LitCovid-sentences  

PMC:7366549 / 2737-26331 JSONTXT 12 Projects

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Id Subject Object Predicate Lexical cue
T26 0-82 Sentence denotes A large number of emerging infectious diseases are known to be zoonotic in origin.
T27 83-160 Sentence denotes In the last two decades, many viruses have been identified from bat species1.
T28 161-304 Sentence denotes Bats have been recognized as the natural reservoirs of a variety of pathogenic viruses such as Rabies, Hendra, Marburg, Nipah and Ebola virus2.
T29 305-382 Sentence denotes Bats are known to harbour coronaviruses (CoVs) and serve as their reservoirs.
T30 383-515 Sentence denotes Alpha-CoV (α-CoV) and beta-CoV (β-CoV) have been detected in bats in Asia, Europe, Africa, North and South America and Australasia3.
T31 516-622 Sentence denotes In the last two decades, bat CoVs (BtCoVs) garnered considerable attention as potential human pathogens45.
T32 623-822 Sentence denotes Severe acute respiratory syndrome (SARS)-CoV-2 causing the current pandemic [CoV disease 2019 (COVID-19)] is also a member of the same genus and found to be similar to bat-derived CoV strain RATG136.
T33 823-997 Sentence denotes SARS-CoV-2 is reported to be 96 per cent identical to BtCoV at the whole genome level, and related viruses were identified in the previously sampled bat population in China7.
T34 998-1185 Sentence denotes CoVs are enveloped, single-stranded, positive-sense RNA viruses with a comparatively large genome size of 26 to 32 kb, classified under the family Coronaviridae in the order Nidovirales8.
T35 1186-1470 Sentence denotes According to the International Committee on Taxonomy of Viruses (ICTV), they are classified into four genera, namely, α-CoV, β-CoV, γ-CoV and δ-CoV)9. β-CoVs are further classified into four different lineages [lineage A (L_A), lineage B (L_B), lineage C (L_C) and lineage D (L_D)]10.
T36 1471-1550 Sentence denotes Most of the human CoVs are either zoonotic in origin or circulate in animals11.
T37 1551-1709 Sentence denotes CoVs can cause a wide range of infections, including respiratory tract infections, gastroenteritis, hepatitis and encephalomyelitis in their respective hosts.
T38 1710-1836 Sentence denotes It is believed that many of the currently circulating α-CoVs and β-CoVs of mammals have evolutionary links to CoVs from bats1.
T39 1837-2131 Sentence denotes India has a diverse population of bats; around 117 species of bats have been recorded, with around 100 subspecies coming under 39 genera belonging to eight families (Pteropodidae, Rhinolophidae, Hipposideridae, Megadermatidae, Rhinopomatidae, Emballonuridae, Molossidae and Vespertilionidae)12.
T40 2132-2397 Sentence denotes The Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) at Pune, India, has detected several viruses in bats, including the Nipah virus in Pteropus medius, Malsoor virus, Tioman virus and a novel adenovirus in Rousettus leschenaultii131415.
T41 2398-2628 Sentence denotes Nipah viral RNA antibodies could be detected in Pteropus bats from many States of India, and the possible link of transmission from bats could be established during the Nipah outbreak which occurred in Kerala in 2018 and 20191617.
T42 2629-2871 Sentence denotes The use of conventional polymerase chain reaction/reverse transcription-polymerase chain reaction (PCR/RT-PCR), as well as metagenomics and next-generation sequencing (NGS) technologies, has led to the discovery of many novel viruses in bats.
T43 2872-3185 Sentence denotes The identification of new CoVs in bats in several neighbouring Asian countries such as China3, Sri Lanka18 and Singapore1920 and the growing threats of novel CoV diseases such as COVID-19 led us to investigate Pteropus and Rousettus bats commonly found in India, for identification and characterization of BtCoVs.
T44 3187-3205 Sentence denotes Material & Methods
T45 3206-3319 Sentence denotes This study was approved by the Institutional Animal Ethics Committee (IAEC) of ICMR-NIV, Pune (IAEC/2019/MEZ/04).
T46 3320-3580 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 3581-3615 Sentence denotes Study sites and sample collection:
T48 3616-3771 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 3772-3866 Sentence denotes Bats were trapped using mist nets and were chemically restrained using isoflurane anaesthesia.
T50 3867-4006 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 4007-4298 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 4299-4353 Sentence denotes These bats were monitored and released after recovery.
T53 4354-4444 Sentence denotes Twelve bats that died during the trapping process were transported to ICMR-NIV on dry ice.
T54 4445-4605 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 4606-4756 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 4757-5015 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 5016-5163 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 5165-5213 Sentence denotes Sequencing of the positive coronavirus specimens
T59 5214-5251 Sentence denotes Sanger sequencing of bat coronavirus:
T60 5252-5346 Sentence denotes The RT-PCR products were separated on 1.5 per cent agarose gel, and 440 bp bands were excised.
T61 5347-5454 Sentence denotes The excised gels were extracted and purified using a QIAQuick gel extraction kit (Qiagen, Hilden, Germany).
T62 5455-5670 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 5671-5749 Sentence denotes BigDye reactions were purified using the DyeEx 2.0 spin kit (Qiagen, Germany).
T64 5750-5887 Sentence denotes The purified chain-terminated reactions were sequenced using the ABI PRISM® 3100 Automated DNA Sequencer (Thermo Fisher Scientific, USA).
T65 5888-5985 Sentence denotes The sequence data generated were assembled using the Sequencer 5.1 software (Accelrys Inc., USA).
T66 5986-6038 Sentence denotes Next-generation sequencing (NGS) of bat coronavirus:
T67 6039-6095 Sentence denotes Selected bat specimens were used for RNA extraction2223.
T68 6096-6183 Sentence denotes RNA libraries were prepared and quantified by Qubit® 2.0 Fluorometer (Invitrogen, USA).
T69 6184-6341 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 6342-6452 Sentence denotes In brief, the RNA library preparation involved fragmentation, adenylation, adapter ligation and amplification.
T71 6453-6681 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 6682-6826 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 6827-6906 Sentence denotes De novo assembly programme was used to assemble contiguous sequences (contigs).
T74 6907-7029 Sentence denotes The contigs generated were analyzed using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to identify matching sequences.
T75 7030-7144 Sentence denotes The closest matching sequence from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) was used for reference mapping.
T76 7145-7227 Sentence denotes Phylogenetic analysis of partial and complete genome sequences of bat coronavirus:
T77 7228-7460 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 7461-7584 Sentence denotes Partial RdRp gene sequences (~419 bp) retrieved by Sanger sequencing, for both the bat species specimens (genomic location:
T79 7585-7694 Sentence denotes 14,701-15,120) were used to construct a phylogenetic tree along with the available RdRp sequences in GenBank.
T80 7695-7895 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 7896-8194 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 8195-8311 Sentence denotes The sequences retrieved in the current study, along with those downloaded from GenBank, were grouped into the genus.
T83 8312-8525 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 8526-8621 Sentence denotes The distance was estimated using a Kimura 2-parameter model with uniform rates among the sites.
T85 8622-8702 Sentence denotes The bootstrap of 500 replicates was used to estimate the variation in the model.
T86 8704-8711 Sentence denotes Results
T87 8712-8874 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 8875-9093 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 9094-9170 Sentence denotes During the trapping process, 12 (8 Rousettus and 4 Pteropus spp.) bats died.
T90 9171-9325 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 9326-9378 Sentence denotes Detection of bat coronavirus using RdRp gene RT-PCR:
T92 9379-9463 Sentence denotes Four of the 78 RS of Rousettus spp. bats screened for the BtCoV were found positive.
T93 9464-9517 Sentence denotes All the positive RS samples belonged to Kerala State.
T94 9518-9596 Sentence denotes Intestinal specimens of two bats were also found to be positive for the BtCoV.
T95 9597-9699 Sentence denotes One bat (MCL-19-Bat-606), from Kerala, was tested positive in both the intestinal specimen and the RS.
T96 9700-9800 Sentence denotes The second bat (MCL-20-Bat-76), from Karnataka, was tested positive only in the intestinal specimen.
T97 9801-9866 Sentence denotes Altogether, five Rousettus spp. bats were positive for the BtCoV.
T98 9867-9944 Sentence denotes All TS specimens from Rousettus spp. were found negative for BtCoV (Table I).
T99 9945-10139 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 10140-10259 Sentence denotes Place of collection Number of positive/number tested (%) for different bat species for BtCoV RdRp gene-specific RT-PCR
T101 10260-10297 Sentence denotes Pteropus bats (%) Rousettus bats (%)
T102 10298-10352 Sentence denotes Rectal swabs Throat swabs Rectal swabs Throat swabs
T103 10353-10412 Sentence denotes Kerala 12/217 (5.53) 0/21 (0.00) 4/42 (9.52) 0/4 (0.00)
T104 10413-10463 Sentence denotes Karnataka 0/78 (0.00) NT 0/4 (0.00) 0/4 (0.00)
T105 10464-10515 Sentence denotes Chandigarh 0/27 (0.00) NT 0/6 (0.00) 0/6 (0.00)
T106 10516-10566 Sentence denotes Gujarat 0/30 (0.00) NT 0/18 (0.00) 0/18 (0.00)
T107 10567-10614 Sentence denotes Odisha 0/30 (0.00) NT 0/2 (0.00) 0/2 (0.00)
T108 10615-10662 Sentence denotes Punjab 0/14 (0.00) NT 0/2 (0.00) 0/2 (0.00)
T109 10663-10713 Sentence denotes Telangana 0/30 (0.00) NT 0/4 (0.00) 0/4 (0.00)
T110 10714-10763 Sentence denotes Himachal Pradesh 2/29 (6.89) 0/6 (0.00) NA NA
T111 10764-10809 Sentence denotes Puducherry 6/23 (26.09) 0/10 (0.00) NA NA
T112 10810-10853 Sentence denotes Tamil Nadu 1/30 (3.33) 0/5 (0.00) NA NA
T113 10854-10906 Sentence denotes 21/508 (4.13) 0/42 (0.00) 4/78 (5.13) 0/40 (0.00)
T114 10907-11069 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 11070-11179 Sentence denotes These positive bats belonged to Kerala (n=12), Himachal Pradesh (n=2), Puducherry (n=6) and Tamil Nadu (n=1).
T116 11180-11245 Sentence denotes The TS specimens of the same bats were tested negative for BtCoV.
T117 11246-11344 Sentence denotes The TS specimens of RS-negative (n=42) bats were also screened and found to be negative (Table I).
T118 11345-11406 Sentence denotes A total of 25 bats from both the species were found positive.
T119 11408-11456 Sentence denotes Sequencing of the positive coronavirus specimens
T120 11457-11494 Sentence denotes Sanger sequencing of bat coronavirus:
T121 11495-11637 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 11638-11759 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 11760-11906 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 11907-12016 Sentence denotes Sanger's sequencing protocol led to retrieval of eight partial RdRp sequences which belonged to Pteropus spp.
T125 12017-12089 Sentence denotes These bats were collected from Kerala (n=5) and Tamil Nadu (n=3) States.
T126 12090-12229 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 12230-12347 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 12348-12482 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 12483-12599 Sentence denotes The remaining four partial RdRp sequences had >97 per cent SI with CoV PREDICT_CoV-17/PB072 (AN: KX284942.1, Nepal).
T130 12600-12794 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 12795-12989 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 12990-13137 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 13138-13408 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 13409-13599 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 13600-13729 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 13730-13839 Sentence denotes The details of the genome recovered reads mapped and the per cent of reads mapped are summarized in Table II.
T137 13840-13958 Sentence denotes Table II Details of the genome recovered reads mapped and the per cent of reads mapped from the Rousettus bat samples
T138 13959-14068 Sentence denotes Sample details Sample type Virus retrieved Relevant reads Per cent of reads Per cent of genome recovered
T139 14069-14143 Sentence denotes MCL-20-Bat-76 Kidney Coronavirus BtRt-BetaCoV/GX2018 1632 0.015 94.39
T140 14144-14187 Sentence denotes Intestine BtCoV HKU9-1 4499 0.056 95.75
T141 14188-14270 Sentence denotes MCL-19-Bat-606 Rectal swab Coronavirus BtRt-BetaCoV/GX2018 13,973 0.114 99.53
T142 14271-14423 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 14424-14558 Sentence denotes A neighbour-joining tree was generated using the partial RdRp region sequences derived from Pteropus and Rousettus spp. bat specimens.
T144 14559-14657 Sentence denotes It was observed that all the BtCoV sequences were clustered within the L_D sequences of beta CoVs.
T145 14658-14769 Sentence denotes A distinct subclustering of the sequences retrieved from Pteropus and Rousettus spp. bats is shown in Figure 1.
T146 14770-14909 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 14910-15141 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 15142-15252 Sentence denotes Fig. 1 Neighbour-joining tree for the RNA-dependent RNA polymerase (RdRp) partial sequence (genomic location:
T149 15253-15301 Sentence denotes 14,701-15,120) generated from Sanger sequencing.
T150 15302-15386 Sentence denotes The tree was constructed using the RdRp sequence available in the GenBank sequences.
T151 15387-15468 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T152 15469-15580 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T153 15581-15723 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 15724-15824 Sentence denotes These sequences were also clustered within L_D of β-CoVs as observed for partial RdRp sequence tree.
T155 15825-15940 Sentence denotes These complete genome sequences were grouped into gene pairs to identify the gene with higher and lower divergence.
T156 15941-16015 Sentence denotes The complete genomes of the Indian BtCoV sequences were grouped under L_D.
T157 16016-16194 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 16195-16283 Sentence denotes E gene sequences had larger divergence within the β-CoV genus ranging from 2.18 to 0.94.
T159 16284-16387 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 16388-16462 Sentence denotes N gene has an overall higher divergence among different lineages (ranging:
T161 16463-16474 Sentence denotes 2.08-0.75).
T162 16475-16647 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 16648-16721 Sentence denotes In contrast, the ORF 1b was less divergent across the genera (Table III).
T164 16722-16777 Sentence denotes Fig. 2 Phylogenetic tree for the complete genome tree:
T165 16778-16902 Sentence denotes A neighbour-joining tree was generated using the representative complete genome sequence available in the GenBank sequences.
T166 16903-16984 Sentence denotes Kimura 2-parameter model was used as the substitution model to generate the tree.
T167 16985-17096 Sentence denotes A bootstrap replication of 1000 cycles was performed to generate the tree to assess the statistical robustness.
T168 17097-17220 Sentence denotes Table III Evolutionary divergence for ORF 1b, S, N and M genes for the retrieved sequences with other reference sequences.
T169 17221-17410 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 17411-17507 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 17508-17594 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 17595-17681 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 17682-17768 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 17769-17851 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 17852-17934 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 17935-18017 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 18018-18099 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 18100-18196 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 18197-18283 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 18284-18370 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 18371-18457 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 18458-18540 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 18541-18623 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 18624-18706 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 18707-18788 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 18789-18885 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 18886-18972 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 18973-19059 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 19060-19146 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 19147-19229 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 19230-19312 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 19313-19395 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 19396-19477 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 19478-19647 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
T195 19649-19659 Sentence denotes Discussion
T196 19660-19842 Sentence denotes As per the available information, the BtCoV causing human infection belongs to α- and β-CoV genera of the Coronaviridae family. β-CoV genus has five strains known to infect humans25.
T197 19843-20002 Sentence denotes The two human-infecting strains (NL63 and 229E) from α-CoV genus which cause mild-to-moderate respiratory infections are believed to have originated in bats25.
T198 20003-20136 Sentence denotes Two members of the β-CoV genus (HCoV-OC43 and HCoV-HKU1) are known to cause the common cold and lower respiratory tract infections26.
T199 20137-20232 Sentence denotes The other three are now shown to be pathogenic to humans (SARS-CoV-1, MERS-CoV and SARS-CoV-2).
T200 20233-20322 Sentence denotes The SARS-CoV-1 and SARS-CoV-2 belong to L_B and MERS CoV belongs to L_C of β-CoV genus27.
T201 20323-20435 Sentence denotes The phylogenetic analysis for the partial RdRp region revealed the presence of distinct BtCoVs in both the bats.
T202 20436-20518 Sentence denotes The genomic sequences retrieved from the Indian sequences form a distinct cluster.
T203 20519-20709 Sentence denotes The three CoV_BtRtBetaCoV/GX2018 sequences retrieved from the Indian Rousettus bats were 5.8-6.7 per cent different from the reference sequence, which was retrieved from Rhinolophus affinis.
T204 20710-20825 Sentence denotes The two CoV_BtRtBetaCoV/GX2018 sequences retrieved from different bats were 1.2 per cent different from each other.
T205 20826-20953 Sentence denotes The effect of host influence on the nt usage of the virus cannot be denied; however, it needs to be explored further in detail.
T206 20954-21071 Sentence denotes Bats are reservoirs for viruses with human pathogenic potential2829, and are known to harbour a broad range of CoVs1.
T207 21072-21260 Sentence denotes The global distribution of bats, along with the different types of cell receptors present within them, favours virus replication, and is a possible link to their intraspecies transmission.
T208 21261-21433 Sentence denotes The interspecies spill-over of a BtCoV to humans is thought to occur through an intermediate host, in which the virus replicates through yet completely unidentified routes.
T209 21434-21555 Sentence denotes In India, regions of the Western Ghats, particularly in Kerala, are reported to have habitat for diverse bat populations.
T210 21556-21688 Sentence denotes The reports of pathogenic human viruses from bat specimens demand enhanced methods to monitor human exposure to various bat species.
T211 21689-21828 Sentence denotes Investigations in unexplored regions/States should be focused on gaining further insights into CoV diversity within Indian bat populations.
T212 21829-21941 Sentence denotes Earlier, we had reported the presence of pathogenic viruses such as the Nipah virus in Pteropus bats in India16.
T213 21942-22108 Sentence denotes In the present scenario of changing demography and ecological manipulations, it is challenging to have checks on the encounters of bats with other animals and humans.
T214 22109-22295 Sentence denotes Therefore, active and continuous surveillance remains crucial for outbreak alerts for bat-associated viral agents with epidemic potential, which would be helpful in timely interventions.
T215 22296-22570 Sentence denotes Although CoVs in the subfamily Coronavirinae do not usually produce clinical symptoms in their natural hosts (bats), accidental transmission of these viruses to humans and other animals may result in respiratory, enteric, hepatic or neurologic diseases of variable severity.
T216 22571-22644 Sentence denotes It is still not understood as to why only certain CoVs can infect people.
T217 22645-22718 Sentence denotes There is a need of proactive surveillance of zoonotic infections in bats.
T218 22719-22935 Sentence denotes Detection and identifications of such aetiological agents will provide leads for the development of diagnostic along with preparedness and readiness to deal with such emergent viruses thereby quickly containing them.
T219 22936-23124 Sentence denotes The detection and identification of such viruses from bats also recommends cross-sectional antibody surveys (human and domestic animals) in localities where the viruses have been detected.
T220 23125-23227 Sentence denotes Similarly, if epidemiological situation demands, evidence-based surveillance should also be conducted.
T221 23228-23395 Sentence denotes There is a need of developing strong mechanisms for working jointly with various stakeholders such as wildlife, poultry, animal husbandry and human health departments.
T222 23396-23487 Sentence denotes In conclusion, our study showed detection of pathogenic CoVs in two species of Indian bats.
T223 23488-23594 Sentence denotes Continuous active surveillance is required to identify the emerging novel viruses with epidemic potential.