Evidence map›Paper›PMID 39707507›Full record

ArticleVirology journal2024

Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis.

Serena Messali, Marta Giovanetti, Alessandro Rondina, Marta Bertelli, Melissa Duheric, Francesca Caccuri, Massimo Ciccozzi, Arnaldo Caruso

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PubMed Full text at PMC Publisher
In one paragraph

Article in Virology journal, 2024. 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
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0citing papers in PubMed
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1 · What the graph read from it

What it found

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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

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

8 authors.

Serena MessaliDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy.
Marta GiovanettiSciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy.
Alessandro RondinaDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy.
Marta BertelliDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy.
Melissa DuhericDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy.
Francesca CaccuriDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy.
Massimo CiccozziSciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy.
Arnaldo CarusoDepartment of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Piazzale Spedali Civili, 1, Brescia, 25123, Italy. arnaldo.caruso@unibs.it.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSince the beginning of the pandemic, contact tracing has been one of the most relevant issues to understand SARS-CoV-2 transmission dynamics and, in this context, the analysis of quasispecies may turn out to be a useful tool for outbreak investigations. Analysis of the intra-host single nucleotide variants (iSNVs) found in the nsp2, ORF3, and ORF7 genes of SARS-CoV-2 was conducted in order to correctly identify virus transmission chain among patients hospitalized in Brescia Civic Hospital.

methodsDuring the period between August and October 2023, 13 nasopharyngeal specimens, collected from patients admitted to Brescia Civic Hospital, were tested for SARS-CoV-2 positivity and molecularly characterized. Firstly, a phylogenetic analysis was performed to evaluate if they were epidemiologically linked and, then, the Beta-binomial method was used to estimate the transmission bottleneck size (Nb) and quantify the number of viral particles transmitted from one individual (donor) to another (recipient).

resultsAccording to the molecular characterization of specimens, we identified two transmission clusters in the cardiology unit: the first cluster concerned patients tested positive for the HV.1/EG.5.1.6 lineage, while the second cluster concerned patients tested positive for the FL.10.1 lineage. Moreover, evaluating the bottleneck size, we were able to solve SARS-CoV-2 transmission chain among infected patients.

conclusionOur method shows that it is possible to conduct a tracing study using a genomic approach based on iSNVs analysis.

Indexed as

COVID-19Disease OutbreaksPhylogenySARS-CoV-2AdultAgedAged, 80 and overContact TracingFemaleHospitalsHumansItalyMaleMiddle AgedNasopharynxQuasispeciesHospital outbreakQuasispeciesSARS-CoV-2TraceabilityWGS

Identifiers

PMID39707507
PMCPMC11662594

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