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

IF 4 3区医学 Q2 VIROLOGY Virology Journal Pub Date : 2024-12-21 DOI:10.1186/s12985-024-02609-2

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

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Abstract

Background: Since 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.

Methods: During 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).

Results: According 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.

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

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通过准种分析跟踪隐匿性SARS-CoV-2医院暴发。

背景：自大流行开始以来，接触者追踪一直是了解SARS-CoV-2传播动力学的最相关问题之一，在此背景下，准物种分析可能成为疫情调查的有用工具。对SARS-CoV-2的nsp2、ORF3和ORF7基因进行宿主内单核苷酸变异（iSNVs）分析，以正确识别布雷西亚市民医院住院患者的病毒传播链。方法：于2023年8月至10月对布雷西亚市属医院收治的13例患者的鼻咽标本进行SARS-CoV-2阳性检测并进行分子表征。首先，进行了系统发育分析，以评估它们是否在流行病学上存在联系，然后，使用β -二项法估计传播瓶颈大小（Nb），并量化病毒颗粒从一个个体（供体）传播到另一个个体（受体）的数量。结果：根据标本的分子特征，我们在心脏科确定了两个传播聚集性：第一个聚集性患者检测出HV.1/EG.5.1.6谱系阳性，而第二个聚集性患者检测出FL.10.1谱系阳性。此外，通过评估瓶颈大小，我们能够解决SARS-CoV-2在感染患者中的传播链。结论：我们的方法表明，利用基于iSNVs分析的基因组方法进行追踪研究是可能的。

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来源期刊

Virology Journal 医学-病毒学

CiteScore

7.40

自引率

2.10%

发文量

186

审稿时长

1 months

期刊介绍： Virology Journal is an open access, peer reviewed journal that considers articles on all aspects of virology, including research on the viruses of animals, plants and microbes. The journal welcomes basic research as well as pre-clinical and clinical studies of novel diagnostic tools, vaccines and anti-viral therapies. The Editorial policy of Virology Journal is to publish all research which is assessed by peer reviewers to be a coherent and sound addition to the scientific literature, and puts less emphasis on interest levels or perceived impact.