LitCovid-sentences  

PMC:7405836 / 63771-83512 JSONTXT 10 Projects

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Id Subject Object Predicate Lexical cue
T429 0-34 Sentence denotes DIAGNOSIS OF SARS-CoV-2 (COVID-19)
T430 35-175 Sentence denotes RNA tests can confirm the diagnosis of SARS-CoV-2 (COVID-19) cases with real-time RT-PCR or next-generation sequencing (148, 149, 245, 246).
T431 176-336 Sentence denotes At present, nucleic acid detection techniques, like RT-PCR, are considered an effective method for confirming the diagnosis in clinical cases of COVID-19 (148).
T432 337-471 Sentence denotes Several companies across the world are currently focusing on developing and marketing SARS-CoV-2-specific nucleic acid detection kits.
T433 472-540 Sentence denotes Multiple laboratories are also developing their own in-house RT-PCR.
T434 541-671 Sentence denotes One of them is the SARS-CoV-2 nucleic acid detection kit produced by Shuoshi Biotechnology (double fluorescence PCR method) (150).
T435 672-701 Sentence denotes Up to 30 March 2020, the U.S.
T436 702-970 Sentence denotes Food and Drug Administration (FDA) had granted 22 in vitro diagnostics Emergency Use Authorizations (EUAs), including for the RT-PCR diagnostic panel for the universal detection of SARS-like betacoronaviruses and specific detection of SARS-CoV-2, developed by the U.S.
T437 971-996 Sentence denotes CDC (Table 1) (258, 259).
T438 997-1113 Sentence denotes TABLE 1 FDA-approved in vitro Emergency Use Authorization diagnostics available for SARS-CoV-2 as of 30 March 2020a
T439 1114-1144 Sentence denotes Developer Diagnostic platform
T440 1145-1242 Sentence denotes Centers for Disease Control and Prevention (CDC) CDC 2019-nCoV real-time RT-PCR diagnostic panel
T441 1243-1388 Sentence denotes Wadsworth Center, New York State Department of Public Health (CDC) New York SARS-CoV-2 real-time reverse transcriptase (RT)-PCR diagnostic panel
T442 1389-1442 Sentence denotes Roche Molecular Systems, Inc. (RMS) cobas SARS-CoV-2
T443 1443-1473 Sentence denotes Thermo Fisher Scientific, Inc.
T444 1475-1501 Sentence denotes TaqPath COVID-19 combo kit
T445 1502-1567 Sentence denotes Laboratory Corporation of America (LabCorp) COVID-19 RT-PCR test
T446 1568-1581 Sentence denotes Hologic, Inc.
T447 1583-1608 Sentence denotes Panther fusion SARS-CoV-2
T448 1609-1651 Sentence denotes Quest Diagnostics Infectious Disease, Inc.
T449 1653-1677 Sentence denotes Quest SARS-CoV-2 rRT-PCR
T450 1678-1719 Sentence denotes Quidel Corporation Lyra SARS-CoV-2 assay
T451 1720-1770 Sentence denotes Abbott Molecular Abbott RealTime SARS-CoV-2 assay
T452 1771-1819 Sentence denotes GenMark Diagnostics, Inc. ePlex SARS-CoV-2 test
T453 1820-1875 Sentence denotes DiaSorin Molecular, LLC Simplexa COVID-19 direct assay
T454 1876-1913 Sentence denotes Cepheid Xpert Xpress SARS-CoV-2 test
T455 1914-1932 Sentence denotes Primerdesign, Ltd.
T456 1934-1970 Sentence denotes COVID-19 Genesig real-time PCR assay
T457 1971-1989 Sentence denotes Mesa Biotech, Inc.
T458 1991-2013 Sentence denotes Accula SARS-Cov-2 test
T459 2014-2057 Sentence denotes BioFire Defense, LLC BioFire COVID-19 test
T460 2058-2075 Sentence denotes PerkinElmer, Inc.
T461 2077-2131 Sentence denotes PerkinElmer new coronavirus nucleic acid detection kit
T462 2132-2154 Sentence denotes Avellino Lab USA, Inc.
T463 2156-2173 Sentence denotes AvellinoCoV2 test
T464 2174-2191 Sentence denotes BGI Genomics, Co.
T465 2192-2196 Sentence denotes Ltd.
T466 2198-2259 Sentence denotes Real-time fluorescent RT-PCR kit for detecting SARS-2019-nCoV
T467 2260-2295 Sentence denotes Luminex Molecular Diagnostics, Inc.
T468 2297-2327 Sentence denotes NxTAG CoV extended panel assay
T469 2328-2364 Sentence denotes Abbott Diagnostics Scarborough, Inc.
T470 2366-2381 Sentence denotes ID Now COVID-19
T471 2382-2434 Sentence denotes Qiagen GmbH QIAstat-Dx respiratory SARS-CoV-2 panel
T472 2435-2458 Sentence denotes NeuMoDx Molecular, Inc.
T473 2460-2484 Sentence denotes NeuMoDx SARS-CoV-2 assay
T474 2485-2525 Sentence denotes a Data are from references 258 and 259.
T475 2526-2798 Sentence denotes Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260).
T476 2799-2947 Sentence denotes All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level.
T477 2948-3075 Sentence denotes Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions.
T478 3076-3205 Sentence denotes Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively.
T479 3206-3336 Sentence denotes Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes.
T480 3337-3551 Sentence denotes The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260).
T481 3552-3831 Sentence denotes Nucleic acids of SARS-CoV-2 can be detected from samples (64) such as bronchoalveolar lavage fluid, sputum, nasal swabs, fiber bronchoscope brush biopsy specimen, pharyngeal swabs, feces, blood, and urine, with different levels of diagnostic performance (Table 2) (80, 245, 246).
T482 3832-3997 Sentence denotes The viral loads of SARS-CoV-2 were measured using N-gene-specific quantitative RT-PCR in throat swab and sputum samples collected from COVID-19-infected individuals.
T483 3998-4165 Sentence denotes The results indicated that the viral load peaked at around 5 to 6 days following the onset of symptoms, and it ranged from 104 to 107 copies/ml during this time (151).
T484 4166-4312 Sentence denotes In another study, the viral load was found to be higher in the nasal swabs than the throat swabs obtained from COVID-19 symptomatic patients (82).
T485 4313-4485 Sentence denotes Although initially it was thought that viral load would be associated with poor outcomes, some case reports have shown asymptomatic individuals with high viral loads (247).
T486 4486-4699 Sentence denotes Recently, the viral load in nasal and throat swabs of 17 symptomatic patients was determined, and higher viral loads were recorded soon after the onset of symptoms, particularly in the nose compared to the throat.
T487 4700-4875 Sentence denotes The pattern of viral nucleic acid shedding of SARS-CoV-2-infected patients was similar to that of influenza patients but seemed to be different from that of SARS-CoV patients.
T488 4876-5108 Sentence denotes The viral load detected in asymptomatic patients resembled that of symptomatic patients as studied in China, which reflects the transmission perspective of asymptomatic or symptomatic patients having minimum signs and symptoms (82).
T489 5109-5317 Sentence denotes Another study, conducted in South Korea, related to SARS-CoV-2 viral load, opined that SARS-CoV-2 kinetics were significantly different from those of earlier reported CoV infections, including SARS-CoV (253).
T490 5318-5516 Sentence denotes SARS-CoV-2 transmission can occur early in the viral infection phase; thus, diagnosing cases and isolation attempts for this virus warrant different strategies than those needed to counter SARS-CoV.
T491 5517-5618 Sentence denotes Studies are required to establish any correlation between SARS-CoV-2 viral load and cultivable virus.
T492 5619-5882 Sentence denotes Recognizing patients with fewer or no symptoms, along with having modest detectable viral RNA in the oropharynx for 5 days, indicates the requirement of data for assessing SARS-CoV-2 transmission dynamics and updating the screening procedures in the clinics (82).
T493 5883-5938 Sentence denotes TABLE 2 Clinical specimens for detection of SARS CoV-2
T494 5939-5962 Sentence denotes Sample Recommendationa
T495 5963-5996 Sentence denotes Bronchoalveolar lavage fluid +++
T496 5997-6008 Sentence denotes Sputum +++
T497 6009-6025 Sentence denotes Nasal swabs +++
T498 6026-6060 Sentence denotes Fibrobronchoscope brush biopsy ++
T499 6061-6081 Sentence denotes Pharyngeal swabs ++
T500 6082-6090 Sentence denotes Feces +
T501 6091-6099 Sentence denotes Blood +
T502 6100-6108 Sentence denotes Urine +
T503 6109-6200 Sentence denotes a Recommendations are based on references 245 and 246. +++, strong; ++, moderate; +, weak.
T504 6201-6409 Sentence denotes The results of the studies related to SARS-CoV-2 viral loads reflect active replication of this virus in the upper respiratory tract and prolonged viral shedding after symptoms disappear, including via stool.
T505 6410-6575 Sentence denotes Thus, the current case definition needs to be updated along with a reassessment of the strategies to be adopted for restraining the SARS-CoV-2 outbreak spread (248).
T506 6576-6730 Sentence denotes In some cases, the viral load studies of SARS-CoV-2 have also been useful to recommend precautionary measures when handling specific samples, e.g., feces.
T507 6731-6954 Sentence denotes In a recent survey from 17 confirmed cases of SARS-CoV-2 infection with available data (representing days 0 to 13 after onset), stool samples from nine cases (53%; days 0 to 11 after onset) were positive on RT-PCR analysis.
T508 6955-7129 Sentence denotes Although the viral loads were lower than those of respiratory samples (range, 550 copies per ml to 1.21 × 105 copies per ml), this has essential biosafety implications (151).
T509 7130-7334 Sentence denotes The samples from 18 SARS-CoV-2-positive patients in Singapore who had traveled from Wuhan to Singapore showed the presence of viral RNA in stool and whole blood but not in urine by real-time RT-PCR (288).
T510 7335-7566 Sentence denotes Further, novel SARS-CoV-2 infections have been detected in a variety of clinical specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs, fibrobronchoscope brush biopsy specimens, pharyngeal swabs, feces, and blood (246).
T511 7567-7650 Sentence denotes The presence of SARS-CoV-2 in fecal samples has posed grave public health concerns.
T512 7651-7893 Sentence denotes In addition to the direct transmission mainly occurring via droplets of sneezing and coughing, other routes, such as fecal excretion and environmental and fomite contamination, are contributing to SARS-CoV-2 transmission and spread (249–252).
T513 7894-8047 Sentence denotes Fecal excretion has also been documented for SARS-CoV and MERS-CoV, along with the potential to stay viable in situations aiding fecal-oral transmission.
T514 8048-8123 Sentence denotes Thus, SARS-CoV-2 has every possibility to be transmitted through this mode.
T515 8124-8313 Sentence denotes Fecal-oral transmission of SARS-CoV-2, particularly in regions having low standards of hygiene and poor sanitation, may have grave consequences with regard to the high spread of this virus.
T516 8314-8416 Sentence denotes Ethanol and disinfectants containing chlorine or bleach are effective against coronaviruses (249–252).
T517 8417-8533 Sentence denotes Appropriate precautions need to be followed strictly while handling the stools of patients infected with SARS-CoV-2.
T518 8534-8645 Sentence denotes Biowaste materials and sewage from hospitals must be adequately disinfected, treated, and disposed of properly.
T519 8646-8763 Sentence denotes The significance of frequent and good hand hygiene and sanitation practices needs to be given due emphasis (249–252).
T520 8764-9046 Sentence denotes Future explorative research needs to be conducted with regard to the fecal-oral transmission of SARS-CoV-2, along with focusing on environmental investigations to find out if this virus could stay viable in situations and atmospheres facilitating such potent routes of transmission.
T521 9047-9338 Sentence denotes The correlation of fecal concentrations of viral RNA with disease severity needs to be determined, along with assessing the gastrointestinal symptoms and the possibility of fecal SARS-CoV-2 RNA detection during the COVID-19 incubation period or convalescence phases of the disease (249–252).
T522 9339-9571 Sentence denotes The lower respiratory tract sampling techniques, like bronchoalveolar lavage fluid aspirate, are considered the ideal clinical materials, rather than the throat swab, due to their higher positive rate on the nucleic acid test (148).
T523 9572-9708 Sentence denotes The diagnosis of COVID-19 can be made by using upper-respiratory-tract specimens collected using nasopharyngeal and oropharyngeal swabs.
T524 9709-9837 Sentence denotes However, these techniques are associated with unnecessary risks to health care workers due to close contact with patients (152).
T525 9838-10094 Sentence denotes Similarly, a single patient with a high viral load was reported to contaminate an entire endoscopy room by shedding the virus, which may remain viable for at least 3 days and is considered a great risk for uninfected patients and health care workers (289).
T526 10095-10220 Sentence denotes Recently, it was found that the anal swabs gave more positive results than oral swabs in the later stages of infection (153).
T527 10221-10398 Sentence denotes Hence, clinicians have to be cautious while discharging any COVID-19-infected patient based on negative oral swab test results due to the possibility of fecal-oral transmission.
T528 10399-10629 Sentence denotes Even though the viral loads in stool samples were found to be less than those of respiratory samples, strict precautionary measures have to be followed while handling stool samples of COVID-19 suspected or infected patients (151).
T529 10630-10743 Sentence denotes Children infected with SARS-CoV-2 experience only a mild form of illness and recover immediately after treatment.
T530 10744-10906 Sentence denotes It was recently found that stool samples of SARS-CoV-2-infected children that gave negative throat swab results were positive within ten days of negative results.
T531 10907-11011 Sentence denotes This could result in the fecal-oral transmission of SARS-CoV-2 infections, especially in children (290).
T532 11012-11194 Sentence denotes Hence, to prevent the fecal-oral transmission of SARS-CoV-2, infected COVID-19 patients should only be considered negative when they test negative for SARS-CoV-2 in the stool sample.
T533 11195-11472 Sentence denotes A suspected case of COVID-19 infection is said to be confirmed if the respiratory tract aspirate or blood samples test positive for SARS-CoV-2 nucleic acid using RT-PCR or by the identification of SARS-CoV-2 genetic sequence in respiratory tract aspirate or blood samples (80).
T534 11473-11569 Sentence denotes The patient will be confirmed as cured when two subsequent oral swab results are negative (153).
T535 11570-11672 Sentence denotes Recently, the live virus was detected in the self-collected saliva of patients infected with COVID-19.
T536 11673-11819 Sentence denotes These findings were confirmative of using saliva as a noninvasive specimen for the diagnosis of COVID-19 infection in suspected individuals (152).
T537 11820-12010 Sentence denotes It has also been observed that the initial screening of COVID-19 patients infected with RT-PCR may give negative results even if they have chest CT findings that are suggestive of infection.
T538 12011-12220 Sentence denotes Hence, for the accurate diagnosis of COVID-19, a combination of repeated swab tests using RT-PCR and CT scanning is required to prevent the possibility of false-negative results during disease screening (154).
T539 12221-12281 Sentence denotes RT-PCR is the most widely used test for diagnosing COVID-19.
T540 12282-12423 Sentence denotes However, it has some significant limitations from the clinical perspective, since it will not give any clarity regarding disease progression.
T541 12424-12555 Sentence denotes Droplet digital PCR (ddPCR) can be used for the quantification of viral load in the samples obtained from lower respiratory tracts.
T542 12556-12647 Sentence denotes Hence, based on the viral load, we can quickly evaluate the progression of infection (291).
T543 12648-13004 Sentence denotes In addition to all of the above findings, sequencing and phylogenetics are critical in the correct identification and confirmation of the causative viral agent and useful to establish relationships with previous isolates and sequences, as well as to know, especially during an epidemic, the nucleotide and amino acid mutations and the molecular divergence.
T544 13005-13230 Sentence denotes The rapid development and implementation of diagnostic tests against emerging novel diseases like COVID-19 pose significant challenges due to the lack of resources and logistical limitations associated with an outbreak (155).
T545 13231-13301 Sentence denotes SARS-CoV-2 infection can also be confirmed by isolation and culturing.
T546 13302-13394 Sentence denotes The human airway epithelial cell culture was found to be useful in isolating SARS-CoV-2 (3).
T547 13395-13478 Sentence denotes The efficient control of an outbreak depends on the rapid diagnosis of the disease.
T548 13479-13672 Sentence denotes Recently, in response to the COVID-19 outbreak, 1-step quantitative real-time reverse transcription-PCR assays were developed that detect the ORF1b and N regions of the SARS-CoV-2 genome (156).
T549 13673-13739 Sentence denotes That assay was found to achieve the rapid detection of SARS-CoV-2.
T550 13740-13905 Sentence denotes Nucleic acid-based assays offer high accuracy in the diagnosis of SARS-CoV-2, but the current rate of spread limits its use due to the lack of diagnostic assay kits.
T551 13906-14031 Sentence denotes This will further result in the extensive transmission of COVID-19, since only a portion of suspected cases can be diagnosed.
T552 14032-14237 Sentence denotes In such situations, conventional serological assays, like enzyme-linked immunosorbent assay (ELISA), that are specific to COVID-19 IgM and IgG antibodies can be used as a high-throughput alternative (149).
T553 14238-14331 Sentence denotes At present, there is no diagnostic kit available for detecting the SARS-CoV-2 antibody (150).
T554 14332-14543 Sentence denotes The specific antibody profiles of COVID-19 patients were analyzed, and it was found that the IgM level lasted more than 1 month, indicating a prolonged stage of virus replication in SARS-CoV-2-infected patients.
T555 14544-14622 Sentence denotes The IgG levels were found to increase only in the later stages of the disease.
T556 14623-14729 Sentence denotes These findings indicate that the specific antibody profiles of SARS-CoV-2 and SARS-CoV were similar (325).
T557 14730-14863 Sentence denotes These findings can be utilized for the development of specific diagnostic tests against COVID-19 and can be used for rapid screening.
T558 14864-15069 Sentence denotes Even though diagnostic test kits are already available that can detect the genetic sequences of SARS-CoV-2 (95), their availability is a concern, as the number of COVID-19 cases is skyrocketing (155, 157).
T559 15070-15243 Sentence denotes A major problem associated with this diagnostic kit is that it works only when the test subject has an active infection, limiting its use to the earlier stages of infection.
T560 15244-15364 Sentence denotes Several laboratories around the world are currently developing antibody-based diagnostic tests against SARS-CoV-2 (157).
T561 15365-15434 Sentence denotes Chest CT is an ideal diagnostic tool for identifying viral pneumonia.
T562 15435-15506 Sentence denotes The sensitivity of chest CT is far superior to that of X-ray screening.
T563 15507-15669 Sentence denotes The chest CT findings associated with COVID-19-infected patients include characteristic patchy infiltration that later progresses to ground-glass opacities (158).
T564 15670-15761 Sentence denotes Early manifestations of COVID-19 pneumonia might not be evident in X-ray chest radiography.
T565 15762-15888 Sentence denotes In such situations, a chest CT examination can be performed, as it is considered highly specific for COVID-19 pneumonia (118).
T566 15889-16007 Sentence denotes Those patients having COVID-19 pneumonia will exhibit the typical ground-glass opacity in their chest CT images (154).
T567 16008-16085 Sentence denotes The patients infected with COVID-19 had elevated plasma angiotensin 2 levels.
T568 16086-16239 Sentence denotes The level of angiotensin 2 was found to be linearly associated with viral load and lung injury, indicating its potential as a diagnostic biomarker (121).
T569 16240-16364 Sentence denotes The chest CT imaging abnormalities associated with COVID-19 pneumonia have also been observed even in asymptomatic patients.
T570 16365-16570 Sentence denotes These abnormalities progress from the initial focal unilateral to diffuse bilateral ground-glass opacities and will further progress to or coexist with lung consolidation changes within 1 to 3 weeks (159).
T571 16571-16645 Sentence denotes The role played by radiologists in the current scenario is very important.
T572 16646-16748 Sentence denotes Radiologists can help in the early diagnosis of lung abnormalities associated with COVID-19 pneumonia.
T573 16749-16931 Sentence denotes They can also help in the evaluation of disease severity, identifying its progression to acute respiratory distress syndrome and the presence of secondary bacterial infections (160).
T574 16932-17230 Sentence denotes Even though chest CT is considered an essential diagnostic tool for COVID-19, the extensive use of CT for screening purposes in the suspected individuals might be associated with a disproportionate risk-benefit ratio due to increased radiation exposure as well as increased risk of cross-infection.
T575 17231-17356 Sentence denotes Hence, the use of CT for early diagnosis of SARS-CoV-2 infection in high-risk groups should be done with great caution (292).
T576 17357-17484 Sentence denotes More recently, other advanced diagnostics have been designed and developed for the detection of SARS-CoV-2 (345, 347, 350–352).
T577 17485-17652 Sentence denotes A reverse transcriptional loop-mediated isothermal amplification (RT-LAMP), namely, iLACO, has been developed for rapid and colorimetric detection of this virus (354).
T578 17653-17793 Sentence denotes RT-LAMP serves as a simple, rapid, and sensitive diagnostic method that does not require sophisticated equipment or skilled personnel (349).
T579 17794-17897 Sentence denotes An interactive web-based dashboard for tracking SARS-CoV-2 in a real-time mode has been designed (238).
T580 17898-18050 Sentence denotes A smartphone-integrated home-based point-of-care testing (POCT) tool, a paper-based POCT combined with LAMP, is a useful point-of-care diagnostic (353).
T581 18051-18261 Sentence denotes An Abbott ID Now COVID-19 molecular POCT-based test, using isothermal nucleic acid amplification technology, has been designed as a point-of-care test for very rapid detection of SARS-CoV-2 in just 5 min (344).
T582 18262-18523 Sentence denotes A CRISPR-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) diagnostic for rapid detection of SARS-CoV-2 without the requirement of specialized instrumentation has been reported to be very useful in the clinical diagnosis of COVID-19 (360).
T583 18524-18628 Sentence denotes A CRISPR-Cas12-based lateral flow assay also has been developed for rapid detection of SARS-CoV-2 (346).
T584 18629-18795 Sentence denotes Artificial intelligence, by means of a three-dimensional deep-learning model, has been developed for sensitive and specific diagnosis of COVID-19 via CT images (332).
T585 18796-19216 Sentence denotes Tracking and mapping of the rising incidence rates, disease outbreaks, community spread, clustered transmission events, hot spots, and superspreader potential of SARS-CoV-2/COVID warrant full exploitation of real-time disease mapping by employing geographical information systems (GIS), such as the GIS software Kosmo 3.1, web-based real-time tools and dashboards, apps, and advances in information technology (356–359).
T586 19217-19741 Sentence denotes Researchers have also developed a few prediction tools/models, such as the prediction model risk of bias assessment tool (PROBAST) and critical appraisal and data extraction for systematic reviews of prediction modeling studies (CHARMS), which could aid in assessing the possibility of getting infection and estimating the prognosis in patients; however, such models may suffer from bias issues and, hence, cannot be considered completely trustworthy, which necessitates the development of new and reliable predictors (360).