Author affiliations: University of Tokyo, Tokyo, Japan (S. Watanabe, N. Ueda, K. Iha, S. Taniguchi, H. Fujii, S. Tsuda, M. Endoh, K. Kato, S. Kyuwa, Y. Yoshikawa, H. Akashi); University of the Philippines Los Baños, Laguna, the Philippines (J.S. Masangkay, P. Alviola); National Institute of Infectious Diseases, Tokyo (N. Nagata, S. Morikawa, T. Mizutani, S. Fukushi, T. Omatsu); Nihon University, Kanagawa, Japan (Y. Tohya)
Figure 1. Phylogenetic tree based on deduced amino acid sequences of partial RNA-dependent RNA polymerase of coronaviruses (CoVs), the Philippines. The 2 new viruses detected in this study are underlined. Percentage of replicate trees in which the associated taxa clustered in the bootstrap test (1,000 replicates) is shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Evolutionary distances were computed by using the Poisson correction method and are shown as number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset. The final dataset included 120 positions. Phylogenetic analyses were conducted in MEGA4 (14). Coronaviruses used for comparisons and their GenBank accession numbers are human coronavirus (HCoV) 229E (HCoV-229E) (NC_002645), porcine epidemic diarrhea virus (PEDV) (NC_003436), transmissible gastroenteritis virus (TGEV) (NC_002306), feline infectious peritonitis virus (FIPV) (AY994055), human coronavirus NL63 (HCoV-NL63) (NC_005831), bat-CoV/A512/2005 (NC_009657), bat-CoV/A515/2005 (DQ648822), bat-CoV/A620/2005 (DQ648828), bat-CoV/A911/2005 (DQ648850), bat-CoV/GhanaKwan/19/2008 (FJ710046), bat-CoV/GhanaKwan/20/2008 (FJ710047), bat-CoV/M.das/Germany/D3.3/2007 (EU375854), bat-CoV/USA/RM-11 (EF544563), bat-CoV HKU2 (EF203064), HKU4 (NC_009019), HKU5 (NC_009020), HKU6 (DQ249224), HKU8 (DQ249228), HKU9 (NC_009021), CoV-HKU1 (NC_006577), human coronavirus (HCoV-OC43) (NC_005147), murine hepatitis virus (MHV) (NC_001846), bovine coronavirus (BCoV) (NC_003045), porcine hemagglutinating encephalomyelitis virus (PHEV) (NC_007732), human severe acute respiratory syndrome coronavirus (SARS) (SARS-human) (NC_004718), civet SARS-like coronavirus (SARS-civet) (AY304488), bat-SARS-like coronavirus HKU3 (bat-SARS-CoV HKU3) (NC_009694), infectious bronchitis virus (IBV) (NC_001451), and turkey coronavirus (AF124991).
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