Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution

Abstract

Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was approximately 0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.

Fig. 1.

Case number of SARS patients in Taiwan in an outbreak that lasted from March to June 2003. There were two stages of SARS infection in the epidemic. The second stage was much more serious.

Fig. 2.

Phylogenetic relationships of SARS virus isolates, including 12 isolates from Taiwan (TW), 16 isolates from other countries, and 1 isolate from a palm civet (SZ3). The neighbor-joining tree was constructed with bootstrap analysis based on the number of mutations in the viral genome, and the bootstrap values are added to the tree. The three clusters of transmission are indicated. The countries of origin of the sequences are as follows: TOR2, Canada; Sin2679, Sin2774, Sin2748, Sin2500, and Sin2677, Singapore; CUHK-Su10, HKU-39849, and CUHK-W1, Hong Kong; Urbani, Vietnam; BJ01, BJ02, BJ03, and BJ04, Beijing, China; HSR1, Italy; Frankfurt1, Germany; the others, Taiwan. Clusters 1 and 2 contain strains related to Hotel M origins.

Fig. 3.

The spectrum of mutation frequency in 28 SARS-CoV genomes. The derived nucleotide was inferred by reference to the sequence recovered from an animal (SZ3). The frequency of occurrences of these mutations in a sample of 28 SARS genomes is depicted on the x axis, whereas the y axis shows the number of sites with the corresponding mutations. The spectrum of mutation frequency showing the neutral equilibrium trend (open bars) is given by θi, where i is the number of occurrences (19); θ is the population parameter (2Nu) and is estimated by θ(1 + 1/2 + · · · + 1/27) = 102 (39).

Fig. 4.

The distribution of the observed and expected pairwise nucleotide site differences. The expected plot for constant (solid line) and growing (dashed line) population is shown with the observed distribution (solid line with squares).