Evolutionary Frequency of Initially Sequenced Human Coronavirus Genomes

Abstract

A novel, human-infecting coronavirus causing COVID-19 was first identified in Wuhan, China in December 2019. Within a short span of time the virus recorded more than 1 million deaths, worldwide. This study addresses the overall evolutionary process from complete genomes of COVID-19. Addressing the complexity of the task, network-based approaches were used in mapping samples to their reported locations. A total of 473 complete human coronavirus genomes from 20 different countries were studied, including samples from 17 states of the United States and samples from the Cruise-Diamond Princess. The phylodynamic network of a global scale was classified into five clusters containing two clusters of the samples from the USA. Cluster B was a shared cluster of samples from China and the USA, while clusters A and C were of a diverse nature. Chinese samples aggregated in clusters A and B which aided in retaining the homogeneous viral genomic pool. In contrast, samples from the USA and Spain were split into distinct clusters which indicated multiple port entries and a possibility of implying a delay in quarantine measures. In the intra-USA samples, we found that sequences reported from Washington and Virginia were scattered indicating evolutionary diversity. This report provides an insight into the transmission pattern of CoV2, which is complicated to evaluate exclusively through the conventional surveillance means.