Phylogenetic analysis in COVID-19 surveillance

Executive summary

Small, often insignificant, changes in viral genomes allow reconstruction of the spread of SARS-CoV-2. Such analysis of viral genomes can complement contact tracing by establishing links between outbreak clusters or by linking new outbreak clusters to viruses circulating outside of Switzerland. While the temporal resolution of such genomic epidemiology is too low to establish direct transmission between two individuals with confidence, genomic information can often rule out that two cases are connected or suggest a linkage between clusters too far apart to be linked by contact tracing. In the current low-incidence situation, analysis of viral genomes can thus provide information to control COVID-19. To maximize impact, sequencing, analysis and sharing of viral genomes have to be fast. To reduce turn-around time, coordination between diagnostic labs, sequencing centers, and data deposition hubs should be improved. Real-time sequencing and phylogenetic analysis should be viewed as an integral part of the continued effort to contain COVID19.