LitCovid-sentences  

PMC:7055038 / 597-11527 JSONTXT 14 Projects

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Id Subject Object Predicate Lexical cue
T6 0-179 Sentence denotes In late December 2019, an outbreak with an initially undiagnosed pneumonia was reported in the city of Wuhan, Hubei Province, China, and linked to the Huanan Seafood Market [1,2].
T7 180-356 Sentence denotes The causative pathogen was identified as a novel betacoronavirus within the severe acute respiratory syndrome (SARS) coronavirus (CoV) family, recently termed SARS-CoV-2 [3-7].
T8 357-511 Sentence denotes In response to the outbreak, several countries including Thailand, established thermal screening at the airport for travellers from Wuhan since 3 January.
T9 512-634 Sentence denotes On 8 January and 13 January, suspected cases of infection with SARS-CoV-2 were identified at Bangkok Suvarnabhumi airport.
T10 635-738 Sentence denotes We report the investigation, basic clinical characteristics and viral genomes derived from these cases.
T11 740-746 Sentence denotes Case 1
T12 747-857 Sentence denotes A woman in her early 60s from Wuhan developed a fever with chills, sore throat and headache on 5 January 2020.
T13 858-939 Sentence denotes She went to a local health facility in China and received undisclosed medication.
T14 940-1092 Sentence denotes On 8 January 2020, she took a direct ca 4 h flight to Thailand from Wuhan, with five family members, as part of a tour group of 16 (including the case).
T15 1093-1210 Sentence denotes Her measured temperature at the arrival gate was 38.6 °C by thermoscanner, and confirmed with a tympanic thermometer.
T16 1211-1399 Sentence denotes After being interviewed by quarantine officers, she was transferred to Bamrasnaradura Infectious Disease Institute (BIDI) Hospital, Nonthaburi, for isolation and laboratory investigations.
T17 1400-1470 Sentence denotes She reported a runny nose and sore throat but no dyspnea or diarrhoea.
T18 1471-1550 Sentence denotes Upon admission, her vital signs were normal except for elevated blood pressure.
T19 1551-1629 Sentence denotes Her physical examination was unremarkable including inconspicuous lung sounds.
T20 1630-1731 Sentence denotes Her complete blood count suggested a viral infection from relatively decreased neutrophil (48%; norm:
T21 1732-1765 Sentence denotes 35–75%) to lymphocyte (40%; norm:
T22 1766-1784 Sentence denotes 20–59%) ratio [8].
T23 1785-1971 Sentence denotes The chest X-ray (CXR) results on 8 January were compatible with pneumonia with mild thickening lung marking at both lower lungs possibly because of crowded lung rather than infiltration.
T24 1972-2011 Sentence denotes It also showed borderline cardiomegaly.
T25 2012-2065 Sentence denotes Repeat CXR after 7 days showed no remarkable changes.
T26 2066-2255 Sentence denotes In the interview, the patient explicitly stated that she had not visited the Huanan Seafood Market but she was living near another local market, which she visited daily until illness onset.
T27 2256-2325 Sentence denotes This market was at ca 7.5 km distance from the Huanan Seafood Market.
T28 2326-2432 Sentence denotes The patient also reported that she had not purchased live animals and or visited stalls with live animals.
T29 2433-2498 Sentence denotes She did not visit Jinyintai Hospital or other hospitals in Wuhan.
T30 2499-2569 Sentence denotes However, she visited local dispensaries in Wuhan to obtain medication.
T31 2570-2638 Sentence denotes She also reported no contact with persons with respiratory symptoms.
T32 2639-2740 Sentence denotes Clinical specimens collected on admission included the upper respiratory tract secretions and sputum.
T33 2741-2848 Sentence denotes These specimens tested positive on 12 January for the CoV family by using a conventional nested RT-PCR [9].
T34 2849-3221 Sentence denotes Genomic sequencing analysis included Sanger and next generation sequencing were performed by the Emerging Infectious Diseases Health Science Center, the Thai Red Cross Society and the Thai National Institute of Health, Department of Medical Sciences and the sequence shared via the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database (EPI_ISL_403962).
T35 3222-3302 Sentence denotes The sequencing protocol and details are provided in the Supplementary Materials.
T36 3303-3432 Sentence denotes The patient recovered after testing negative for SARS-CoV-2, and returned to China without signs and symptoms on 18 January 2020.
T37 3434-3440 Sentence denotes Case 2
T38 3441-3520 Sentence denotes A woman in her mid-70s from Wuhan landed at Suvarnabhumi airport on 13 January.
T39 3521-3624 Sentence denotes She travelled to Thailand with three family members as part of a tour group of 20 (including the case).
T40 3625-3725 Sentence denotes An airport thermoscanner detected a fever of 38.0 °C that was confirmed with a tympanic thermometer.
T41 3726-3855 Sentence denotes The patient reported a sore throat, that her fever onset date was 13 January and that she had a cough for an undetermined period.
T42 3856-3893 Sentence denotes The patient was hospitalised at BIDI.
T43 3894-3982 Sentence denotes Upon admission, she reported mild tachypnoea, and her CXR was compatible with pneumonia.
T44 3983-4232 Sentence denotes Similar to case 1, the first CXR taken on 13 January, showed thickening interstitial lung marking at both lower lung fields and both perihilar regions because of interstitial infiltration or crowded lung marking, mild cardiomegaly and dilated aorta.
T45 4233-4344 Sentence denotes Follow-up CXR on 17 January additionally showed recent hazy with reticular opacities at left middle lung field.
T46 4345-4396 Sentence denotes The patient was not in severe condition but stable.
T47 4397-4502 Sentence denotes In the patient interview, she reported that she did not visit the Huanan Seafood Market or other markets.
T48 4503-4640 Sentence denotes She also reported no contact with pigs, camels, other mammals (or areas with dead birds), or any consumption of raw or undercooked foods.
T49 4641-4719 Sentence denotes She stated that she was not in contact with persons with respiratory symptoms.
T50 4720-4806 Sentence denotes A conventional nested RT-PCR test of this patient was positive for the CoV family [9].
T51 4807-4936 Sentence denotes Subsequent genome sequencing was again compatible with the SARS-CoV-2 and shared via the GISAID EpiCoV database (EPI_ISL_403963).
T52 4937-5005 Sentence denotes A nasopharyngeal swab also tested positive by RT-PCR for adenovirus.
T53 5006-5180 Sentence denotes The patient was no longer febrile as of 17 January, and after testing negative for the CoV family by conventional nested RT-PCR, she was discharged and she returned to China.
T54 5182-5206 Sentence denotes Genome sequence analysis
T55 5207-5622 Sentence denotes Comparing the two genome sequences with a non-redundant selection of representatives from all known CoV families by alignment [10] and phylogenetic tree (Figure 1A) [11] shows that they belong to the SARS family of betacoronaviruses and while related to SARS-CoV (80% genome identity), they were most closely related to SARS-like bat CoV from China (88% identity) as closest known sequence at the time of emergence.
T56 5623-5855 Sentence denotes Figure 1 Phylogenetic trees of Thai sequences in context of all coronavirus families (A) and structural mapping of mutations in the spike glycoprotein between SARS CoV (PDB:6CG [12]) and the current SARS-CoV-2 using YASARA [20] (B)
T57 5856-5879 Sentence denotes CoV: coronavirus; MERS:
T58 5880-5966 Sentence denotes Middle East respiratory syndrome coronavirus; SARS: severe acute respiratory syndrome.
T59 5967-6038 Sentence denotes Panel A: blue: SARS-CoV-2; red: SARS; purple: MERS; green: common cold.
T60 6039-6085 Sentence denotes Panel B: cyan: ACE2 human host receptor; grey:
T61 6086-6174 Sentence denotes CoV spike glycoprotein trimer (PDB:6ACG); red: mutations between SARS-CoV vs SARS-CoV-2.
T62 6175-6386 Sentence denotes The phylogenetic tree was created from whole genome alignment with MAFFT using the neighbour-joining method with maximum composite likelihood (MCL) model, uniform site rates and 500 bootstrap tests using MEGA X.
T63 6387-6569 Sentence denotes Structural mapping of mutations in the spike glycoprotein between SARS CoV and the two cases of the SARS-CoV-2 reported here shows only 76% identity at the protein level (Figure 1B).
T64 6570-6690 Sentence denotes This surface protein is critical for ACE2 host receptor interaction and is also a target of the immune response [12,13].
T65 6691-6892 Sentence denotes Given several mutations in the binding interface, it may differ in host cell binding efficiency compared with SARS-CoV which could result in differences in virulence and transmission potential [14,15].
T66 6893-7279 Sentence denotes The genomes of the two separate cases of coronavirus disease 2019 (COVID-19) are identical over the full length of close to 30 kb and are furthermore identical to five other sequences (four from Wuhan and one from Zhejiang); together these sequences form the largest cluster of identical cases within the early outbreak, comprising a core of at least indirectly linked cases (Figure 2).
T67 7280-7526 Sentence denotes Within-outbreak sequence divergence is generally low with 0–9 nt differences over the whole genome and mutations unique to individual strains are possibly related to quality differences of the samples and noise of the methods used for sequencing.
T68 7527-7630 Sentence denotes Figure 2 Within-outbreak SARS-CoV-2 sequence divergence and clusters, China and Thailand, January 2020
T69 7631-7732 Sentence denotes Number of pair-wise nt differences across whole genomes colour-coded from zero (green) to nine (red).
T70 7733-7738 Sentence denotes Blue:
T71 7739-7757 Sentence denotes Thai sample names.
T72 7758-7836 Sentence denotes Orange: samples with sequences identical to each other and the Thai sequences.
T73 7837-8044 Sentence denotes We gratefully acknowledge the authors, the originating and submitting laboratories for their sequence and metadata shared through GISAID, on which this research is based (as listed in Supplementary Table 1).
T74 8046-8067 Sentence denotes Follow-up of contacts
T75 8068-8154 Sentence denotes Case 1 travelled in a tour group with 15 others and 40 close contacts were identified:
T76 8155-8327 Sentence denotes 15 members of the tour group, 15 people sitting within two rows in front and back of the seat of case 1 on the same airplane, nine crew members and one port health officer.
T77 8328-8422 Sentence denotes They were monitored for COVID-19 with RT-PCR tests on days 1, 12 and 14 ; all tested negative.
T78 8423-8509 Sentence denotes Case 2 travelled in a tour group with 19 others and 44 close contacts were identified:
T79 8510-8643 Sentence denotes 19 members of the tour group, 15 within two rows front and back of the seat of case 2, nine crew members and one port health officer.
T80 8644-8739 Sentence denotes All were monitored for COVID-19 with RT-PCR tests on days 1, 12 and 14 and all tested negative.
T81 8741-8766 Sentence denotes Discussion and conclusion
T82 8767-8904 Sentence denotes According to the cases’ history, the two imported COVID-19 cases described here are not directly linked, yet their genomes are identical.
T83 8905-9206 Sentence denotes Further, according to information provided by the cases, they have no direct link to the Huanan Seafood Market but their genomes are identical to four sequences from Wuhan collected on 30 December 2019 and sequenced by three different laboratories, indicating potential wider distribution in the city.
T84 9207-9439 Sentence denotes Although within-outbreak sequence divergence is low for this virus, identical genomes of up to 30 kb are rare and a strong sign of recent transmission linkage, albeit with unknown number of generations within the transmission chain.
T85 9440-9599 Sentence denotes The missing link to the market, the time of travel and onset of symptoms in the two COVID-19 cases together with the incubation period of mean 6.4 days (range:
T86 9600-9829 Sentence denotes 5.6–7.7) [16] and the time of closest genome neighbours obtained from sequences in Wuhan, suggest that transmission within Wuhan beyond the Huanan Seafood Market is likely to have occurred in the first week of January or earlier.
T87 9830-9969 Sentence denotes People travelling out of the city since then may have spread the virus further before travel restrictions were enforced on 23 January [17].
T88 9970-10195 Sentence denotes Thailand implemented measures for screening patients travelling from Wuhan since 3 January 2020 at Suvarnabhumi Airport, Don Mueang, Phuket and Chiang Mai airports, and stepped up surveillance at public and private hospitals.
T89 10196-10350 Sentence denotes The two cases described here who tested positive for SARS-CoV-2 were the first confirmed exported cases from China, suggesting early international spread.
T90 10351-10720 Sentence denotes Therefore, while one cannot exclude the possibility that asymptomatic cases in their incubation period would be missed and become infectious later, screening of incoming travellers from an affected area proved successful at least in these two instances, when COVID-19 cases were detected, isolated, observed and only discharged once they tested negative for SARS-CoV-2.
T91 10721-10930 Sentence denotes Rapid response including genome sequencing and sharing via GISAID [18,19] (https://www.gisaid.org/) enabled fast dissemination of results and provided a glimpse of early transmission patterns in this outbreak.