LitCovid-sentences  

PMC:7366549 / 11441-22384 JSONTXT 10 Projects

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Id Subject Object Predicate Lexical cue
T86 0-7 Sentence denotes Results
T87 8-170 Sentence denotes The TS and RS specimens for 78 Rousettus spp. bats were collected in VTM from seven States (Kerala, Karnataka, Chandigarh, Gujarat, Odisha, Punjab and Telangana).
T88 171-389 Sentence denotes The TS and RS specimens of 508 Pteropus spp. bats were also collected in VTM from 10 States/UTs in India (Kerala, Karnataka, Chandigarh, Gujarat, Himachal Pradesh, Odisha, Puducherry, Punjab, Tamil Nadu and Telangana).
T89 390-466 Sentence denotes During the trapping process, 12 (8 Rousettus and 4 Pteropus spp.) bats died.
T90 467-621 Sentence denotes Organ specimens (intestine and kidney) were collected from these bats (TS and RS specimens of these 12 bats were included in the total number of samples).
T91 622-674 Sentence denotes Detection of bat coronavirus using RdRp gene RT-PCR:
T92 675-759 Sentence denotes Four of the 78 RS of Rousettus spp. bats screened for the BtCoV were found positive.
T93 760-813 Sentence denotes All the positive RS samples belonged to Kerala State.
T94 814-892 Sentence denotes Intestinal specimens of two bats were also found to be positive for the BtCoV.
T95 893-995 Sentence denotes One bat (MCL-19-Bat-606), from Kerala, was tested positive in both the intestinal specimen and the RS.
T96 996-1096 Sentence denotes The second bat (MCL-20-Bat-76), from Karnataka, was tested positive only in the intestinal specimen.
T97 1097-1162 Sentence denotes Altogether, five Rousettus spp. bats were positive for the BtCoV.
T98 1163-1240 Sentence denotes All TS specimens from Rousettus spp. were found negative for BtCoV (Table I).
T99 1241-1435 Sentence denotes Table I Bat coronavirus positivity in bat specimens screened using RNA-dependent RNA polymerase (RdRp) gene-specific reverse transcription-polymerase chain reaction (RT-PCR) in different States
T100 1436-1555 Sentence denotes Place of collection Number of positive/number tested (%) for different bat species for BtCoV RdRp gene-specific RT-PCR
T101 1556-1593 Sentence denotes Pteropus bats (%) Rousettus bats (%)
T102 1594-1648 Sentence denotes Rectal swabs Throat swabs Rectal swabs Throat swabs
T103 1649-1708 Sentence denotes Kerala 12/217 (5.53) 0/21 (0.00) 4/42 (9.52) 0/4 (0.00)
T104 1709-1759 Sentence denotes Karnataka 0/78 (0.00) NT 0/4 (0.00) 0/4 (0.00)
T105 1760-1811 Sentence denotes Chandigarh 0/27 (0.00) NT 0/6 (0.00) 0/6 (0.00)
T106 1812-1862 Sentence denotes Gujarat 0/30 (0.00) NT 0/18 (0.00) 0/18 (0.00)
T107 1863-1910 Sentence denotes Odisha 0/30 (0.00) NT 0/2 (0.00) 0/2 (0.00)
T108 1911-1958 Sentence denotes Punjab 0/14 (0.00) NT 0/2 (0.00) 0/2 (0.00)
T109 1959-2009 Sentence denotes Telangana 0/30 (0.00) NT 0/4 (0.00) 0/4 (0.00)
T110 2010-2059 Sentence denotes Himachal Pradesh 2/29 (6.89) 0/6 (0.00) NA NA
T111 2060-2105 Sentence denotes Puducherry 6/23 (26.09) 0/10 (0.00) NA NA
T112 2106-2149 Sentence denotes Tamil Nadu 1/30 (3.33) 0/5 (0.00) NA NA
T113 2150-2202 Sentence denotes 21/508 (4.13) 0/42 (0.00) 4/78 (5.13) 0/40 (0.00)
T114 2203-2365 Sentence denotes NT, not tested; NA, not available; BtCoV, bat coronavirus Twenty one of the 508 RSs from Pteropus spp. bats screened were tested positive for the BtCoV (Table I).
T115 2366-2475 Sentence denotes These positive bats belonged to Kerala (n=12), Himachal Pradesh (n=2), Puducherry (n=6) and Tamil Nadu (n=1).
T116 2476-2541 Sentence denotes The TS specimens of the same bats were tested negative for BtCoV.
T117 2542-2640 Sentence denotes The TS specimens of RS-negative (n=42) bats were also screened and found to be negative (Table I).
T118 2641-2702 Sentence denotes A total of 25 bats from both the species were found positive.
T119 2704-2752 Sentence denotes Sequencing of the positive coronavirus specimens
T120 2753-2790 Sentence denotes Sanger sequencing of bat coronavirus:
T121 2791-2933 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 2934-3055 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 3056-3202 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 3203-3312 Sentence denotes Sanger's sequencing protocol led to retrieval of eight partial RdRp sequences which belonged to Pteropus spp.
T125 3313-3385 Sentence denotes These bats were collected from Kerala (n=5) and Tamil Nadu (n=3) States.
T126 3386-3525 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 3526-3643 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 3644-3778 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 3779-3895 Sentence denotes The remaining four partial RdRp sequences had >97 per cent SI with CoV PREDICT_CoV-17/PB072 (AN: KX284942.1, Nepal).
T130 3896-4090 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 4091-4285 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 4286-4433 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 4434-4704 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 4705-4895 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 4896-5025 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 5026-5135 Sentence denotes The details of the genome recovered reads mapped and the per cent of reads mapped are summarized in Table II.
T137 5136-5254 Sentence denotes Table II Details of the genome recovered reads mapped and the per cent of reads mapped from the Rousettus bat samples
T138 5255-5364 Sentence denotes Sample details Sample type Virus retrieved Relevant reads Per cent of reads Per cent of genome recovered
T139 5365-5439 Sentence denotes MCL-20-Bat-76 Kidney Coronavirus BtRt-BetaCoV/GX2018 1632 0.015 94.39
T140 5440-5483 Sentence denotes Intestine BtCoV HKU9-1 4499 0.056 95.75
T141 5484-5566 Sentence denotes MCL-19-Bat-606 Rectal swab Coronavirus BtRt-BetaCoV/GX2018 13,973 0.114 99.53
T142 5567-5719 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 5720-5854 Sentence denotes A neighbour-joining tree was generated using the partial RdRp region sequences derived from Pteropus and Rousettus spp. bat specimens.
T144 5855-5953 Sentence denotes It was observed that all the BtCoV sequences were clustered within the L_D sequences of beta CoVs.
T145 5954-6065 Sentence denotes A distinct subclustering of the sequences retrieved from Pteropus and Rousettus spp. bats is shown in Figure 1.
T146 6066-6205 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 6206-6437 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 6438-6548 Sentence denotes Fig. 1 Neighbour-joining tree for the RNA-dependent RNA polymerase (RdRp) partial sequence (genomic location:
T149 6549-6597 Sentence denotes 14,701-15,120) generated from Sanger sequencing.
T150 6598-6682 Sentence denotes The tree was constructed using the RdRp sequence available in the GenBank sequences.
T151 6683-6764 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T152 6765-6876 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T153 6877-7019 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 7020-7120 Sentence denotes These sequences were also clustered within L_D of β-CoVs as observed for partial RdRp sequence tree.
T155 7121-7236 Sentence denotes These complete genome sequences were grouped into gene pairs to identify the gene with higher and lower divergence.
T156 7237-7311 Sentence denotes The complete genomes of the Indian BtCoV sequences were grouped under L_D.
T157 7312-7490 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 7491-7579 Sentence denotes E gene sequences had larger divergence within the β-CoV genus ranging from 2.18 to 0.94.
T159 7580-7683 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 7684-7758 Sentence denotes N gene has an overall higher divergence among different lineages (ranging:
T161 7759-7770 Sentence denotes 2.08-0.75).
T162 7771-7943 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 7944-8017 Sentence denotes In contrast, the ORF 1b was less divergent across the genera (Table III).
T164 8018-8073 Sentence denotes Fig. 2 Phylogenetic tree for the complete genome tree:
T165 8074-8198 Sentence denotes A neighbour-joining tree was generated using the representative complete genome sequence available in the GenBank sequences.
T166 8199-8280 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T167 8281-8392 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T168 8393-8516 Sentence denotes Table III Evolutionary divergence for ORF 1b, S, N and M genes for the retrieved sequences with other reference sequences.
T169 8517-8706 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 8707-8803 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 8804-8890 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 8891-8977 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 8978-9064 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 9065-9147 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 9148-9230 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 9231-9313 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 9314-9395 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 9396-9492 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 9493-9579 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 9580-9666 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 9667-9753 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 9754-9836 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 9837-9919 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 9920-10002 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 10003-10084 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 10085-10181 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 10182-10268 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 10269-10355 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 10356-10442 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 10443-10525 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 10526-10608 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 10609-10691 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 10692-10773 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 10774-10943 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