20210209

Contents

1. 1. Working directories
2. 2. Password protected PDF
3. 3. A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived | Zenodo
4. 4. Fastest MUSCLE
5. 5. A pneumonia outbreak associated with a new coronavirus of probable bat origin | Nature
   1. 5.1. Extended data figures and tables
      1. 5.1.1. Extended Data Fig. 1 NGS raw reads of sample WIV04 mapping to the 2019-nCoV sequence.
      2. 5.1.2. Extended Data Fig. 2 Phylogenetic trees based on the complete S and RdRp gene sequences of coronaviruses.
      3. 5.1.3. Extended Data Fig. 3 Amino acid sequence alignment of the S1 protein of the 2019-nCoV to SARS-CoV and selected bat SARSr-CoVs.
      4. 5.1.4. Extended Data Fig. 4 Molecular detection method used to detect 2019-nCoV.
      5. 5.1.5. Extended Data Fig. 5 Amino acid sequence alignment of the nucleocapsid protein of 2019-nCoV to bat SARSr-CoV Rp3 and SARS-CoV BJ01.
      6. 5.1.6. Extended Data Fig. 6 Isolation and antigenic characterization of 2019-nCoV.
      7. 5.1.7. Extended Data Fig. 7 Analysis of 2019-nCoV receptor usage.
      8. 5.1.8. Extended Data Table 1 Patient information and diagnosis history
      9. 5.1.9. Extended Data Table 2 Laboratory results
      10. 5.1.10. Extended Data Table 3 Genomic comparison of 2019-nCoV WIV04 with SARS-CoVs and bat SARSr-CoVs
      11. 5.1.11. Extended Data Table 4 Virus neutralization test of serum samples

Working directories

i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/CRAN/Manuals/R_Learning/A_Little_Book_of_R_For_Bioinformatics.pdf
setsid okular ${i} # downloaded by Zhang Li
#
i=/media/ht/ht_5T/Work/Projects/Other_Projects/Coronavirus_Project/Ref/Not_Classified/SQuay_Bayesian_Analysis_of_SARS-CoV-2_FINAL_V.2.pdf
setsid okular ${i} # Steven C. Quay, MD, PhD
#
i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/Aligner/Ref/Evaluating_the_Accuracy_and_Efficiency_of_Multiple_Sequence_Alignment_Methods.pdf
setsid okular ${i} # speed up MUSCLE
#
i=/media/ht/ht_5T_9/YouTubes/书斋夜话/1
pcmanfm -n ${i}; cd ${i} # to be organized
#
i=/media/ht/ht_5T_9/YouTubes/History/Wuhan/新冠杂谈
pcmanfm -n ${i}; cd ${i} # to be organized

Password protected PDF

pdftk input.pdf output output.pdf user_pw abc
#
pdftk input.pdf output output.pdf owner_pw xyz user_pw abc

A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived | Zenodo

• Quay MD PhD, Steven Carl

i=/media/ht/ht_5T/Work/Projects/Other_Projects/Coronavirus_Project/Ref/Not_Classified/SQuay_Bayesian_Analysis_of_SARS-CoV-2_FINAL_V.2.pdf
setsid okular ${i} # Steven C. Quay, MD, PhD

Fastest MUSCLE

muscle -in seqs.fa -out seqs.afa -maxiters 1 - diags -sv -distance1 kbit20_3

Comfirmed by Yao Yuan

A pneumonia outbreak associated with a new coronavirus of probable bat origin | Nature

Extended data figures and tables

Extended Data Fig. 1 NGS raw reads of sample WIV04 mapping to the 2019-nCoV sequence.

The x axis indicates the genome nucleotide position and the y axis represents the read depth of the mapping.

Extended Data Fig. 2 Phylogenetic trees based on the complete S and RdRp gene sequences of coronaviruses.

a, b, Phylogenetic trees on the basis of the gene sequences of S (a) and RdRp (b) are shown. 2019-nCoV and bat CoV RaTG13 are shown in bold and in red. The trees were constructed using the maximum likelihood method using the GTR + G substitution model with bootstrap values determined by 1,000 replicates. Bootstraps values of more than 50% are shown.

Extended Data Fig. 3 Amino acid sequence alignment of the S1 protein of the 2019-nCoV to SARS-CoV and selected bat SARSr-CoVs.

The receptor-binding motif of SARS-CoV and the homologous region of other coronaviruses are indicated by the red box. The key amino acid residues involved in the interaction with human ACE2 are numbered at the top of the aligned sequences. The short insertions in the N-terminal domain of the 2019-nCoV are indicated by the blue boxes. Bat CoV RaTG13 was obtained from R. affinis, found in Yunnan province. Bat CoV ZC45 was obtained from R. sinicus, found in Zhejiang province.

Extended Data Fig. 4 Molecular detection method used to detect 2019-nCoV.

a, Standard curve for qPCR primers. The PCR product of the S gene that was serial diluted in the range of 108 to 101 (lines from left to right) was used as a template. Primer sequences and experimental conditions are described in the Methods. b, Specificity of the qPCR primers. Nucleotide samples from the indicated pathogens were used.

Extended Data Fig. 5 Amino acid sequence alignment of the nucleocapsid protein of 2019-nCoV to bat SARSr-CoV Rp3 and SARS-CoV BJ01.

Bat SARSr-CoV Rp3 was obtained from R. sinicus, which is found in Guangxi province.

Extended Data Fig. 6 Isolation and antigenic characterization of 2019-nCoV.

a, b, Vero E6 cells are shown at 24 h after infection with mock virus (a) or 2019-nCoV (b). c, d, Mock-virus-infected (c) or 2019-nCoV-infected (d) samples were stained with rabbit serum raised against recombinant SARSr-CoV Rp3 N protein (red) and DAPI (blue). The experiment was conducted twice independently with similar results. e, The ratio of the number of reads related to 2019-nCoV among the total number of virus-related reads in metagenomics analysis of supernatants from Vero E6 cell cultures. f, Virus growth in Vero E6 cells. g, Viral particles in the ultrathin sections were imaged using electron microscopy at 200 kV. The sample was from virus-infected Vero E6 cells. The inset shows the viral particles in an intra-cytosolic vacuole.

Extended Data Fig. 7 Analysis of 2019-nCoV receptor usage.

Determination of virus infectivity in HeLa cells with or without the expression of human APN and DPP4. The expression of ACE2, APN and DPP4 plasmids with S tag were detected using mouse anti-S tag monoclonal antibody. ACE2, APN and DPP4 proteins (green), viral protein (red) and nuclei (blue) are shown. Scale bars, 10 μm.

Extended Data Table 1 Patient information and diagnosis history

Extended Data Table 2 Laboratory results

Extended Data Table 3 Genomic comparison of 2019-nCoV WIV04 with SARS-CoVs and bat SARSr-CoVs

Extended Data Table 4 Virus neutralization test of serum samples

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