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. 2008 Jul 30:552–560. doi: 10.1016/B978-012374410-4.00780-9

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Copyright © 2008 Elsevier Ltd. All rights reserved.

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Phylogenetic analysis of RNA sequences coding for the RNA-dependent RNA polymerase (partial sequence). The phylogenetic tree was constructed by the neighbor-joining method and bootstrap values were determined with 1000 replicates. Human SARS CoV (GenBank accession AY278491.2), SARS CoVs isolated from palm civets in 2003 (AY304486.1) and 2004 (AY613948.1) and bat CoVs [Bat CoV 1A (DQ666337.1), Bat CoV 1B (DQ666338.1), Bat CoV HKU2 (DQ249235.1), Bat-SARS CoV HKU3–1 (DQ022305), Bat CoV HKU4 (DQ249214.1), Bat CoV HKU5 (DQ249217.1), Bat CoV HKU6 (DQ249224.1), Bat CoV HKU7 (DQ249226.1), Bat CoV HKU8 (DQ249228.1), Bat-SARS CoV Rp3 (DQ071615), Bat-SARS CoV Rm1 (DQ412043), Bat-SARS CoV Rf1 (DQ412042), Bat CoV/A434/2005 (DQ648819.1), Bat CoV/A701/2005 (DQ648833.1), Bat CoV/A773/2005 (DQ648835.1) Bat CoV/A821/2005 (DQ648837.1), Bat CoV/A970/2005 (DQ648854.1) Bat CoV/A911/2005 (DQ648850.1), Bat CoV/A1018/2005 (DQ648795.1), Bat CoV/133/2005 (NC_008315), Bat CoV/273/2005 (DQ648856), Bat CoV/279/2005 (DQ648857), Bat CoV/355A/2005 (DQ648809.1), Bat CoV/512/2005 (DQ648858)] were aligned with references sequences as indicated. Reference sequences are: transmissible gastroenteritis virus, TGEV (DQ811789); HCoV 229E (AF304460); HCoV NL63 (AY567487); HCoV-OC43 (AY391777); HCoV-HKU1 (DQ415903 HKU1); porcine epidemic diarrhea virus, PEDV (AF353511); avian infectious bronchitis virus, AIBV (AY646283); mouse hepatitis virus, MHV (AY700211); bovine coronavirus, BCoV (AF220295); feline infectious peritonitis virus, FIPV (AY994055).