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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T16","span":{"begin":841,"end":845},"obj":"Body_part"},{"id":"T17","span":{"begin":851,"end":857},"obj":"Body_part"},{"id":"T18","span":{"begin":875,"end":881},"obj":"Body_part"},{"id":"T19","span":{"begin":1147,"end":1150},"obj":"Body_part"},{"id":"T20","span":{"begin":2092,"end":2098},"obj":"Body_part"},{"id":"T21","span":{"begin":2891,"end":2894},"obj":"Body_part"}],"attributes":[{"id":"A16","pred":"uberon_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A17","pred":"uberon_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"},{"id":"A18","pred":"uberon_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A19","pred":"uberon_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/UBERON_0000970"},{"id":"A20","pred":"uberon_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A21","pred":"uberon_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/UBERON_0000970"}],"text":"2.7 Safety testing\n\n2.7.1 Assessment of pathogenicity in one-day-old SPF chickens\nThe chickens were separately housed in isolators under consistent conditions, and food and water was provided ad libitum. A total of 120 one-day-old SPF chickens were randomly divided into four groups (n = 30 per group). The chickens in the experimental groups were intranasally inoculated with 200 μL allantoic fluid per chick containing 105EID50 of the rH120, rIBYZ, and rH120-S1/YZ strains. The control group (n = 30) was inoculated with 200 μL sterile PBS via the same route. The morbidity and mortality was followed-up for 14 days. All experimental groups were monitored daily for clinical signs related to IB infection for 14 days post-infection (dpi), including coughing, sneezing, and tracheal rales. Dead chickens were examined for gross tracheal, lung, and kidney lesions.\n\n2.7.2 Tissue tropism of early viral infection in vivo\nA total of 100 1-day-old SPF chickens were assigned to four groups (n = 25 per group). The birds were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively via eye drop and the intranasal route and 200 μL PBS per chick was administered to the control group (n = 25) via the same route. The tracheas, lungs, kidneys, and bursa from the 5 inoculated birds per group were harvested at 1, 3, 5, and 7 dpi, weighed, and collected into 1 mL PBS per sample and frozen at −80 °C. After grinding the samples, the viral RNA was extracted using TRIzol, and the cDNA was obtained by reverse transcription using a PrimeScript RT Master Mix Perfect Real Time Kit (TaKaRa, Otsu, Shiga, Japan). The viral RNA copies from each of the different samples were detected by real-time PCR as described above. All assays were run in triplicate and the copy number for each virus was calculated according to the standard curve.\n\n2.7.3 Histopathology\nAfter inoculation with 105 EID50 dose of the rH120, rIBYZ, and rH120-S1/YZ strains, three infected chickens per group were randomly selected to be euthanized by bleeding, and the tissue pathology was examined in the different groups at 3, 5, 7, 10 dpi. The tracheas, lungs, kidneys, and bursas of three dead or other randomly-selected chickens from the experimental and control groups (inoculated with PBS) were collected at 5 or 7 dpi and further processed for histopathology. The samples were fixed in formalin, embedded in paraffin, cut into 5 μm sections, and stained with hematoxylin and eosin. The slides were examined under light microscopy for the presence of lesions.\n\n2.7.4 Viral shedding\nTo determine the level of viral shedding of the different recombinants, 10 birds per group were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively. 200 μL PBS per chick was administered to the control group via eye drop and the intranasal route. . Oral and cloacal swabs were collected from each bird into 1 mL PBS at 7, 14, 18, 22, 26, and 30 dpi and stored at −80 °C. After freezing and thawing three times and centrifuging at 8,000 × g for 5 min at 4 °C, relative amount of virus present in 200 μL of supernatants of each sample was quantified by RNA extraction, reverse transcription, and real-time PCR as described previously."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T24","span":{"begin":532,"end":539},"obj":"Disease"},{"id":"T25","span":{"begin":699,"end":708},"obj":"Disease"},{"id":"T26","span":{"begin":726,"end":735},"obj":"Disease"},{"id":"T27","span":{"begin":899,"end":914},"obj":"Disease"},{"id":"T28","span":{"begin":905,"end":914},"obj":"Disease"}],"attributes":[{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005047"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"2.7 Safety testing\n\n2.7.1 Assessment of pathogenicity in one-day-old SPF chickens\nThe chickens were separately housed in isolators under consistent conditions, and food and water was provided ad libitum. A total of 120 one-day-old SPF chickens were randomly divided into four groups (n = 30 per group). The chickens in the experimental groups were intranasally inoculated with 200 μL allantoic fluid per chick containing 105EID50 of the rH120, rIBYZ, and rH120-S1/YZ strains. The control group (n = 30) was inoculated with 200 μL sterile PBS via the same route. The morbidity and mortality was followed-up for 14 days. All experimental groups were monitored daily for clinical signs related to IB infection for 14 days post-infection (dpi), including coughing, sneezing, and tracheal rales. Dead chickens were examined for gross tracheal, lung, and kidney lesions.\n\n2.7.2 Tissue tropism of early viral infection in vivo\nA total of 100 1-day-old SPF chickens were assigned to four groups (n = 25 per group). The birds were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively via eye drop and the intranasal route and 200 μL PBS per chick was administered to the control group (n = 25) via the same route. The tracheas, lungs, kidneys, and bursa from the 5 inoculated birds per group were harvested at 1, 3, 5, and 7 dpi, weighed, and collected into 1 mL PBS per sample and frozen at −80 °C. After grinding the samples, the viral RNA was extracted using TRIzol, and the cDNA was obtained by reverse transcription using a PrimeScript RT Master Mix Perfect Real Time Kit (TaKaRa, Otsu, Shiga, Japan). The viral RNA copies from each of the different samples were detected by real-time PCR as described above. All assays were run in triplicate and the copy number for each virus was calculated according to the standard curve.\n\n2.7.3 Histopathology\nAfter inoculation with 105 EID50 dose of the rH120, rIBYZ, and rH120-S1/YZ strains, three infected chickens per group were randomly selected to be euthanized by bleeding, and the tissue pathology was examined in the different groups at 3, 5, 7, 10 dpi. The tracheas, lungs, kidneys, and bursas of three dead or other randomly-selected chickens from the experimental and control groups (inoculated with PBS) were collected at 5 or 7 dpi and further processed for histopathology. The samples were fixed in formalin, embedded in paraffin, cut into 5 μm sections, and stained with hematoxylin and eosin. The slides were examined under light microscopy for the presence of lesions.\n\n2.7.4 Viral shedding\nTo determine the level of viral shedding of the different recombinants, 10 birds per group were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively. 200 μL PBS per chick was administered to the control group via eye drop and the intranasal route. . Oral and cloacal swabs were collected from each bird into 1 mL PBS at 7, 14, 18, 22, 26, and 30 dpi and stored at −80 °C. After freezing and thawing three times and centrifuging at 8,000 × g for 5 min at 4 °C, relative amount of virus present in 200 μL of supernatants of each sample was quantified by RNA extraction, reverse transcription, and real-time PCR as described previously."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T16","span":{"begin":882,"end":889},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T17","span":{"begin":899,"end":914},"obj":"http://purl.obolibrary.org/obo/GO_0016032"},{"id":"T18","span":{"begin":1558,"end":1579},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T19","span":{"begin":1566,"end":1579},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T20","span":{"begin":2598,"end":2612},"obj":"http://purl.obolibrary.org/obo/GO_0019076"},{"id":"T21","span":{"begin":2639,"end":2653},"obj":"http://purl.obolibrary.org/obo/GO_0019076"},{"id":"T22","span":{"begin":3246,"end":3267},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T23","span":{"begin":3254,"end":3267},"obj":"http://purl.obolibrary.org/obo/GO_0006351"}],"text":"2.7 Safety testing\n\n2.7.1 Assessment of pathogenicity in one-day-old SPF chickens\nThe chickens were separately housed in isolators under consistent conditions, and food and water was provided ad libitum. A total of 120 one-day-old SPF chickens were randomly divided into four groups (n = 30 per group). The chickens in the experimental groups were intranasally inoculated with 200 μL allantoic fluid per chick containing 105EID50 of the rH120, rIBYZ, and rH120-S1/YZ strains. The control group (n = 30) was inoculated with 200 μL sterile PBS via the same route. The morbidity and mortality was followed-up for 14 days. All experimental groups were monitored daily for clinical signs related to IB infection for 14 days post-infection (dpi), including coughing, sneezing, and tracheal rales. Dead chickens were examined for gross tracheal, lung, and kidney lesions.\n\n2.7.2 Tissue tropism of early viral infection in vivo\nA total of 100 1-day-old SPF chickens were assigned to four groups (n = 25 per group). The birds were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively via eye drop and the intranasal route and 200 μL PBS per chick was administered to the control group (n = 25) via the same route. The tracheas, lungs, kidneys, and bursa from the 5 inoculated birds per group were harvested at 1, 3, 5, and 7 dpi, weighed, and collected into 1 mL PBS per sample and frozen at −80 °C. After grinding the samples, the viral RNA was extracted using TRIzol, and the cDNA was obtained by reverse transcription using a PrimeScript RT Master Mix Perfect Real Time Kit (TaKaRa, Otsu, Shiga, Japan). The viral RNA copies from each of the different samples were detected by real-time PCR as described above. All assays were run in triplicate and the copy number for each virus was calculated according to the standard curve.\n\n2.7.3 Histopathology\nAfter inoculation with 105 EID50 dose of the rH120, rIBYZ, and rH120-S1/YZ strains, three infected chickens per group were randomly selected to be euthanized by bleeding, and the tissue pathology was examined in the different groups at 3, 5, 7, 10 dpi. The tracheas, lungs, kidneys, and bursas of three dead or other randomly-selected chickens from the experimental and control groups (inoculated with PBS) were collected at 5 or 7 dpi and further processed for histopathology. The samples were fixed in formalin, embedded in paraffin, cut into 5 μm sections, and stained with hematoxylin and eosin. The slides were examined under light microscopy for the presence of lesions.\n\n2.7.4 Viral shedding\nTo determine the level of viral shedding of the different recombinants, 10 birds per group were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively. 200 μL PBS per chick was administered to the control group via eye drop and the intranasal route. . Oral and cloacal swabs were collected from each bird into 1 mL PBS at 7, 14, 18, 22, 26, and 30 dpi and stored at −80 °C. After freezing and thawing three times and centrifuging at 8,000 × g for 5 min at 4 °C, relative amount of virus present in 200 μL of supernatants of each sample was quantified by RNA extraction, reverse transcription, and real-time PCR as described previously."}

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T9","span":{"begin":753,"end":761},"obj":"Phenotype"},{"id":"T10","span":{"begin":786,"end":791},"obj":"Phenotype"},{"id":"T11","span":{"begin":1147,"end":1155},"obj":"Phenotype"},{"id":"T12","span":{"begin":2891,"end":2899},"obj":"Phenotype"}],"attributes":[{"id":"A9","pred":"hp_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/HP_0012735"},{"id":"A10","pred":"hp_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/HP_0030830"},{"id":"A11","pred":"hp_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/HP_0000508"},{"id":"A12","pred":"hp_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/HP_0000508"}],"text":"2.7 Safety testing\n\n2.7.1 Assessment of pathogenicity in one-day-old SPF chickens\nThe chickens were separately housed in isolators under consistent conditions, and food and water was provided ad libitum. A total of 120 one-day-old SPF chickens were randomly divided into four groups (n = 30 per group). The chickens in the experimental groups were intranasally inoculated with 200 μL allantoic fluid per chick containing 105EID50 of the rH120, rIBYZ, and rH120-S1/YZ strains. The control group (n = 30) was inoculated with 200 μL sterile PBS via the same route. The morbidity and mortality was followed-up for 14 days. All experimental groups were monitored daily for clinical signs related to IB infection for 14 days post-infection (dpi), including coughing, sneezing, and tracheal rales. Dead chickens were examined for gross tracheal, lung, and kidney lesions.\n\n2.7.2 Tissue tropism of early viral infection in vivo\nA total of 100 1-day-old SPF chickens were assigned to four groups (n = 25 per group). The birds were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively via eye drop and the intranasal route and 200 μL PBS per chick was administered to the control group (n = 25) via the same route. The tracheas, lungs, kidneys, and bursa from the 5 inoculated birds per group were harvested at 1, 3, 5, and 7 dpi, weighed, and collected into 1 mL PBS per sample and frozen at −80 °C. After grinding the samples, the viral RNA was extracted using TRIzol, and the cDNA was obtained by reverse transcription using a PrimeScript RT Master Mix Perfect Real Time Kit (TaKaRa, Otsu, Shiga, Japan). The viral RNA copies from each of the different samples were detected by real-time PCR as described above. All assays were run in triplicate and the copy number for each virus was calculated according to the standard curve.\n\n2.7.3 Histopathology\nAfter inoculation with 105 EID50 dose of the rH120, rIBYZ, and rH120-S1/YZ strains, three infected chickens per group were randomly selected to be euthanized by bleeding, and the tissue pathology was examined in the different groups at 3, 5, 7, 10 dpi. The tracheas, lungs, kidneys, and bursas of three dead or other randomly-selected chickens from the experimental and control groups (inoculated with PBS) were collected at 5 or 7 dpi and further processed for histopathology. The samples were fixed in formalin, embedded in paraffin, cut into 5 μm sections, and stained with hematoxylin and eosin. The slides were examined under light microscopy for the presence of lesions.\n\n2.7.4 Viral shedding\nTo determine the level of viral shedding of the different recombinants, 10 birds per group were inoculated with 200 μL allantoic fluid containing 105 EID50 of the rH120, rIBYZ, or rH120-S1/YZ strains, respectively. 200 μL PBS per chick was administered to the control group via eye drop and the intranasal route. . Oral and cloacal swabs were collected from each bird into 1 mL PBS at 7, 14, 18, 22, 26, and 30 dpi and stored at −80 °C. After freezing and thawing three times and centrifuging at 8,000 × g for 5 min at 4 °C, relative amount of virus present in 200 μL of supernatants of each sample was quantified by RNA extraction, reverse transcription, and real-time PCR as described previously."}

LitCovid-PubTator

PMC:7115396 / 13641-16952 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7115396 / 13641-16952 JSON TXT