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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sample-MedDRA

{"project":"LitCovid-sample-MedDRA","denotations":[{"id":"T6","span":{"begin":788,"end":800},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T7","span":{"begin":1113,"end":1129},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T8","span":{"begin":1965,"end":1987},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T9","span":{"begin":2762,"end":2787},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T10","span":{"begin":2789,"end":2792},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T11","span":{"begin":3720,"end":3729},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"}],"attributes":[{"id":"A6","pred":"meddra_id","subj":"T6","obj":"http://purl.bioontology.org/ontology/MEDDRA/10062026"},{"id":"A7","pred":"meddra_id","subj":"T7","obj":"http://purl.bioontology.org/ontology/MEDDRA/10025251"},{"id":"A8","pred":"meddra_id","subj":"T8","obj":"http://purl.bioontology.org/ontology/MEDDRA/10049413"},{"id":"A9","pred":"meddra_id","subj":"T9","obj":"http://purl.bioontology.org/ontology/MEDDRA/10050967"},{"id":"A10","pred":"meddra_id","subj":"T10","obj":"http://purl.bioontology.org/ontology/MEDDRA/10050967"},{"id":"A11","pred":"meddra_id","subj":"T11","obj":"http://purl.bioontology.org/ontology/MEDDRA/10050417"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

LitCovid-sample-PD-IDO

LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

LitCovid-sample-sentences

LitCovid-sample-PD-UBERON

LitCovid-sample-Pubtator

LitCovid-sample-UniProt

LitCovid-sample-Enju

LitCovid-sample-PD-MAT

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T1","span":{"begin":4967,"end":4973},"obj":"http://purl.obolibrary.org/obo/MAT_0000119"},{"id":"T2","span":{"begin":5745,"end":5749},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"},{"id":"T3","span":{"begin":5796,"end":5800},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"},{"id":"T4","span":{"begin":5961,"end":5965},"obj":"http://purl.obolibrary.org/obo/MAT_0000135"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T20","span":{"begin":6481,"end":6485},"obj":"http://purl.obolibrary.org/obo/GO_0004617"},{"id":"T21","span":{"begin":7168,"end":7172},"obj":"http://purl.obolibrary.org/obo/GO_0004617"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

LitCovid-sample-PD-FMA

LitCovid-sample-PD-MONDO

LitCovid-sample-PD-HP

{"project":"LitCovid-sample-PD-HP","denotations":[{"id":"T3","span":{"begin":5745,"end":5756},"obj":"Phenotype"}],"attributes":[{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0100526"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T3","span":{"begin":5745,"end":5756},"obj":"Phenotype"}],"attributes":[{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0100526"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

2_test

{"project":"2_test","denotations":[{"id":"32413736-25030060-48112969","span":{"begin":632,"end":634},"obj":"25030060"},{"id":"32413736-16195424-48112970","span":{"begin":1956,"end":1958},"obj":"16195424"},{"id":"32413736-16195424-48112971","span":{"begin":2757,"end":2759},"obj":"16195424"},{"id":"32413736-16195424-48112972","span":{"begin":2948,"end":2950},"obj":"16195424"},{"id":"32413736-16195424-48112973","span":{"begin":3086,"end":3088},"obj":"16195424"},{"id":"32413736-12730501-48112974","span":{"begin":3155,"end":3157},"obj":"12730501"},{"id":"32413736-16195424-48112975","span":{"begin":3368,"end":3370},"obj":"16195424"},{"id":"32413736-23181222-48112976","span":{"begin":6926,"end":6928},"obj":"23181222"},{"id":"32413736-8565784-48112977","span":{"begin":7035,"end":7037},"obj":"8565784"},{"id":"T58999","span":{"begin":632,"end":634},"obj":"25030060"},{"id":"T82223","span":{"begin":1956,"end":1958},"obj":"16195424"},{"id":"T62085","span":{"begin":2757,"end":2759},"obj":"16195424"},{"id":"T33865","span":{"begin":2948,"end":2950},"obj":"16195424"},{"id":"T81204","span":{"begin":3086,"end":3088},"obj":"16195424"},{"id":"T68046","span":{"begin":3155,"end":3157},"obj":"12730501"},{"id":"T5396","span":{"begin":3368,"end":3370},"obj":"16195424"},{"id":"T44869","span":{"begin":6926,"end":6928},"obj":"23181222"},{"id":"T36197","span":{"begin":7035,"end":7037},"obj":"8565784"}],"text":"4.1 Serum therapy\n\n4.1.1 Convalescent plasma from patients recovered from COVID-19\n\n4.1.1.1 Hypothesis: Plasma from patients recovered from COVID-19 contain antibodies against 2019-nCoV\nA look at the history of viral outbreaks offers convalescent plasma as the only remedy to avoid further fatalities. The most recent examples include the pandemic of influenza A H1N1 (H1N1pdm09) in virus infection 2009, the Western African Ebola virus epidemic in 2014, and the outbreak of MERS-CoV in 2015 [9]. Meta-analysis studies have shown a reduced risk of mortality in patients with SARS-CoV and influenza receiving convalescent plasma [10].\n\n4.1.1.2 Rationale: Convalescent plasma from patients recovered from COVID-19 can treat patients with severe COVID-19\nA pilot study [11] recently has investigated the safety and effect of convalescent plasma that contain antibody levels higher than 1:640 combined with regular anti-viral agents and standard supportive care on clinical outcomes of ten patients with severe COVID-19. The study showed clinical improvement of all the ten patients accompanied by an increase in lymphocyte count and a decrease in CRP. Following transfusion of convalescent plasma, all the seven patients who were SARS-CoV2 RNA positive before transfusion of convalescent plasma turned SARS-CoV2 negative. There were no control groups receiving convalescent plasma alone or standard therapy without convalescent therapy to evaluate the main effect of convalescent plasma.\n\n4.1.2 Serum from bats with SARS-like CoV\n\n4.1.2.1 Hypothesis: whole-genome sequencing and phylogenetic analysis shed light on the origin of the 2019-nCoV virus – It has been probably introduced from bats to men\nGenome sequencing of a fecal bat sample, Rp3, could detect an isolate of coronaviruses, which was almost identical to the causative agent of the SARS-CoV outbreak of 2002–2003. Hence, it attained the name SARS-like coronavirus isolate Rp3 (SL-CoV Rp3) [12]. The bronchoalveolar lavage fluid (BALF) of a patient with SARS contained the 2019-nCoV. RNA sequencing could reveal about 90% similarity in nucleotides of the novel coronavirus and of SARS-like coronavirus that had previously related to bats [13], [14]. In particular, the S protein of the 2019-nCoV has a high sequence identity of 80–98% with the S protein of bat SARS-like CoVs, such as SARSr-CoV ZXC21 S, ZC45 S, and RaTG13 [3]. Moreover, in phylogenomic trees, branches for the 2019-nCoV are of greater length than those for the 2003 SARS-CoV, and therefore more favorable to bats.\n\n4.1.2.2 Rationale: Bat serum is not able to efficiently neutralize SARS-CoV\nThe range of bats, belonging to the genus Rhinolophus (horseshoe bats) and the family Rhinolophidae, produce the SARS-CoV antibody [12]. Polymerase chain reaction (PCR) will confirm the presence of SARS-CoV nucleocapsid (N) and polymerase (P) proteins in fecal samples if an individual bat being seropositive for SARS-CoV [12]. There is a significant degree of resemblance of greater than 90% in the nucleotide sequence of the viral genomes between SL-CoV Rp3 [12] and the Tor2 strain of SARS-CoV – which was isolated in Toronto [15]. The differences in the genome sequences of SARS-CoV in the two species occur merely in the S gene – which encodes the S1 domain of the coronavirus spike protein and contains regions with high mutation rates [12]. The coronaviruses commonly possess five open reading frames (ORF) that correlate with the production of the replicase polyprotein (P), the spike (S), envelope (E), and membrane (M) glycoproteins and the nucleocapsid (N) protein. The human SARS-CoV Tor2 and bat SL-CoV Rp3 strains remain more than 90% identical at the proteins P, E, M, and N. the protein S consists of two main domains: 1) the S1 domain conveys the role of receptor binding and 2) the S2 domain assumes the role of the fusion of viral and host-cell membranes. In particular, the human SARS-CoV Tor2 strain shows a noticeable degree of difference in the S1 domain from the bat SL-CoV Rp3 strain. This diversity would suffice to produce functional differences between the species, and is an apparent reason why bat sera having high levels of cross-reactive antibodies not acted efficiently to neutralize SARS-CoV.\n\n4.1.3 Serum from convalescent SARS patients\n\n4.1.3.1 Hypothesis: SARS-CoV and SARS-CoV2 are ideally similar in the structure and the cell entry receptor and protease\nSARS-CoV and SARS-CoV2 share absolutely the same cleavage junctions, almost the same sequence (96%) of their main protease, a high degree (76%) of similarity in the amino acid sequence of their S protein, a similar S2′ cleavage site, a similar spectrum of cells they can enter, and the similarity of the most residues essential for binding ACE2 [16], [17], [18]. Also, both of them utilize the same domain of S1B to interact with the ACE2 receptor. However, they differ in proteolytic processing to some degree. Study [16] of the human embryonic kidney (HEK) cell line, 293 T, has shown that a signal for the S2 subunit is present in cells inoculated with SARS-2-S, but not in cells inoculated with SARS-S.\nTwo main proteases for both SARS-S and SARS-2-S are endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane protease, serine 2TMPRSS2 [16]. In 293 T cells lacking 2TMPRSS2, blocking CatB/L activity through increasing the endosomal pH by ammonium chloride could significantly limit the entry of both SARS-S and SARS-2-S. In TMPRSS2 + Caco-2 cells, the effect of ammonium chloride existed to a lesser extent. A combination of camostat mesylate, a blocker of TMPRSS2, and E-64d, an inhibitor of CatB/L, yielded the complete inhibition of SARS-2-S entry in TMPRSS2 + Caco-2 cells. In both the human lung cancer cell line Calu-3 and the primary human lung cells, there was a reduction of the entry of both SARS-S and SARS-2-S by camostat mesylate, indicating that SARS-S and SARS-2-S partially require TMPRSS2 for a lung infection.\n\n4.1.3.2 Rational: Serum from convalescent SARS patients is able to neutralize SARS-CoV2 efficiently\nAntiserum that contains antibodies against human ACE2 could hinder the entry of both SARS-S and SARS-2-S pseudotypes while not affected the entry of VSV-G and MERS-S pseudotypes. It supports the notion that SARS-S and SARS-2-S utilize the same primary entry receptor, i.e., ACE2, which is different from the primary receptors VSV-G and MERS-S engage for cell entry that is LDLR and DPP4, respectively.\nSera from three convalescent SARS patients reduced the SARS-S entry and, to e lesser degree, the SARS-2-S entry. The patient serum effect was in a dose-dependent manner [16].\n\n4.1.4 Serum from rabbits immunized with SARS\n\n4.1.4.1 Hypotheses: Serum from rabbits immunized with SARS is more effective than serum from convalescent SARS patients\nParaoxonases (PON) are mammalian enzymes associated with anti-oxidant and anti-inflammatory effects [19]. Rabbit PON differs from human PON in terms of more activity and more stability under the circumstances [20].\n\n4.1.4.2 Rational: Serum from rabbits immunized with the S1 subunit of SARS-S is able to neutralize SARS-CoV2 very efficiently\nSera from rabbits immunized with the S1 subunit of SARS-S could effectively reduce the entry of both SARS-S and SARS-2-S [16]. When compared with patient serum, rabbit serum revealed to us higher efficiency in inhibition of SARS-2-S entry at the same concentration."}

PMC:7205724 / 9970-17403 JSONTXT

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PMC:7205724 / 9970-17403 JSON TXT