Trevor BedfordVerified account

As noted by @Tuliodna these viruses bear a remarkable constellation of mutations in the spike protein that are concerning in terms of predicted immune escape coupled with increased transmissibility. 6/16https://twitter.com/nicd_sa/status/1463833794276900864 …

Besides this mutational profile, the other critical data point is apparent rapid spread in South Africa. Here, I wouldn't trust frequencies of genome data at the moment as there has been urgent sequencing and deposition of S dropout samples collected from Gauteng. 8/16

This rapid increase across provinces is concerning and suggests that Omicron is outcompeting Delta in the current context in South Africa. I'd hope for modeling work using this S dropout data to better quantify relative fitness of Omicron vs Delta in the following days. 10/16

However, rather than looking at raw frequency of genomic lineage or clade assignments, we can take a phylodynamic approach to estimate clade growth. This approach uses a molecular clock along with branching patterns in the phylogeny to infer viral population dynamics. 11/16