Rapid Identification of Emerging Pathogens: Coronavirus
Rangarajan Sampath* , Steven A. Hofstadler*, Lawrence B. Blyn*, Mark W. Eshoo*, Thomas A. Hall*, Christian Massire*, Harold M. Levene*, James C. Hannis*, Patina M. Harrell*, Benjamin Neuman†, Michael J. Buchmeier†, Yun Jiang*, Raymond Ranken*, Jared J. Drader*, Vivek Samant*, Richard H. Griffey*, John A. McNeil*, Stanley T. Crooke*, and David J. Ecker*
Author affiliations: *Ibis Therapeutics, Carlsbad, California, USA; †The Scripps Research Institute, La Jolla, California, USA
Figure 3. . Spatial representation of base compositions for the 3 coronavirus (CoV) species known to infect humans. Severe acute respiratory syndrome (SARS), HCoV-OC43, and HCoV-229E base compositions in the region amplified by RNA-dependent RNA polymerase primers (Table 1) are plotted on the A, G, and C axes. T counts are shown by the tilt of the symbol. Within a species, all known isolates of each virus (37 isolates for SARS, 4 for HCoV-229E, and 2 for OC43) had identical sequences in this region. Δbc represents the number of changes in the A, G, C, and T bases needed for 1 species to be misidentified as another in the direction of the arrow. Δm represents the pairwise mutation distance between 2 species, or the cumulative probability of Δbc occurring.
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