Evaluation of saliva and nasopharyngeal swab sampling for genomic detection of SARS-CoV-2 in children accessing a pediatric emergency department during the second pandemic wave

Diani, Erica; Silvagni, D.; Lotti, Virginia; Lagni, Anna; Baggio, Laura; Medaina, Nicoletta; Biban, Paolo; Gibellini, Davide

doi:10.3389/fmicb.2023.1163438

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…The analysis of nasopharyngeal samples for SARS-CoV-2 genome detection was performed by a commercial multiplex real-time RT–PCR platform, as described before [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 Positivity in Foreign-Born Adults: A Retrospective Study in Verona, Northeast Italy

Lotti,

Spiteri,

Caliskan

et al. 2024

Life

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We compared SARS-CoV-2 positivity between the foreign-born adult working population and Italians living in the Verona area to investigate whether being a foreign-born adult could confer an increased risk of infection or lead to a diagnostic delay. The present study included 105,774 subjects, aged 18–65 years, tested for SARS-CoV-2 by nasopharyngeal swabs and analyzed at the University Hospital of Verona between January 2020 and September 2022. A logistic regression model was used, controlling for gender, age, time of sampling, and source of referral. A higher proportion of SARS-CoV-2 positivity in Italian (30.09%) than in foreign-born (25.61%) adults was reported, with a higher proportion of SARS-CoV-2 positivity in men than women in both cohorts analyzed. The difference in swab positivity among Italian and foreign-born adults was the highest in people aged 18–29 years (31.5% vs. 23.3%) and tended to disappear thereafter. Swab positivity became comparable between Italian and foreign-born adults during the vaccination campaign. Multivariable analysis confirmed the lower risk of swab positivity among foreign-born adults (OR = 0.85, 95%CI 0.82–0.89). In the Verona area, foreign-born adults showed a lower rate of SARS-CoV-2 positivity than the native population, likely because of underdiagnosis. Hence, public health should increase attention toward these particularly vulnerable populations.

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“…The analysis of nasopharyngeal samples for SARS-CoV-2 genome detection was performed by a commercial multiplex real-time RT–PCR platform, as described before [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 Positivity in Foreign-Born Adults: A Retrospective Study in Verona, Northeast Italy

Lotti,

Spiteri,

Caliskan

et al. 2024

Life

Self Cite

View full text Add to dashboard Cite

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“…Nasopharyngeal swab samples collected from patients and medical surveillance personnel at the AOUI Hospital of Verona as previously described [14] were processed for SARS-CoV-2 infection diagnosis. RNA extraction from nasopharyngeal swab maintenance solution was performed with the semi-automated Nimbus apparatus (Seegene, Seoul, Republic of Korea) following the manufacturer's instructions.…”

Section: Sample Collection and Rna Extraction And Quantificationmentioning

confidence: 99%

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Tonon,

Cecchetto,

Diani

et al. 2024

Microorganisms

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The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.

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Mass Spectrometry-Based Metabolomics Reveals a Salivary Signature for Low-Severity COVID-19

Lopes de Lima,

Ap. Rosini Silva,

Brites

et al. 2024

IJMS

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Omics approaches were extensively applied during the coronavirus disease 2019 (COVID-19) pandemic to understand the disease, identify biomarkers with diagnostic and prognostic value, and discover new molecular targets for medications. COVID-19 continues to challenge the healthcare system as the virus mutates, becoming more transmissible or adept at evading the immune system, causing resurgent epidemic waves over the last few years. In this study, we used saliva from volunteers who were negative and positive for COVID-19 when Omicron and its variants became dominant. We applied a direct solid-phase extraction approach followed by non-target metabolomics analysis to identify potential salivary signatures of hospital-recruited volunteers to establish a model for COVID-19 screening. Our model, which aimed to differentiate COVID-19-positive individuals from controls in a hospital setting, was based on 39 compounds and achieved high sensitivity (85%/100%), specificity (82%/84%), and accuracy (84%/92%) in training and validation sets, respectively. The salivary diagnostic signatures were mainly composed of amino acids and lipids and were related to a heightened innate immune antiviral response and an attenuated inflammatory profile. The higher abundance of thyrotropin-releasing hormone in the COVID-19 positive group highlighted the endocrine imbalance in low-severity disease, as first reported here, underscoring the need for further studies in this area.

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Evaluation of saliva and nasopharyngeal swab sampling for genomic detection of SARS-CoV-2 in children accessing a pediatric emergency department during the second pandemic wave

Cited by 3 publications

References 29 publications

SARS-CoV-2 Positivity in Foreign-Born Adults: A Retrospective Study in Verona, Northeast Italy

SARS-CoV-2 Positivity in Foreign-Born Adults: A Retrospective Study in Verona, Northeast Italy

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Mass Spectrometry-Based Metabolomics Reveals a Salivary Signature for Low-Severity COVID-19

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