LitCovid-sentences  

PMC:7366549 / 5924-11439 JSONTXT 11 Projects

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Id Subject Object Predicate Lexical cue
T44 0-18 Sentence denotes Material & Methods
T45 19-132 Sentence denotes This study was approved by the Institutional Animal Ethics Committee (IAEC) of ICMR-NIV, Pune (IAEC/2019/MEZ/04).
T46 133-393 Sentence denotes Permissions were also obtained from the Principal Chief Conservators of Forests (PCCF)/wildlife wardens of different States/Union Territories (UT) (Kerala, Karnataka, Tamil Nadu, Himachal Pradesh, Punjab, Gujarat, Odisha, Telangana, Chandigarh and Puducherry).
T47 394-428 Sentence denotes Study sites and sample collection:
T48 429-584 Sentence denotes Upon obtaining permission from the respective State authorities, bat-roosting sites in each State/UT were identified with the help of the forest officials.
T49 585-679 Sentence denotes Bats were trapped using mist nets and were chemically restrained using isoflurane anaesthesia.
T50 680-819 Sentence denotes Throat swabs (TS) and rectal swabs (RSs) were collected in virus transport medium (VTM) and were transported to ICMR-NIV, Pune, on dry ice.
T51 820-1111 Sentence denotes The specimens were collected from Pteropus spp. bats from Kerala, Karnataka, Chandigarh, Gujarat, Himachal Pradesh, Odisha, Puducherry, Punjab, Tamil Nadu and Telangana and Rousettus spp. bats from Kerala, Karnataka, Chandigarh, Gujarat, Odisha, Punjab and Telangana States during 2018-2019.
T52 1112-1166 Sentence denotes These bats were monitored and released after recovery.
T53 1167-1257 Sentence denotes Twelve bats that died during the trapping process were transported to ICMR-NIV on dry ice.
T54 1258-1418 Sentence denotes Necropsy of these bats was carried out in the Biosafety Level 4 (BSL-4) containment facility, and tissue specimens (intestine and kidney) collected were tested.
T55 1419-1569 Sentence denotes Detection of bat coronavirus using RT-PCR: RNA was extracted from the bat specimens using the MagMAX pathogen RNA/DNA isolation kit (Invitrogen, USA).
T56 1570-1828 Sentence denotes RT-PCR was performed using Superscript III one-step RT-PCR (Invitrogen, USA) with Platinum High-Fidelity Taq polymerase (Invitrogen, USA) using the published BtCoV-specific primers targeting the conserved region of RNA-dependent RNA polymerase (RdRp) gene21.
T57 1829-1976 Sentence denotes The amplicon of 440 bp was separated on 1.5 per cent agarose gel and visualized under VersaDoc MP 4000 ultraviolet transilluminator (Bio-Rad, USA).
T58 1978-2026 Sentence denotes Sequencing of the positive coronavirus specimens
T59 2027-2064 Sentence denotes Sanger sequencing of bat coronavirus:
T60 2065-2159 Sentence denotes The RT-PCR products were separated on 1.5 per cent agarose gel, and 440 bp bands were excised.
T61 2160-2267 Sentence denotes The excised gels were extracted and purified using a QIAQuick gel extraction kit (Qiagen, Hilden, Germany).
T62 2268-2483 Sentence denotes The purified products were quantified, and chain-terminated PCR reactions were performed using pathogen-specific forward and reverse primers21 with the BigDye Terminator 3.1 sequencing kit (Applied Biosystems, USA).
T63 2484-2562 Sentence denotes BigDye reactions were purified using the DyeEx 2.0 spin kit (Qiagen, Germany).
T64 2563-2700 Sentence denotes The purified chain-terminated reactions were sequenced using the ABI PRISM® 3100 Automated DNA Sequencer (Thermo Fisher Scientific, USA).
T65 2701-2798 Sentence denotes The sequence data generated were assembled using the Sequencer 5.1 software (Accelrys Inc., USA).
T66 2799-2851 Sentence denotes Next-generation sequencing (NGS) of bat coronavirus:
T67 2852-2908 Sentence denotes Selected bat specimens were used for RNA extraction2223.
T68 2909-2996 Sentence denotes RNA libraries were prepared and quantified by Qubit® 2.0 Fluorometer (Invitrogen, USA).
T69 2997-3154 Sentence denotes NEB NextrRNA depletion kit (New England Biolabs, USA) was used to remove host ribosomal RNA and re-quantified using Qubit® 2.0 Fluorometer (Invitrogen, USA).
T70 3155-3265 Sentence denotes In brief, the RNA library preparation involved fragmentation, adenylation, adapter ligation and amplification.
T71 3266-3494 Sentence denotes The amplified libraries were quantified using KAPA Library Quantification Kit (KapaBiosystems, Roche, Switzerland) as per the manufacturer's protocol and further loaded onto the Illumina Miniseq NGS platform (Illumina, USA)2223.
T72 3495-3639 Sentence denotes The FASTQ files generated after the completion of the run were analyzed using CLC Genomics Workbench software version 11 (CLC, Qiagen, Germany).
T73 3640-3719 Sentence denotes De novo assembly programme was used to assemble contiguous sequences (contigs).
T74 3720-3842 Sentence denotes The contigs generated were analyzed using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to identify matching sequences.
T75 3843-3957 Sentence denotes The closest matching sequence from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) was used for reference mapping.
T76 3958-4040 Sentence denotes Phylogenetic analysis of partial and complete genome sequences of bat coronavirus:
T77 4041-4273 Sentence denotes The CoV sequences retrieved from RS specimens of Rousettus spp. bats (n=4) were aligned with whole-genome sequences from GenBank using the create alignment function of the CLC genomics workbench (https://digitalinsights.qiagen.com).
T78 4274-4397 Sentence denotes Partial RdRp gene sequences (~419 bp) retrieved by Sanger sequencing, for both the bat species specimens (genomic location:
T79 4398-4507 Sentence denotes 14,701-15,120) were used to construct a phylogenetic tree along with the available RdRp sequences in GenBank.
T80 4508-4708 Sentence denotes Phylogenetic analysis was carried out using the neighbour-joining method available in MEGA v7 software24 using the Kimura 2-parameter nucleotide (nt) substitution model with 1000 bootstrap replicates.
T81 4709-5007 Sentence denotes The nt divergence for the open reading frame (ORF) 1a polyprotein (ORF 1a), ORF 1b polyprotein (ORF 1b), spike protein (S), nucleocapsid phospoprotein (N), envelope protein (E) and membrane glycoprotein (M) genes was estimated using the Kimura 2-parameter model as implemented in the MEGA software.
T82 5008-5124 Sentence denotes The sequences retrieved in the current study, along with those downloaded from GenBank, were grouped into the genus.
T83 5125-5338 Sentence denotes The viruses from the β-CoV genus were further grouped into lineages, L_A, L_B, L_C and L_D, to estimate the evolutionary divergence over the respective gene sequence pairs between groups using the MEGA software24.
T84 5339-5434 Sentence denotes The distance was estimated using a Kimura 2-parameter model with uniform rates among the sites.
T85 5435-5515 Sentence denotes The bootstrap of 500 replicates was used to estimate the variation in the model.