CORD-19-Sentences  

CORD-19:0015023cc06b5362d332b3baf348d11567ca2fbb JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-144 Sentence denotes The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication but essential for the production of infectious virus.
TextSentencer_T1 0-144 Sentence denotes The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication but essential for the production of infectious virus.
TextSentencer_T2 145-148 Sentence denotes 2 3
TextSentencer_T2 145-148 Sentence denotes 2 3
TextSentencer_T3 150-158 Sentence denotes Abstract
TextSentencer_T3 150-158 Sentence denotes Abstract
TextSentencer_T4 159-170 Sentence denotes word count:
TextSentencer_T4 159-170 Sentence denotes word count:
TextSentencer_T5 171-194 Sentence denotes 194 22 Text word count:
TextSentencer_T5 171-194 Sentence denotes 194 22 Text word count:
TextSentencer_T6 195-223 Sentence denotes 5168 23 24 25 author/funder.
TextSentencer_T6 195-223 Sentence denotes 5168 23 24 25 author/funder.
TextSentencer_T7 224-244 Sentence denotes All rights reserved.
TextSentencer_T7 224-244 Sentence denotes All rights reserved.
TextSentencer_T8 245-281 Sentence denotes No reuse allowed without permission.
TextSentencer_T8 245-281 Sentence denotes No reuse allowed without permission.
TextSentencer_T9 282-441 Sentence denotes Abstract 27 The positive stranded RNA genomes of picornaviruses comprise a single large open reading 28 frame flanked by 5′ and 3′ untranslated regions (UTRs).
TextSentencer_T9 282-441 Sentence denotes Abstract 27 The positive stranded RNA genomes of picornaviruses comprise a single large open reading 28 frame flanked by 5′ and 3′ untranslated regions (UTRs).
TextSentencer_T10 442-555 Sentence denotes Foot-and-mouth disease virus (FMDV) 29 has an unusually large 5′ UTR (1.3 kb) containing five structural domains.
TextSentencer_T10 442-555 Sentence denotes Foot-and-mouth disease virus (FMDV) 29 has an unusually large 5′ UTR (1.3 kb) containing five structural domains.
TextSentencer_T11 556-707 Sentence denotes These include the 30 internal ribosome entry site (IRES), which facilitates initiation of translation, and the cis-acting 31 replication element (cre).
TextSentencer_T11 556-707 Sentence denotes These include the 30 internal ribosome entry site (IRES), which facilitates initiation of translation, and the cis-acting 31 replication element (cre).
TextSentencer_T12 708-925 Sentence denotes Less well characterised structures are a 5′ terminal 360 nucleotide 32 stem-loop, a variable length poly-C-tract of approximately 100-200 nucleotides and a series of 33 two to four tandemly repeated pseudoknots (PKs).
TextSentencer_T12 708-925 Sentence denotes Less well characterised structures are a 5′ terminal 360 nucleotide 32 stem-loop, a variable length poly-C-tract of approximately 100-200 nucleotides and a series of 33 two to four tandemly repeated pseudoknots (PKs).
TextSentencer_T13 926-1150 Sentence denotes We investigated the structures of the PKs 34 by selective 2′ hydroxyl acetylation analysed by primer extension (SHAPE) analysis and 35 determined their contribution to genome replication by mutation and deletion experiments.
TextSentencer_T13 926-1150 Sentence denotes We investigated the structures of the PKs 34 by selective 2′ hydroxyl acetylation analysed by primer extension (SHAPE) analysis and 35 determined their contribution to genome replication by mutation and deletion experiments.
TextSentencer_T14 1151-1274 Sentence denotes 36 SHAPE and mutation experiments confirmed the importance of the previously predicted PK 37 structures for their function.
TextSentencer_T14 1151-1274 Sentence denotes 36 SHAPE and mutation experiments confirmed the importance of the previously predicted PK 37 structures for their function.
TextSentencer_T15 1275-1341 Sentence denotes Deletion experiments showed that although PKs are not essential 38
TextSentencer_T15 1275-1341 Sentence denotes Deletion experiments showed that although PKs are not essential 38
TextSentencer_T16 1342-1409 Sentence denotes for replication, they provide genomes with a competitive advantage.
TextSentencer_T16 1342-1409 Sentence denotes for replication, they provide genomes with a competitive advantage.
TextSentencer_T17 1410-1590 Sentence denotes However, although 39 replicons and full-length genomes lacking all PKs were replication competent, no infectious 40 virus was rescued from genomes containing less than one PK copy.
TextSentencer_T17 1410-1590 Sentence denotes However, although 39 replicons and full-length genomes lacking all PKs were replication competent, no infectious 40 virus was rescued from genomes containing less than one PK copy.
TextSentencer_T18 1591-1708 Sentence denotes This is consistent with our 41 earlier report describing the presence of putative packaging signals in the PK region.
TextSentencer_T18 1591-1708 Sentence denotes This is consistent with our 41 earlier report describing the presence of putative packaging signals in the PK region.
TextSentencer_T19 1709-1729 Sentence denotes 42 43 author/funder.
TextSentencer_T19 1709-1729 Sentence denotes 42 43 author/funder.
TextSentencer_T20 1730-1750 Sentence denotes All rights reserved.
TextSentencer_T20 1730-1750 Sentence denotes All rights reserved.
TextSentencer_T21 1751-1787 Sentence denotes No reuse allowed without permission.
TextSentencer_T21 1751-1787 Sentence denotes No reuse allowed without permission.
TextSentencer_T22 1789-1872 Sentence denotes VP3, and VP0 (which is further processed to VP2 and VP4 during virus assembly) (6).
TextSentencer_T22 1789-1872 Sentence denotes VP3, and VP0 (which is further processed to VP2 and VP4 during virus assembly) (6).
TextSentencer_T23 1873-2152 Sentence denotes The P2 64 and P3 regions encode the non-structural proteins 2B and 2C and 3A, 3B (1-3) (VPg), 3C pro and 4 structural protein-coding region is replaced by reporter genes, allow the study of genome 68 replication without the requirement for high containment (9, 10) ( figure 1A ).
TextSentencer_T23 1873-2152 Sentence denotes The P2 64 and P3 regions encode the non-structural proteins 2B and 2C and 3A, 3B (1-3) (VPg), 3C pro and 4 structural protein-coding region is replaced by reporter genes, allow the study of genome 68 replication without the requirement for high containment (9, 10) ( figure 1A ).
TextSentencer_T24 2153-2302 Sentence denotes The FMDV 5′ UTR is the largest known picornavirus UTR, comprising approximately 1300 71 nucleotides and containing several highly structured regions.
TextSentencer_T24 2153-2302 Sentence denotes The FMDV 5′ UTR is the largest known picornavirus UTR, comprising approximately 1300 71 nucleotides and containing several highly structured regions.
TextSentencer_T25 2303-2630 Sentence denotes The first 360 nucleotides at the 5′ 72 end are predicted to fold into a single large stem loop termed the S-fragment, followed by a The PKs were originally predicted in 1987 and consist of two to four tandem repeats of a ~48 86 nucleotide region containing a small stem loop and downstream interaction site (figure 1B) 87 (12).
TextSentencer_T25 2303-2630 Sentence denotes The first 360 nucleotides at the 5′ 72 end are predicted to fold into a single large stem loop termed the S-fragment, followed by a The PKs were originally predicted in 1987 and consist of two to four tandem repeats of a ~48 86 nucleotide region containing a small stem loop and downstream interaction site (figure 1B) 87 (12).
TextSentencer_T26 2631-2814 Sentence denotes Due to the sequence similarity between the PKs (figure 1C), it is speculated that they 88 were formed by duplication events during viral replication, probably involving recombination.
TextSentencer_T26 2631-2814 Sentence denotes Due to the sequence similarity between the PKs (figure 1C), it is speculated that they 88 were formed by duplication events during viral replication, probably involving recombination.
TextSentencer_T27 2815-3020 Sentence denotes 89 Between two and four PKs are present in different virus isolates but no strain has been 90 identified with less than two PKs, emphasising their potential importance in the viral life cycle 91 (19, 20) .
TextSentencer_T27 2815-3020 Sentence denotes 89 Between two and four PKs are present in different virus isolates but no strain has been 90 identified with less than two PKs, emphasising their potential importance in the viral life cycle 91 (19, 20) .
TextSentencer_T28 3021-3122 Sentence denotes The presence of PKs has been reported in the 5′ UTR of other picornaviruses such as 92 author/funder.
TextSentencer_T28 3021-3122 Sentence denotes The presence of PKs has been reported in the 5′ UTR of other picornaviruses such as 92 author/funder.
TextSentencer_T29 3123-3143 Sentence denotes All rights reserved.
TextSentencer_T29 3123-3143 Sentence denotes All rights reserved.
TextSentencer_T30 3144-3269 Sentence denotes No reuse allowed without permission. can occur in the absence of PKs at least one is required for wild-type (wt) replication.
TextSentencer_T30 3144-3269 Sentence denotes No reuse allowed without permission. can occur in the absence of PKs at least one is required for wild-type (wt) replication.
TextSentencer_T31 3270-3392 Sentence denotes 104 Furthermore, competition experiments showed that extra copies of PKs conferred a replicative 105 advantage to genomes.
TextSentencer_T31 3270-3392 Sentence denotes 104 Furthermore, competition experiments showed that extra copies of PKs conferred a replicative 105 advantage to genomes.
TextSentencer_T32 3393-3562 Sentence denotes Although replicons and full-length genomes lacking PKs were 106 replication-competent, no infectious virus was rescued from genomes containing less than one 107 PK copy.
TextSentencer_T32 3393-3562 Sentence denotes Although replicons and full-length genomes lacking PKs were 106 replication-competent, no infectious virus was rescued from genomes containing less than one 107 PK copy.
TextSentencer_T33 3563-3686 Sentence denotes This is consistent with our earlier report describing the presence of putative 108 packaging signals in the PK region (22).
TextSentencer_T33 3563-3686 Sentence denotes This is consistent with our earlier report describing the presence of putative 108 packaging signals in the PK region (22).
TextSentencer_T34 3687-3709 Sentence denotes 109 110 author/funder.
TextSentencer_T34 3687-3709 Sentence denotes 109 110 author/funder.
TextSentencer_T35 3710-3730 Sentence denotes All rights reserved.
TextSentencer_T35 3710-3730 Sentence denotes All rights reserved.
TextSentencer_T36 3731-3767 Sentence denotes No reuse allowed without permission.
TextSentencer_T36 3731-3767 Sentence denotes No reuse allowed without permission.
TextSentencer_T37 3768-3789 Sentence denotes Plasmid construction.
TextSentencer_T37 3768-3789 Sentence denotes Plasmid construction.
TextSentencer_T38 3790-3936 Sentence denotes 117 The FMDV replicon plasmids, pRep-ptGFP, and the replication-defective polymerase mutant 118 control, 3D-GNN, have already been described (10).
TextSentencer_T38 3790-3936 Sentence denotes 117 The FMDV replicon plasmids, pRep-ptGFP, and the replication-defective polymerase mutant 118 control, 3D-GNN, have already been described (10).
TextSentencer_T39 3937-4157 Sentence denotes To introduce mutations into the PK region, the pRep-ptGFP replicon plasmid was digested 121 with SpeI and KpnI and the resulting fragment inserted into a sub-cloning vector (pBluescript) 122 to create the pBluescript PK.
TextSentencer_T39 3937-4157 Sentence denotes To introduce mutations into the PK region, the pRep-ptGFP replicon plasmid was digested 121 with SpeI and KpnI and the resulting fragment inserted into a sub-cloning vector (pBluescript) 122 to create the pBluescript PK.
TextSentencer_T40 4158-4292 Sentence denotes PKs 3 and 4 were removed by digestion with HindIII and AatII 123 before insertion of a synthetic DNA sequence with PK 3 and 4 deleted.
TextSentencer_T40 4158-4292 Sentence denotes PKs 3 and 4 were removed by digestion with HindIII and AatII 123 before insertion of a synthetic DNA sequence with PK 3 and 4 deleted.
TextSentencer_T41 4293-4519 Sentence denotes PKs 2, 3 and 4 were 124 deleted by PCR amplification using ΔPK 234 Forward primer and FMDV 1331-1311 reverse 125 primer, the resultant product was digested with HindIII and AatII and ligated into the 126 pBluescript PK vector.
TextSentencer_T41 4293-4519 Sentence denotes PKs 2, 3 and 4 were 124 deleted by PCR amplification using ΔPK 234 Forward primer and FMDV 1331-1311 reverse 125 primer, the resultant product was digested with HindIII and AatII and ligated into the 126 pBluescript PK vector.
TextSentencer_T42 4520-4828 Sentence denotes Complete PK deletion was achieved by introduction of an AflII site at 127 the 3′ end of the poly-C tract by PCR mutagenesis to create the sub-cloning vector, pBluescript 128 C11, which was then used to remove all the PKs by PCR mutagenesis using ΔPK 1234 forward 129 primer and FMDV 1331-1311 reverse primer.
TextSentencer_T42 4520-4828 Sentence denotes Complete PK deletion was achieved by introduction of an AflII site at 127 the 3′ end of the poly-C tract by PCR mutagenesis to create the sub-cloning vector, pBluescript 128 C11, which was then used to remove all the PKs by PCR mutagenesis using ΔPK 1234 forward 129 primer and FMDV 1331-1311 reverse primer.
TextSentencer_T43 4829-4972 Sentence denotes The modified PK sequences were removed from 130 the sub-cloning vectors and inserted into the pRep-ptGFP plasmid using NheI-HF and KpnI-131 HF.
TextSentencer_T43 4829-4972 Sentence denotes The modified PK sequences were removed from 130 the sub-cloning vectors and inserted into the pRep-ptGFP plasmid using NheI-HF and KpnI-131 HF.
TextSentencer_T44 4973-4995 Sentence denotes 132 133 author/funder.
TextSentencer_T44 4973-4995 Sentence denotes 132 133 author/funder.
TextSentencer_T45 4996-5016 Sentence denotes All rights reserved.
TextSentencer_T45 4996-5016 Sentence denotes All rights reserved.
TextSentencer_T46 5017-5053 Sentence denotes No reuse allowed without permission.
TextSentencer_T46 5017-5053 Sentence denotes No reuse allowed without permission.
TextSentencer_T47 5054-5378 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 7 Mutations to disrupt and reform PK structure were introduced using synthetic DNA by 134 digestion with AflII and AatII and ligation into a similarly digested pBluescript PK vector.
TextSentencer_T47 5054-5378 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 7 Mutations to disrupt and reform PK structure were introduced using synthetic DNA by 134 digestion with AflII and AatII and ligation into a similarly digested pBluescript PK vector.
TextSentencer_T48 5379-5455 Sentence denotes Mutations were then introduced into the replicon plasmid as described above.
TextSentencer_T48 5379-5455 Sentence denotes Mutations were then introduced into the replicon plasmid as described above.
TextSentencer_T49 5456-5563 Sentence denotes To assess the effects of truncation of the poly-C-tract on replication the entire sequence was 137 removed.
TextSentencer_T49 5456-5563 Sentence denotes To assess the effects of truncation of the poly-C-tract on replication the entire sequence was 137 removed.
TextSentencer_T50 5564-5663 Sentence denotes This was performed by PCR mutagenesis using primers C0 SpeI, and FMDV 1331- In vitro transcription.
TextSentencer_T50 5564-5663 Sentence denotes This was performed by PCR mutagenesis using primers C0 SpeI, and FMDV 1331- In vitro transcription.
TextSentencer_T51 5664-5765 Sentence denotes 143 In vitro transcription reactions for replicon assays were performed as described previously (28).
TextSentencer_T51 5664-5765 Sentence denotes 143 In vitro transcription reactions for replicon assays were performed as described previously (28).
TextSentencer_T52 5766-6155 Sentence denotes Transcription reactions to produce large amounts of RNA for SHAPE analysis were performed 145 with purified linear DNA as described above, and 1 μg of linearised DNA was then used in a 146 HiScribe T7 synthesis kit (NEB), before DNase treatment and purification using a PureLink FastQ files were quality checked using FastQC with poor quality reads filtered using the 225 Sickle algorithm.
TextSentencer_T52 5766-6155 Sentence denotes Transcription reactions to produce large amounts of RNA for SHAPE analysis were performed 145 with purified linear DNA as described above, and 1 μg of linearised DNA was then used in a 146 HiScribe T7 synthesis kit (NEB), before DNase treatment and purification using a PureLink FastQ files were quality checked using FastQC with poor quality reads filtered using the 225 Sickle algorithm.
TextSentencer_T53 6156-6283 Sentence denotes Host cell reads were removed using FastQ Screen algorithm and FMDV 226 reads assembled de novo into contigs using IDBA-UD (35).
TextSentencer_T53 6156-6283 Sentence denotes Host cell reads were removed using FastQ Screen algorithm and FMDV 226 reads assembled de novo into contigs using IDBA-UD (35).
TextSentencer_T54 6284-6421 Sentence denotes Contigs that matched the FMDV 227 library (identified using Basic Local ALighnment Search Tool (BLAST)) were assembled 228 author/funder.
TextSentencer_T54 6284-6421 Sentence denotes Contigs that matched the FMDV 227 library (identified using Basic Local ALighnment Search Tool (BLAST)) were assembled 228 author/funder.
TextSentencer_T55 6422-6442 Sentence denotes All rights reserved.
TextSentencer_T55 6422-6442 Sentence denotes All rights reserved.
TextSentencer_T56 6443-6479 Sentence denotes No reuse allowed without permission.
TextSentencer_T56 6443-6479 Sentence denotes No reuse allowed without permission.
TextSentencer_T57 6480-6730 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint into consensus sequences using SeqMan Pro software in the DNA STAR Lasergene 13 229 package (DNA STAR) (36).
TextSentencer_T57 6480-6730 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint into consensus sequences using SeqMan Pro software in the DNA STAR Lasergene 13 229 package (DNA STAR) (36).
TextSentencer_T58 6731-6938 Sentence denotes The SHAPE data largely agreed with the predicted structures with the stems of PK 1, 2 and 3, interacting nucleotides showed little to no reactivity, suggesting NMIA could not interact with 300 author/funder.
TextSentencer_T58 6731-6938 Sentence denotes The SHAPE data largely agreed with the predicted structures with the stems of PK 1, 2 and 3, interacting nucleotides showed little to no reactivity, suggesting NMIA could not interact with 300 author/funder.
TextSentencer_T59 6939-6959 Sentence denotes All rights reserved.
TextSentencer_T59 6939-6959 Sentence denotes All rights reserved.
TextSentencer_T60 6960-6996 Sentence denotes No reuse allowed without permission.
TextSentencer_T60 6960-6996 Sentence denotes No reuse allowed without permission.
TextSentencer_T61 6997-7233 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 14 these nucleotides either due to the predicted base pairing or steric hindrance (figure 2B).
TextSentencer_T61 6997-7233 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 14 these nucleotides either due to the predicted base pairing or steric hindrance (figure 2B).
TextSentencer_T62 7234-7237 Sentence denotes The
TextSentencer_T62 7234-7237 Sentence denotes The
TextSentencer_T63 7238-7503 Sentence denotes NMIA reactivity for the interacting nucleotides in the stem-loops with downstream residues of 302 PK 1, 2 and 3 again largely agreed with the predicted structure, although the SHAPE data 303 suggests that there might be fewer interactions than previously predicted.
TextSentencer_T63 7238-7503 Sentence denotes NMIA reactivity for the interacting nucleotides in the stem-loops with downstream residues of 302 PK 1, 2 and 3 again largely agreed with the predicted structure, although the SHAPE data 303 suggests that there might be fewer interactions than previously predicted.
TextSentencer_T64 7504-7607 Sentence denotes However, differences 304 here could be due to heterogeneity in the formation of PKs in this experiment.
TextSentencer_T64 7504-7607 Sentence denotes However, differences 304 here could be due to heterogeneity in the formation of PKs in this experiment.
TextSentencer_T65 7608-7676 Sentence denotes The evidence 305 for loop-downstream interaction was weaker for PK4.
TextSentencer_T65 7608-7676 Sentence denotes The evidence 305 for loop-downstream interaction was weaker for PK4.
TextSentencer_T66 7677-7818 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint
TextSentencer_T66 7677-7818 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint
TextSentencer_T67 7819-7831 Sentence denotes orientation.
TextSentencer_T67 7819-7831 Sentence denotes orientation.
TextSentencer_T68 7832-8001 Sentence denotes 351 Since removal of all four PKs resulted in a significant decrease in replication, the minimal 352 requirements to maintain wt levels of replication were investigated.
TextSentencer_T68 7832-8001 Sentence denotes 351 Since removal of all four PKs resulted in a significant decrease in replication, the minimal 352 requirements to maintain wt levels of replication were investigated.
TextSentencer_T69 8002-8170 Sentence denotes As near wt level of 353 replication was observed when only one PK was present, all further mutagenesis was 354 performed in a C11 replicon plasmid containing only PK 1.
TextSentencer_T69 8002-8170 Sentence denotes As near wt level of 353 replication was observed when only one PK was present, all further mutagenesis was 354 performed in a C11 replicon plasmid containing only PK 1.
TextSentencer_T70 8171-8362 Sentence denotes In addition, the orientation of PK 1 was reversed by "flipping" the nucleotide sequence to 367 potentially facilitate hybridisation of the loop with upstream rather than downstream sequences.
TextSentencer_T70 8171-8362 Sentence denotes In addition, the orientation of PK 1 was reversed by "flipping" the nucleotide sequence to 367 potentially facilitate hybridisation of the loop with upstream rather than downstream sequences.
TextSentencer_T71 8363-8571 Sentence denotes Changing the orientation of the PK reduced replicon replication to a similar level seen in the replication decreased until at passage three there is a 2.5 fold reduction compared to that of 398 author/funder.
TextSentencer_T71 8363-8571 Sentence denotes Changing the orientation of the PK reduced replicon replication to a similar level seen in the replication decreased until at passage three there is a 2.5 fold reduction compared to that of 398 author/funder.
TextSentencer_T72 8572-8592 Sentence denotes All rights reserved.
TextSentencer_T72 8572-8592 Sentence denotes All rights reserved.
TextSentencer_T73 8593-8629 Sentence denotes No reuse allowed without permission.
TextSentencer_T73 8593-8629 Sentence denotes No reuse allowed without permission.
TextSentencer_T74 8630-8794 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint passage 0 (figure 5B).
TextSentencer_T74 8630-8794 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint passage 0 (figure 5B).
TextSentencer_T75 8795-8922 Sentence denotes Therefore, it appears that replicons with a single PK are at a competitive 399 disadvantage compared to those with two or more.
TextSentencer_T75 8795-8922 Sentence denotes Therefore, it appears that replicons with a single PK are at a competitive 399 disadvantage compared to those with two or more.
TextSentencer_T76 8923-9261 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 20 of infectious virus despite being able to replicate after transfection into cells, is consistent with 448 a requirement for RNA structure within the PK region being required for virus assembly.
TextSentencer_T76 8923-9261 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 20 of infectious virus despite being able to replicate after transfection into cells, is consistent with 448 a requirement for RNA structure within the PK region being required for virus assembly.
TextSentencer_T77 9262-9425 Sentence denotes The 5′ UTR of FMDV is unique amongst picornaviruses due to its large size and the presence 454 of multiple RNA elements, some of which still have unknown function.
TextSentencer_T77 9262-9425 Sentence denotes The 5′ UTR of FMDV is unique amongst picornaviruses due to its large size and the presence 454 of multiple RNA elements, some of which still have unknown function.
TextSentencer_T78 9426-9534 Sentence denotes One of these features 455 is a series of repeated PKs varying in number from 2-4, depending on virus strain.
TextSentencer_T78 9426-9534 Sentence denotes One of these features 455 is a series of repeated PKs varying in number from 2-4, depending on virus strain.
TextSentencer_T79 9535-9651 Sentence denotes In this study, 456 we sequentially deleted or mutated the PKs to help understand their role in the viral life cycle.
TextSentencer_T79 9535-9651 Sentence denotes In this study, 456 we sequentially deleted or mutated the PKs to help understand their role in the viral life cycle.
TextSentencer_T80 9652-9887 Sentence denotes 457 We also confirmed the predicted PK structures by SHAPE mapping, although there may be Although all viruses isolated to date contain at least two PKs, replicons or viruses containing a 464 single PK were still replication competent.
TextSentencer_T80 9652-9887 Sentence denotes 457 We also confirmed the predicted PK structures by SHAPE mapping, although there may be Although all viruses isolated to date contain at least two PKs, replicons or viruses containing a 464 single PK were still replication competent.
TextSentencer_T81 9888-10044 Sentence denotes However, replicons with more than a single PK 465 were found to have a competitive advantage over replicons with a single PK when sequentially 466 passaged.
TextSentencer_T81 9888-10044 Sentence denotes However, replicons with more than a single PK 465 were found to have a competitive advantage over replicons with a single PK when sequentially 466 passaged.
TextSentencer_T82 10045-10219 Sentence denotes Replicons lacking all PKs displayed poor passaging potential even when co-467 transfected with yeast tRNA, reinforcing the observation of a significant impact in replication.
TextSentencer_T82 10045-10219 Sentence denotes Replicons lacking all PKs displayed poor passaging potential even when co-467 transfected with yeast tRNA, reinforcing the observation of a significant impact in replication.
TextSentencer_T83 10220-10342 Sentence denotes Moreover, viruses recovered from genomes with reduced numbers of PKs were slower growing 469 and produced smaller plaques.
TextSentencer_T83 10220-10342 Sentence denotes Moreover, viruses recovered from genomes with reduced numbers of PKs were slower growing 469 and produced smaller plaques.
TextSentencer_T84 10343-10514 Sentence denotes In addition, these differences were more pronounced in more PKs is functionally competent as no differences was seen between replicons congaing a single 472 author/funder.
TextSentencer_T84 10343-10514 Sentence denotes In addition, these differences were more pronounced in more PKs is functionally competent as no differences was seen between replicons congaing a single 472 author/funder.
TextSentencer_T85 10515-10535 Sentence denotes All rights reserved.
TextSentencer_T85 10515-10535 Sentence denotes All rights reserved.
TextSentencer_T86 10536-10572 Sentence denotes No reuse allowed without permission.
TextSentencer_T86 10536-10572 Sentence denotes No reuse allowed without permission.
TextSentencer_T87 10573-10737 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 21 copy of PK1 or PK4.
TextSentencer_T87 10573-10737 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 21 copy of PK1 or PK4.
TextSentencer_T88 10738-10894 Sentence denotes This observation is consistent with a previous report of deletion of PK1, 473 along with the Poly-C-tract, with no adverse effect in viral replication (37).
TextSentencer_T88 10738-10894 Sentence denotes This observation is consistent with a previous report of deletion of PK1, 473 along with the Poly-C-tract, with no adverse effect in viral replication (37).
TextSentencer_T89 10895-11066 Sentence denotes This also supports 474 our findings that the truncation of the Poly-C-tract to create the C11 construct had no effect on 475 replicon replication in the cell lines tested.
TextSentencer_T89 10895-11066 Sentence denotes This also supports 474 our findings that the truncation of the Poly-C-tract to create the C11 construct had no effect on 475 replicon replication in the cell lines tested.
TextSentencer_T90 11067-11288 Sentence denotes As has been described with Mengo virus, it is 476 possible that the role of the poly-C-tract is essential in other aspects of the viral lifecycle which 477 cannot be recapitulated in a standard tissue culture system (39).
TextSentencer_T90 11067-11288 Sentence denotes As has been described with Mengo virus, it is 476 possible that the role of the poly-C-tract is essential in other aspects of the viral lifecycle which 477 cannot be recapitulated in a standard tissue culture system (39).
TextSentencer_T91 11289-11438 Sentence denotes The presence of at least two PKs in all viral isolates sequenced so far suggests that multiple 480 PKs confer a competitive advantage in replication.
TextSentencer_T91 11289-11438 Sentence denotes The presence of at least two PKs in all viral isolates sequenced so far suggests that multiple 480 PKs confer a competitive advantage in replication.
TextSentencer_T92 11439-11634 Sentence denotes Here we showed by sequential passage that 481 replicons containing at least two PKs were maintained at a level similar to wt, but replicons 482 containing only one PK showed a persistent decline.
TextSentencer_T92 11439-11634 Sentence denotes Here we showed by sequential passage that 481 replicons containing at least two PKs were maintained at a level similar to wt, but replicons 482 containing only one PK showed a persistent decline.
TextSentencer_T93 11635-11840 Sentence denotes It is unclear why some viral isolates 483 contain two, three or four PKs is still unknown, but this may be stochastic variation or may 484 reflect subtle effects of host range or geographical localisation.
TextSentencer_T93 11635-11840 Sentence denotes It is unclear why some viral isolates 483 contain two, three or four PKs is still unknown, but this may be stochastic variation or may 484 reflect subtle effects of host range or geographical localisation.
TextSentencer_T94 11841-11997 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint author/funder.
TextSentencer_T94 11841-11997 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint author/funder.
TextSentencer_T95 11998-12018 Sentence denotes All rights reserved.
TextSentencer_T95 11998-12018 Sentence denotes All rights reserved.
TextSentencer_T96 12019-12055 Sentence denotes No reuse allowed without permission.
TextSentencer_T96 12019-12055 Sentence denotes No reuse allowed without permission.
TextSentencer_T97 12056-12431 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint Significance is shown comparing the replication of C11 PK disrupt and C11 PK restore (Aii).
TextSentencer_T97 12056-12431 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint Significance is shown comparing the replication of C11 PK disrupt and C11 PK restore (Aii).
TextSentencer_T98 12432-12478 Sentence denotes Significance shown is compared to wt replicon.
TextSentencer_T98 12432-12478 Sentence denotes Significance shown is compared to wt replicon.
TextSentencer_T99 12479-12552 Sentence denotes Error bars are calculated by SEM, n = 3, * P 673 < 0.05, **** P < 0.0001.
TextSentencer_T99 12479-12552 Sentence denotes Error bars are calculated by SEM, n = 3, * P 673 < 0.05, **** P < 0.0001.
TextSentencer_T100 12553-12571 Sentence denotes 674 author/funder.
TextSentencer_T100 12553-12571 Sentence denotes 674 author/funder.
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TextSentencer_T101 12572-12592 Sentence denotes All rights reserved.
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TextSentencer_T102 12593-12629 Sentence denotes No reuse allowed without permission.
TextSentencer_T103 12630-12793 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 33 675 author/funder.
TextSentencer_T103 12630-12793 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 33 675 author/funder.
TextSentencer_T104 12794-12814 Sentence denotes All rights reserved.
TextSentencer_T104 12794-12814 Sentence denotes All rights reserved.
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TextSentencer_T106 12852-12993 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint
TextSentencer_T106 12852-12993 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint