LitCovid-sentences  

PMC:7366549 / 14145-22384 JSONTXT 9 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T119 0-48 Sentence denotes Sequencing of the positive coronavirus specimens
T120 49-86 Sentence denotes Sanger sequencing of bat coronavirus:
T121 87-229 Sentence denotes Using the Sanger sequencing protocol, partial RdRp sequences of BtCoV were retrieved from two (out of 4 amplicons) specimens of Rousettus spp.
T122 230-351 Sentence denotes One of the sequences (MCL-19-bat-588/2) showed close identity to BtCoV HKU9-5-2 (AN): HM211099.1; sequence identity (SI):
T123 352-498 Sentence denotes 99.2 per cent, whereas the second RdRp sequence (MCL-20-bat-76/10) had an SI of 98.8 per cent with BtCoV HKU9-1 (AN: EF065513.1), both from China.
T124 499-608 Sentence denotes Sanger's sequencing protocol led to retrieval of eight partial RdRp sequences which belonged to Pteropus spp.
T125 609-681 Sentence denotes These bats were collected from Kerala (n=5) and Tamil Nadu (n=3) States.
T126 682-821 Sentence denotes One of the three partial RdRp sequences from Tamil Nadu had 97.93 per cent SI with BtCoV/B55951/Pte_lyl/CB2-THA (AN: MG256459.1, Thailand).
T127 822-939 Sentence denotes The other two sequences had a minimum of 99.48 per cent SI with the CoV PREDICT_CoV-17/PB072 (AN: KX284942.1, Nepal).
T128 940-1074 Sentence denotes One of the five partial RdRp sequences from Kerala had 98.88 per cent SI with BtCoV/B55951/Pte_lyl/CB2-THA (AN: MG256459.1, Thailand).
T129 1075-1191 Sentence denotes The remaining four partial RdRp sequences had >97 per cent SI with CoV PREDICT_CoV-17/PB072 (AN: KX284942.1, Nepal).
T130 1192-1386 Sentence denotes Next-generation sequencing of bat coronavirus: NGS was performed on 10 specimens [4 RS, 2 kidney and 4 intestinal tissue) of the five Rousettus bats to retrieve the complete genome of the BtCoV.
T131 1387-1581 Sentence denotes Kidney and intestine tissues of the bats from Karnataka State (MCL-20-Bat-76) and RS along with intestine tissue of bats from Kerala State (MCL-19-Bat-606) were used for sequencing and analysis.
T132 1582-1729 Sentence denotes Two different viruses were retrieved based on the BLAST analysis of the sequences from the kidney and intestine tissues of the bats from Karnataka.
T133 1730-2000 Sentence denotes Kidney specimen of MCL-20-Bat-76 had an SI of 94 per cent and query coverage (QC) of 94 per cent with CoV BtRt-BetaCoV/GX2018 (AN: MK211379.1), whereas the intestine tissue of the MCL-20-Bat-76 had an SI of 96.8 and 95 per cent QC with the BtCoV HKU9-1 (AN: EF065513.1).
T134 2001-2191 Sentence denotes The sequences from RS and intestine tissue of the MCL-19-Bat-606 from Kerala, had 93.69 and 93.99 per cent SI to CoV BtRt-BetaCoV/GX2018 (AN: MK211379.1), respectively, with 100 per cent QC.
T135 2192-2321 Sentence denotes Further, 99.8 per cent of the CoV BtRt-BetaCoV/GX2018 sequences were retrieved from the intestine specimen of the MCL-19-Bat-606.
T136 2322-2431 Sentence denotes The details of the genome recovered reads mapped and the per cent of reads mapped are summarized in Table II.
T137 2432-2550 Sentence denotes Table II Details of the genome recovered reads mapped and the per cent of reads mapped from the Rousettus bat samples
T138 2551-2660 Sentence denotes Sample details Sample type Virus retrieved Relevant reads Per cent of reads Per cent of genome recovered
T139 2661-2735 Sentence denotes MCL-20-Bat-76 Kidney Coronavirus BtRt-BetaCoV/GX2018 1632 0.015 94.39
T140 2736-2779 Sentence denotes Intestine BtCoV HKU9-1 4499 0.056 95.75
T141 2780-2862 Sentence denotes MCL-19-Bat-606 Rectal swab Coronavirus BtRt-BetaCoV/GX2018 13,973 0.114 99.53
T142 2863-3015 Sentence denotes Intestine Coronavirus BtRt-BetaCoV/GX2018 10,214,492 93.476 99.87 Phylogenetic analysis of partial and complete genome sequences of bat coronavirus:
T143 3016-3150 Sentence denotes A neighbour-joining tree was generated using the partial RdRp region sequences derived from Pteropus and Rousettus spp. bat specimens.
T144 3151-3249 Sentence denotes It was observed that all the BtCoV sequences were clustered within the L_D sequences of beta CoVs.
T145 3250-3361 Sentence denotes A distinct subclustering of the sequences retrieved from Pteropus and Rousettus spp. bats is shown in Figure 1.
T146 3362-3501 Sentence denotes The sequences in the light pink colour are retrieved from the Pteropus spp., whereas those in the dark pink region belong to Rousettus spp.
T147 3502-3733 Sentence denotes The sequence divergence of 0.35 was observed between Pteropus spp. and Rousettus spp., which was obtained by averaging over all the sequence pairs between the two species, determining those to be distinct sequences to each species.
T148 3734-3844 Sentence denotes Fig. 1 Neighbour-joining tree for the RNA-dependent RNA polymerase (RdRp) partial sequence (genomic location:
T149 3845-3893 Sentence denotes 14,701-15,120) generated from Sanger sequencing.
T150 3894-3978 Sentence denotes The tree was constructed using the RdRp sequence available in the GenBank sequences.
T151 3979-4060 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T152 4061-4172 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T153 4173-4315 Sentence denotes The complete genome sequences of four BtCoV obtained from Rousettus spp. specimens were used for generating a neighbour-joining tree (Fig. 2).
T154 4316-4416 Sentence denotes These sequences were also clustered within L_D of β-CoVs as observed for partial RdRp sequence tree.
T155 4417-4532 Sentence denotes These complete genome sequences were grouped into gene pairs to identify the gene with higher and lower divergence.
T156 4533-4607 Sentence denotes The complete genomes of the Indian BtCoV sequences were grouped under L_D.
T157 4608-4786 Sentence denotes The evolutionary divergence of ORF 1b was <0.54 between the different β-CoV lineages with a maximum score of 0.7 between different BtCoV sequences used in this study (Table III).
T158 4787-4875 Sentence denotes E gene sequences had larger divergence within the β-CoV genus ranging from 2.18 to 0.94.
T159 4876-4979 Sentence denotes Lineages L_A and L_C had the maximum divergence of 2.18, whereas the L_B and L_C were the least (0.94).
T160 4980-5054 Sentence denotes N gene has an overall higher divergence among different lineages (ranging:
T161 5055-5066 Sentence denotes 2.08-0.75).
T162 5067-5239 Sentence denotes Overall, evolutionary divergence for the sequences of each gene pair demonstrated that S, N, E and M genes from the α- and δ-CoV highly diverged across the different genus.
T163 5240-5313 Sentence denotes In contrast, the ORF 1b was less divergent across the genera (Table III).
T164 5314-5369 Sentence denotes Fig. 2 Phylogenetic tree for the complete genome tree:
T165 5370-5494 Sentence denotes A neighbour-joining tree was generated using the representative complete genome sequence available in the GenBank sequences.
T166 5495-5576 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T167 5577-5688 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T168 5689-5812 Sentence denotes Table III Evolutionary divergence for ORF 1b, S, N and M genes for the retrieved sequences with other reference sequences.
T169 5813-6002 Sentence denotes The lower right-check hand matrix of the table depicts the divergence and the upper left-check matrix of the matrix (blue colour) depicts the variation observed in the bootstrap replication
T170 6003-6099 Sentence denotes N gene Alpha Delta Gamma L_A L_B L_C L_D M gene Alpha Delta Gamma L_A L_B L_C L_D
T171 6100-6186 Sentence denotes Alpha 0.15 0.09 0.10 0.08 0.08 0.09 Alpha 0.11 0.12 0.05 0.06 0.05 0.06
T172 6187-6273 Sentence denotes Delta 2.08 0.11 0.16 0.09 0.11 0.10 Delta 1.50 0.26 0.08 0.16 0.10 0.11
T173 6274-6360 Sentence denotes Gamma 1.57 1.49 0.08 0.08 0.09 0.08 Gamma 1.53 1.84 0.10 0.12 0.11 0.09
T174 6361-6443 Sentence denotes L_A 1.84 1.73 1.37 0.05 0.05 0.06 L_A 0.92 1.24 1.30 0.06 0.05 0.05
T175 6444-6526 Sentence denotes L_B 1.48 1.37 1.32 1.09 0.03 0.04 L_B 1.05 1.51 1.37 0.92 0.05 0.05
T176 6527-6609 Sentence denotes L_C 1.57 1.52 1.42 1.07 0.75 0.04 L_C 0.99 1.35 1.27 0.80 0.82 0.05
T177 6610-6691 Sentence denotes L_D 1.64 1.46 1.36 1.27 0.90 0.97 L_D 0.99 1.42 1.23 0.84 0.79 0.82
T178 6692-6788 Sentence denotes ORF 1b Alpha Delta Gamma L_A L_B L_C L_D ORF 1a Alpha Delta Gamma L_A L_B L_C L_D
T179 6789-6875 Sentence denotes Alpha 0.01 0.01 0.01 0.01 0.01 0.01 Alpha 0.02 0.02 0.01 0.02 0.02 0.03
T180 6876-6962 Sentence denotes Delta 0.70 0.01 0.02 0.01 0.01 0.01 Delta 1.32 0.03 0.02 0.03 0.03 0.04
T181 6963-7049 Sentence denotes Gamma 0.62 0.67 0.01 0.01 0.01 0.01 Gamma 1.14 1.33 0.02 0.03 0.02 0.04
T182 7050-7132 Sentence denotes L_A 0.61 0.69 0.60 0.01 0.01 0.01 L_A 1.22 1.01 1.30 0.02 0.02 0.04
T183 7133-7215 Sentence denotes L_B 0.60 0.70 0.65 0.54 0.01 0.01 L_B 1.26 1.42 1.41 1.19 0.01 0.02
T184 7216-7298 Sentence denotes L_C 0.58 0.69 0.62 0.53 0.50 0.01 L_C 1.35 1.41 1.44 1.19 0.97 0.03
T185 7299-7380 Sentence denotes L_D 0.60 0.67 0.61 0.53 0.50 0.52 L_D 1.26 1.27 1.39 1.09 0.90 1.03
T186 7381-7477 Sentence denotes S gene Alpha Delta Gamma L_A L_B L_C L_D E gene Alpha Delta Gamma L_A L_B L_C L_D
T187 7478-7564 Sentence denotes Alpha 0.02 0.02 0.03 0.03 0.03 0.02 Alpha 0.12 0.18 0.09 0.15 0.15 0.12
T188 7565-7651 Sentence denotes Delta 0.86 0.03 0.04 0.04 0.06 0.03 Delta 1.14 0.47 0.22 0.41 0.28 0.17
T189 7652-7738 Sentence denotes Gamma 1.14 0.96 0.04 0.05 0.06 0.04 Gamma 1.59 1.64 0.22 0.24 0.32 0.19
T190 7739-7821 Sentence denotes L_A 1.36 1.28 1.43 0.03 0.03 0.02 L_A 1.03 1.58 1.57 0.23 0.21 0.25
T191 7822-7904 Sentence denotes L_B 1.33 1.23 1.34 1.19 0.04 0.02 L_B 1.24 1.75 1.40 1.83 0.11 0.14
T192 7905-7987 Sentence denotes L_C 1.42 1.32 1.46 1.17 1.03 0.03 L_C 1.37 1.64 1.83 2.18 0.94 0.17
T193 7988-8069 Sentence denotes L_D 1.34 1.24 1.41 1.16 1.00 1.11 L_D 1.25 1.42 1.52 1.95 1.16 1.37
T194 8070-8239 Sentence denotes ORF 1a, open reading frame 1a polyprotein; ORF 1b, ORF 1b polyprotein; S, spike glycoprotein; N, nuclocapsid phospoptotein; M, membrane glycoprotein; E, envelope protein