Affiliation:
1. Department of Molecular and Translational Medicine, Section of Microbiology University of Brescia Brescia Italy
2. Instituto Rene Rachou Fundação Oswaldo Cruz Belo Horizonte Minas Gerais Brazil
3. Sciences and Technologies for Sustainable Development and One Health University of Campus Bio‐Medico Rome Italy
4. Clinical Pathology and Microbiology Laboratory, Unit of Medical Statistics and Molecular Epidemiology University Hospital Campus Biomedico Rome Italy
Abstract
AbstractDuring COVID‐19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS‐CoV‐2 consists in an ensemble of replicating and closely related viral variants so‐called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS‐CoV‐2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well‐conserved genes, namely nsp2, ORF3, and ORF7.
Subject
Infectious Diseases,Virology
Cited by
1 articles.
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1. Virus Engineering and Applications;International Journal of Molecular Sciences;2023-11-27