Phylogenetic Analysis of Coronavirus Genomes

For the newly identified virus genome, the potential ORFs were predicted and annotated using the conserved signatures of the cleavage sites recognized by coronavirus proteinases, and were processed in the Lasergene software package (v.7.1, DNAstar). The viral genes were aligned using the L-INS-i algorithm implemented in MAFFT (v.7.407)^{37 (link)}.
Phylogenetic analyses were then performed using the nucleotide sequences of various CoV gene datasets: (1) whole genome, (2) ORF1a, (3) ORF1b, (4) nsp5 (3CLpro), (5) RdRp (nsp12), (6) nsp13 (Hel), (7) nsp14 (ExoN), (8) nsp15 (NendoU), (9) nsp16 (O-MT), (10) spike (S) and (11) nucleocapsid (N). Phylogenetic trees were inferred using the maximum likelihood method implemented in the PhyML program (v.3.0)^{38 (link)}, using the generalized time reversible substitution model and subtree pruning and regrafting branch swapping. Bootstrap support values were calculated from 1,000 pseudo-replicate trees. The best-fitting model of nucleotide substitution was determined using MEGA (v.5)^{39 (link)}. Amino acid identities among sequences were calculated using the MegAlign program implemented in the Lasergene software package (v.7.1, DNAstar).

Free full text: Click here

Wu F., Zhao S., Yu B., Chen Y.M., Wang W., Song Z.G., Hu Y., Tao Z.W., Tian J.H., Pei Y.Y., Yuan M.L., Zhang Y.L., Dai F.H., Liu Y., Wang Q.M., Zheng J.J., Xu L., Holmes E.C, & Zhang Y.Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265-269.

Publication 2020

Amino acid sequences Cleavage Coronavirus Exon Gene Genome Nendou Nucleocapsid Nucleotide Nucleotide sequences Orfs Proteinases Replicate Trees Viral genes Virus genome

Corresponding Organization :

Other organizations : Shanghai Public Health Clinical Center, Huazhong University of Science and Technology, Central Hospital of Wuhan, Wuhan Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, University of Sydney

Top 5 similar protocols

Protocol cited in 53 other protocols

Variable analysis

independent variables

Nucleotide sequences of various CoV gene datasets: (1) whole genome, (2) ORF1a, (3) ORF1b, (4) nsp5 (3CLpro), (5) RdRp (nsp12), (6) nsp13 (Hel), (7) nsp14 (ExoN), (8) nsp15 (NendoU), (9) nsp16 (O-MT), (10) spike (S) and (11) nucleocapsid (N)

dependent variables

Phylogenetic trees inferred using the maximum likelihood method

control variables

Generalized time reversible substitution model
Subtree pruning and regrafting branch swapping
Bootstrap support values calculated from 1,000 pseudo-replicate trees
Best-fitting model of nucleotide substitution determined using MEGA (v.5)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!