LitCovid-sentences  

PMC:7335631 / 1475-9584 JSONTXT 10 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T15 0-15 Sentence denotes 1 Introduction
T16 16-240 Sentence denotes The present pandemic situation of the Severe Acute Respiratory Syndrome (COVID-19) is caused by the RNA virus SARS-CoV2 which is characterized by its rapid mutations up to a million times higher than that of their hosts [1].
T17 241-408 Sentence denotes Several mutations have been detected in various proteins of the SARS-CoV2 over a short period of time, which are recently reported in various articles [[2], [3], [4]].
T18 409-490 Sentence denotes Genomic variations and evolution enabled the virus to escape host immunity [5,6].
T19 491-571 Sentence denotes So, such variability would help the scientists towards the drug development [1].
T20 572-789 Sentence denotes Among various proteins of SARS-CoV2, spike(S), envelope (E), membrane(M) and nucleocapsid (N) are the four structural proteins which help them in assembling and releasing new copies of the virus within human cell [7].
T21 790-991 Sentence denotes The CoV envelope (E) protein is the smallest among the four structural proteins involved in several aspects of the virus life cycle, such as assembly, budding, envelope formation, and pathogenesis [7].
T22 992-1091 Sentence denotes However, the molecular mechanism involving E-protein in pathogenesis is not yet clearly understood.
T23 1092-1208 Sentence denotes Notably, this protein interacts with other structural proteins such as membrane(M) and other accessory proteins viz.
T24 1209-1249 Sentence denotes ORF3a, ORF7a and host cell proteins [8].
T25 1250-1414 Sentence denotes Envelope protein of SARS-CoV2 is 76 amino acids long and possesses three important domains viz. (N)-terminus, transmembrane domain (TMD) and (C)-terminus (Fig. 1 ).
T26 1415-1629 Sentence denotes The (C)-terminal domain of envelope protein in SARS-CoV2 binds to human PALS1, a tight junction-associated protein, which is essential for the establishment and maintenance of epithelial polarity in mammals [9,10].
T27 1630-1710 Sentence denotes Fig. 1 Amino acid sequence and domains of the envelope protein of SARS-CoV2 [7].
T28 1711-1932 Sentence denotes Red and blue colors are representing hydrophobic and hydrophilic amino acid, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
T29 1933-2139 Sentence denotes Four mutations including one deletion have been found in the envelope protein of SARS-CoV2 with reference to the SARS-CoV1, a species of coronavirus that also infects humans, bats and certain other mammals.
T30 2140-2230 Sentence denotes The alignment of the envelope proteins of the SARS-CoV1 and SARS-CoV2 is given in Fig. 2 .
T31 2231-2307 Sentence denotes Fig. 2 Clustal alignment of the envelope protein of SARS-CoV1 and SARS-CoV2.
T32 2308-2659 Sentence denotes Mutations in (C)-terminus domain in the E protein protein of SARS-CoV2 are T55S, V56F, E69R (the mutation of an amino acid A1 to an amino acid A2 is denoted by A1pA2 where p denotes location in the reference amino acid sequence).The deletion mutation of G at the 70th position with respect to the reference envelope protein of SARS-CoV1 is also noted.
T33 2660-2827 Sentence denotes It is reported that the C-terminus domain of the envelope protein contains the motif DLLV which binds to the host cell PALS1 protein to facilitate infection [9,11,12].
T34 2828-3056 Sentence denotes In this present study, non-synonymous mutations over the envelope protein of SARS-CoV2 across the available 3617 SARS-CoV2 genomes (as on 6th June 2020), have been found and accordingly their probable consequences are discussed.
T35 3058-3068 Sentence denotes 2 Methods
T36 3069-3164 Sentence denotes From the NCBI virus database, all the protein sequences of 3617 SARS-CoV2 genomes were fetched.
T37 3165-3294 Sentence denotes Then the amino acid sequences of envelope protein of SARS-CoV2 are exported in fasta format using file operations through Matlab.
T38 3295-3461 Sentence denotes These sequences (fasta formatted) are blasted using Clustal-Omega and found the mismatched and from their mutations and their associated positions were detected [13].
T39 3463-3473 Sentence denotes 3 Results
T40 3474-3631 Sentence denotes Among these virus genomes from 3617 patients; 2588 were from the USA, 372 were from Asia, 287 were from Europe, 365 were from Oceania and 5 were from Africa.
T41 3632-3756 Sentence denotes Here, we present the non-synonymous mutations of the E-protein protein over the available 3617 SARS-CoV2 genomes (Table 1 ).
T42 3757-3985 Sentence denotes It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contained the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes.
T43 3986-4084 Sentence denotes Changes of the R-group of each amino acid according to the mutations are also presented (Table-1).
T44 4085-4370 Sentence denotes It is to be noted that the mutation of an amino acid A 1 to an amino acid A 2 is denoted by A 1 pA 2 where p denotes location in the reference amino acid sequence.• In less than 0.5% of the SARS-CoV2 genomes, the E-protein possesses the missense mutations as adumbrated in the Table 1.
T45 4371-4471 Sentence denotes In TMD and C-terminus domain, there are nine different mutations where the R-group property changes.
T46 4472-4612 Sentence denotes But only in QHZ00381, for the mutation L37H in the TMD of the envelope protein causes changes in amino acid from hydrophobic to hydrophilic.
T47 4613-4808 Sentence denotes • TMD was also observed to be conserved over the SARS-CoV1 and COV2 genomes, but the protein sequences of QJA42107 (USA: VA), QJQ84222(USA: KENNER, LA), QHZ00381(South Korea) and QJS53352(Greece:
T48 4809-4916 Sentence denotes Athens) possess four mutations A36V, L26F, L37H and L39M, respectively, in the TMD of the envelope protein.
T49 4917-5105 Sentence denotes Change in the R-group property from Hydrophobic to Hydrophilic in the TMD of the envelope protein of the virus from South Korea may affect the ion channel activity of the envelope protein.
T50 5106-5199 Sentence denotes • The motif ′DLLV′ has been changed to ′DFLV′ and ′YLLV′ in the proteins QJR88103 (Australia:
T51 5200-5230 Sentence denotes Victoria) and QKI36831 (China:
T52 5231-5290 Sentence denotes Guangzhou) due to the mutations L73F and D72Y respectively.
T53 5291-5481 Sentence denotes These mutations having changes in the motif ′DFLV′ may mis-target the PALS1 at Golgi and delaying TJ formation and accordingly may influence replication and/or infectivity of the virus [10].
T54 5482-5659 Sentence denotes • In the C-terminus domain of the E-protein of SARS-CoV2 the amino acid S at 68th position changes to the amino acids F and C in the proteins {QKG87268,  QKG88576} from the USA:
T55 5660-5698 Sentence denotes Massachusetts and QKI36855 from China:
T56 5699-5722 Sentence denotes Guangzhou respectively.
T57 5723-5930 Sentence denotes Note that the mutation of the amino acid S to F keeps the R-group property unchanged (i.e. hydrophobic to hydrophilic) while that of the amino acid S to C changes the R-group from Hydrophilic to Hydrophobic.
T58 5931-6002 Sentence denotes This would possibly make changes in protein functions and interactions.
T59 6003-6066 Sentence denotes Table 1 Non- synonymous mutation in the E-protein of SARS-CoV2.
T60 6067-6124 Sentence denotes Protein-ID Geo-location Mutation Domain Change of R-group
T61 6125-6178 Sentence denotes QJA42107 USA: VA A36V TMDa Hydrophobic to Hydrophobic
T62 6179-6239 Sentence denotes QJQ84222 USA: KENNER, LA L26F TMD Hydrophobic to Hydrophobic
T63 6240-6296 Sentence denotes QHZ00381 South Korea L37H TMD Hydrophobic to Hydrophilic
T64 6297-6313 Sentence denotes QJS53352 Greece:
T65 6314-6356 Sentence denotes Athens L39M TMD Hydrophobic to Hydrophobic
T66 6357-6376 Sentence denotes QJR88103 Australia:
T67 6377-6428 Sentence denotes Victoria L73F C-terminus Hydrophobic to Hydrophobic
T68 6429-6488 Sentence denotes QKE45838 USA: CA P71L C-terminus Hydrophobic to Hydrophobic
T69 6489-6548 Sentence denotes QKE45886 USA: CA P71L C-terminus Hydrophobic to Hydrophobic
T70 6549-6608 Sentence denotes QKE45898 USA: CA P71L C-terminus Hydrophobic to Hydrophobic
T71 6609-6668 Sentence denotes QKE45910 USA: CA P71L C-terminus Hydrophobic to Hydrophobic
T72 6669-6728 Sentence denotes QJE38284 USA: CA P71L C-terminus Hydrophobic to Hydrophobic
T73 6729-6788 Sentence denotes QIU81527 USA: WA P71L C-terminus Hydrophobic to Hydrophobic
T74 6789-6802 Sentence denotes QKG87268 USA:
T75 6803-6859 Sentence denotes Massachusetts S68F C-terminus Hydrophobic to Hydrophobic
T76 6860-6873 Sentence denotes QKG88576 USA:
T77 6874-6930 Sentence denotes Massachusetts S68F C-terminus Hydrophobic to Hydrophobic
T78 6931-6946 Sentence denotes QKI36831 China:
T79 6947-6999 Sentence denotes Guangzhou D72Y C-terminus Hydrophilic to Hydrophobic
T80 7000-7015 Sentence denotes QKI36855 China:
T81 7016-7068 Sentence denotes Guangzhou S68C C-terminus Hydrophilic to Hydrophobic
T82 7069-7097 Sentence denotes a TMD: transmembrane domain.
T83 7099-7120 Sentence denotes 4 Concluding remarks
T84 7121-7329 Sentence denotes Among all the proteins present in the novel RNA virus, some accessory proteins such as ORF6, ORF7b, ORF8, ORF10 contain the least number of missense mutation as reported in various studies [[14], [15], [16]].
T85 7330-7361 Sentence denotes And same is true for E-protein.
T86 7362-7507 Sentence denotes We find 15 among 3617 (0.414%) of the SARS-CoV2 genome contains eight different types of mutations in TMD and C-terminus of the envelope protein.
T87 7508-7659 Sentence denotes Mutated E-protein might affect replication and propagation of the SARS-CoV2 as has been observed in cases of SARS-CoV and MERS-CoV in mouse model [17].
T88 7660-7787 Sentence denotes Potential studies have also shown that vaccine against the E-protein mutated viruses can reduce the infectivity in mouse model.
T89 7789-7809 Sentence denotes Author contributions
T90 7810-7862 Sentence denotes SH conceived the problem and examined the mutations.
T91 7863-7904 Sentence denotes SH, PPC, BR analyzed the data and result.
T92 7905-8012 Sentence denotes SH wrote the initial draft which was checked and edited by all other authors to generate the final version.
T93 8014-8047 Sentence denotes Declaration of Competing Interest
T94 8048-8109 Sentence denotes The authors do not have any conflicts of interest to declare.