LitCovid-sentences  

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Id Subject Object Predicate Lexical cue
T59 0-22 Sentence denotes THE VIRUS (SARS-CoV-2)
T60 23-164 Sentence denotes Coronaviruses are positive-sense RNA viruses having an extensive and promiscuous range of natural hosts and affect multiple systems (23, 24).
T61 165-319 Sentence denotes Coronaviruses can cause clinical diseases in humans that may extend from the common cold to more severe respiratory diseases like SARS and MERS (17, 279).
T62 320-586 Sentence denotes The recently emerging SARS-CoV-2 has wrought havoc in China and caused a pandemic situation in the worldwide population, leading to disease outbreaks that have not been controlled to date, although extensive efforts are being put in place to counter this virus (25).
T63 587-917 Sentence denotes This virus has been proposed to be designated/named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV), which determined the virus belongs to the Severe acute respiratory syndrome-related coronavirus category and found this virus is related to SARS-CoVs (26).
T64 918-1145 Sentence denotes SARS-CoV-2 is a member of the order Nidovirales, family Coronaviridae, subfamily Orthocoronavirinae, which is subdivided into four genera, viz., Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (3, 27).
T65 1146-1321 Sentence denotes The genera Alphacoronavirus and Betacoronavirus originate from bats, while Gammacoronavirus and Deltacoronavirus have evolved from bird and swine gene pools (24, 28, 29, 275).
T66 1322-1466 Sentence denotes Coronaviruses possess an unsegmented, single-stranded, positive-sense RNA genome of around 30 kb, enclosed by a 5′-cap and 3′-poly(A) tail (30).
T67 1467-1542 Sentence denotes The genome of SARS-CoV-2 is 29,891 bp long, with a G+C content of 38% (31).
T68 1543-1618 Sentence denotes These viruses are encircled with an envelope containing viral nucleocapsid.
T69 1619-1751 Sentence denotes The nucleocapsids in CoVs are arranged in helical symmetry, which reflects an atypical attribute in positive-sense RNA viruses (30).
T70 1752-1997 Sentence denotes The electron micrographs of SARS-CoV-2 revealed a diverging spherical outline with some degree of pleomorphism, virion diameters varying from 60 to 140 nm, and distinct spikes of 9 to 12 nm, giving the virus the appearance of a solar corona (3).
T71 1998-2108 Sentence denotes The CoV genome is arranged linearly as 5′-leader-UTR-replicase-structural genes (S-E-M-N)-3′ UTR-poly(A) (32).
T72 2109-2246 Sentence denotes Accessory genes, such as 3a/b, 4a/b, and the hemagglutinin-esterase gene (HE), are also seen intermingled with the structural genes (30).
T73 2247-2424 Sentence denotes SARS-CoV-2 has also been found to be arranged similarly and encodes several accessory proteins, although it lacks the HE, which is characteristic of some betacoronaviruses (31).
T74 2425-2534 Sentence denotes The positive-sense genome of CoVs serves as the mRNA and is translated to polyprotein 1a/1ab (pp1a/1ab) (33).
T75 2535-2693 Sentence denotes A replication-transcription complex (RTC) is formed in double-membrane vesicles (DMVs) by nonstructural proteins (nsps), encoded by the polyprotein gene (34).
T76 2694-2806 Sentence denotes Subsequently, the RTC synthesizes a nested set of subgenomic RNAs (sgRNAs) via discontinuous transcription (35).
T77 2807-2934 Sentence denotes Based on molecular characterization, SARS-CoV-2 is considered a new Betacoronavirus belonging to the subgenus Sarbecovirus (3).
T78 2935-3038 Sentence denotes A few other critical zoonotic viruses (MERS-related CoV and SARS-related CoV) belong to the same genus.
T79 3039-3222 Sentence denotes However, SARS-CoV-2 was identified as a distinct virus based on the percent identity with other Betacoronavirus; conserved open reading frame 1a/b (ORF1a/b) is below 90% identity (3).
T80 3223-3399 Sentence denotes An overall 80% nucleotide identity was observed between SARS-CoV-2 and the original SARS-CoV, along with 89% identity with ZC45 and ZXC21 SARS-related CoVs of bats (2, 31, 36).
T81 3400-3521 Sentence denotes In addition, 82% identity has been observed between SARS-CoV-2 and human SARS-CoV Tor2 and human SARS-CoV BJ01 2003 (31).
T82 3522-3635 Sentence denotes A sequence identity of only 51.8% was observed between MERS-related CoV and the recently emerged SARS-CoV-2 (37).
T83 3636-3746 Sentence denotes Phylogenetic analysis of the structural genes also revealed that SARS-CoV-2 is closer to bat SARS-related CoV.
T84 3747-3894 Sentence denotes Therefore, SARS-CoV-2 might have originated from bats, while other amplifier hosts might have played a role in disease transmission to humans (31).
T85 3895-4007 Sentence denotes Of note, the other two zoonotic CoVs (MERS-related CoV and SARS-related CoV) also originated from bats (38, 39).
T86 4008-4109 Sentence denotes Nevertheless, for SARS and MERS, civet cat and camels, respectively, act as amplifier hosts (40, 41).
T87 4110-4166 Sentence denotes Coronavirus genomes and subgenomes encode six ORFs (31).
T88 4167-4241 Sentence denotes The majority of the 5′ end is occupied by ORF1a/b, which produces 16 nsps.
T89 4242-4364 Sentence denotes The two polyproteins, pp1a and pp1ab, are initially produced from ORF1a/b by a −1 frameshift between ORF1a and ORF1b (32).
T90 4365-4533 Sentence denotes The virus-encoded proteases cleave polyproteins into individual nsps (main protease [Mpro], chymotrypsin-like protease [3CLpro], and papain-like proteases [PLPs]) (42).
T91 4534-4625 Sentence denotes SARS-CoV-2 also encodes these nsps, and their functions have been elucidated recently (31).
T92 4626-4855 Sentence denotes Remarkably, a difference between SARS-CoV-2 and other CoVs is the identification of a novel short putative protein within the ORF3 band, a secreted protein with an alpha helix and beta-sheet with six strands encoded by ORF8 (31).
T93 4856-5014 Sentence denotes Coronaviruses encode four major structural proteins, namely, spike (S), membrane (M), envelope (E), and nucleocapsid (N), which are described in detail below.
T94 5016-5030 Sentence denotes S Glycoprotein
T95 5031-5117 Sentence denotes Coronavirus S protein is a large, multifunctional class I viral transmembrane protein.
T96 5118-5284 Sentence denotes The size of this abundant S protein varies from 1,160 amino acids (IBV, infectious bronchitis virus, in poultry) to 1,400 amino acids (FCoV, feline coronavirus) (43).
T97 5285-5380 Sentence denotes It lies in a trimer on the virion surface, giving the virion a corona or crown-like appearance.
T98 5381-5534 Sentence denotes Functionally it is required for the entry of the infectious virion particles into the cell through interaction with various host cellular receptors (44).
T99 5535-5637 Sentence denotes Furthermore, it acts as a critical factor for tissue tropism and the determination of host range (45).
T100 5638-5756 Sentence denotes Notably, S protein is one of the vital immunodominant proteins of CoVs capable of inducing host immune responses (45).
T101 5757-5873 Sentence denotes The ectodomains in all CoVs S proteins have similar domain organizations, divided into two subunits, S1 and S2 (43).
T102 5874-5971 Sentence denotes The first one, S1, helps in host receptor binding, while the second one, S2, accounts for fusion.
T103 5972-6092 Sentence denotes The former (S1) is further divided into two subdomains, namely, the N-terminal domain (NTD) and C-terminal domain (CTD).
T104 6093-6208 Sentence denotes Both of these subdomains act as receptor-binding domains, interacting efficiently with various host receptors (45).
T105 6209-6262 Sentence denotes The S1 CTD contains the receptor-binding motif (RBM).
T106 6263-6366 Sentence denotes In each coronavirus spike protein, the trimeric S1 locates itself on top of the trimeric S2 stalk (45).
T107 6367-6508 Sentence denotes Recently, structural analyses of the S proteins of COVID-19 have revealed 27 amino acid substitutions within a 1,273-amino-acid stretch (16).
T108 6509-6649 Sentence denotes Six substitutions are located in the RBD (amino acids 357 to 528), while four substitutions are in the RBM at the CTD of the S1 domain (16).
T109 6650-6797 Sentence denotes Of note, no amino acid change is seen in the RBM, which binds directly to the angiotensin-converting enzyme-2 (ACE2) receptor in SARS-CoV (16, 46).
T110 6798-6905 Sentence denotes At present, the main emphasis is knowing how many differences would be required to change the host tropism.
T111 6906-7036 Sentence denotes Sequence comparison revealed 17 nonsynonymous changes between the early sequence of SARS-CoV-2 and the later isolates of SARS-CoV.
T112 7037-7229 Sentence denotes The changes were found scattered over the genome of the virus, with nine substitutions in ORF1ab, ORF8 (4 substitutions), the spike gene (3 substitutions), and ORF7a (single substitution) (4).
T113 7230-7394 Sentence denotes Notably, the same nonsynonymous changes were found in a familial cluster, indicating that the viral evolution happened during person-to-person transmission (4, 47).
T114 7395-7527 Sentence denotes Such adaptive evolution events are frequent and constitute a constantly ongoing process once the virus spreads among new hosts (47).
T115 7528-7732 Sentence denotes Even though no functional changes occur in the virus associated with this adaptive evolution, close monitoring of the viral mutations that occur during subsequent human-to-human transmission is warranted.
T116 7734-7743 Sentence denotes M Protein
T117 7744-7876 Sentence denotes The M protein is the most abundant viral protein present in the virion particle, giving a definite shape to the viral envelope (48).
T118 7877-7967 Sentence denotes It binds to the nucleocapsid and acts as a central organizer of coronavirus assembly (49).
T119 7968-8105 Sentence denotes Coronavirus M proteins are highly diverse in amino acid contents but maintain overall structural similarity within different genera (50).
T120 8106-8257 Sentence denotes The M protein has three transmembrane domains, flanked by a short amino terminus outside the virion and a long carboxy terminus inside the virion (50).
T121 8258-8319 Sentence denotes Overall, the viral scaffold is maintained by M-M interaction.
T122 8320-8432 Sentence denotes Of note, the M protein of SARS-CoV-2 does not have an amino acid substitution compared to that of SARS-CoV (16).
T123 8434-8443 Sentence denotes E Protein
T124 8444-8543 Sentence denotes The coronavirus E protein is the most enigmatic and smallest of the major structural proteins (51).
T125 8544-8637 Sentence denotes It plays a multifunctional role in the pathogenesis, assembly, and release of the virus (52).
T126 8638-8726 Sentence denotes It is a small integral membrane polypeptide that acts as a viroporin (ion channel) (53).
T127 8727-8870 Sentence denotes The inactivation or absence of this protein is related to the altered virulence of coronaviruses due to changes in morphology and tropism (54).
T128 8871-9038 Sentence denotes The E protein consists of three domains, namely, a short hydrophilic amino terminal, a large hydrophobic transmembrane domain, and an efficient C-terminal domain (51).
T129 9039-9136 Sentence denotes The SARS-CoV-2 E protein reveals a similar amino acid constitution without any substitution (16).
T130 9138-9147 Sentence denotes N Protein
T131 9148-9193 Sentence denotes The N protein of coronavirus is multipurpose.
T132 9194-9408 Sentence denotes Among several functions, it plays a role in complex formation with the viral genome, facilitates M protein interaction needed during virion assembly, and enhances the transcription efficiency of the virus (55, 56).
T133 9409-9545 Sentence denotes It contains three highly conserved and distinct domains, namely, an NTD, an RNA-binding domain or a linker region (LKR), and a CTD (57).
T134 9546-9693 Sentence denotes The NTD binds with the 3′ end of the viral genome, perhaps via electrostatic interactions, and is highly diverged both in length and sequence (58).
T135 9694-9800 Sentence denotes The charged LKR is serine and arginine rich and is also known as the SR (serine and arginine) domain (59).
T136 9801-9919 Sentence denotes The LKR is capable of direct interaction with in vitro RNA interaction and is responsible for cell signaling (60, 61).
T137 9920-10048 Sentence denotes It also modulates the antiviral response of the host by working as an antagonist for interferon (IFN) and RNA interference (62).
T138 10049-10306 Sentence denotes Compared to that of SARS-CoV, the N protein of SARS-CoV-2 possess five amino acid mutations, where two are in the intrinsically dispersed region (IDR; positions 25 and 26), one each in the NTD (position 103), LKR (position 217), and CTD (position 334) (16).
T139 10308-10335 Sentence denotes nsps and Accessory Proteins
T140 10336-10523 Sentence denotes Besides the important structural proteins, the SARS-CoV-2 genome contains 15 nsps, nsp1 to nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b, and ORF14) (16).
T141 10524-10590 Sentence denotes All these proteins play a specific role in viral replication (27).
T142 10591-10721 Sentence denotes Unlike the accessory proteins of SARS-CoV, SARS-CoV-2 does not contain 8a protein and has a longer 8b and shorter 3b protein (16).
T143 10722-10901 Sentence denotes The nsp7, nsp13, envelope, matrix, and p6 and 8b accessory proteins have not been detected with any amino acid substitutions compared to the sequences of other coronaviruses (16).
T144 10902-10958 Sentence denotes The virus structure of SARS-CoV-2 is depicted in Fig. 2.
T145 10959-10993 Sentence denotes FIG 2 SARS-CoV-2 virus structure.
T146 10995-11038 Sentence denotes SARS-CoV-2 Spike Glycoprotein Gene Analysis
T147 11040-11077 Sentence denotes Sequence percent similarity analysis.
T148 11078-11254 Sentence denotes We assessed the nucleotide percent similarity using the MegAlign software program, where the similarity between the novel SARS-CoV-2 isolates was in the range of 99.4% to 100%.
T149 11255-11442 Sentence denotes Among the other Serbecovirus CoV sequences, the novel SARS-CoV-2 sequences revealed the highest similarity to bat-SL-CoV, with nucleotide percent identity ranges between 88.12 and 89.65%.
T150 11443-11551 Sentence denotes Meanwhile, earlier reported SARS-CoVs showed 70.6 to 74.9% similarity to SARS-CoV-2 at the nucleotide level.
T151 11552-11764 Sentence denotes Further, the nucleotide percent similarity was 55.4%, 45.5% to 47.9%, 46.2% to 46.6%, and 45.0% to 46.3% to the other four subgenera, namely, Hibecovirus, Nobecovirus, Merbecovirus, and Embecovirus, respectively.
T152 11765-11925 Sentence denotes The percent similarity index of current outbreak isolates indicates a close relationship between SARS-CoV-2 isolates and bat-SL-CoV, indicating a common origin.
T153 11926-12216 Sentence denotes However, particular pieces of evidence based on further complete genomic analysis of current isolates are necessary to draw any conclusions, although it was ascertained that the current novel SARS-CoV-2 isolates belong to the subgenus Sarbecovirus in the diverse range of betacoronaviruses.
T154 12217-12367 Sentence denotes Their possible ancestor was hypothesized to be from bat CoV strains, wherein bats might have played a crucial role in harboring this class of viruses.
T155 12369-12399 Sentence denotes SplitsTree phylogeny analysis.
T156 12400-12561 Sentence denotes In the unrooted phylogenetic tree of different betacoronaviruses based on the S protein, virus sequences from different subgenera grouped into separate clusters.
T157 12562-12687 Sentence denotes SARS-CoV-2 sequences from Wuhan and other countries exhibited a close relationship and appeared in a single cluster (Fig. 1).
T158 12688-12869 Sentence denotes The CoVs from the subgenus Sarbecovirus appeared jointly in SplitsTree and divided into three subclusters, namely, SARS-CoV-2, bat-SARS-like-CoV (bat-SL-CoV), and SARS-CoV (Fig. 1).
T159 12870-13135 Sentence denotes In the case of other subgenera, like Merbecovirus, all of the sequences grouped in a single cluster, whereas in Embecovirus, different species, comprised of canine respiratory CoVs, bovine CoVs, equine CoVs, and human CoV strain (OC43), grouped in a common cluster.
T160 13136-13284 Sentence denotes Isolates in the subgenera Nobecovorus and Hibecovirus were found to be placed separately away from other reported SARS-CoVs but shared a bat origin.