A Novel Construction of Genome Space with Biological Geometry

Yu, Chenglong; Liang, Qian; Yin, Changchuan; He, Rong L.; Yau, Stephen S.-T.

genome space. We also find that the newly discovered human coronavirus NL63 is very close to the human coronavirus 229E, and thus it is classified into group 1. This result is the same as the identification by van der Hoek et al. 27 Our two-dimensional genome space reveals that for human SARS-CoV, the most closely related coronavirus is from a small infected mammal, the palm civet (not a bird as initially suspected). This result coincides with those found by Guan et al. 28 For another newly discovered human coronavirus HCoV-HKU1, Woo et al. 30 classified it into group 2 because HCoV-HKU1 contains certain features that are characteristic of group 2 coronaviruses. However, these authors also stated that the proteins of HCoV-HKU1 formed distinct branches in the phylogenetic trees, indicating that HCoV-HKU1 is a distinct member within the group and is not very closely related to any other known member of group 2 coronaviruses. In our two-dimensional genome space, we found that HCoV-HKU1 is an individual coronavirus between the SARS group (which we suggest as group 4) and the traditional group 2, thus we propose that HCoV-HKU1 belongs to a new group 5. By computing the distances between the genomes in Fig. 5A , we also reconstructed the phylogenetic tree of these coronaviruses (Fig. 6 ) using UPGMA program in the MEGA 4 package. 23 Thus, the evolutionary relationship of these genomes is clearer.