Journal: Journal of Neurovirology

Article Title: Potential neuroinvasive and neurotrophic properties of SARS-CoV-2 in pediatric patients: comparison of SARS-CoV-2 with non-segmented RNA viruses

doi: 10.1007/s13365-020-00913-5

Figure Lengend Snippet: Evolutionary history of SARS-CoV-2 compared with selected CoVs and neuroinvasive and neurotropic non-segmented RNA viruses. Evolutionary analyses were conducted in MEGAX. The nucleotide sequences were aligned with ClustalW and the results were visualized by Dendroscope-3. The percentage of replicate trees in which the associated clusters was found by the bootstrap test (1000 replicates) is shown next to the branches. The accession numbers for the viruses studied in this present study are shown. The highest log likelihood of the tree is − 541499.02. The branch of SARS-CoV-2 was labelled with blue color, whereas the branches of other viruses infecting infants and children nervous system were labelled with red color. This analysis involved 32 nucleotide sequences and contained a total of 32822 positions in the final dataset. The distance scale bar suggests a 0.2 (20%) genetic variation for the length of the scale between sequences

Article Snippet: RStudio with msa package including ClustalW command was used for multiple sequence alignment.

Techniques:

Journal: Journal of Neurovirology

Article Title: Potential neuroinvasive and neurotrophic properties of SARS-CoV-2 in pediatric patients: comparison of SARS-CoV-2 with non-segmented RNA viruses

doi: 10.1007/s13365-020-00913-5

Figure Lengend Snippet: a Schematic representation of SARS-CoV-2 complete genome (accession number: NC_04551) and selected ORF and encoded conserved domains. Macrodomain (macro_X_nsp3-like), S protein, and viroporin (E protein), investigated in the present study, are highlighted in blue color. The arrows indicate the protease priming sites on S protein. b The macrodomain (macro_X_nsp3-like) sequence of SARS-CoV-2 was compared with SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-HKU1, HCoV-NL63, MHV-JHM, rubella, eastern equine encephalitis virus, western equine encephalitis virus, Venezuelan equine encephalitis virus, and Chikungunya virus. c The viroporin sequence of SARS-CoV-2 was compared with SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-HKU1, HCoV-NL63, MHV-JHM, coxsackievirus, echovirus, poliovirus, and HIV-1. RStudio with msa package including ClustalW command was used for multiple sequence alignment. The results were visualized by RStudio and LaTeX with TEXshade package. All identical residues at a position were shaded in blue or purple if the number of matching residues is higher than 50% or 80%, respectively. The residues that are not identical but similar to the consensus sequence were shaded in red. Furthermore, the degree of protein sequence conservation and amino acid properties such as charge and hydrophobicity were shown as color scales and bar graph along the alignment. On the top of the plot, residue conservation was shown as bars and the charge of amino acid side chain was shown as color scales (red: acidic; blue: basic). Hydrophobicity was shown at the bottom of the plot (upper red box: hydrophobic; underside box: hydrophilic). The degree of similarity and identity between all sequences in the alignment were shown in tables (b-II, c-II). The bootstrap consensus trees inferred from 1000 replicates to represent the evolutionary history of the macrodomain (macro_X_nsp3-like) (b-III) and viroporin (c-III) between the viruses analyzed. The percentage of replicate trees in which the associated viruses clustered together in the bootstrap test is shown next to the branches. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed

Article Snippet: RStudio with msa package including ClustalW command was used for multiple sequence alignment.

Techniques: Sequencing, Virus, Western Blot, Residue