A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China

Abstract

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.

Fig. 1

The GD-Ins29 in the genome of Isolate GD01. Solid arrows indicate ORFs and the gray arrows denote the BGI-PUPs. Open arrows highlight the region of interest. The position of the insertion and related annotations are in the parentheses.

Fig. 2

Phylogenetic analysis of the 17 SARS-CoV isolates based on completed genomes. The proposed rectangular cladogram was generated by Clustalw 1.81 and the bootstrap values were deducted from 1,000 replicates. The sources and abbreviations of the sequences are referred to the text of Table 1.