Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human

TLDR

Genomic sequences of SARS‑CoV from humans and palm civets in the 2003/2004 Guangzhou outbreak were nearly identical. We identified 202 single‑nucleotide variations by combining all existing data while excluding singletons. Phylogenetic analysis indicated an independent animal‑to‑human spillover, with 202 identified SNPs—including 17 civet‑specific polymorphisms—and a high nonsynonymous/synonymous ratio in civet isolates suggesting rapid evolution, while key Spike gene variations likely facilitated the shift to human‑to‑human transmission that triggered the 2002/2003 outbreak.

Abstract

The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode. Combining all existing data but excluding singletons, we identified 202 single-nucleotide variations. Among them, 17 are polymorphic in palm civets only. The ratio of nonsynonymous/synonymous nucleotide substitution in palm civets collected 1 yr apart from different geographic locations is very high, suggesting a rapid evolving process of viral proteins in civet as well, much like their adaptation in the human host in the early 2002–2003 epidemic. Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome outbreak of 2002/2003.