Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

Jing Lu

Jing Lu, Guangdong Provincial Center for Disease Control & Prevention, China


COVID-19 is caused by the SARS-CoV-2 coronavirus and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China’s most populous province, during early 2020 resulted in 1,388 reported RNA positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China, we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain due to low virus genetic variation early in the pandemic. Our results illustrate how the timing, size and duration of putative local transmission chains were constrained by national travel restrictions and by the province’s large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required as the number of cases imported from other countries is increasing.


Jing Lu’s research focuses on studying the evolutionary dynamics and infection mechanisms of human pathogens, particularly rapidly-evolving clinical viruses, by using phylogenetic methods and functional experiments. Jing is also interested in novel tools and methods for pathogen diagnosis, like metagenomic analysis of pathogens directly from environmental and clinical samples.