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PMC:7126159 JSONTXT 21 Projects

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Id Subject Object Predicate Lexical cue
T1 0-89 Sentence denotes Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2
T2 91-102 Sentence denotes Dear editor
T3 103-304 Sentence denotes A recent study in this journal studied the genomes of the novel SARS-like coronavirus (SARS-CoV-2) in China and suggested that the SARS-CoV-2 had undergone genetic recombination with SARS-related CoV1.
T4 305-516 Sentence denotes By February 14, 2020, a total of 66,576 confirmed cases of COVID-19, people infected with SARS-CoV-2, were reported in China, leading to 1524 deaths, per the Chinese CDC (http://2019ncov.chinacdc.cn/2019-nCoV/).
T5 517-659 Sentence denotes Several full genomic sequences of this virus have been released for the study of its evolutionary origin and molecular characteristics2, 3, 4.
T6 660-826 Sentence denotes Here, we analyzed the potential mutations that may have evolved after the virus became epidemic among humans and also the mutations resulting in the human adaptation.
T7 827-914 Sentence denotes The sequences of BetaCoV were downloaded on February 3, 2020 from the GISAID platform5.
T8 915-1039 Sentence denotes A total of 58 accessions were available, among which BetaCoV/bat/Yunnan/RaTG13/2013 is a known close relative of SARS-CoV-2.
T9 1040-1255 Sentence denotes Four accessions, namely, BetaCov/Italy/INM1/2020, BetaCov/Italy/INM2/2020, BetaCoV/Kanagawa/1/2020, and BetaCoV/USA/IL1/2020, were excluded because of the short-truncated sequences or multiple ambiguous nucleotides.
T10 1256-1366 Sentence denotes A total of 54 accessions (Supplementary Table 1) isolated from humans were utilized in the following analysis.
T11 1367-1479 Sentence denotes The sequences NC_004718.3 of SARS coronavirus6 genes were utilized to define the protein products of SARS-CoV-2.
T12 1480-1616 Sentence denotes The protein sequences of ORF1ab, S, E, M, and N genes were translated, and all of the loci without experimental evidences were excluded.
T13 1617-1832 Sentence denotes First, the protein sequences of SARS-CoV-2 were compared with RaTG13, human SARS (NC_004718.3), bat SARS (DQ022305.2), and human MERS (NC_019843.3) by calculating the similarity in a given sliding window (Fig. 1 A).
T14 1833-1951 Sentence denotes The sliding window was set to 500 for ORF1ab and S, and to 50 for proteins E, M, and N considering their short length.
T15 1952-2161 Sentence denotes SARS-CoV-2 were highly similar to RaTG13 isolated from bats, showing 96% identity based on the whole-nucleotide sequences and 83% based on the protein sequences, suggesting a bat zoonotic origin of SARS-CoV-2.
T16 2162-2241 Sentence denotes ORF1a, and the head of S seemed to have diverged from other beta coronaviruses.
T17 2242-2769 Sentence denotes Fig. 1 (A) The similarity between SARS-CoV-2 and other beta coronaviruses using the sliding window showed that SARS-CoV-2 was similar to bat virus RaTG13. (B) The molecular phylogenetic tree based on protein sequences established the high similarity among SARS-CoV-2 and its near relatives. (C) The mutations that developed after it came to circulate among humans did not include any mutation with high occurrence. (D) The graphs show all of the differences between SARS-CoV-2 and its close relative strains isolated from bats.
T18 2770-2898 Sentence denotes The molecular phylogenetic tree (Fig. 1B) was built by using the maximum likelihood method based on the JTT matrix-based model7.
T19 2899-2974 Sentence denotes It hinted that the protein sequences of SARS-CoV-2 had over 99% similarity.
T20 2975-3093 Sentence denotes Twenty-eight viruses had shared the same protein sequences, and could be the original strain circulated in the humans.
T21 3094-3145 Sentence denotes The other viruses had only a few mutations from it.
T22 3146-3295 Sentence denotes This indicates that the virus could have evolved for only a very short time after gaining the efficient human to human transmissibility, as expected.
T23 3296-3444 Sentence denotes Next, we analyzed the mutations that occurred after infecting humans (Fig. 1C) in order to identify mutations associated with more severe infection.
T24 3445-3653 Sentence denotes Here, two accessions (BetaCoV/Shenzhen/SZTH-001/2020 and BetaCoV/Shenzhen/SZTH-004/2020) from Shenzhen, which had 5 and 16 mutations, respectively, were excluded, considering the possible experimental issues.
T25 3654-3810 Sentence denotes All of the mutations only occurred once, so it is possible that all of these mutations occur naturally and are associated with viral survival and infection.
T26 3811-3903 Sentence denotes Several mutations were clustered in peptides nsp3 and nsp4 of ORF1ab and in the header of S.
T27 3904-4030 Sentence denotes These results suggested that there had probably been no hyper-variable genomic hotspot in the SARS-CoV-2 population until now.
T28 4031-4215 Sentence denotes We compared these results with those of the work of Ceraolo and Giorgi8, who reported at least two hyper-variable genomic hotspots based on the Shannon entropy of nucleotide sequences.
T29 4216-4353 Sentence denotes They utilized all of the sequences, while we merged all of the fully identical sequences into one during our Shannon entropy calculation.
T30 4354-4551 Sentence denotes As shown in Fig. 1B, 28 sequences were merged into one in present study because they had been collected in such a short time, so collection time and location could not have produced any large bias.
T31 4552-4692 Sentence denotes If those identical sequences were calculated individually, any mutations on these 28 sequences would have sharply increased Shannon entropy.
T32 4693-4769 Sentence denotes The protein sequences were used to exclude any unimportant silent mutations.
T33 4770-4862 Sentence denotes Finally, the sequences of earliest SARS-CoV-2 were compared with RaTG13 from bats (Fig. 1D).
T34 4863-5065 Sentence denotes Fisher's exact test with post hoc test suggested that nsp1, nsp3, and nsp15 of ORF1ab and gene S had significantly more mutations than other genes, which might facilitate human adaptation and infection.
T35 5066-5182 Sentence denotes S gene encodes spike glycoprotein, which binds host ACE2 receptors and is required for initiation of the infection9.
T36 5183-5298 Sentence denotes They reported that a 193-amino acid fragment was able to bind ACE2 more efficiently than its unmutated counterpart.
T37 5299-5446 Sentence denotes This region in which spike glycoprotein binds to ACE2 had 21 mutations not found in RaTG13, suggesting their role in the adaptation to human hosts.
T38 5447-5538 Sentence denotes Peptide nsp1 facilitated viral gene expression and evasion from the host immune response10.
T39 5539-5685 Sentence denotes Peptide nsp3, named papain-like proteinase, was found to be associated with the cleavages, viral replication, and antagonization of innate immune.
T40 5686-5778 Sentence denotes These two peptides are probably associated with the latent period after infection in humans.
T41 5779-5838 Sentence denotes Peptide nsp15 acted as uridylate-specific endoribonuclease.
T42 5839-5979 Sentence denotes These results collectively suggest that peptides nsp1, nsp3, and nsp15 might have unclear but critical roles in this outbreak of SARS-CoV-2.
T43 5980-6100 Sentence denotes To summarize, this study confirmed the relationship of SARS-CoV-2 with other beta coronaviruses on the amino acid level.
T44 6101-6290 Sentence denotes The hyper-variable genomic hotspot has been established in the SARS-CoV-2 population at the nucleotide but not the amino acid level, suggesting that there have been no beneficial mutations.
T45 6291-6449 Sentence denotes The mutations in nsp1, nsp3, nsp15, and gene S that identified in this study would be associated with the SARS-CoV-2 epidemic and was worthy of further study.
T46 6451-6484 Sentence denotes Declaration of Competing Interest
T47 6485-6490 Sentence denotes None.
T48 6492-6525 Sentence denotes Appendix Supplementary materials
T49 6527-6534 Sentence denotes Funding
T50 6535-6838 Sentence denotes This study was supported by Key Laboratory for Preventive Research of Emerging Animal Diseases in Foshan University (KLPREAD201801-06), (KLPREAD201801-10), Youth Innovative Talents Project of Guangdong Province (2018KQNCX280), and National Key Research and Development Project (grant No.2017YFD0500800).
T51 6840-6855 Sentence denotes Acknowledgement
T52 6856-6934 Sentence denotes We thank the researchers who deposited the SARS-CoV-2 sequences in the GISAID.
T53 6935-7023 Sentence denotes We thank LetPub for its linguistic assistance during the preparation of this manuscript.
T54 7024-7147 Sentence denotes Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.jinf.2020.02.027.