We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)âassociated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.
The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing ϳ440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1-to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.The notion that sequence-based methodologies will take their place in routine clinical laboratories is an increasing reality. The initial cost of equipment, i.e., automated sequencers, can quickly be recovered with savings in personnel, time, and ultimately in health care costs. Laboratories are beginning to rely more on genotypic characterization, which is more specific and easier to standardize than conventional tests (14).Leaders in the field of diagnostic mycobacteriology acknowledge the need for advanced methods for more accurate identification of mycobacteria to the species level (36,39,44). The number of members within the genus is highly underestimated, and of the 92 currently established species, as listed in J. P. Euzéby's: "List of bacterial names with standing in nomenclature" (http://www.bacterio.cict.fr/m/mycobacterium.html), many are considered potentially pathogenic. Biochemical characteristics have been well established for the most well-known Mycobacterium species, but with a rapid increase of newly described species, this becomes more and more complex, difficult, and perhaps obsolete. Also, many species that are biochemically inert or extremely slow growing contribute further to these problems.The 16S rRNA gene is the most widely accepte...
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