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

The SARS-CoV-2 coronavirus demonstrates significant genomic diversity and plasticity within its hosts, and has regions in its genome that are prone to genomic alterations - including a potential recombination hotspot - according to a pioneering study by scientists at the Hellenic Pasteur Institute (EIP), in collaboration with Professor of epidemiology at the Athens University Medical School, Sotiris Tsiodras. 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.