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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
275 1105-1109 Gene denotes LAMP Gene:27074
276 553-563 Species denotes SARS-CoV-2 Tax:2697049
277 1380-1391 Species denotes Lassa virus Tax:11620
278 1601-1611 Species denotes Zika virus Tax:64320
279 1786-1796 Species denotes SARS-CoV-2 Tax:2697049
280 1393-1397 Species denotes LASV Tax:11620
281 1522-1526 Species denotes LASV Tax:11620
282 82-103 Disease denotes SARS-CoV-2 infections MESH:C000657245
283 300-308 Disease denotes COVID-19 MESH:C000657245
294 1971-1981 Species denotes SARS-CoV-2 Tax:2697049
295 2636-2644 Species denotes SARS-CoV Tax:694009
296 2754-2762 Species denotes MERS-CoV Tax:1335626
297 2912-2920 Species denotes MERS-CoV Tax:1335626
298 3034-3045 Species denotes coronavirus Tax:11118
299 2012-2032 Disease denotes coronavirus diseases MESH:D018352
300 2102-2134 Disease denotes Middle East respiratory syndrome MESH:D018352
301 2136-2140 Disease denotes MERS MESH:D018352
302 2367-2387 Disease denotes coronavirus diseases MESH:D018352
303 2809-2813 Disease denotes MERS MESH:D018352
318 3178-3186 Species denotes patients Tax:9606
319 3407-3415 Species denotes patients Tax:9606
320 3567-3581 Species denotes rhesus monkeys Tax:9544
321 3783-3793 Species denotes SARS-CoV-2 Tax:2697049
322 3898-3908 Species denotes SARS-CoV-2 Tax:2697049
323 3925-3933 Species denotes patients Tax:9606
324 4250-4260 Species denotes SARS-CoV-2 Tax:2697049
325 4584-4589 Species denotes women Tax:9606
326 4756-4760 Chemical denotes HBSS
327 4832-4836 Chemical denotes HBSS
328 4967-4970 Chemical denotes PBS
329 3169-3177 Disease denotes COVID-19 MESH:C000657245
330 3543-3563 Disease denotes SARS-CoV-2 infection MESH:C000657245
331 4509-4517 Disease denotes COVID-19 MESH:C000657245
335 5251-5259 Disease denotes COVID-19 MESH:C000657245
336 5454-5462 Disease denotes COVID-19 MESH:C000657245
337 5552-5568 Disease denotes viral infections MESH:D001102

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T262 0-10 Sentence denotes Discussion
T263 11-131 Sentence denotes In this study, we developed a rapid and sensitive diagnostic assay for SARS-CoV-2 infections, which is based on RT-LAMP.
T264 132-250 Sentence denotes The assay could detect 23.7 copies of viral RNA within 15 min from clinical specimens (Fig 1A, Table 6, and S1 Table).
T265 251-468 Sentence denotes Currently, RT-qPCR is the gold standard assay of COVID-19 diagnosis and takes at least 2–3 hours to complete all processes including RNA extraction followed by a quantitative PCR step using a real-time thermal cycler.
T266 469-639 Sentence denotes To shorten the assay time, several research groups developed RT-LAMP assays against SARS-CoV-2 [16–21]; however, the detection sensitivity and assay time can be improved.
T267 640-832 Sentence denotes Huang et al. reported a novel RT-LAMP assay that could detect 2 copies of viral RNA after an additional gel electrophoresis step, requiring more assay time than the normal RT-LAMP method [21].
T268 833-991 Sentence denotes In addition to RT-LAMP, we also developed a remarkable rapid assay, Direct RT-LAMP, that does not require the extraction of viral RNA from clinical specimens.
T269 992-1100 Sentence denotes This assay could detect 203 copies of viral RNA in the virus-spiked swab solution within 10.5 min (Table 5).
T270 1101-1229 Sentence denotes The LAMP method has an excellent specificity accomplished by 6 to 8 different primer binding regions in the target DNA sequence.
T271 1230-1379 Sentence denotes Nevertheless, several viruses require multiple sets of primers to detect whole lineages/genotypes due to genetic diversity of their genome sequences.
T272 1380-1473 Sentence denotes Lassa virus (LASV) has 6 lineages and has highly diverse genome even within the same lineage.
T273 1474-1600 Sentence denotes There is a single report of a RT-LAMP assay for LASV, and the assay requires 3 sets of primers to detect only lineage II [22].
T274 1601-1772 Sentence denotes Zika virus also shows diversity in genome sequences between Asian and African genotypes, requiring the mixture of 2 primer sets to detect all strains in one reaction [13].
T275 1773-1946 Sentence denotes Fortunately, SARS-CoV-2 shows lower genetic diversity worldwide, and therefore would be suitable to be diagnosed using the simple RT-LAMP assay with one primer set (S1 Fig).
T276 1947-2158 Sentence denotes Before the emergence of SARS-CoV-2, two large outbreaks of novel coronavirus diseases were reported: severe acute respiratory syndrome (SARS) in 2002, and Middle East respiratory syndrome (MERS) in 2012 [23,24].
T277 2159-2323 Sentence denotes For the molecular diagnosis for these diseases, RT-PCR and RT-qPCR were used as gold standard assays with an immediate announcement of recommended protocols by WHO.
T278 2324-2448 Sentence denotes Several years since the emergence of these coronavirus diseases, RT-LAMP assays were developed for faster diagnosis [25,26].
T279 2449-2677 Sentence denotes For SARS, Thai et al. developed a RT-LAMP assay which is 100-fold more sensitive than RT-PCR [25] and showed clear linearity between viral titer and detection time, and that could detect SARS-CoV even in RT-PCR negative samples.
T280 2678-2763 Sentence denotes Similar to SARS, several RT-LAMP assays were developed for the detection of MERS-CoV.
T281 2764-2960 Sentence denotes Shirato et al. developed a RT-LAMP assay for MERS with a sensitivity comparable to standard RT-qPCR, and with sufficient specificity to distinguish MERS-CoV from 20 other respiratory viruses [26].
T282 2961-3098 Sentence denotes These past reports indicate advantages in using RT-LAMP assays to detect coronavirus from clinical specimens with sufficient sensitivity.
T283 3099-3303 Sentence denotes A recent clinical study that evaluated respiratory tract specimens of COVID-19 patients with severe and mild symptoms showed the initial viral load of 6.17 and 5.11 log10 copies per mL, respectively [27].
T284 3304-3518 Sentence denotes Posterior oropharyngeal saliva, which might represent a non-invasive reasonable specimen acceptable by patients, contained 4 to 8 log10 copies of viral genome per mL in the first 5 days from the symptom onset [27].
T285 3519-3729 Sentence denotes Similarly, experimental SARS-CoV-2 infection of rhesus monkeys showed that the initial viral load in nasal or throat swabs also contained 4 to 8 log10 copies of viral genome per mL within the first 5 days [28].
T286 3730-3992 Sentence denotes Again, our RT-LAMP assay could detect 23.7 copies of SARS-CoV-2 viral RNA, approximately equivalent to 1,778 copies per mL in clinical specimens, effectively detecting SARS-CoV-2 in samples from patients with both severe and mild symptoms during the acute phase.
T287 3993-4200 Sentence denotes Whereas, our Direct RT-LAMP is approximately 60-fold less sensitive than RT-LAMP in the assay for clinical specimens, indicating the reliable detection limit of approximately 5 log10 copies per mL (Table 6).
T288 4201-4416 Sentence denotes Thus, although this Direct RT-LAMP assay detects SARS-CoV-2 in high viral titer samples, it should not be used as a sole molecular diagnostic method but used with another assay such as qPCR to avoid false negatives.
T289 4417-4736 Sentence denotes Nevertheless, Direct RT-LAMP would significantly contribute to the rapid first screening of COVID-19 during an outbreak (1) in the high-risk population (e.g. pregnant women, individuals with a pre-existing illness) who needs an immediate care, and (2) in the resource-limited settings where a centrifuge is unavailable.
T290 4737-4882 Sentence denotes We also found that HBSS affected the detection time of Direct RT-LAMP (Fig 2), indicating that HBSS contains inhibitors of RT-LAMP amplification.
T291 4883-4971 Sentence denotes Therefore, in the Direct RT-LAMP assay, it is preferable to suspend swab samples in PBS.
T292 4972-5123 Sentence denotes Since the RT-LAMP assay can be performed with a portable battery-driven device, it may be available at point-of-care, even in poorly-equipped settings.
T293 5124-5372 Sentence denotes Taken together, our results suggest that this new RT-LAMP protocol can be useful as a rapid and sensitive diagnostic assay for COVID-19, and that the Direct RT-LAMP version could also be made available as a much simpler, faster, and low-cost assay.
T294 5373-5569 Sentence denotes These new assays may contribute to public health control in countries undergoing COVID-19 epidemics, not only for early disease detection, but also to monitor future expansion of viral infections.