Traceability of SARS-CoV-2 transmission through quasispecies analysis

During 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.

Automated summary

During the COVID-19 pandemic, consensus genomic sequences were used to monitor the global spread of the virus quickly. However, there was less focus on intrahost genetic diversity. This study shows that intrahost single nucleotide variants (iSNVs) can be used for contact tracing analysis. The research demonstrates that iSNVs can propagate among individuals during the acute phase of infection, and transmission chains can be reconstructed by investigating iSNVs during SARS-CoV-2 outbreaks.