Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries

Abstract

A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2.

Keywords: COVID-19; SARS-CoV-2; phylodynamic analysis; super-spreader; transmission.

Figure 1.

Phylogentic analysis of SARS-CoV-2 genomes. Four super-spreader clusters (SSs) were identified. Each SS was found to exhibit a signature mutation profile.

Figure 2.

Changes in the distribution pattern and mutation rate of different super-spreader clusters in various continents over time. Distribution of different SSs and their mutations (a) Overall, (b) in China, (c), in Asian countries excluding China, (d) in Europe, (e) in Oceania, and (f) in North America. Two genomes with over 20 mutations were not included to facilitate easy visualization of the graphs.

Figure 3.

Transmission of super-spreaders and other derivatives of the original SARS-CoV-2 in different parts of world. Derivative strains of the original virus have been transmitted worldwide and contributed to the early outbreak of COVID-19. SS1 strains were transmitted mainly in Asia and the US but were less prevalent in other parts of the world. SS2 and SS3 strains were transmitted mainly in Asian countries other than China, as well as Europe from mid January to mid February. SS4 strains were transmitted mainly in Europe at the beginning of the pandemic and were then transmitted to all over the world.