Tracking the Genomic Footprints of SARS-CoV-2 Transmission

Abstract

There is considerable public and scientific interest in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.

Figure 1

Illustration of Comparative Analysis of Different Types of Data Related to Emerging Infections. The disease transmission chain in an outbreak is depicted in the last layer. The penultimate layer shows the genomic samples of the pathogen from the outbreak which are connected in a phylogenetic tree. A newly emerged lineage is highlighted in green and is characterized by the mutation X in red. Other related data such as virus phenotypes, clinical manifestations, population demography, geography, and environmental features can be mapped to the phylogenetic tree based on the information associated with the genomic samples, as shown in the first to fourth (from top down) layers. Comparison to the genomic sequences in the phylogenetic tree can identify the association with the emerged lineage (green), and some examples of such an interpretation are indicated in the text in the right column. Notably, an association may also be established between two or more layers – for example, the emerged lineage carries mutation X (fifth layer), which increases virus shedding titer and duration of infection (fourth layer), and hence causes higher disease severity (third layer).