective StudiesCOVID-19GISAIDSARS-CoV-2Variant transition

Identifiers

PMID37004335
PMCPMC10065418

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.