A review of studies on animal reservoirs of the SARS coronavirus

Abstract

In this review, we summarize the researches on animal reservoirs of the SARS coronavirus (SARS-CoV). Masked palm civets were suspected as the origin of the SARS outbreak in 2003 and was confirmed as the direct origin of SARS cases with mild symptom in 2004. Sequence analysis of the SARS-CoV-like virus in masked palm civets indicated that they were highly homologous to human SARS-CoV with nt identity over 99.6%, indicating the virus has not been circulating in the population of masked palm civets for a very long time. Alignment of 10 complete viral genome sequences from masked palm civets with those of human SARS-CoVs revealed 26 conserved single-nucleotide variations (SNVs) in the viruses from masked palm civets. These conserved SNVs were gradually lost from the genomes of viruses isolated from the early phase to late phase human patients of the 2003 SARS epidemic. In 2005, horseshoe bats were identified as the natural reservoir of a group of coronaviruses that are distantly related to SARS-CoV. The genome sequences of bat SARS-like coronavirus had about 88-92% nt identity with that of the SARS-CoV. The prevalence of antibodies and viral RNA in different bat species and the characteristics of the bat SARS-like coronavirus were elucidated. Apart from masked palm civets and bats, 29 other animal species had been tested for the SARS-CoV, and the results are summarized in this paper.

Fig. 1

The genome organization of SARS-CoV in human and masked palm civet, and SL-CoV in bat. The black arrows indicate the conserved genes of the family Coronaviridae; the gray arrows indicate SARS-CoV unique genes; the red indicate the most variable regions in SARS-CoV and SL-CoV. The bar scale may not represent the real size of the genes.

Fig. 2

Phylogenetic trees based on aa sequence of ORF1b, nucleotide sequence of S, N and ORF8 gene. Sequence used for analysis in this study are as follows (GenBank accession number given in parenthesis): Tor2 (NC-004718), human isolate from late phase of the 2002/3 oubreaks; GD01 (AY278489), human isolate from early phase of the 2002/3 outbreaks; SZ3 (AY304486), masked palm civet isolate from 2003; PC4-227 (AY613950), masked palm civet isolate from 2004; HKU3-1 (DQ022305), isolate from Rhinolophus sinicus; Rp3 (DQ071615), isolate from Rhinolophus pearsoni; Rf1 partial sequence (DQ71611, DQ159956), isolate from Rhinolophus ferrumequinum; Rm1 partial sequence (DQ71612, DQ159957), isolate from Rhinolophus macrotis. The phylogenetic trees were constructed using the Neighbor-Joining algorithm in the MEGA3.1 software with a bootstrap of 1000 replicates. Other coronavirus sequences used in this study: HCoV-229E (AF304460), HCoV-OC43 (AY391777), PEDV (AF353511), MHV (AY700211), IBV (AY851295), and BCoV (AF391542) and TGEV (NC_002306). Genetic variation scales are indicated for each tree and different genetic scales are used for different trees.

Fig. 3

Comparison of the receptor binding motif of S protein of bat SL-CoV with that of SARS-CoV. Alignment between the receptor binding motif of S protein (RBM) of SARS-CoV Tor2, SZ3 (masked palm civet) and the corresponding regions of bat SL-CoVs S proteins is shown. The displayed RBM region represents aa 424–495 of the Tor2 spike protein sequence.