PMC:3713832 / 3989-5823
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3713832","sourcedb":"PMC","sourceid":"3713832","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3713832","text":"The RNA-dependent RNA polymerase (RdRp, the 12th nonstructural protein codified to open reading frame 1a,b) is a highly conserved gene of CoVs, which is frequently used for phylogenetic comparison (8,9). MEGA5.0 (www.megasoftware.net) was used to construct the phylogenetic trees on the basis of the nucleotide sequences and deduced amino acid sequences. First, we used the MUSCLE package and default parameters (www.megasoftware.net/) to construct the alignment. The best substitution model was then evaluated with the Model Selection package implemented in MEGA5. Finally, we used the maximum-likelihood method with an appropriate model to process the phylogenetic analysis with 1,000 bootstrap replicates. We constructed a phylogenetic tree based on the nucleotide sequences of the RdRp gene to show the evolutionary relationship between these 2 betacoronaviruses and other CoVs (Figure 1). Reference CoV genome sequences were downloaded from GenBank and aligned with the fragments of the newly discovered CoVs. The RdRp genes of Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011 were highly similar, sharing 93.1% nt identity. The phylogenetic analysis demonstrated that betacoronaviruses and the bat SARS-like CoVs in our study are clustered (93.1%–93.4% nt identity) and are close in distance to SARS-CoVs (92.9%–94.8% nt identity) and civet SARS-like CoVs (93.1%–94.8% nt identity) but that bat CoV (BtCoV-HKU9) and HCoV-OC43 are placed among the relatively distant groups (65.8%–65.9% and 62.9%–63.5% nt identities with the betacoronaviruses, respectively). Therefore, collectively we called these betacoronaviruses and bat SARS-like CoVs the bat SARS-like cluster of CoVs. Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011 showed little genetic similarity (\u003c66.2%–67.3% nt identity) to HCoV-EMC.","tracks":[{"project":"2_test","denotations":[{"id":"23739658-15613317-27697036","span":{"begin":198,"end":199},"obj":"15613317"},{"id":"23739658-22933277-27697037","span":{"begin":200,"end":201},"obj":"22933277"}],"attributes":[{"subj":"23739658-15613317-27697036","pred":"source","obj":"2_test"},{"subj":"23739658-22933277-27697037","pred":"source","obj":"2_test"}]},{"project":"MyTest","denotations":[{"id":"23739658-15613317-27697036","span":{"begin":198,"end":199},"obj":"15613317"},{"id":"23739658-22933277-27697037","span":{"begin":200,"end":201},"obj":"22933277"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"23739658-15613317-27697036","pred":"source","obj":"MyTest"},{"subj":"23739658-22933277-27697037","pred":"source","obj":"MyTest"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93bdec","default":true},{"id":"MyTest","color":"#d7ec93"}]}]}}