CORD-19-Sentences  

CORD-19:0c6ba9dd4563409e699feb39f57f540fd4c4e4f4 JSONTXT 9 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-8 Sentence denotes Abstract
TextSentencer_T1 0-8 Sentence denotes Abstract
TextSentencer_T2 9-107 Sentence denotes Porcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years.
TextSentencer_T2 9-107 Sentence denotes Porcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years.
TextSentencer_T3 108-258 Sentence denotes In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection.
TextSentencer_T3 108-258 Sentence denotes In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection.
TextSentencer_T4 259-394 Sentence denotes The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively.
TextSentencer_T4 259-394 Sentence denotes The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively.
TextSentencer_T5 395-470 Sentence denotes The entire spike (S) genes of eleven detected PDCoV strains were sequenced.
TextSentencer_T5 395-470 Sentence denotes The entire spike (S) genes of eleven detected PDCoV strains were sequenced.
TextSentencer_T6 471-659 Sentence denotes Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/ Thailand lineage.
TextSentencer_T6 471-659 Sentence denotes Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/ Thailand lineage.
TextSentencer_T7 660-789 Sentence denotes The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage.
TextSentencer_T7 660-789 Sentence denotes The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage.
TextSentencer_T8 790-996 Sentence denotes The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage.
TextSentencer_T8 790-996 Sentence denotes The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage.
TextSentencer_T9 997-1120 Sentence denotes The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234.
TextSentencer_T9 997-1120 Sentence denotes The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234.
TextSentencer_T10 1121-1247 Sentence denotes Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram.
TextSentencer_T10 1121-1247 Sentence denotes Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram.
TextSentencer_T11 1248-1418 Sentence denotes The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein.
TextSentencer_T11 1248-1418 Sentence denotes The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein.
TextSentencer_T12 1420-1671 Sentence denotes Porcine deltacoronavirus (PDCoV) is a newly emerging enteropathogenic swine coronavirus that can cause acute diarrhoea and vomiting in pigs, leading to dehydration and death in newborn piglets (Chen et al., 2015b; Jung et al., 2015; Ma et al., 2015) .
TextSentencer_T12 1420-1671 Sentence denotes Porcine deltacoronavirus (PDCoV) is a newly emerging enteropathogenic swine coronavirus that can cause acute diarrhoea and vomiting in pigs, leading to dehydration and death in newborn piglets (Chen et al., 2015b; Jung et al., 2015; Ma et al., 2015) .
TextSentencer_T13 1672-1801 Sentence denotes The clinical infection symptoms caused by PDCoV are similar to but milder than those of porcine epidemic diarrhoea virus (PEDV) .
TextSentencer_T13 1672-1801 Sentence denotes The clinical infection symptoms caused by PDCoV are similar to but milder than those of porcine epidemic diarrhoea virus (PEDV) .
TextSentencer_T14 1802-1967 Sentence denotes PDCoV is an enveloped, single-stranded, positive-sense RNA virus that belongs to the genus Deltacoronavirus within the family Coronaviridae of the order Nidovirales.
TextSentencer_T14 1802-1967 Sentence denotes PDCoV is an enveloped, single-stranded, positive-sense RNA virus that belongs to the genus Deltacoronavirus within the family Coronaviridae of the order Nidovirales.
TextSentencer_T15 1968-2114 Sentence denotes PDCoV was first discovered in Hong Kong, China, in 2012 in a territory-wide molecular epidemiology study in mammals and birds (Woo et al., 2012) .
TextSentencer_T15 1968-2114 Sentence denotes PDCoV was first discovered in Hong Kong, China, in 2012 in a territory-wide molecular epidemiology study in mammals and birds (Woo et al., 2012) .
TextSentencer_T16 2115-2424 Sentence denotes PDCoV was subsequently reported in the United States in 2014 (Castro et al., 2012; Wang et al., 2014) and then in South Korea, mainland China, Japan, Thailand, Viet Nam and Lao People's Democratic Republic (Lao PDR) (Lee and Lee, 2014; Lorsirigool et al., 2016; Saeng-Chuto et al., 2017a; Song et al., 2015) .
TextSentencer_T16 2115-2424 Sentence denotes PDCoV was subsequently reported in the United States in 2014 (Castro et al., 2012; Wang et al., 2014) and then in South Korea, mainland China, Japan, Thailand, Viet Nam and Lao People's Democratic Republic (Lao PDR) (Lee and Lee, 2014; Lorsirigool et al., 2016; Saeng-Chuto et al., 2017a; Song et al., 2015) .
TextSentencer_T17 2425-2614 Sentence denotes The coinfection of PDCoV with other enteric viral pathogens such as PEDV, rotavirus or kobuvirus are commonly reported (Mai et al., 2018; Marthaler et al., 2014a; Marthaler et al., 2014b) .
TextSentencer_T17 2425-2614 Sentence denotes The coinfection of PDCoV with other enteric viral pathogens such as PEDV, rotavirus or kobuvirus are commonly reported (Mai et al., 2018; Marthaler et al., 2014a; Marthaler et al., 2014b) .
TextSentencer_T18 2615-3153 Sentence denotes The genome of PDCoV is composed of approximately 25.4 kb nucleotides and has a genomic organization similar to other coronaviruses: a 5′ untranslated region (UTR), open reading frame 1a (ORF1a) and ORF1b encoding two overlapping polyprotein precursors; four structural protein genes encoding spike (S), envelope (E), membrane (M), and nucleocapsid (N); three accessory protein genes encoding NS6, NS7, and NS7a; and a 3' UTR and poly (A) tail (Chen et al., 2015a; Fang et al., 2017; Fang et al., 2016; Li et al., 2014; Woo et al., 2012) .
TextSentencer_T18 2615-3153 Sentence denotes The genome of PDCoV is composed of approximately 25.4 kb nucleotides and has a genomic organization similar to other coronaviruses: a 5′ untranslated region (UTR), open reading frame 1a (ORF1a) and ORF1b encoding two overlapping polyprotein precursors; four structural protein genes encoding spike (S), envelope (E), membrane (M), and nucleocapsid (N); three accessory protein genes encoding NS6, NS7, and NS7a; and a 3' UTR and poly (A) tail (Chen et al., 2015a; Fang et al., 2017; Fang et al., 2016; Li et al., 2014; Woo et al., 2012) .
TextSentencer_T19 3154-3269 Sentence denotes For coronaviruses, the function of the S protein is to recognize receptors and mediate viral entry into host cells.
TextSentencer_T19 3154-3269 Sentence denotes For coronaviruses, the function of the S protein is to recognize receptors and mediate viral entry into host cells.
TextSentencer_T20 3270-3415 Sentence denotes The S protein is composed of an N-terminal S1 subunit for receptor binding and a Cterminal S2 subunit for the fusion of host and viral membranes.
TextSentencer_T20 3270-3415 Sentence denotes The S protein is composed of an N-terminal S1 subunit for receptor binding and a Cterminal S2 subunit for the fusion of host and viral membranes.
TextSentencer_T21 3416-3718 Sentence denotes The cryo-electron microscopy structure of PDCoV S protein ectodomain (Se) without the transmembrane anchor or intracellular tail in the prefusion state (Shang et al., 2018) showed that the S1 subunit contained an N-terminal domain (S1-NTD), a C-terminal domain (S1-CTD) and connecting subdomains (SDs).
TextSentencer_T21 3416-3718 Sentence denotes The cryo-electron microscopy structure of PDCoV S protein ectodomain (Se) without the transmembrane anchor or intracellular tail in the prefusion state (Shang et al., 2018) showed that the S1 subunit contained an N-terminal domain (S1-NTD), a C-terminal domain (S1-CTD) and connecting subdomains (SDs).
TextSentencer_T22 3719-3879 Sentence denotes The S2 subunit contained two central helices (CH-N and CH-C), a hydrophobic fusion peptide (FP), two heptad repeat (HR-N and HR-C) regions and connecting loops.
TextSentencer_T22 3719-3879 Sentence denotes The S2 subunit contained two central helices (CH-N and CH-C), a hydrophobic fusion peptide (FP), two heptad repeat (HR-N and HR-C) regions and connecting loops.
TextSentencer_T23 3880-3933 Sentence denotes Between S1 and S2 are connecting SDs and a long loop.
TextSentencer_T23 3880-3933 Sentence denotes Between S1 and S2 are connecting SDs and a long loop.
TextSentencer_T24 3934-4161 Sentence denotes Because the S protein of the coronavirus is the major surface protein and the main target of the host humoural immune response, it is considered to be evolutionarily related and a focus of vaccine design (Graham et al., 2013) .
TextSentencer_T24 3934-4161 Sentence denotes Because the S protein of the coronavirus is the major surface protein and the main target of the host humoural immune response, it is considered to be evolutionarily related and a focus of vaccine design (Graham et al., 2013) .
TextSentencer_T25 4162-4482 Sentence denotes Several genetic and phylogenetic analyses using S genes or complete genomes have indicated that the global PDCoV strains separated clearly into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage (Mai et al., 2018; Saeng-Chuto et al., 2017b; Suzuki et al., 2018) .
TextSentencer_T25 4162-4482 Sentence denotes Several genetic and phylogenetic analyses using S genes or complete genomes have indicated that the global PDCoV strains separated clearly into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage (Mai et al., 2018; Saeng-Chuto et al., 2017b; Suzuki et al., 2018) .
TextSentencer_T26 4483-4704 Sentence denotes In the present study, to further investigate the epidemiology and phylogenetics of PDCoV in China, a total of 719 porcine samples from 18 provinces in China from 2016 to 2018 were simultaneously tested for PDCoV and PEDV.
TextSentencer_T26 4483-4704 Sentence denotes In the present study, to further investigate the epidemiology and phylogenetics of PDCoV in China, a total of 719 porcine samples from 18 provinces in China from 2016 to 2018 were simultaneously tested for PDCoV and PEDV.
TextSentencer_T27 4705-4802 Sentence denotes The S gene sequences of 11 PDCoV strains from PDCoV-positive samples were sequenced and analysed.
TextSentencer_T27 4705-4802 Sentence denotes The S gene sequences of 11 PDCoV strains from PDCoV-positive samples were sequenced and analysed.
TextSentencer_T28 4803-4873 Sentence denotes Phylogenetic, sequence and recombination analyses were also performed.
TextSentencer_T28 4803-4873 Sentence denotes Phylogenetic, sequence and recombination analyses were also performed.
TextSentencer_T29 4874-5044 Sentence denotes The results from this study will help to understand the prevalence of PDCoV strains in China and further provide more insights into the evolution and diversity of PDCoVs.
TextSentencer_T29 4874-5044 Sentence denotes The results from this study will help to understand the prevalence of PDCoV strains in China and further provide more insights into the evolution and diversity of PDCoVs.
TextSentencer_T30 5045-5307 Sentence denotes A total of 719 porcine samples, including faeces, fecal swabs or small intestines, were collected from sows, boars, finishers, or nursing piglets showing signs of diarrhoea in different commercial pig farms over a 27-month period (March 2016-June 2018) in China.
TextSentencer_T30 5045-5307 Sentence denotes A total of 719 porcine samples, including faeces, fecal swabs or small intestines, were collected from sows, boars, finishers, or nursing piglets showing signs of diarrhoea in different commercial pig farms over a 27-month period (March 2016-June 2018) in China.
TextSentencer_T31 5308-5356 Sentence denotes The 18 sampling provinces are shown in Fig. 1A .
TextSentencer_T31 5308-5356 Sentence denotes The 18 sampling provinces are shown in Fig. 1A .
TextSentencer_T32 5357-5521 Sentence denotes All of the samples were placed into separate clean containers with phosphate buffered saline, frozen, thawed three times, and then centrifuged for 10 min at 845 ×g.
TextSentencer_T32 5357-5521 Sentence denotes All of the samples were placed into separate clean containers with phosphate buffered saline, frozen, thawed three times, and then centrifuged for 10 min at 845 ×g.
TextSentencer_T33 5522-5608 Sentence denotes The supernatants from the 719 samples were mixed with TRIzol for viral RNA extraction.
TextSentencer_T33 5522-5608 Sentence denotes The supernatants from the 719 samples were mixed with TRIzol for viral RNA extraction.
TextSentencer_T34 5609-5705 Sentence denotes Total RNA was dissolved in RNase-free water and carefully preserved at −70°C before further use.
TextSentencer_T34 5609-5705 Sentence denotes Total RNA was dissolved in RNase-free water and carefully preserved at −70°C before further use.
TextSentencer_T35 5706-5876 Sentence denotes Synthesis of cDNA for each sample was carried out using a RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, USA) according to the manufacturer's instructions.
TextSentencer_T35 5706-5876 Sentence denotes Synthesis of cDNA for each sample was carried out using a RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, USA) according to the manufacturer's instructions.
TextSentencer_T36 5877-5936 Sentence denotes The cDNAs were screened for the presence of PDCoV and PEDV.
TextSentencer_T36 5877-5936 Sentence denotes The cDNAs were screened for the presence of PDCoV and PEDV.
TextSentencer_T37 5937-6233 Sentence denotes The detection of PDCoV by using real-time reverse transcription PCR (rRT-PCR) targeting the membrane (M) gene was performed as reported previously (Marthaler et al., 2014b) , using AceQ qPCR Probe Master Mix (Vazyme, China) and performed on Light Cycler96, the specific procedure was as followed:
TextSentencer_T37 5937-6233 Sentence denotes The detection of PDCoV by using real-time reverse transcription PCR (rRT-PCR) targeting the membrane (M) gene was performed as reported previously (Marthaler et al., 2014b) , using AceQ qPCR Probe Master Mix (Vazyme, China) and performed on Light Cycler96, the specific procedure was as followed:
TextSentencer_T38 6234-6304 Sentence denotes 5 min at 95°C, followed by 40 cycles of 15 s at 95°C and 30 s at 60°C.
TextSentencer_T38 6234-6304 Sentence denotes 5 min at 95°C, followed by 40 cycles of 15 s at 95°C and 30 s at 60°C.
TextSentencer_T39 6305-6396 Sentence denotes Primers and procedure used for detecting PEDV was as previous report (Chiou et al., 2017) .
TextSentencer_T39 6305-6396 Sentence denotes Primers and procedure used for detecting PEDV was as previous report (Chiou et al., 2017) .
TextSentencer_T40 6397-6593 Sentence denotes To obtain the complete sequence of the PDCoV S gene, three pairs of primers established previously were synthesized to amplify three DNA fragments spanning each entire S gene (Wang et al., 2014) .
TextSentencer_T40 6397-6593 Sentence denotes To obtain the complete sequence of the PDCoV S gene, three pairs of primers established previously were synthesized to amplify three DNA fragments spanning each entire S gene (Wang et al., 2014) .
TextSentencer_T41 6594-6818 Sentence denotes Phanta HS Super-Fidelity DNA Polymerase (Vazyme, China) was used and the overlapping sequences of the PCR products were sequenced (Sangon Biotech, China) and assembled into full-length S gene sequences using DNAMAN software.
TextSentencer_T41 6594-6818 Sentence denotes Phanta HS Super-Fidelity DNA Polymerase (Vazyme, China) was used and the overlapping sequences of the PCR products were sequenced (Sangon Biotech, China) and assembled into full-length S gene sequences using DNAMAN software.
TextSentencer_T42 6819-6934 Sentence denotes Nucleotide and deduced amino acid sequences of the complete S gene of PDCoVs were aligned by the Clustal W program.
TextSentencer_T42 6819-6934 Sentence denotes Nucleotide and deduced amino acid sequences of the complete S gene of PDCoVs were aligned by the Clustal W program.
TextSentencer_T43 6935-7169 Sentence denotes Phylogenetic trees were constructed using the maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 7.0) (http://www.megasoftware.net/), and bootstrap values were estimated for 1000 replicates.
TextSentencer_T43 6935-7169 Sentence denotes Phylogenetic trees were constructed using the maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 7.0) (http://www.megasoftware.net/), and bootstrap values were estimated for 1000 replicates.
TextSentencer_T44 7170-7381 Sentence denotes To characterize the genetic divergence within and between the lineages, the distances within and between lineages were calculated by the Tamura-Nei model, and bootstrap values were estimated for 1000 replicates.
TextSentencer_T44 7170-7381 Sentence denotes To characterize the genetic divergence within and between the lineages, the distances within and between lineages were calculated by the Tamura-Nei model, and bootstrap values were estimated for 1000 replicates.
TextSentencer_T45 7382-7671 Sentence denotes The significant substitutions displayed on the three-dimensional cartoon diagram of PDCoV S-e were performed with PyMOL software, the cryo-electron microscopy structure of prefusion PDCoV S-e was downloaded from the PDB protein data bank (http://www.rcsb.org/), and the PDB entry was 6B7n.
TextSentencer_T45 7382-7671 Sentence denotes The significant substitutions displayed on the three-dimensional cartoon diagram of PDCoV S-e were performed with PyMOL software, the cryo-electron microscopy structure of prefusion PDCoV S-e was downloaded from the PDB protein data bank (http://www.rcsb.org/), and the PDB entry was 6B7n.
TextSentencer_T46 7672-7858 Sentence denotes Prediction of the recombinant events within PDCoV strains was conducted using the Recombination Detection Program version 4.0 (RDP4) package with default settings (Martin et al., 2015) .
TextSentencer_T46 7672-7858 Sentence denotes Prediction of the recombinant events within PDCoV strains was conducted using the Recombination Detection Program version 4.0 (RDP4) package with default settings (Martin et al., 2015) .
TextSentencer_T47 7859-8002 Sentence denotes Six recombination detection methods, including RDP, Chimaera, BootScan, GENECONV, MaxChi and SiScan, were implemented to analyse the sequences.
TextSentencer_T47 7859-8002 Sentence denotes Six recombination detection methods, including RDP, Chimaera, BootScan, GENECONV, MaxChi and SiScan, were implemented to analyse the sequences.
TextSentencer_T48 8003-8172 Sentence denotes The criteria for determining recombination and breakpoints were a P-value < .05, and only putative recombination events detected by more than three methods were adopted.
TextSentencer_T48 8003-8172 Sentence denotes The criteria for determining recombination and breakpoints were a P-value < .05, and only putative recombination events detected by more than three methods were adopted.
TextSentencer_T49 8173-8306 Sentence denotes Eleven PDCoV S genes sequenced in this study have been deposited in GenBank under the following accession numbers: MK040445-MK040455.
TextSentencer_T49 8173-8306 Sentence denotes Eleven PDCoV S genes sequenced in this study have been deposited in GenBank under the following accession numbers: MK040445-MK040455.
TextSentencer_T50 8307-8602 Sentence denotes In total, 719 porcine samples collected from 18 provinces of China were used for PDCoV and PEDV infection detection; 94 samples were detected as PDCoV positive (13.07%), 267 samples were PEDV positive (36.72%), and 34 samples were PDCoV and PEDV copositive, yielding a coinfection rate of 4.73%.
TextSentencer_T50 8307-8602 Sentence denotes In total, 719 porcine samples collected from 18 provinces of China were used for PDCoV and PEDV infection detection; 94 samples were detected as PDCoV positive (13.07%), 267 samples were PEDV positive (36.72%), and 34 samples were PDCoV and PEDV copositive, yielding a coinfection rate of 4.73%.
TextSentencer_T51 8603-8862 Sentence denotes Eleven diarrhoea samples derived from 4 provinces of China ( Fig. 1B ) yielding low cycle threshold (lower than 25) in the rRT-PCR assay were chosen for PDCoV entire S gene sequencing, the full-length S genes were submitted to the GenBank database (Table 1 ).
TextSentencer_T51 8603-8862 Sentence denotes Eleven diarrhoea samples derived from 4 provinces of China ( Fig. 1B ) yielding low cycle threshold (lower than 25) in the rRT-PCR assay were chosen for PDCoV entire S gene sequencing, the full-length S genes were submitted to the GenBank database (Table 1 ).
TextSentencer_T52 8863-9044 Sentence denotes In the 11 detected PDCoV strains, 9 strains contained a 3480 nt length S gene with a 3-nt deletion (AAT, from 154 to 156), which is common in the majority of PDCoV strains in China.
TextSentencer_T52 8863-9044 Sentence denotes In the 11 detected PDCoV strains, 9 strains contained a 3480 nt length S gene with a 3-nt deletion (AAT, from 154 to 156), which is common in the majority of PDCoV strains in China.
TextSentencer_T53 9045-9214 Sentence denotes Another 2 strains (CH-HA1-2017 and CH-HA3-2017) had a 3483 nt length S gene, which is common in the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage.
TextSentencer_T53 9045-9214 Sentence denotes Another 2 strains (CH-HA1-2017 and CH-HA3-2017) had a 3483 nt length S gene, which is common in the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage.
TextSentencer_T54 9215-9385 Sentence denotes Phylogenetic analysis and genetic divergence of the 11 sequenced S genes were constructed together with 51 other PDCoV isolate sequences available in GenBank (Table S1) .
TextSentencer_T54 9215-9385 Sentence denotes Phylogenetic analysis and genetic divergence of the 11 sequenced S genes were constructed together with 51 other PDCoV isolate sequences available in GenBank (Table S1) .
TextSentencer_T55 9386-9455 Sentence denotes A phylogenetic tree was analysed using the maximum likelihood method.
TextSentencer_T55 9386-9455 Sentence denotes A phylogenetic tree was analysed using the maximum likelihood method.
TextSentencer_T56 9456-9779 Sentence denotes As shown in Fig. 2 , most of the global PDCoV strains could be divided into three lineages: the China (2019) To analyse the global genetic divergence of PDCoV strains, the genetic distances of the China, USA/Japan/South Korea PDCoVs and Viet Nam/Laos/Thailand lineages were calculated using the Tamura-Nei model (Table 2) .
TextSentencer_T56 9456-9779 Sentence denotes As shown in Fig. 2 , most of the global PDCoV strains could be divided into three lineages: the China (2019) To analyse the global genetic divergence of PDCoV strains, the genetic distances of the China, USA/Japan/South Korea PDCoVs and Viet Nam/Laos/Thailand lineages were calculated using the Tamura-Nei model (Table 2) .
TextSentencer_T57 9780-10186 Sentence denotes Of these three lineages, the China lineage showed the largest genetic divergence with an average distance ( ± standard error) of 0.019 ± 0.001, the Viet Nam/Laos/Thailand lineage showed a slightly less genetic divergence of 0.018 ± 0.002 than that in China lineage, and the USA/Japan/South Korea lineage showed the least genetic divergence of 0.002 ± 0.000, which was nearly one-tenth of the China lineage.
TextSentencer_T57 9780-10186 Sentence denotes Of these three lineages, the China lineage showed the largest genetic divergence with an average distance ( ± standard error) of 0.019 ± 0.001, the Viet Nam/Laos/Thailand lineage showed a slightly less genetic divergence of 0.018 ± 0.002 than that in China lineage, and the USA/Japan/South Korea lineage showed the least genetic divergence of 0.002 ± 0.000, which was nearly one-tenth of the China lineage.
TextSentencer_T58 10187-10544 Sentence denotes Among the three lineages, the genetic divergence between the China lineage and the Viet Nam/Laos/Thailand lineage was 0.037 ± 0.003, The genetic divergence between the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage was 0.036 ± 0.003, and the divergence between the China lineage and the USA/Japan/South Korea lineage was 0.017 ± 0.002.
TextSentencer_T58 10187-10544 Sentence denotes Among the three lineages, the genetic divergence between the China lineage and the Viet Nam/Laos/Thailand lineage was 0.037 ± 0.003, The genetic divergence between the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage was 0.036 ± 0.003, and the divergence between the China lineage and the USA/Japan/South Korea lineage was 0.017 ± 0.002.
TextSentencer_T59 10545-10706 Sentence denotes To further analyse the genetic divergence of the 11 sequenced China PDCoV strains, the distances of China-reported strains and sequenced strains were calculated.
TextSentencer_T59 10545-10706 Sentence denotes To further analyse the genetic divergence of the 11 sequenced China PDCoV strains, the distances of China-reported strains and sequenced strains were calculated.
TextSentencer_T60 10707-11027 Sentence denotes Compared with the reported China strains, the 11 strains showed a larger genetic divergence (0.021 > 0.016); additionally, the divergence of sequenced China strains and the USA/Japan/South Korea lineage was also greater than the divergence of reported China strains and the USA/Japan/South Korea lineage (0.021 > 0.016).
TextSentencer_T60 10707-11027 Sentence denotes Compared with the reported China strains, the 11 strains showed a larger genetic divergence (0.021 > 0.016); additionally, the divergence of sequenced China strains and the USA/Japan/South Korea lineage was also greater than the divergence of reported China strains and the USA/Japan/South Korea lineage (0.021 > 0.016).
TextSentencer_T61 11028-11477 Sentence denotes To analyse the genetic characteristics of the 11 sequenced China strains, the sequence alignment of the deduced amino acids of the S protein was compared with that of the representative reference PDCoV Using the cryo-electron microscopy structure of PDCoV S-e (residues 52-1017) (Shang et al., 2018) , these significant amino acid substitutions were displayed on a three-dimensional cartoon diagram to analyse their possible significance (Fig. 3B) .
TextSentencer_T61 11028-11477 Sentence denotes To analyse the genetic characteristics of the 11 sequenced China strains, the sequence alignment of the deduced amino acids of the S protein was compared with that of the representative reference PDCoV Using the cryo-electron microscopy structure of PDCoV S-e (residues 52-1017) (Shang et al., 2018) , these significant amino acid substitutions were displayed on a three-dimensional cartoon diagram to analyse their possible significance (Fig. 3B) .
TextSentencer_T62 11478-11699 Sentence denotes For the S1 ectodomain (residues 52-552), except for the substitution (residue 307) mapped on the S1-CTD, 11 other substitutions mapped on the S1-NTD and 3 substitutions mapped on the SDs were all located on surface loops.
TextSentencer_T62 11478-11699 Sentence denotes For the S1 ectodomain (residues 52-552), except for the substitution (residue 307) mapped on the S1-CTD, 11 other substitutions mapped on the S1-NTD and 3 substitutions mapped on the SDs were all located on surface loops.
TextSentencer_T63 11700-11790 Sentence denotes The residue 307 located on a β-sheet of S1-CTD was exposed on the surface of the S trimer.
TextSentencer_T63 11700-11790 Sentence denotes The residue 307 located on a β-sheet of S1-CTD was exposed on the surface of the S trimer.
TextSentencer_T64 11791-12139 Sentence denotes For the S2 ectodomain (residues 553-1017), 2 substitutions were located on the loop of the FP, 6 substitutions were located on the helix of CH and HR, 3 on CH-N (residues 624, 630, 639), 2 on HR-N and 1 on CH-C (residues 867), 2 substitutions (residues 557, 571) on SDs and 5 substitutions (residues 642, 666, 668, 670 and 907) on connecting loops.
TextSentencer_T64 11791-12139 Sentence denotes For the S2 ectodomain (residues 553-1017), 2 substitutions were located on the loop of the FP, 6 substitutions were located on the helix of CH and HR, 3 on CH-N (residues 624, 630, 639), 2 on HR-N and 1 on CH-C (residues 867), 2 substitutions (residues 557, 571) on SDs and 5 substitutions (residues 642, 666, 668, 670 and 907) on connecting loops.
TextSentencer_T65 12140-12358 Sentence denotes To further analyse the possible recombinant events of these 11 PDCoV strains sequenced in this study, alignments of S genes of the 11 PDCoVs along with reference sequences were analysed by six methods included in RDP4.
TextSentencer_T65 12140-12358 Sentence denotes To further analyse the possible recombinant events of these 11 PDCoV strains sequenced in this study, alignments of S genes of the 11 PDCoVs along with reference sequences were analysed by six methods included in RDP4.
TextSentencer_T66 12359-12615 Sentence denotes A significant (P < .05) recombination event was detected by five methods (RDP, Chimaera, BootScan, MaxChi and SiScan) in the CH-HA2-2017 S gene between positions 27 and 1234, with CH-HA3-2017 as the major parent and HKU15-155 as the minor parent (Fig. 4) .
TextSentencer_T66 12359-12615 Sentence denotes A significant (P < .05) recombination event was detected by five methods (RDP, Chimaera, BootScan, MaxChi and SiScan) in the CH-HA2-2017 S gene between positions 27 and 1234, with CH-HA3-2017 as the major parent and HKU15-155 as the minor parent (Fig. 4) .
TextSentencer_T67 12616-12624 Sentence denotes Fig. 2 .
TextSentencer_T67 12616-12624 Sentence denotes Fig. 2 .
TextSentencer_T68 12625-12670 Sentence denotes Phylogenetic analysis of the S gene of PDCoV.
TextSentencer_T68 12625-12670 Sentence denotes Phylogenetic analysis of the S gene of PDCoV.
TextSentencer_T69 12671-12758 Sentence denotes The tree was constructed using the maximum likelihood method in the MEGA V.7.0 program.
TextSentencer_T69 12671-12758 Sentence denotes The tree was constructed using the maximum likelihood method in the MEGA V.7.0 program.
TextSentencer_T70 12759-12859 Sentence denotes Numbers at nodes represent the percentages of 1000 bootstrap replicates (values < 50 are not shown).
TextSentencer_T70 12759-12859 Sentence denotes Numbers at nodes represent the percentages of 1000 bootstrap replicates (values < 50 are not shown).
TextSentencer_T71 12860-12932 Sentence denotes The scale bar indicates the number of nucleotide substitutions per site.
TextSentencer_T71 12860-12932 Sentence denotes The scale bar indicates the number of nucleotide substitutions per site.
TextSentencer_T72 12933-13002 Sentence denotes The 11 S genes sequenced in this study are indicated with "red dots".
TextSentencer_T72 12933-13002 Sentence denotes The 11 S genes sequenced in this study are indicated with "red dots".
TextSentencer_T73 13003-13477 Sentence denotes The reference sequences obtained from GenBank are indicated by strain name and accession number. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) Table 2 The average genetic distances within and between PDCoV lineages, which include S gene sequences of 25 China-reported PDCoVs, 20 USA/Japan/South Korea PDCoVs, 6 Viet Nam/Laos/Thailand PDCoVs and the 11 China PDCoVs sequenced in this study.
TextSentencer_T73 13003-13477 Sentence denotes The reference sequences obtained from GenBank are indicated by strain name and accession number. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) Table 2 The average genetic distances within and between PDCoV lineages, which include S gene sequences of 25 China-reported PDCoVs, 20 USA/Japan/South Korea PDCoVs, 6 Viet Nam/Laos/Thailand PDCoVs and the 11 China PDCoVs sequenced in this study.
TextSentencer_T74 13478-13580 Sentence denotes The numbers of base differences per site from averaging total sequence pairs between groups are shown.
TextSentencer_T74 13478-13580 Sentence denotes The numbers of base differences per site from averaging total sequence pairs between groups are shown.
TextSentencer_T75 13581-13752 Sentence denotes Standard error (SE) estimates are shown and were obtained by a bootstrap procedure (1000 replicates); evolutionary analyses were conducted under Tamura-Nei model in MEGA7.
TextSentencer_T75 13581-13752 Sentence denotes Standard error (SE) estimates are shown and were obtained by a bootstrap procedure (1000 replicates); evolutionary analyses were conducted under Tamura-Nei model in MEGA7.
TextSentencer_T76 13753-13766 Sentence denotes Zhang, et al.
TextSentencer_T76 13753-13766 Sentence denotes Zhang, et al.
TextSentencer_T77 13767-13821 Sentence denotes Infection, Genetics and Evolution 73 (2019) 151-158 4.
TextSentencer_T77 13767-13821 Sentence denotes Infection, Genetics and Evolution 73 (2019) 151-158 4.
TextSentencer_T78 13822-13832 Sentence denotes Discussion
TextSentencer_T78 13822-13832 Sentence denotes Discussion
TextSentencer_T79 13833-13993 Sentence denotes Since PDCoV was discovered in Hong Kong, China, in 2012, epidemiological investigations of PDCoV and other relevant enteroviruses have been reported frequently.
TextSentencer_T79 13833-13993 Sentence denotes Since PDCoV was discovered in Hong Kong, China, in 2012, epidemiological investigations of PDCoV and other relevant enteroviruses have been reported frequently.
TextSentencer_T80 13994-14240 Sentence denotes Previous studies revealed that, as a very common coinfection pathogen with PDCoV, PEDV was more prevalent and more pathogenic than PDCoV in pig diarrhoeal samples (Jang et al., 2017; Mai et al., 2018; Marthaler et al., 2014b; Song et al., 2015) .
TextSentencer_T80 13994-14240 Sentence denotes Previous studies revealed that, as a very common coinfection pathogen with PDCoV, PEDV was more prevalent and more pathogenic than PDCoV in pig diarrhoeal samples (Jang et al., 2017; Mai et al., 2018; Marthaler et al., 2014b; Song et al., 2015) .
TextSentencer_T81 14241-14526 Sentence denotes In the present study, the positive rate of PEDV (36.72%) was higher than that of PDCoV (13.07%) in the 719 porcine diarrheic samples, and this prevalence was relatively consistent with that of other studies (Ajayi et al., 2018; Hsu et al., 2018; Song et al., 2015; Wang et al., 2018) .
TextSentencer_T81 14241-14526 Sentence denotes In the present study, the positive rate of PEDV (36.72%) was higher than that of PDCoV (13.07%) in the 719 porcine diarrheic samples, and this prevalence was relatively consistent with that of other studies (Ajayi et al., 2018; Hsu et al., 2018; Song et al., 2015; Wang et al., 2018) .
TextSentencer_T82 14527-14817 Sentence denotes In the phylogenetic analysis, most of the global PDCoV strains could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage, this is consistent with previous reports (Lorsirigool et al., 2016; Saeng-Chuto et al., 2017b) .
TextSentencer_T82 14527-14817 Sentence denotes In the phylogenetic analysis, most of the global PDCoV strains could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage, this is consistent with previous reports (Lorsirigool et al., 2016; Saeng-Chuto et al., 2017b) .
TextSentencer_T83 14818-14983 Sentence denotes Three sequenced strains (CH-HA1, CH-HA2 and CH-HA3), which formed a new monophyletic branch, were most closely related to the Viet Nam/Laos/Thailand lineage strains.
TextSentencer_T83 14818-14983 Sentence denotes Three sequenced strains (CH-HA1, CH-HA2 and CH-HA3), which formed a new monophyletic branch, were most closely related to the Viet Nam/Laos/Thailand lineage strains.
TextSentencer_T84 14984-15231 Sentence denotes This is the first report of China PDCoV strains having such a close relationship with the Viet Nam/Laos/Thailand lineage and separated from the China lineage, strains collected from China normally clustered to the China lineage Liu et al., 2018) .
TextSentencer_T84 14984-15231 Sentence denotes This is the first report of China PDCoV strains having such a close relationship with the Viet Nam/Laos/Thailand lineage and separated from the China lineage, strains collected from China normally clustered to the China lineage Liu et al., 2018) .
TextSentencer_T85 15232-15333 Sentence denotes Do these strains clustered in this new monophyletic branch originate from recombination or evolution?
TextSentencer_T85 15232-15333 Sentence denotes Do these strains clustered in this new monophyletic branch originate from recombination or evolution?
TextSentencer_T86 15334-15459 Sentence denotes The recombination analysis showed that the strain CH-HA2-2017 in this special branch indeed had a possible recombinant event.
TextSentencer_T86 15334-15459 Sentence denotes The recombination analysis showed that the strain CH-HA2-2017 in this special branch indeed had a possible recombinant event.
TextSentencer_T87 15460-15622 Sentence denotes The minor parent HKU15-155 was from the China lineage, and the major parent CH-HA3-2017 was from this same new branch but not the Viet Nam/ Laos/Thailand lineage.
TextSentencer_T87 15460-15622 Sentence denotes The minor parent HKU15-155 was from the China lineage, and the major parent CH-HA3-2017 was from this same new branch but not the Viet Nam/ Laos/Thailand lineage.
TextSentencer_T88 15623-15690 Sentence denotes Is there any possibility that the major parent is recombinant also?
TextSentencer_T88 15623-15690 Sentence denotes Is there any possibility that the major parent is recombinant also?
TextSentencer_T89 15691-15765 Sentence denotes It needs to be further studied until enough PDCoV sequences are available.
TextSentencer_T89 15691-15765 Sentence denotes It needs to be further studied until enough PDCoV sequences are available.
TextSentencer_T90 15766-16260 Sentence denotes However, the global genetic divergence analysis of PDCoV showed that the relationship between the China and Viet Nam/Laos/Thailand lineages (0.037 ± 0.003) was farther than that of the China and USA/Japan/South Korea lineages (0.017 ± 0.001), this result makes the close relationship between China's new branch and the Viet Nam/Laos/Thailand lineage incomprehensible, as these three lineages originated from the same or different ancestors and need to be intensely analysed with more sequences.
TextSentencer_T90 15766-16260 Sentence denotes However, the global genetic divergence analysis of PDCoV showed that the relationship between the China and Viet Nam/Laos/Thailand lineages (0.037 ± 0.003) was farther than that of the China and USA/Japan/South Korea lineages (0.017 ± 0.001), this result makes the close relationship between China's new branch and the Viet Nam/Laos/Thailand lineage incomprehensible, as these three lineages originated from the same or different ancestors and need to be intensely analysed with more sequences.
TextSentencer_T91 16261-16473 Sentence denotes Furthermore, the greater genetic divergence (0.036 and 0.037) of the Viet Nam/Laos/Thailand lineage among three lineages suggesting that the Viet Nam/Laos/ Thailand strains may diverged from other early lineages.
TextSentencer_T91 16261-16473 Sentence denotes Furthermore, the greater genetic divergence (0.036 and 0.037) of the Viet Nam/Laos/Thailand lineage among three lineages suggesting that the Viet Nam/Laos/ Thailand strains may diverged from other early lineages.
TextSentencer_T92 16474-16718 Sentence denotes Because it has a non-swine ancestor, PDCoV may not yet be fully adapted to pigs, and it appears to continue to undergo genetic drift to become more adapted to pigs, even if pigs are considered the initial susceptible hosts (Jung et al., 2017) .
TextSentencer_T92 16474-16718 Sentence denotes Because it has a non-swine ancestor, PDCoV may not yet be fully adapted to pigs, and it appears to continue to undergo genetic drift to become more adapted to pigs, even if pigs are considered the initial susceptible hosts (Jung et al., 2017) .
TextSentencer_T93 16719-16934 Sentence denotes The S protein of the coronavirus is the main determinant of viral host range and tissue tropism; thus, substitutions in the S protein are critical for analysing the evolution, infectivity and pathogenicity of PDCoV.
TextSentencer_T93 16719-16934 Sentence denotes The S protein of the coronavirus is the main determinant of viral host range and tissue tropism; thus, substitutions in the S protein are critical for analysing the evolution, infectivity and pathogenicity of PDCoV.
TextSentencer_T94 16935-17054 Sentence denotes In the present study, significant amino acid substitutions of the S protein between global PDCoV strains were analysed.
TextSentencer_T94 16935-17054 Sentence denotes In the present study, significant amino acid substitutions of the S protein between global PDCoV strains were analysed.
TextSentencer_T95 17055-17271 Sentence denotes Although the significance of these substitutions is almost obscured currently, the three-dimensional cartoon diagram displaying gave a visual spatial location and made it possible to deduce their potential functions.
TextSentencer_T95 17055-17271 Sentence denotes Although the significance of these substitutions is almost obscured currently, the three-dimensional cartoon diagram displaying gave a visual spatial location and made it possible to deduce their potential functions.
TextSentencer_T96 17272-17591 Sentence denotes The substitutions mapped on the surface loops of S1-NTD and SDs may be associated with the connection of different S1 and S2 subunits to form the crown-like structure, the residue 307 located on a β-sheet of S1-CTD was exposed on the surface of the S trimer and may be responsible for the antigenicity of the S protein.
TextSentencer_T96 17272-17591 Sentence denotes The substitutions mapped on the surface loops of S1-NTD and SDs may be associated with the connection of different S1 and S2 subunits to form the crown-like structure, the residue 307 located on a β-sheet of S1-CTD was exposed on the surface of the S trimer and may be responsible for the antigenicity of the S protein.
TextSentencer_T97 17592-17742 Sentence denotes Thus, all of the substitutions of S1 were located on the surface of the "crown" and may be associated with receptor binding capacity and antigenicity.
TextSentencer_T97 17592-17742 Sentence denotes Thus, all of the substitutions of S1 were located on the surface of the "crown" and may be associated with receptor binding capacity and antigenicity.
TextSentencer_T98 17743-17842 Sentence denotes Similarly, substitutions of S2 may be responsible for the viral characteristics of membrane fusion.
TextSentencer_T98 17743-17842 Sentence denotes Similarly, substitutions of S2 may be responsible for the viral characteristics of membrane fusion.
TextSentencer_T99 17843-18254 Sentence denotes A previous study revealed that the non-synonymous substitutions L107Q, A698S, A551V, L670I, and I111V, which were also analysed in this study, were shared by the branches leading to Korean PDCoV isolates in 2014 and 2015 in the reconstruction of ancestral amino acid changes (Lee et al., 2016) , further implying the significance of substitutions related to the ongoing potential adaptation to the natural host.
TextSentencer_T99 17843-18254 Sentence denotes A previous study revealed that the non-synonymous substitutions L107Q, A698S, A551V, L670I, and I111V, which were also analysed in this study, were shared by the branches leading to Korean PDCoV isolates in 2014 and 2015 in the reconstruction of ancestral amino acid changes (Lee et al., 2016) , further implying the significance of substitutions related to the ongoing potential adaptation to the natural host.
TextSentencer_T100 18255-18347 Sentence denotes In summary, PDCoV strains circulating in pig farms in China may not separate evolutionarily.
TextSentencer_T100 18255-18347 Sentence denotes In summary, PDCoV strains circulating in pig farms in China may not separate evolutionarily.
TextSentencer_T101 18348-18580 Sentence denotes A new monophyletic branch of China strains closely related to the Viet Nam/Laos/Thailand lineage was detected in this study, although the ancestor or source has not been elucidated due to the limitation of available PDCoV sequences.
TextSentencer_T101 18348-18580 Sentence denotes A new monophyletic branch of China strains closely related to the Viet Nam/Laos/Thailand lineage was detected in this study, although the ancestor or source has not been elucidated due to the limitation of available PDCoV sequences.
TextSentencer_T102 18581-18757 Sentence denotes The sites and locations of significant amino acid substitutions in the PDCoV S protein were analysed, but the exact biological functions need more experiments to be elucidated.
TextSentencer_T102 18581-18757 Sentence denotes The sites and locations of significant amino acid substitutions in the PDCoV S protein were analysed, but the exact biological functions need more experiments to be elucidated.
TextSentencer_T103 18758-18990 Sentence denotes Our study provides useful insights into the molecular characteristics of prevalent China PDCoV strains and provides references for further biological research on potential functional sites of the S protein and pathogenicity studies.
TextSentencer_T103 18758-18990 Sentence denotes Our study provides useful insights into the molecular characteristics of prevalent China PDCoV strains and provides references for further biological research on potential functional sites of the S protein and pathogenicity studies.
TextSentencer_T104 18991-19101 Sentence denotes Moreover, further analysis of molecular epidemiology based on the complete genome sequence is urgently needed.
TextSentencer_T104 18991-19101 Sentence denotes Moreover, further analysis of molecular epidemiology based on the complete genome sequence is urgently needed.