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. 2009 Sep 30;9(6):1185–1196. doi: 10.1016/j.meegid.2009.09.015

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Copyright © 2009 Published by Elsevier B.V.

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Fig. 2 — A phylogeny of all known CoVs (n = 40). The phylogeny was constructed based on the amino acid sequences of the RNA-dependent RNA Polymerase region (length = 163 a.a.). The phylogeny was constructed using BEAST (Drummond and Rambaut, 2007) under a uncorrelated lognormally relaxed clock model (Drummond et al., 2006). The number at the nodes indicates the Bayesian posterior probability support (as percentages) summarized from trees sampled at every 1000th step of a BMCMC chain of 10,000,000 steps where values lower than 80% were not shown. The mean substitution rate was fixed at 1.0 and the branch length was expressed in units of substitutions per site. FIPV, Feline infectious peritonitis virus (AY994055); CFBGDDM9503, Chinese ferret badger CoV 2003 (EU769560); PRCV, Porcine respiratory CoV (DQ811787); TGEV, Transmissible gastroenteritis virus (NC_002306); PEDV, Porcine epidemic diahrrea virus (NC_003436); BtCoV5122005, Bat CoV 512-2005 (NC_009657); BatCoVHKU6, Bat CoV HKU6 (DQ249224); BtCoV1A, Bat CoV 1A (NC_010437); BtCoV1B, Bat CoV 1B (NC_010436); BatCoVHKU8, Bat CoV HKU8 (NC_010438); HCoV229E, Human CoV 229E (NC_002645); HCoVNL63, Human CoV NL63 (NC_005831); BatCoVHKU2, Bat CoV HKU2 (EF203064); HCoVOC43, Human CoV OC43 (NC_005147); BCoV, Bovine CoV (NC_003045); AntelopeCoV, Sable antelope CoV (EF424621); GiCoV, Giraffe CoV (EF424622); PHEV, Porcine hemagglutinating encephalomyelitis virus (NC_007732); SDAV, Rat sialodacryoadenitis CoV (AF124990); MHV, Mouse hepatitis virus (NC_006852); HCoVHKU1, Human CoV HKU1 (NC_006577); BatCoVHKU9, Bat CoV HKU9 (NC_009021); SCoV (NC_004718); Rp3, Bat SLCoV (NC_009693); BatSCoVHKU3, Bat SLCoV HKU3 (NC_009694); Rm1, Bat SLCoV (NC_009696); Rf1, Bat SLCoV (NC_009695); BtCoV1332005, Bat CoV-133-2005 (NC_008315); BatCoVHKU4, Bat CoV HKU4 (NC_009019); BatCoVHKU5, Bat CoV HKU5 (NC_009020); IBV, Infectious bronchitis virus (NC_001451); IBVpeafowl, peafowl CoV (AY641576); IBVpartridge, partridge CoV (AY646283); TCoV, Turkey CoV (NC_010800); SW1, Beluga whale CoV (NC_010646); BuCoVHKU11, Bulbul CoV (NC_011548); ThCoVHKU12, Thrush CoV (NC_011549); MuCoVHKU13, Munia CoV (NC_011550); ALCGXF23006, Asian leopard cat CoV 2006 (EF584908); CFBGXF24706, Chinese ferret badger CoV 2006 (EF584911).