tetano
Editor, Senior Moderator
Virol J
. 2024 Dec 21;21(1):331.
doi: 10.1186/s12985-024-02609-2. Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis
Serena Messali[SUP] 1 [/SUP], Marta Giovanetti[SUP] 2 3 [/SUP], Alessandro Rondina[SUP] 1 [/SUP], Marta Bertelli[SUP] 1 [/SUP], Melissa Duheric[SUP] 1 [/SUP], Francesca Caccuri[SUP] 1 [/SUP], Massimo Ciccozzi[SUP] 2 4 [/SUP], Arnaldo Caruso[SUP] 5 [/SUP]
Affiliations
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.
Keywords: Hospital outbreak; Quasispecies; SARS-CoV-2; Traceability; WGS.
. 2024 Dec 21;21(1):331.
doi: 10.1186/s12985-024-02609-2. Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis
Serena Messali[SUP] 1 [/SUP], Marta Giovanetti[SUP] 2 3 [/SUP], Alessandro Rondina[SUP] 1 [/SUP], Marta Bertelli[SUP] 1 [/SUP], Melissa Duheric[SUP] 1 [/SUP], Francesca Caccuri[SUP] 1 [/SUP], Massimo Ciccozzi[SUP] 2 4 [/SUP], Arnaldo Caruso[SUP] 5 [/SUP]
Affiliations
- PMID: 39707507
- PMCID: PMC11662594
- DOI: 10.1186/s12985-024-02609-2
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.
Keywords: Hospital outbreak; Quasispecies; SARS-CoV-2; Traceability; WGS.