https://orcid.org/0000-0001-6336-6657
Figures & data
Table 1. List of coronaviruses used in this study.
Figure 1. Betacoronavirus genome organization. The betacoronavirus genome comprises of the 5'-untranslated region (5'-UTR), open reading frame (orf) 1a/b (yellow box) encoding non-structural proteins (nsp) for replication, structural proteins including spike (blue box), envelop (orange box), membrane (red box), and nucleocapsid (cyan box) proteins, accessory proteins (purple boxes) such as orf 3, 6, 7a, 7b, 8 and 9b in the 2019-nCoV (HKU-SZ-005b) genome, and the 3'-untranslated region (3'-UTR). Examples of lineages A to D betacoronaviruses include human coronavirus (HCoV) HKU1 (lineage A), 2019-nCoV (HKU-SZ-005b) and SARS-CoV (lineage B), MERS-CoV and Tylonycteris bat CoV HKU4 (lineage C), and Rousettus bat CoV HKU9 (lineage D). The length of nsps and orfs are not drawn in scale.
Table 2. Putative functions and proteolytic cleavage sites of 16 nonstructural proteins in orf1a/b as predicted by bioinformatics.
Table 3. Amino acid identity between the 2019 novel coronavirus and bat SARS-like coronavirus or human SARS-CoV.
Figure 2. Comparison of protein sequences of Spike stalk S2 subunit. Multiple alignment of Spike S2 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number NC004718) was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21 respectively. The black boxes represent the identity while the grey boxes represent the similarity of the four amino acid sequences.
Figure 4. Analysis of orf3b. A. Multiple alignment of orf3b protein sequence between 2019-nCoV (HKU-SZ-005b), SARS-CoV and SARS-related CoV. B. A novel putative short protein found in orf3b.
Figure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively.
