Pioneering study by Pasteur Institute, with Prof. Tsiodras, on SARS-CoV-2 genomic variability within hosts

The publication of the study is expected in the near future.

Researchers analysed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. They identified tens of low- or higher-frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs corresponded to missense changes.

The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host but also strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, they de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene.

The research is available at: https://www.pasteur.gr/wp-content/uploads/2020/04/SARS-CoV-2-exhibits-intra-host-genomic-plasticity-and-low-frequency-polymorphic-quasispecies..pdf