Table S1 TW and non-TW MRSA importation and acquisition events under different assumptions. The baseline assumption classifies all episodes where MRSA was recovered from an isolate taken within 48 hours of admission as importations. The SA1 assumption uses a 24 hour cutoff instead. See protocol S1 in supporting material for full details of baseline and SA1 assumptions. (PDF) Table S2 Estimated ward-level reproduction numbers (s.e.) for TW and non-TW MRSA clones under alternative assumptions. Phase-specific estimates of ward-level reproduction numbers for TW MRSA and Non-TW MRSA derived using Method 1 under baseline assumptions with perfect ward coupling (applies to combined ICU estimates only) and under SA1 assumptions (see protocol S1 in supporting material for details of baseline and SA1 assumptions). (PDF) Table S3 q estimates for TW and non-TW combined under SA1 and SA2 assumptions. Sensitivity analysis for phase-specific estimates for q, the daily probability of a susceptible patient acquiring MRSA from an MRSA positive patient in the same ward, for ICU 1 and ICU 2 (without distinguishing between TW and non-TW strains). In the Combined row, the estimates are constrained to be the same in both wards, and the All phases column constrains the estimates to be the same in the four phases. See protocol S1 in supporting material for details of the SA1 and SA2 assumptions used in the sensitivity analyses. 1 P-values test the null hypothesis that transmission does not vary between study phase (likelihood ratio test, df = 3). 2 P-values test the null hypothesis that transmission in the current phase does not differ between wards (likelihood ratio test, df = 1). (PDF) Table S4 Estimates of the daily transmission probability (q) from one exposed to one susceptible patient under SA1 and SA2 assumptions. Estimates of the daily transmission probability (q) from one exposed to one susceptible patient under assumptions SA1 and SA2. See protocol S1 in supporting material for details of the SA1 and SA2 assumptions used in thesse sensitivity analyses. 1. P-values test the null hypothesis that transmission varies between study phases but not MRSA types against the alternative that it varies between study phases and MRSA types (likelihood ratio test, df = 4). 2 P-values test the null hypothesis that transmission in the study phase does not differ between TW and Non-TW MRSA using combined data from both wards (likelihood ratio test, df = 1). (PDF) Table S5 Estimates of the daily transmission probability (q) from one exposed to one susceptible patient and from background transmission sources. 'Patient to patient' estimates corresponds to the daily transmission probability (q) from one exposed to one susceptible patient. Background estimates corresponds to the daily probability of acquisition from background sources (such as environmental contamination). This probability is assumed to remain constant within each phase for each of the two MRSA types. In some cases confidence intervals could not be estimated for numerical reasons, while in others the very wide confidence intervals indicate that parameters are weakly identifiable. For both ICUs we compared the model with background and patient-to-patient transmission (with both phase and MRSA-type specific parameters) with nested models with only background transmission (but still with both phase and MRSAtype specific parameters) using a likelihood ratio test based on the chi-squared distribution with eight degrees of freedom. The results gave strong evidence to prefer the more complex model in the case of ICU2 (p = 0.008), but no evidence to prefer it in the case of ICU 1 (p = 0.70). (PDF) Discovery and Genomic Characterization of a Novel Bat Sapovirus with Unusual Genomic Features and Phylogenetic Position Sapovirus is a genus of caliciviruses that are known to cause enteric disease in humans and animals. There is considerable genetic diversity among the sapoviruses, which are classified into different genogroups based on phylogenetic analysis of the full-length capsid protein sequence. While several mammalian species, including humans, pigs, minks, and dogs, have been identified as animal hosts for sapoviruses, there were no reports of sapoviruses in bats in spite of their biological diversity. In this report, we present the results of a targeted surveillance study in different bat species in Hong Kong. Five of the 321 specimens from the bat species, Hipposideros pomona, were found to be positive for sapoviruses by RT-PCR. Complete or nearly full-length genome sequences of approximately 7.7 kb in length were obtained for three strains, which showed similar organization of the genome compared to other sapoviruses. Interestingly, they possess many genomic features atypical of most sapoviruses, like high G+C content and minimal CpG suppression. Phylogenetic analysis of the viral proteins suggested that the bat sapovirus descended from an ancestral sapovirus lineage and is most closely related to the porcine sapoviruses. Codon usage analysis showed that the bat sapovirus genome has greater codon usage bias relative to other sapovirus genomes. In summary, we report the discovery and genomic characterization of the first bat calicivirus, which appears to have evolved under different conditions after early divergence from other sapovirus lineages. The caliciviruses are a family of small non-enveloped viruses, and can be classified into five genera: Vesivirus, Lagovirus, Norovirus, Sapovirus and Nebovirus. They possess a non-segmented, polyadenylated, positive-sense ssRNA genome of about 7.5 to 8.5 kb in length, enclosed in an icosahedral capsid of 27 to 40 nm in diameter. Among them, noroviruses and sapoviruses (SaVs) are well known to cause enteric disease in a range of mammals, including humans, while vesiviruses and lagoviruses cause systemic diseases in specific animal hosts. Nebovirus is the most recently established genus in the family Caliciviridae [1] , and its members are associated with enteric diseases in cattle [2, 3] . A putative sixth genus, Recovirus, has been proposed for a novel calicivirus detected in stool specimens from rhesus monkeys [4, 5] . Another new genus, Valovirus, has been proposed for a novel group of swine caliciviruses known as the St-Valérien-like viruses [6] . In addition, there exist other unclassified caliciviruses, such as the recently described chicken calicivirus [7] .