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LitCovid-OGER-BB

Id Subject Object Predicate Lexical cue
T1 38-48 SP_7 denotes SARS-CoV-2
T2 107-114 SO:0001026 denotes genomic
T3 135-143 SP_7 denotes COVID-19
T4 186-196 SP_7 denotes SARS-CoV-2
T5 253-260 SO:0000704 denotes genetic
T6 280-285 NCBITaxon:10239 denotes virus
T7 418-428 SP_7 denotes SARS-CoV-2
T8 429-436 SO:0001026 denotes genomes
T9 496-506 SP_7 denotes SARS-CoV-2
T10 507-513 SO:0000112 denotes primer
T11 644-651 SO:0000704 denotes genetic
T12 694-703 GO:0097617 denotes annealing
T13 755-762 SO:0001026 denotes genomes
T14 799-808 GO:0097617 denotes annealing
T15 856-863 SO:0001026 denotes genomes
T16 927-934 SO:0001026 denotes genomes
T17 1055-1065 SP_7 denotes SARS-CoV-2
T18 1087-1094 SO:0001026 denotes genomes
T19 1321-1326 NCBITaxon:10239 denotes viral
T20 1327-1333 SO:0001026 denotes genome
T21 1338-1348 SP_7 denotes SARS-CoV-2
T22 1448-1458 SP_7 denotes SARS-CoV-2
T23 1507-1554 SP_7 denotes Severe Acute Respiratory Syndrome Coronavirus 2
T24 1556-1566 SP_7 denotes SARS-CoV-2
T25 1765-1776 NCBITaxon:11118 denotes Coronavirus
T26 1793-1801 SP_7 denotes COVID-19
T27 1865-1871 NCBITaxon:9606 denotes people
T28 1940-1946 GO:0016265 denotes deaths
T29 2010-2020 SP_7 denotes SARS-CoV-2
T30 2036-2047 NCBITaxon:11118 denotes coronavirus
T31 2064-2070 NCBITaxon:9606 denotes humans
T32 2143-2151 SP_10 denotes SARS-CoV
T33 2163-2171 SP_9 denotes MERS-CoV
T34 2204-2214 SP_7 denotes SARS-CoV-2
T35 2285-2296 SO:0000704 denotes genetically
T36 2305-2313 SP_10 denotes SARS-CoV
T37 2314-2321 NCBITaxon:species denotes species
T38 2332-2336 SP_2 denotes bats
T39 2332-2336 NCBITaxon:9397 denotes bats
T40 2373-2378 SP_6 denotes human
T41 2373-2378 NCBITaxon:9606 denotes human
T42 2379-2392 NCBITaxon:11118 denotes coronaviruses
T43 2482-2492 SP_7 denotes SARS-CoV-2
T44 2530-2541 UBERON:0001004 denotes respiratory
T45 2580-2593 NCBITaxon:11118 denotes coronaviruses
T46 2598-2604 SO:0000984 denotes single
T47 2606-2623 SO:0000984 denotes positive-stranded
T48 2628-2635 NCBITaxon:10239 denotes viruses
T49 2649-2656 SO:0001026 denotes genomic
T50 2689-2694 SO:0000704 denotes genes
T51 2756-2767 GO:0006260 denotes replication
T52 2827-2835 GO:0031975 denotes envelope
T53 2841-2849 GO:0016020 denotes membrane
T54 2904-2909 NCBITaxon:10239 denotes virus
T55 2973-2978 NCBITaxon:10239 denotes viral
T56 3007-3012 NCBITaxon:10239 denotes virus
T57 3033-3054 GO:0001171 denotes reverse transcription
T58 3132-3137 NCBITaxon:10239 denotes virus
T59 3153-3163 SP_7 denotes SARS-CoV-2
T60 3521-3531 SP_7 denotes SARS-CoV-2
T61 3532-3539 SO:0001026 denotes genomic
T62 3606-3613 SO:0000704 denotes genetic
T63 3627-3637 SP_7 denotes SARS-CoV-2
T64 3706-3711 NCBITaxon:10239 denotes virus
T65 3828-3835 NCBITaxon:10239 denotes viruses
T66 3869-3879 SP_7 denotes SARS-CoV-2
T67 4084-4091 SO:0000704 denotes genetic
T68 4106-4116 SP_7 denotes SARS-CoV-2
T69 4311-4316 NCBITaxon:10239 denotes virus
T70 4355-4360 NCBITaxon:10239 denotes viral
T71 4445-4454 GO:0097617 denotes annealing
T72 4591-4598 SO:0001026 denotes genomic
T73 4709-4716 NCBITaxon:10239 denotes viruses
T74 4730-4737 SO:0000704 denotes genetic
T75 4755-4765 SP_7 denotes SARS-CoV-2
T76 4806-4816 SP_7 denotes SARS-CoV-2
T77 4869-4874 NCBITaxon:10239 denotes viral
T78 4875-4881 SO:0001026 denotes genome
T79 4955-4965 SP_7 denotes SARS-CoV-2
T80 5167-5177 SP_7 denotes SARS-CoV-2
T81 5314-5324 SP_7 denotes SARS-CoV-2
T82 5395-5405 SP_7 denotes SARS-CoV-2
T83 5406-5413 SO:0001026 denotes genomes
T84 5466-5479 NCBITaxon:11118 denotes coronaviruses
T85 5535-5540 SP_6 denotes human
T86 5535-5540 NCBITaxon:9606 denotes human
T87 5541-5554 NCBITaxon:11118 denotes coronaviruses
T88 5577-5580 SP_2 denotes bat
T89 5577-5580 NCBITaxon:8342 denotes bat
T90 5581-5585 SP_10 denotes SARS
T91 5591-5604 NCBITaxon:11118 denotes coronaviruses
T92 5669-5676 SO:0000704 denotes genetic
T93 5705-5715 SP_7 denotes SARS-CoV-2
T94 5716-5722 SO:0001026 denotes genome
T95 5790-5800 SP_7 denotes SARS-CoV-2
T96 5925-5935 SP_7 denotes SARS-CoV-2
T97 5973-5983 SP_7 denotes SARS-CoV-2
T98 6043-6053 SP_7 denotes SARS-CoV-2
T99 6054-6061 SO:0001026 denotes genomes
T100 6276-6283 SO:0001026 denotes genomes
T101 6535-6545 SP_7 denotes SARS-CoV-2
T102 6546-6552 SO:0000112 denotes primer
T103 6693-6700 SO:0000704 denotes genetic
T104 6743-6752 GO:0097617 denotes annealing
T105 6757-6766 GO:0097617 denotes annotated
T106 7208-7215 SO:0001026 denotes genomes
T107 7596-7600 SO:0000704 denotes gene
T108 7671-7677 PR:P06174 denotes Orf1ab
T109 7678-7682 SO:0000704 denotes gene
T110 7705-7712 SO:0000704 denotes genetic
T111 7737-7748 NCBITaxon:11118 denotes coronavirus
T112 7749-7756 SO:0001026 denotes genomes
T113 7821-7836 SO:0000409 denotes binding regions
T114 7967-7974 SO:0001026 denotes genomes
T115 8011-8020 GO:0097617 denotes annealing
T116 8068-8075 SO:0001026 denotes genomes
T117 8187-8194 SO:0001026 denotes genomes
T118 8226-8230 SO:0000704 denotes gene
T119 8242-8256 SO:0000121 denotes forward primer
T120 8342-8349 SO:0000112 denotes primers
T121 8376-8383 SO:0000704 denotes Genetic
T122 8405-8414 GO:0097617 denotes annealing
T123 8518-8525 SO:0001026 denotes genomes
T124 8558-8572 SO:0000132 denotes Reverse primer
T125 8680-8686 SO:0000121 denotes primer
T126 8687-8702 SO:0000409 denotes binding regions
T127 8727-8734 SO:0001026 denotes genomes
T128 8880-8894 SO:0000132 denotes Reverse primer
T129 8895-8910 SO:0000409 denotes binding regions
T130 8920-8926 SO:0001026 denotes genome
T131 9205-9212 SO:0001026 denotes genomes
T132 9657-9664 SO:0001026 denotes genomes
T133 10087-10097 SP_7 denotes SARS-CoV-2
T134 10135-10145 SP_7 denotes SARS-CoV-2
T135 10199-10205 SO:0000985 denotes duplex
T136 10249-10254 SO:0001867 denotes genes
T137 10291-10302 CHEBI:51217 denotes fluorophore
T138 10291-10302 CHEBI:51217 denotes fluorophore
T139 10421-10431 SP_7 denotes SARS-CoV-2
T140 10550-10560 SP_7 denotes SARS-CoV-2
T141 10598-10608 SP_7 denotes SARS-CoV-2
T142 10641-10648 SO:0001026 denotes genomes
T143 10685-10694 GO:0097617 denotes annealing
T144 10748-10755 SO:0001026 denotes genomes
T145 10810-10816 SO:0000112 denotes primer
T146 10957-10964 SO:0000112 denotes primers
T147 10968-10975 SO:0001026 denotes genomes
T148 11116-11123 SO:0001026 denotes genomic
T149 11402-11412 SP_7 denotes SARS-CoV-2
T150 11464-11474 SP_7 denotes SARS-CoV-2
T151 11606-11616 SP_7 denotes SARS-CoV-2
T152 11669-11679 SP_7 denotes SARS-CoV-2
T153 11697-11704 SO:0001026 denotes genomic
T154 11751-11759 SP_7 denotes COVID-19
T155 11838-11848 SP_7 denotes SARS-CoV-2
T156 11849-11856 SO:0001026 denotes genomes
T157 11968-11977 GO:0097617 denotes annealing
T158 11985-11995 SP_7 denotes SARS-CoV-2
T159 12241-12251 SP_7 denotes SARS-CoV-2
T160 12311-12318 SO:0000704 denotes genetic
T161 12338-12348 SP_7 denotes SARS-CoV-2
T162 12349-12355 SO:0001026 denotes genome
T163 12401-12406 NCBITaxon:10239 denotes viral
T164 12525-12535 SP_7 denotes SARS-CoV-2
T165 12646-12653 SO:0001026 denotes genomic
T166 13314-13324 SP_7 denotes SARS-CoV-2
T167 13443-13454 NCBITaxon:11118 denotes coronavirus
T168 13456-13465 SP_7 denotes 2019-nCoV
T169 13491-13498 SO:0000112 denotes primers
T170 13577-13588 NCBITaxon:11118 denotes coronavirus
T171 13589-13598 SP_7 denotes 2019-ncov
T172 13622-13628 SO:0000112 denotes primer
T173 13705-13716 NCBITaxon:11118 denotes coronavirus
T174 13718-13727 SP_7 denotes 2019-nCoV
T175 13907-13914 SO:0001026 denotes Genomic
T176 13950-13955 SP_6 denotes human
T177 13950-13955 NCBITaxon:9606 denotes human
T178 13967-13978 NCBITaxon:11118 denotes coronavirus
T179 14227-14238 NCBITaxon:11118 denotes coronavirus
T180 14240-14249 SP_7 denotes 2019-nCoV
T181 14444-14455 NCBITaxon:11118 denotes coronavirus
T182 14457-14466 SP_7 denotes 2019-nCoV
T183 14653-14658 SP_6 denotes human
T184 14653-14658 NCBITaxon:9606 denotes human
T185 14659-14672 NCBITaxon:11118 denotes coronaviruses
T186 14851-14858 NCBITaxon:species denotes species
T187 14872-14883 UBERON:0001004 denotes respiratory
T188 14901-14912 NCBITaxon:11118 denotes coronavirus
T189 14926-14935 SP_7 denotes 2019-nCoV
T190 14950-14960 SP_7 denotes SARS-CoV-2
T191 15304-15315 NCBITaxon:11118 denotes coronavirus
T192 15330-15338 SP_7 denotes COVID-19
T193 15495-15506 NCBITaxon:11118 denotes coronavirus
T194 15656-15666 SP_7 denotes SARS-CoV-2
T195 15697-15707 SP_7 denotes SARS-CoV-2
T196 15830-15840 SP_7 denotes sars-cov-2
T197 15971-15978 GO:0005634 denotes Nucleic
T198 16124-16130 SO:0000112 denotes primer
T199 16190-16197 GO:0005634 denotes nucleic
T200 16359-16367 SP_7 denotes COVID-19
T201 16583-16590 SO:0001026 denotes Genomic
T202 16613-16624 NCBITaxon:11118 denotes coronavirus
T203 16783-16794 NCBITaxon:11118 denotes coronavirus
T204 16796-16805 SP_7 denotes 2019-nCoV
T205 16820-16825 SP_6 denotes human
T206 16820-16825 NCBITaxon:9606 denotes human
T207 16908-16912 CHEBI:50845 denotes docs
T208 16908-16912 CHEBI:50845 denotes docs
T209 16928-16940 NCBITaxon:11118 denotes coronaviruse
T210 17108-17118 SP_7 denotes SARS-CoV-2
T211 17177-17187 SP_7 denotes SARS-CoV-2
T212 17318-17324 SO:0000112 denotes primer
T213 17357-17362 NCBITaxon:10239 denotes viral
T214 17488-17499 NCBITaxon:11118 denotes Coronavirus
T215 17514-17522 SP_7 denotes COVID-19
T216 17639-17650 NCBITaxon:11118 denotes coronavirus
T217 17731-17742 NCBITaxon:11118 denotes coronavirus
T218 17757-17765 SP_7 denotes COVID-19
T219 17780-17785 SP_6 denotes human
T220 17780-17785 NCBITaxon:9606 denotes human
T221 17860-17864 UBERON:0001769 denotes iris
T222 17957-17968 NCBITaxon:11118 denotes coronavirus
T223 17985-17990 SP_6 denotes human
T224 17985-17990 NCBITaxon:9606 denotes human
T225 17991-18002 UBERON:0001004 denotes respiratory
T226 18107-18118 NCBITaxon:11118 denotes coronavirus
T227 18362-18373 NCBITaxon:11118 denotes coronavirus
T228 19127-19137 SP_7 denotes SARS-CoV-2
T229 19240-19244 SO:0000704 denotes gene
T230 19343-19347 SO:0000704 denotes gene
T231 19361-19365 SO:0000704 denotes gene
T232 19589-19599 SP_7 denotes SARS-CoV-2
T233 19639-19648 SP_7 denotes 2019-nCoV
T234 19924-19934 SP_7 denotes SARS-CoV-2
T235 19974-19983 SP_7 denotes 2019-nCoV
T236 20075-20079 SO:0000704 denotes gene
T237 20172-20176 SO:0000704 denotes gene
T238 20225-20228 SO:0000236 denotes ORF
T239 20232-20236 SO:0000704 denotes gene
T240 20550-20560 SP_7 denotes SARS-CoV-2
T241 20595-20602 NCBITaxon:10239 denotes viruses
T242 20607-20615 NCBITaxon:2 denotes bacteria
T243 20638-20649 UBERON:0001004 denotes respiratory
T244 20685-20705 NCBITaxon:11118 denotes coronavirusesQIAstat
T245 20722-20732 SP_7 denotes SARS-CoV-2
T246 20779-20783 SO:0000704 denotes gene
T247 20796-20802 PR:P06174 denotes Orf1ab
T248 20815-20819 SO:0000704 denotes gene
T249 20833-20837 SO:0000704 denotes gene
T250 20856-20860 SO:0000704 denotes gene
T251 21137-21141 SP_10 denotes SARS
T252 21147-21160 NCBITaxon:11118 denotes coronaviruses
T253 21887-21892 NCBITaxon:10239 denotes viral
T254 21897-21906 NCBITaxon:2 denotes bacterial
T255 21907-21918 UBERON:0001004 denotes respiratory
T256 21940-21950 SP_7 denotes SARS-CoV-2
T257 21988-22001 NCBITaxon:11118 denotes coronaviruses
T258 22048-22057 SP_7 denotes 2019-nCoV
T259 22059-22067 SP_10 denotes SARS-CoV
T260 22072-22075 SP_2 denotes bat
T261 22076-22080 SP_10 denotes SARS
T262 22086-22099 NCBITaxon:11118 denotes coronaviruses
T263 22107-22111 SP_10 denotes SARS
T264 22130-22136 NCBITaxon:9606 denotes humans
T265 22149-22160 NCBITaxon:1 denotes individuals
T266 22241-22250 SP_7 denotes 2019-nCoV
T267 22266-22272 NCBITaxon:33208 denotes animal
T268 22273-22286 NCBITaxon:11118 denotes coronaviruses
T269 22307-22314 SO:0001026 denotes genomic
T270 22350-22365 SO:0000409 denotes binding regions
T271 22388-22398 SP_7 denotes SARS-CoV-2
T272 22465-22472 SO:0001026 denotes genomes
T273 22522-22529 SO:0001026 denotes genomes
T274 22931-22940 SP_7 denotes 2019-nCoV
T275 22968-22977 SP_7 denotes 2019-nCoV
T276 22981-22984 PR:000003035 denotes P53
T277 23009-23018 SP_7 denotes 2019-nCoV
T278 23050-23059 SP_7 denotes 2019-nCoV
T279 23077-23086 SP_7 denotes 2019-nCoV
T280 23118-23127 SP_7 denotes 2019-nCoV
T281 23148-23157 SP_7 denotes 2019-nCoV
T282 23177-23186 SP_7 denotes 2019-nCoV
T283 23217-23226 SP_7 denotes 2019-nCoV
T284 23277-23285 SO:0000112 denotes primer23
T285 23347-23355 SO:0000112 denotes primer30
T286 23386-23395 SO:0000112 denotes primer337
T287 23470-23478 SO:0000112 denotes primer56
T288 23741-23749 SO:0000112 denotes primer15
T289 23822-23830 SO:0000112 denotes primer27
T290 23862-23870 SO:0000112 denotes primer57
T291 24045-24059 SO:0000121 denotes Forward primer
T292 24076-24083 SO:0001031 denotes Reverse
T293 24084-24093 SO:0000132 denotes primerTwo
T294 24094-24100 SO:0001026 denotes genome
T295 24208-24215 SO:0001026 denotes genomes
T296 24310-24317 SO:0001026 denotes genomes
T297 24408-24415 SO:0001026 denotes genomes
T298 24573-24580 SO:0001026 denotes genomes
T299 24673-24680 SO:0001026 denotes genomes
T300 24738-24744 SO:0001026 denotes genome
T301 24812-24819 SO:0001026 denotes genomes
T302 24899-24906 SO:0001026 denotes genomes
T303 25004-25011 SO:0001026 denotes genomes
T304 25087-25094 SO:0001026 denotes genomes
T305 25171-25178 SO:0001026 denotes genomes
T306 25247-25254 SO:0001026 denotes genomes
T307 25338-25345 SO:0001026 denotes genomes
T308 25427-25434 SO:0001026 denotes genomes
T309 25529-25535 SO:0001026 denotes genome
T310 25614-25621 SO:0001026 denotes genomes
T311 25780-25787 SO:0001026 denotes genomes
T312 25859-25866 SO:0001026 denotes genomes
T313 25953-25960 SO:0001026 denotes genomes
T314 26048-26055 SO:0001026 denotes genomes
T315 26141-26148 SO:0001026 denotes genomes
T316 26236-26243 SO:0001026 denotes genomes
T317 26309-26316 SO:0001026 denotes genomes
T318 26402-26409 SO:0001026 denotes genomes
T319 26547-26554 SO:0001026 denotes genomes
T320 26633-26640 SO:0001026 denotes genomes
T321 26700-26707 SO:0001026 denotes genomes
T322 26790-26797 SO:0001026 denotes genomes
T323 26856-26862 SO:0001026 denotes genome
T324 26920-26927 SO:0001026 denotes genomes
T325 26996-27002 SO:0001026 denotes genome

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 429-436 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T2 755-762 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T3 856-863 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T4 927-934 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T5 1087-1094 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T6 1327-1333 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T7 2624-2627 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 2717-2725 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T9 2806-2814 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T10 2969-2972 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 3121-3124 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 3824-3827 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 3841-3851 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T14 4875-4881 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T15 5406-5413 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T16 5716-5722 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T17 6054-6061 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T18 6081-6092 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T19 6276-6283 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T20 6859-6870 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T21 7208-7215 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T22 7337-7347 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T23 7596-7600 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T24 7678-7682 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T25 7749-7756 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T26 7967-7974 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T27 8068-8075 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T28 8187-8194 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T29 8226-8230 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T30 8518-8525 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T31 8727-8734 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T32 8920-8926 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T33 9205-9212 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T34 9657-9664 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T35 10641-10648 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T36 10748-10755 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T37 10968-10975 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T38 11849-11856 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T39 11933-11943 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T40 12072-12082 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T41 12349-12355 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T42 15097-15100 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T43 17860-17864 Body_part denotes iris http://purl.org/sig/ont/fma/fma58235
T44 19240-19244 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T45 19343-19347 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T46 19361-19365 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T47 20075-20079 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T48 20172-20176 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T49 20232-20236 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T50 20750-20753 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T51 20764-20767 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 20779-20783 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T53 20815-20819 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T54 20833-20837 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T55 22465-22472 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T56 22522-22529 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T57 24094-24100 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T58 24208-24215 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T59 24310-24317 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T60 24408-24415 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T61 24573-24580 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T62 24673-24680 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T63 24738-24744 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T64 24812-24819 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T65 24899-24906 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T66 25004-25011 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T67 25087-25094 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T68 25171-25178 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T69 25247-25254 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T70 25338-25345 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T71 25427-25434 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T72 25529-25535 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T73 25614-25621 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T74 25780-25787 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T75 25859-25866 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T76 25953-25960 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T77 26048-26055 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T78 26141-26148 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T79 26236-26243 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T80 26309-26316 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T81 26402-26409 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T82 26547-26554 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T83 26633-26640 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T84 26700-26707 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T85 26790-26797 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T86 26856-26862 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T87 26920-26927 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T88 26996-27002 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 17860-17864 Body_part denotes iris http://purl.obolibrary.org/obo/UBERON_0001769

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 38-46 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 135-143 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 186-194 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 418-426 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 496-504 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1055-1063 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 1338-1346 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1448-1456 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1507-1554 Disease denotes Severe Acute Respiratory Syndrome Coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1556-1564 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 1765-1789 Disease denotes Coronavirus Disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1793-1801 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 2010-2018 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 2143-2151 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 2204-2212 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2305-2313 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 2482-2490 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 2503-2512 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T19 2517-2550 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T20 3153-3161 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 3521-3529 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 3627-3635 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 3869-3877 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 4106-4114 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 4755-4763 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 4806-4814 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4955-4963 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 5167-5175 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 5314-5322 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 5395-5403 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 5581-5585 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T32 5705-5713 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 5790-5798 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 5925-5933 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 5973-5981 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 6043-6051 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 10087-10095 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 10135-10143 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 10421-10429 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 10550-10558 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 10598-10606 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 11402-11410 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 11464-11472 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 11606-11614 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 11669-11677 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 11751-11759 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 11838-11846 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 11985-11993 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 12241-12249 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 12338-12346 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 12525-12533 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 13051-13053 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T54 13062-13064 Disease denotes JP http://purl.obolibrary.org/obo/MONDO_0010820
T55 13314-13322 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 13866-13868 Disease denotes KH http://purl.obolibrary.org/obo/MONDO_0016236
T57 14017-14026 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T58 14156-14159 Disease denotes SMS http://purl.obolibrary.org/obo/MONDO_0008434|http://purl.obolibrary.org/obo/MONDO_0008491
T60 14274-14283 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T61 14799-14801 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725
T62 14859-14892 Disease denotes Severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T63 14950-14958 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 15203-15205 Disease denotes AM http://purl.obolibrary.org/obo/MONDO_0020320
T65 15304-15328 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T66 15330-15338 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T67 15656-15664 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 15697-15705 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 16089-16092 Disease denotes Mes http://purl.obolibrary.org/obo/MONDO_0009571
T70 16359-16367 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T71 17108-17116 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 17177-17185 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 17278-17280 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T75 17488-17512 Disease denotes Coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T76 17514-17522 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T77 17731-17755 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T78 17757-17765 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T79 17991-18010 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T80 18393-18402 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T81 19127-19135 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 19589-19597 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 19924-19932 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 20550-20558 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 20632-20660 Disease denotes upper respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T86 20722-20730 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T87 21137-21141 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T88 21429-21442 Disease denotes Viral Disease http://purl.obolibrary.org/obo/MONDO_0005108
T89 21940-21948 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 22059-22067 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T91 22076-22080 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T92 22107-22111 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T93 22388-22396 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 19-20 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 154-164 http://purl.obolibrary.org/obo/BFO_0000030 denotes OBJECTIVES
T3 280-285 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 561-564 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T5 728-729 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T6 1108-1109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1175-1181 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T8 1644-1647 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T9 1745-1757 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T10 1828-1831 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T11 1989-2001 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T12 2064-2070 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T13 2283-2284 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2332-2336 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T15 2373-2378 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T16 2475-2479 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T17 2628-2635 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T18 2689-2694 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T19 2841-2849 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T20 2904-2909 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T21 3007-3012 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T22 3132-3137 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 3448-3449 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 3598-3599 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 3646-3647 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 3706-3711 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 3828-3835 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T28 3940-3941 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3982-3990 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T30 4309-4310 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 4311-4316 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T32 4348-4354 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T33 4709-4716 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T34 5235-5247 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T35 5535-5540 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T36 5577-5580 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T37 5743-5746 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T38 5846-5847 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 6238-6239 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 6324-6326 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T41 6441-6442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 6600-6603 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T43 6774-6776 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T44 6774-6776 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T45 7040-7048 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T46 7159-7160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 7596-7600 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T48 7678-7682 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T49 8106-8110 http://purl.obolibrary.org/obo/CLO_0001627 denotes a) a
T50 8226-8230 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T51 8258-8259 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T52 8485-8489 http://purl.obolibrary.org/obo/CLO_0001627 denotes a) a
T53 8531-8532 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 8658-8660 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T55 8704-8705 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T56 9026-9029 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T57 9067-9070 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T58 9562-9563 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 9639-9640 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T60 9695-9698 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T61 9888-9891 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T62 10180-10181 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 10249-10254 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T64 10315-10316 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 10446-10447 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T66 10497-10498 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 10656-10657 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 10724-10726 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T69 10766-10767 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 10897-10898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 10993-10994 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 11145-11151 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T73 11184-11185 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T74 12689-12690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 13038-13040 http://purl.obolibrary.org/obo/CLO_0007860 denotes MR
T76 13256-13257 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T77 13277-13279 http://purl.obolibrary.org/obo/CLO_0002878 denotes EC
T78 13426-13429 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T79 13684-13687 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T80 13690-13693 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T81 13950-13955 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T82 13993-13994 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 14084-14086 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T84 14143-14146 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes Pan
T85 14219-14220 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 14402-14403 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T87 14409-14411 http://purl.obolibrary.org/obo/CLO_0002781 denotes DK
T88 14561-14563 http://purl.obolibrary.org/obo/CLO_0053755 denotes ES
T89 14653-14658 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T90 14678-14683 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T91 14688-14692 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T92 14698-14701 http://purl.obolibrary.org/obo/CLO_0001003 denotes 163
T93 14779-14781 http://purl.obolibrary.org/obo/CLO_0051456 denotes AE
T94 14789-14791 http://purl.obolibrary.org/obo/CLO_0008954 denotes SC
T95 14799-14801 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T96 14836-14838 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T97 14982-14988 http://purl.obolibrary.org/obo/CLO_0001416 denotes 5: 536
T98 15101-15108 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T99 16251-16256 http://purl.obolibrary.org/obo/CLO_0001053 denotes 12(1)
T100 16336-16337 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T101 16820-16825 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T102 16996-16997 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T103 17400-17402 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T104 17468-17480 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T105 17688-17700 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T106 17719-17726 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T107 17780-17785 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T108 17915-17916 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T109 17951-17952 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T110 17985-17990 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T111 18034-18037 http://purl.obolibrary.org/obo/CLO_0001423 denotes 579
T112 18133-18139 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T113 18246-18248 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T114 18246-18248 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T115 18257-18258 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T116 18282-18283 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T117 18354-18355 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T118 19240-19244 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T119 19322-19329 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T120 19343-19347 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T121 19361-19365 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T122 19469-19481 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T123 19601-19602 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T124 19936-19937 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T125 20075-20079 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T126 20105-20106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 20146-20147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T128 20172-20176 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T129 20232-20236 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T130 20382-20383 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 20595-20602 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T132 20607-20615 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T133 20779-20783 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T134 20815-20819 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T135 20833-20837 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T136 20931-20937 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T137 21026-21038 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T138 21055-21058 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T139 21216-21219 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T140 21767-21768 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 22072-22075 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T142 22130-22136 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T143 22266-22272 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T144 22690-22693 http://purl.obolibrary.org/obo/CLO_0002990 denotes F95
T145 22864-22866 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T146 23103-23105 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T147 23230-23233 http://purl.obolibrary.org/obo/CLO_0008722 denotes R86
T148 23879-23881 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T149 24116-24117 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 24221-24222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 24280-24281 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T152 24323-24324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T153 24382-24383 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T154 24510-24511 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T155 24518-24519 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T156 24549-24550 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 24586-24587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 24686-24687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 24750-24751 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T160 24825-24826 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 24874-24875 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 24884-24885 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T163 24918-24919 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 24984-24985 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 25017-25018 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T166 25070-25071 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 25073-25074 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 25084-25086 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T169 25100-25101 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 25148-25149 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T171 25156-25157 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T172 25260-25261 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 25351-25352 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 25377-25378 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T175 25396-25397 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T176 25501-25502 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T177 25517-25518 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T178 25520-25521 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T179 25541-25542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 25595-25596 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T181 25598-25599 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T182 25872-25873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 25966-25967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T184 25996-25997 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T185 26014-26015 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T186 26061-26062 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 26154-26155 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 26249-26250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 26322-26323 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 26353-26354 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T191 26366-26367 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T192 26415-26416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 26459-26460 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T194 26560-26561 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 26646-26647 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 26713-26714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 26803-26804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 26868-26869 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 26933-26934 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 27008-27009 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 678-693 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T2 1128-1144 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T3 2717-2725 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T4 2806-2814 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T5 3471-3475 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T7 3841-3851 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T8 4429-4444 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T9 6081-6092 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T10 6727-6742 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T11 6774-6776 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T12 6859-6870 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T13 6996-7001 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T14 7337-7347 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T15 8136-8139 Chemical denotes GGG http://purl.obolibrary.org/obo/CHEBI_63961
T16 8432-8447 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T17 8658-8660 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T18 8793-8796 Chemical denotes GGG http://purl.obolibrary.org/obo/CHEBI_63961
T19 9071-9073 Chemical denotes N2 http://purl.obolibrary.org/obo/CHEBI_17997
T20 9147-9163 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T21 10104-10119 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T22 10517-10533 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T23 10703-10718 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T24 10820-10825 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T25 11548-11550 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T26 11933-11943 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T27 12072-12082 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T28 13030-13032 Chemical denotes LP http://purl.obolibrary.org/obo/CHEBI_46895|http://purl.obolibrary.org/obo/CHEBI_73580
T30 13034-13036 Chemical denotes RP http://purl.obolibrary.org/obo/CHEBI_141419
T31 13038-13040 Chemical denotes MR http://purl.obolibrary.org/obo/CHEBI_74698
T32 13051-13053 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T33 13244-13246 Chemical denotes KG http://purl.obolibrary.org/obo/CHEBI_73604
T34 13266-13268 Chemical denotes WI http://purl.obolibrary.org/obo/CHEBI_141448
T35 13287-13289 Chemical denotes RF http://purl.obolibrary.org/obo/CHEBI_73818
T36 13866-13868 Chemical denotes KH http://purl.obolibrary.org/obo/CHEBI_32589
T37 14359-14361 Chemical denotes VM http://purl.obolibrary.org/obo/CHEBI_75015
T38 14409-14411 Chemical denotes DK http://purl.obolibrary.org/obo/CHEBI_73829
T39 14561-14563 Chemical denotes ES http://purl.obolibrary.org/obo/CHEBI_73509
T40 14589-14591 Chemical denotes VM http://purl.obolibrary.org/obo/CHEBI_75015
T41 14779-14781 Chemical denotes AE http://purl.obolibrary.org/obo/CHEBI_61565
T42 14799-14801 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819
T43 14836-14838 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T45 15869-15871 Chemical denotes PA http://purl.obolibrary.org/obo/CHEBI_30745|http://purl.obolibrary.org/obo/CHEBI_30768|http://purl.obolibrary.org/obo/CHEBI_74753|http://purl.obolibrary.org/obo/CHEBI_7959|http://purl.obolibrary.org/obo/CHEBI_8429
T50 15908-15923 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T51 16064-16066 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T52 16190-16203 Chemical denotes nucleic acids http://purl.obolibrary.org/obo/CHEBI_33696
T53 16198-16203 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T54 16320-16322 Chemical denotes WT http://purl.obolibrary.org/obo/CHEBI_141450
T55 17278-17280 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T56 17292-17294 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T57 17923-17925 Chemical denotes YM http://purl.obolibrary.org/obo/CHEBI_134468
T58 18246-18248 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T59 18292-18294 Chemical denotes Lu http://purl.obolibrary.org/obo/CHEBI_33382
T60 18343-18345 Chemical denotes GF http://purl.obolibrary.org/obo/CHEBI_73912
T61 19550-19552 Chemical denotes N2 http://purl.obolibrary.org/obo/CHEBI_17997
T62 24473-24478 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T63 25752-25755 Chemical denotes GGG http://purl.obolibrary.org/obo/CHEBI_63961

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2990-3012 http://purl.obolibrary.org/obo/GO_0009597 denotes detection of the virus
T2 3033-3054 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T3 3041-3054 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T4 7024-7048 http://purl.obolibrary.org/obo/GO_0004528 denotes 5'- exonuclease activity
T5 7028-7048 http://purl.obolibrary.org/obo/GO_0004527 denotes exonuclease activity
T6 15085-15093 http://purl.obolibrary.org/obo/GO_0007610 denotes Behavior

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 2503-2512 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 14017-14026 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 14274-14283 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 17045-17050 Phenotype denotes S, Le http://purl.obolibrary.org/obo/HP_0002725
T5 18393-18402 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T6 20638-20660 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-153 Sentence denotes Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak.
T2 154-165 Sentence denotes OBJECTIVES:
T3 166-347 Sentence denotes In this study, five SARS-CoV-2 PCR assay panels were evaluated against the accumulated genetic variability of the virus to assess the effect on sensitivity of the individual assays.
T4 348-366 Sentence denotes DESIGN OR METHODS:
T5 367-495 Sentence denotes As of week 21, 2020, the complete set of available SARS-CoV-2 genomes from GISAID and GenBank databases were used in this study.
T6 496-718 Sentence denotes SARS-CoV-2 primer sequences from publicly available panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx were included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated.
T7 719-727 Sentence denotes RESULTS:
T8 728-826 Sentence denotes A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay.
T9 827-1028 Sentence denotes Variations in 8,773 (25.94%) genomes were considered as high risk, whereas additional 2,854 (8.43%) genomes presented low frequent single mutations and were predicted to yield no impact on sensitivity.
T10 1029-1228 Sentence denotes In case of the QIAstat-Dx SARS-CoV-2 Panel, 99.11% of the genomes matched with a 100% coverage all oligonucleotides, and critical variations were tested in vitro corroborating no loss of sensitivity.
T11 1229-1241 Sentence denotes CONCLUSIONS:
T12 1242-1704 Sentence denotes This analysis stresses the importance of targeting more than one region in the viral genome for SARS-CoV-2 detection to mitigate the risk of loss of sensitivity due to the unknown mutation rate during this SARS-CoV-2 outbreak.INTRODUCTIONSince the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 (Zhu et al., 2020), the number of confirmed cases has been rising dramatically (The Open Science Prize, 2020).
T13 1705-2203 Sentence denotes According to data from the World Health Organization (WHO), Coronavirus Disease 2019 or COVID-19 (Gorbalenya et al., 2020) has been diagnosed in over 6,057,853 people from more than 200 countries or territories and caused over 371,166 deaths worldwide as of 1 June 2020 (World Health Organization, 2020a).SARS-CoV-2 is the seventh coronavirus known to infect humans and it appears to have its origin from zoonotic transmission similar to SARS-CoV (2002) and MERS-CoV (2012) (Andersen et al., 2020).
T14 2204-2356 Sentence denotes SARS-CoV-2 is hypothesised to be the product of recombination or mutation from a genetically related SARS-CoV species hosted by bats (Sun et al., 2020).
T15 2357-2575 Sentence denotes Unlike seasonal human coronaviruses HKU1, NL63, OC43 and 229E which are associated with mild symptoms (Corman et al., 2018), SARS-CoV-2 can cause pneumonia and severe acute respiratory syndrome (Andersen et al., 2020).
T16 2576-2682 Sentence denotes All coronaviruses are single, positive-stranded RNA viruses with similar genomic ∼30kb size and structure.
T17 2683-3311 Sentence denotes These genes encode non-structural proteins (ORF1a and ORF1b) involved in replication at the 5'-end and multiple structural proteins (spike (S), envelope (E), membrane (M) and nucleocapsid (N)) downstream that make up the virus particle (Chan et al., 2020; Wu et al., 2020).During novel RNA viral outbreaks, detection of the virus relies on real-time reverse transcription polymerase chain reaction (real-time RT-PCR) for detection of the RNA of the virus In the case of SARS-CoV-2, RT-PCR is used for confirmatory diagnosis of symptomatic patients as well as increasingly screening of asymptomatic contacts and subjects at risk.
T18 3312-3793 Sentence denotes The unprecedented outbreak posed the challenge of evaluating the different diagnostic RT-PCR assays sensitivity and specificity without a previous established gold standard.Since the availability of the first SARS-CoV-2 genomic sequence (Wu et al., 2020), several studies have reported a rapid genetic evolution of SARS-CoV-2 through a phylogenetic tree tracking the geographical spread of the virus (Andersen et al., 2020; The Open Science Prize, 2020; Wu et al., 2020; Yi, 2020).
T19 3794-4063 Sentence denotes As previously established for RNA viruses, the nucleotide mutation rate of SARS-CoV-2 is estimated to be 8E-04 substitutions per site per year as a consequence of the lack of proofreading activity of polymerases (Lauring and Andino, 2020; The Open Science Prize, 2020).
T20 4064-4608 Sentence denotes It evinces that new genetic variations of SARS-CoV-2 that will most likely occur during this evolving outbreak could compromise the sensitivity and specificity of RT-PCR detection (Lippi et al., 2020).Specifically, both natural mutation rate of a virus (Lauring and Andino, 2020) and active viral recombination (Yi, 2020) could potentially impair the efficiency of oligonucleotide annealing (Lippi et al., 2020), affecting sensitivity (increasing the limit of detection) or inclusivity (missed detection of some strains due to genomic changes).
T21 4609-4882 Sentence denotes We hypothesize that in order to minimize the risk of sensitivity loss of RT-PCR for detecting novel viruses with unknown genetic variability like SARS-CoV-2, published RT-PCR design strategies for SARS-CoV-2 detection should target more than one region in the viral genome.
T22 4883-5341 Sentence denotes This was the general approach followed to obtain the earliest available SARS-CoV-2 RT-PCR assays in panels used worldwide (Centers for Disease Control and Prevention, 2020a, 2020b; Chu et al., 2020; Corman et al., 2020; National Microbiology Data Center, 2020; QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020; University of Hong Kong, 2020; World Health Organization, 2020b), including the syndromic multiplex QIAstat-Dx Respiratory SARS-CoV-2 Panel (Table 1).
T23 5342-5831 Sentence denotes The selected conserved target regions from available SARS-CoV-2 genomes minimizes the potential cross-reactivity with other coronaviruses (Gorbalenya et al., 2020; Zhu et al., 2020), including human coronaviruses (Wu et al., 2020) and bat-SARS-like coronaviruses (Chan et al., 2020).The goal of this study is to assess how the genetic variability observed in the SARS-CoV-2 genome as of week 21, 2020 has affected sensitivity of publicly available SARS-CoV-2 real-time RT-PCR Panel assays.
T24 5832-6216 Sentence denotes Additionally, a detailed characterization and evaluation of the impact on performance of the SARS-CoV-2 assays in the QIAstat-Dx Respiratory SARS-CoV-2 Panel was carried out.METHODSThe complete set of available SARS-CoV-2 genomes larger than 26,000 nucleotides from GISAID (https://www.gisaid.org/) and GenBank (http://www.ncbi.nlm.nih.gov/genbank/) databases were used in this study.
T25 6217-6492 Sentence denotes As of week 21, 2020, a total of 30,090 and 3,729 available genomes (GISAID and GenBank respectively, Table S1) were aligned using ClustalW algorithm implemented in Geneious software v.10.0.3. (http://www.geneious.com), with a gap open and extent cost of 5 and 3 respectively.
T26 6493-6778 Sentence denotes The output alignment was curated manually.SARS-CoV-2 primer sequences from publicly available panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx (Table 1) were included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated (Table S2).
T27 6779-7089 Sentence denotes Variations were considered as high risk when they were placed in the three last nucleotides of the 3'-end, affecting the PCR elongation step (Stadhouders et al., 2010; Whiley and Sloots, 2005) or in the 5'-end of the probe affecting the natural 5'- exonuclease activity of the polymerases (Smith et al., 2002).
T28 7090-7786 Sentence denotes In addition, were also considered as high risk those variations with a significant presence (>1%) among all published genomes that could become more extended worldwide in the current or potential future spread episodes.RESULTSResults showed large nucleotide insertions (EPI_ISL_416672, EPI_ISL_418061, EPI_ISL_418066, EPI_ISL_416720, EPI_ISL_423027, EPI_ISL_424274, EPI_ISL_424327, EPI_ISL_426134, EPI_ISL_427267, EPI_ISL_429646, EPI_ISL_430896, EPI_ISL_434554, EPI_ISL_437867, EPI_ISL_445217) or fragment gene inversions (EPI_ISL_427289, EPI_ISL_427291) mainly in the polyprotein Orf1ab gene, typically indicating genetic recombination common in coronavirus genomes (Sun et al., 2020; Yi, 2020).
T29 7787-8038 Sentence denotes Since none of them were placed in binding regions of any of the PCR assays, recombination analysis was considered out of the scope of this current study.A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay.
T30 8039-9342 Sentence denotes Variations in 8,773 (25.94%) genomes were considered as high risk: a) a trinucleotide variation (GGG to AAC) present in 8,251 of the 8,257 (24.41%) genomes affecting the binding of the N gene NMDC assay forward primer; b) different single variations in the last three positions of the 3'-end or 5'-end (primers and probes respectively)..Genetic variations affecting annealing of more than one oligonucleotide of the same assay were not frequent: a) a total of 126 out of the 128 genomes with a non-critical mismatch in Reverse primer of the WHO RdRp assay (Table 2) present any other variation in the Probe (RdRp_SARSr-P2) or in the Forward primer binding regions, b) 17 out of the 8,251 genomes with multiple three consecutive mismatches at the 5'-end (GGG to AAC) of the NMDC N assay presented additional single variations in the Probe or Reverse primer binding regions; c) five genome sequences (EPI_ISL_444736 for the WHO N assay; EPI_ISL_437536, EPI_ISL_422983 and MT293178 for the CDC N1 assay; and EPI_ISL_446918 for the CDC N2 assay) presented combinations of non-critical mismatches among different oligonucleotides of the same set.Additional 2,854 (8.44%) genomes presented low frequent single mutations considered to be low risk (Table 2) and were predicted to yield no impact on sensitivity.
T31 9343-9477 Sentence denotes However, the effect in every PCR performance must be evaluated individually based on the corresponding PCR thermal profile conditions.
T32 9478-9748 Sentence denotes The impact of non-3 terminal mismatches should not be underestimated, especially in a diagnostic environment (Stadhouders et al., 2010; Whiley and Sloots, 2005).A large number of genomes with variations affecting the CDC N3 assay were also found (546 variations, 1.61%).
T33 9749-10130 Sentence denotes Although they cannot be classified as critical based on the parameters defined in the present study, this data supports why the initial N3 CDC assay was removed from the official panel due to inconclusive results (Centers of Disease Control and Prevention, 2020a, 2020b).This same method of evaluation was carried out with the QIAstat-Dx SARS-CoV-2 Panel oligonucleotide sequences.
T34 10131-10445 Sentence denotes The SARS-CoV-2 assay was originally developed as a real-time RT-PCR duplex assay covering two highly conserved target genes (RdRp and E) reported with the same fluorophore and showing a verified combined limit of detection (LoD) of 500 copies/mL in clinical samples (QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020).
T35 10446-10615 Sentence denotes A total of 33,518 (99.11 %) of 33,819 matched with a 100% coverage all oligonucleotides included in the SARS-CoV-2 assays of the QIAstat-Dx Respiratory SARS-CoV-2 Panel.
T36 10616-10830 Sentence denotes In contrast, 301 (0.89%) genomes showed a single variation affecting annealing for any oligonucleotide, and 35 (0.10%) of those 301 genomes contained a variation in any critical position of any primer or probe end.
T37 10831-10984 Sentence denotes Among these latter ones, the most frequent variation consisted of a mismatch in the last position of the 3'-end of one of the primers (7 genomes, 0.02%).
T38 10985-11183 Sentence denotes Because a mismatch in this position might impair the elongation PCR step (Stadhouders et al., 2010; Whiley and Sloots, 2005), this genomic mutation was further tested in vitro re-evaluating the LoD.
T39 11184-11579 Sentence denotes A total of twenty replicates of quantified synthetic dsDNA reproducing the sequence containing this mutation were run at the LoD concentration (500 copies/mL) described in the publicly available QIAstat-Dx Respiratory SARS-CoV-2 Panel instructions for use (QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020), and 19 out of the 20 (95%) replicates were positive (Table S3) confirming the defined LoD.
T40 11580-12034 Sentence denotes Therefore, the QIAstat-Dx SARS-CoV-2 assay remains highly specific and sensitive against SARS-CoV-2 even in light of genomic variations from the first three months of the COVID-19 outbreak (Visseaux et al., 2020).DISCUSSIONGenetic variability observed among SARS-CoV-2 genomes available until week 15, 2020 after the onset of the outbreak showed single nucleotide mutations affecting the annealing of all SARS-CoV-2 RT-PCR panels evaluated in this study.
T41 12035-12202 Sentence denotes The majority of the annotated single nucleotide variations are predicted to have no effect on sensitivity at panel level, including those placed in critical positions.
T42 12203-12603 Sentence denotes This was confirmed for the QIAstat-Dx SARS-CoV-2 Panel to show no effect on the LoD of the panel.Given that genetic variability in the SARS-CoV-2 genome is expected to increase based on the natural viral mutation and recombination rates, our results show that combination of more than one assay target in real-time RT-PCR SARS-CoV-2 panels can mitigate the risk of loss of sensitivity or specificity.
T43 12604-12915 Sentence denotes In this regards, continuous monitoring of genomic variations is essential to provide a rapid response in case assay re-design is needed.AcknowledgementsWe thank all those who have contributed sequences to the GISAID database (https://www.gisaid.org/) and to NCBI database (http://www.ncbi.nlm.nih.gov/genbank/).
T44 12916-13140 Sentence denotes We also thank the QIAstat-Dx Barcelona team for their support in their corresponding roles.Conflict of interests: LP, RP, MR, SNR, MJF,DM,MLF and JP are QIAGEN employees.No ethical approval was required to conduct this work.
T45 13141-13290 Sentence denotes The work described in this paper was funded by the employer of the authors (QIAGEN).ReferencesAndersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF.
T46 13291-13325 Sentence denotes The proximal origin of SARS-CoV-2.
T47 13326-13431 Sentence denotes Nat Med 2020. https://doi.org/10.1038/s41591-020-0820-9.Centers for Disease Control and Prevention (CDC).
T48 13432-13510 Sentence denotes 2019-novel coronavirus (2019-nCoV) real-time rRT-PCR panel primers and probes.
T49 13511-13527 Sentence denotes 2020a; Accessed:
T50 13528-13540 Sentence denotes 09 Apr 2020.
T51 13541-13689 Sentence denotes Available from: https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf.Centers for Disease Control and Prevention (CDC).
T52 13690-13763 Sentence denotes CDC 2019-novel coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel.
T53 13764-13780 Sentence denotes 2020b; Accessed:
T54 13781-13793 Sentence denotes 09 Apr 2020.
T55 13794-13906 Sentence denotes Available from: https://www.fda.gov/media/134922/download.Chan JFW, Kok KH, Zhu Z, Chu H, To KKW, Yuan S, et al.
T56 13907-14048 Sentence denotes Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.
T57 14049-14079 Sentence denotes Emerg Microbes Infect 2020; 9:
T58 14080-14195 Sentence denotes 221-36. https://doi.org/10.1080/22221751.2020.1719902.Chu DKV, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, et al.
T59 14196-14284 Sentence denotes Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia.
T60 14285-14419 Sentence denotes Clin Chem 2020; 0(0):1-7. https://doi.org/10.1093/clinchem/hvaa029.Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al.
T61 14420-14486 Sentence denotes Detection of 2019 novel coronavirus (2019-nCoV) by realtimeRT-PCR.
T62 14487-14623 Sentence denotes Euro Surveill 2020; 25(3): pii=2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045.Corman VM, Muth D, Niemeyer D, Drosten C.
T63 14624-14673 Sentence denotes Hosts and sources of endemic human coronaviruses.
T64 14674-14706 Sentence denotes Adv Virus Res 2018; 100:163-188.
T65 14707-14846 Sentence denotes ISSN 0065-3527. https://doi.org/10.1016/bs.aivir.2018.01.001.Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, et al.
T66 14847-14961 Sentence denotes The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.
T67 14962-14984 Sentence denotes Nat Microbiol 2020; 5:
T68 14985-15056 Sentence denotes 536-44. https://doi.org/10.1038/s41564-020-0695-z.Lauring AS, Andino R.
T69 15057-15109 Sentence denotes Quasispecies Theory and the Behavior of RNA Viruses.
T70 15110-15217 Sentence denotes PLoS Pathog 2010; 6(7): e1001005. https://doi:10.1371/journal.ppat.1001005.Lippi G, Simundic AM, Plebani M.
T71 15218-15340 Sentence denotes Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19).
T72 15341-15488 Sentence denotes Clin Chem Lab Med 2020; 20200285, eISSN 1437-4331, ISSN 1434-6621. https://doi.org/10.1515/cclm-2020-0285.National Microbiology Data Center (NMDC).
T73 15489-15563 Sentence denotes Novel coronavirus national science and technology resource service system.
T74 15564-15579 Sentence denotes 2020; Accessed:
T75 15580-15593 Sentence denotes 09 Apr 2020..
T76 15594-15673 Sentence denotes Available from: http://nmdc.cn/nCov/en.QIAstat-Dx Respiratory SARS-CoV-2 Panel.
T77 15674-15746 Sentence denotes QIAstat-Dx Respiratory SARS-CoV-2 Panel instructions for use (Handbook).
T78 15747-15762 Sentence denotes 2020; Accessed:
T79 15763-15775 Sentence denotes 09 Apr 2020.
T80 15776-15872 Sentence denotes Available from: https://qiastat-dx.com/row/qiastat-dx-sars-cov-2/.Smith S, Vigilant L, Morin PA.
T81 15873-15970 Sentence denotes The effects of sequence length and oligonucleotide mismatches on 5' exonuclease assay efficiency.
T82 15971-15989 Sentence denotes Nucleic Acids Res.
T83 15990-16109 Sentence denotes 2002; 30(20): e111. https://doi.org/10.1093/nar/gnf110.Stadhouders R, Pas SD, Anber J, Voermans J, Mes THM, Schutten M.
T84 16110-16232 Sentence denotes The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay.
T85 16233-16257 Sentence denotes J Mol Diagn 2010; 12(1):
T86 16258-16358 Sentence denotes 109-117. https://doi.org/10.2353/jmoldx.2010.090035.Sun J, He WT, Wang L, Lai A, Ji X, Zhai X et al.
T87 16359-16368 Sentence denotes COVID-19:
T88 16369-16430 Sentence denotes Epidemiology, Evolution, and Cross-Disciplinary Perspectives.
T89 16431-16442 Sentence denotes Trends Mol.
T90 16443-16528 Sentence denotes Med0 2020; 1550. https://doi.org/10.1016/j.molmed.2020.02.008.The Open Science Prize.
T91 16529-16540 Sentence denotes Nextstrain:
T92 16541-16582 Sentence denotes Real-time tracking of pathogen evolution.
T93 16583-16625 Sentence denotes Genomic epidemiology of novel coronavirus.
T94 16626-16641 Sentence denotes 2020; Accessed:
T95 16642-16654 Sentence denotes 09 Apr 2020.
T96 16655-16758 Sentence denotes Available from: https://nextstrain.org/ncov.The University of Hong Kong (HKU), School of Public Health.
T97 16759-16842 Sentence denotes Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR.
T98 16843-16858 Sentence denotes 2020; Accessed:
T99 16859-16871 Sentence denotes 09 Apr 2020.
T100 16872-17066 Sentence denotes Available from: https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4.Visseaux B, Le Hingrat Q, Collin G, Bouzid D, Lebourgeois S, Le Pluart D et al.
T101 17067-17198 Sentence denotes Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the first rapid multiplex PCR commercial assay for SARS-CoV-2 detection.
T102 17199-17295 Sentence denotes J Clin Microbiol 2020;JCM.00630-20. https//doi.org/10.1128/JCM.00630-20.Whiley DM and Sloots TP.
T103 17296-17380 Sentence denotes Sequence variation in primer targets affects the accuracy of viral quantitative PCR.
T104 17381-17403 Sentence denotes J Clin Virol 2005; 34:
T105 17404-17487 Sentence denotes 104-107. https://doi.org/10.1016/j.jcv.2005.02.010.World Health Organization (WHO).
T106 17488-17545 Sentence denotes Coronavirus disease 2019 (COVID-19) situation report -79.
T107 17546-17562 Sentence denotes 2020a; Accessed:
T108 17563-17575 Sentence denotes 09 Apr 2020.
T109 17576-17707 Sentence denotes Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/.World Health Organization (WHO).
T110 17708-17792 Sentence denotes Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases.
T111 17793-17809 Sentence denotes 2020b; Accessed:
T112 17810-17822 Sentence denotes 09 Apr 2020.
T113 17823-17950 Sentence denotes Available from: https://apps.who.int/iris/rest/bitstreams/1271387/retrieve.Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al.
T114 17951-18020 Sentence denotes A new coronavirus associated with human respiratory disease in China.
T115 18021-18038 Sentence denotes Nature 2020; 579:
T116 18039-18095 Sentence denotes 265-269. https://doi.org/10.1038/s41586-020-2008-3.Yi H.
T117 18096-18154 Sentence denotes 2019 novel coronavirus is undergoing active recombination.
T118 18155-18353 Sentence denotes Clin Infect Dis 2020; ciaa219. https://doi.org/10.1093/cid/ciaa219.Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W.
T119 18354-18418 Sentence denotes A novel coronavirus from patients with pneumonia in China, 2019.
T120 18419-18445 Sentence denotes N Engl J Med 2020; 382(8):
T121 18446-18516 Sentence denotes 727-33. https://doi.org/10.1056/NEJMoa2001017.Authors contributionsLP:
T122 18517-18638 Sentence denotes Planned experiments, conceptualised the laboratory work, conceptualised the overall study, wrote the manuscript draft.MR:
T123 18639-18676 Sentence denotes Planned and conducted experiments.RP:
T124 18677-18714 Sentence denotes Planned and conducted experiments.SR:
T125 18715-18785 Sentence denotes Contributed to overall study planning and review of the manuscript.MJ:
T126 18786-18856 Sentence denotes Contributed to overall study planning and review of the manuscript.DM:
T127 18857-18937 Sentence denotes Contributed to overall study conceptualization and review of the manuscript.MLF:
T128 18938-19008 Sentence denotes Contributed to overall study planning and review of the manuscript.JP:
T129 19009-19092 Sentence denotes Contributed to overall study conceptualization, co-wrote of the manuscript.Table 1.
T130 19093-19354 Sentence denotes Description of earliest available SARS-CoV-2 RT-PCR assaysRT-qPCR panelAssays includedTarget genesDescriptionfReferencesWHO panela3RdRp, E, Nthe E gene assay is used as the firstline screening tool, then followed by confirmatory testing with an RdRp gene assay.
T131 19355-19600 Sentence denotes The N gene assay can eventually be analyzed as an additional confirmatory assay.Corman et al., 2020; World Health Organization, 2020bCDC (US) panelb2NThis panel contains two monoplex assays (N1, N2) designed for specific detection of SARS-CoV-2.
T132 19601-19935 Sentence denotes A specimen is considered positive for 2019-nCoV if both assays are positive, whereas if only one assay resulted positive the result is inconclusive and it should be retested.Centers of Disease Control and Prevention, 2020a, 2020bNMDC panelc2RdRp, NThis panel contains two monoplex assays designed for specific detection of SARS-CoV-2.
T133 19936-20841 Sentence denotes A specimen is considered positive for 2019-nCoV if both assays are positive.National Microbiology Data Center, 2020HKU paneld2RdRp, NThe N gene RT-PCR is recommended as a screening assay and the Orf1b assay as a confirmatory one (the N gene assay is about 10 times more sensitive than the ORF-1b gene assay in detecting positive clinical specimens).Chu et al., 2020; The University of Hong Kong, 2020.QIAstat-Dx Panele2RdRp, EThis panel contains a Duplex assay in the same optical channel to report an additive performance (including CT and endpoint fluorescence values) of the two PCR assays and it discriminates SARS-CoV-2 detection from more than other 20 viruses and bacteria responsible for upper respiratory infections including other endemic coronavirusesQIAstat-Dx Respiratoyry SARS-CoV-2 Panel, 2020RdRp: RNA-dependent RNA polymerase gene (inside the Orf1ab polyprotein gene), E: envelop gene, N:
T134 20842-22100 Sentence denotes Nucleocaspide gene.This panel was originally proposed by the Charité-Universitätsmedizin Berlin Institute of Virology (Corman et al., 2020), and then endorsed by the WHO (World Helath Organization, 2020b).Initial CDC panel contained one additional assay (N3) designed for universal detection of SARS-like coronaviruses (Centers of Disease Control and Prevention, 2020a) but has been removed due to inconclusive results based on low performance (Centers of Disease Control and Prevention, 2020b).National Microbiology Data Center (NMDC) works in collaboration with National Institute for Viral Disease Control and Prevention under Chinese Center for Disease Control and Prevention.The School of Public Health of the University of Hong Kong (HKU) developed the assay (Chu et al., 2020) and it was later established as official protocol under the WHO Network Laboratories (The University of Hong Kong, 2020).QIAstat-Dx Panel is a syndromic Point-of-Care system incorporating sample purification and real time RT-qPCR amplification for more than 20 viral and bacterial respiratory pathogens, including SARS-CoV-2.WHO and HKU assays are reactive with coronaviruses under the subgenus Sarbecovirus that includes 2019-nCoV, SARS-CoV and bat SARS-like coronaviruses.
T135 22101-22295 Sentence denotes Since SARS was eliminated in humans since 2004, individuals with samples that are positive in these RT-PCR assays should be infected by the 2019-nCoV or its related animal coronaviruses.Table 2.
T136 22296-24044 Sentence denotes Summary of genomic variants detected in complementary binding regions of earliest available SARS-CoV-2 RT-PCR assays.RT-qPCR panelassayTypeOligonucleotide nameNumber of genomes (%) with non-critical single variationsNumber of genomes (%) with high risk single variationsWHO panelEFwE_Sarbeco_F10 (0.030%)2 (0.006%)aPE_Sarbeco_P134 (0.101%)9 (0.027%)bRevE_Sarbeco_R14 (0.4041%)-RdRpFwRdRp_SARSr-F95 (0.281%)5 (0.015%)cPRdRp_SARSr-P1126 (0.373%)2 (0.006%)dPRdRp_SARSr-P215 (0.044%)-RevRdRp_SARSr-R128 (0.378%)-NFwN_Sarbeco_F70 (0.207%)4 (0.012%)ePN_Sarbeco_P169 (0.204%)11 (0.033%)fRevN_Sarbeco_R119 (0.352%)1 (0.003%)gCDC (US) panelN1Fw2019-nCoV_N1-F40 (0.118%)3 (0.009%)hP2019-nCoV_N1-P53 (0.157%)353 (1.044%)iRev2019-nCoV_N1-R168 (0.497%)4 (0.012%)jN2Fw2019-nCoV_N2-F58 (0.172%)-P2019-nCoV_N2-P102 (0.302%)41 (0.121%)kRev2019-nCoV_N2-R41 (0.121%)-N3Fw2019-nCoV_N3-F344 (1.017%)l-P2019-nCoV_N3-P107 (0.316%)6 (0.018%)mRev2019-nCoV_N3-R86 (0.254%)3 (0.009%)nNMDC panelRdRpFwForward primer23 (0.068%)-PFluorescent probe48 (0.142%)10 (0.030%)oRevReverse primer30 (0.089%)1 (0.003%)pNFwForward primer337 (0.996%)8257 (24.415%)qPFluorescent probe15 (0.044%)3 (0.009%)rRevReverse primer56 (0.166%)5 (0.015%)sHKU panelRdRpFwHKU-ORF1b-nsp14F84 (0.248%)5 (0.015%)PHKU-ORF1b-nsp14P45 (0.133%)-RevHKU-ORF1b-nsp14R62 (0.183%)2 (0.006%)uNFwHKU-NF73 (0.216%)3 (0.009%)vPHKU-NP53 (0.157%)6 (0.018%)wRevHKU-NR83 (0.245%)2 (0.006%)xQIAstat-Dx PanelRdRpFwForward primer15 (0.044%)1 (0.003%)yPFluorescent probe133 (0.393%)12 (0.035%)zRevReverse primer27 (0.080%)3 (0.009%)aaEFwForward primer57 (0.169%)11 (0.032%)bbPFluorescent probe10 (0.030%)1 (0.003%)ccRevReverse primer24 (0.071%)7 (0.021%)ddTOTALS2,854 (8.434%)8,773 (25,941%)ACUMMULATED TOTAL11,627 (34.380%)Fw:
T137 24045-24063 Sentence denotes Forward primer, P:
T138 24064-24075 Sentence denotes Probe, Rev:
T139 24076-25764 Sentence denotes Reverse primerTwo genome sequences with a mismatch in in the three last positions of the 3'-end (U to C and G to respectively).Nine genomes with a mismatch in the last three positions of the 5'-end (five A to G, and four C to U).Five genomes with a mismatch in the last three positions of the 3'-end (G to A, C to U, or G to U).Two genomes with multiple mismatches in the binding position of this probe (positions 1 (C to U), 7 (G to A), 10 (A to G), 12 (R to C), 21 (U to A) of the 5'-end)).Four genomes with a mismatch in any of the three last positions at the 3'-end (C to U, or U to C).Eleven genomes with a mismatch in position 2 of the 5'-end (C to U).One genome with a mismatch in the first position of the 3'-end (G to C).Three genomes with a mismatch in the second position of the 3'-end (A to C/G).A total of 353 genomes containing a mismatch in any of the last three positions of the 5'-end (C to A/U, C to U/G).Four genomes with a mismatch in the third position of the 3'-end (C to A).A total of 41 genomes with a mismatch in the first position of the 5'-end (A to U).A total of 292 genomes present the same mismatch in position 15 of the 3'-end (U to C).Six genomes with a mismatch in second (Y to G) or third (C to U) positions of the 5'-end.Three genomes with a mismatch in first (G to A) or second (U to A) positions of the 3'-end.Ten genomes with any mismatch in the last three positions of the 5'-end (C to A, C to U, G to A).A single genome with a mismatch in the second position of the 3'-end (G to A).A total of 8251 genomes with multiple three consecutive mismatches in positions 20,21,22 of the 3'-end, corresponding to positions 1, 2, 3 of the 5'-end (GGG to AAC).
T140 25765-27040 Sentence denotes Six additional genomes with mismatches in any of the three last positions of the 3'-end.Three genomes with a mismatch in the second (U to C) or third (G to U) positions of the 5'-end.Five genomes with a mismatch in the first (G to A) or third (C to A/U) positions of the 3'-end.Five genomes with a mismatch in the second (C to U) or third (C to U) positions of the 3'-end.Two genomes with a mismatch in the second (U to C) or third (C to U) positions of the 3'-end.Three genomes with a mismatch in the third (U to C) position of the 3'-end.Six genomes with a mismatch in the second (C to A) or third (A to G) positions of the 5'-end.Two genomes with a mismatch in the second (U to C) or third (A to G) positions of the 3'-end.One mismatch in the third position of the 3'-end.Twelve genomes with a single mismatch in any of the three last positions of the 5'-end.Three genomes with a mismatch in the second position of the 3'-end.Seven genomes with a mismatch in the last position of the 3'-end, together with four additional genomes with a mismatch in the second or third positions.A single genome with a mismatch in the second position of the 5'-end.Six genomes with a mismatch in third position of the 3'-end, and one additional genome with a double mismatch in position 1.