Corpus overview


MeSH Disease

HGNC Genes

There are no HGNC terms in the subcorpus

SARS-CoV-2 proteins

There are no SARS-CoV-2 protein terms in the subcorpus


SARS-CoV-2 Proteins
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    Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19 MESHD

    Authors: Dr. Sally Mahmoud; Ms.Esra Ibrahim; Subhashini Ganesan; Dr. Bhagyashree Thakre; Dr.Juliet Teddy; Ms.Preety Raheja; Dr.Walid Zaher

    doi:10.1101/2021.03.15.21253570 Date: 2021-03-17 Source: medRxiv

    In this current COVID 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS COV 2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS MESHD samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer- Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS MESHD samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS CoV 2 testing.

    Coinfection with Respiratory Pathogens in COVID-19 MESHD in Korea

    Authors: Kyung Ho Roh; Yu Kyung Kim; Shin-Woo Kim; Eun-Rim Kang; Yong-Jin Yang; Sun-Kyung Jung; Sun-Hwa Lee; Nackmoon Sung

    doi:10.1101/2020.12.18.20248449 Date: 2020-12-19 Source: medRxiv

    Detection of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 MESHD ( COVID-19 MESHD) were investigated. From the study subjects (N = 258) retrospectively enrolled when confirmed as SARS-CoV-2 positive, nasopharyngeal ( NPS MESHD), oropharyngeal swabs (OPS), and sputum specimens were restored for retesting SARS-CoV-2 and detecting respiratory pathogens. Majority of the study subjects (95.7%, N = 247) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens, suggesting that the upper respiratory specimen is most valuable in detecting SARS-CoV-2. Coinfection rates in COVID-19 MESHD patients (N = 258) with respiratory pathogens were 9.7% (N = 25); 8.5% (N = 22) respiratory viruses and 1.2% (N = 3) Mycoplasma pneumoniae MESHD, an atypical bacterium. Of the respiratory virus coinfection cases (N = 22), 20 (90.9%) were co-infected MESHD with a single respiratory virus and 2 (0.8%) (metapneumovirus/adenovirus and rhinovirus/bocavirus 1/2/3/4) with two viruses. Respiratory viruses in single viral coinfection cases with SARS-CoV-2 were as follows: non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.9%), rhinovirus (N = 4, 1.6%), metapneumovirus (N = 3, 1.2%), influenza A (N = 3, 1.2%), respiratory syncytial virus A and B (N = 3, 1.2%), and adenovirus (N = 2, 0.8%). No mixed coinfections with respiratory viruses and M. pneumoniae were found. In conclusion, the diagnostic value of utilizing NPS MESHD/OPS specimen is excellent, and, as the first report in Korea, coinfection with respiratory pathogens were detected at a rate of 9.7% in patients with COVID-19 MESHD.

    Performance of qualitative and quantitative antigen tests for SARS-CoV-2 in early symptomatic patients using saliva

    Authors: Isao Yokota; Takayo Sakurazawa; Junichi Sugita; Sumio Iwasaki; Keiko Yasuda; Naoki Yamashita; Shinichi Fujisawa; Mutsumi Nishida; Satoshi Konno; Takanori Teshima

    doi:10.1101/2020.11.06.20227363 Date: 2020-11-10 Source: medRxiv

    Background: The rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent need for the prevention and containment of disease outbreaks in communities. Although the gold standard is polymerase chain reaction (PCR), antigen tests such as immunochromatographic assay (ICA) and chemiluminescent enzyme immunoassay (CLEIA) that can yield results within 30 minutes. Methods: We evaluated performance of ICA and CLEIA using 34 frozen PCR-positive specimens (17 saliva and 17 nasopharyngeal swab) and 307 PCR-negative samples. Results: ICA detected SARS-CoV-2 in only 14 (41%) samples, with positivity of 24% in saliva and 59% in NPS MESHD. Notably, ICA detected SARS-CoV-2 in 5 (83%) of 6 samples collected within 4 days after symptom onset. CLEIA detected SARS-CoV-2 in 31 (91%) samples, with positivity of 82% in saliva and 100% in NPS MESHD. CLEIA was negative in 3 samples with low viral load by PCR. Conclusions: These results suggest that use of ICA should be limited to earlier time after symptom onset and CLEIA is more sensitive and can be used in situations where quick results are required.

    Mass screening of asymptomatic persons for SARS-CoV-2 using saliva

    Authors: Isao Yokota; Peter Y Shane; Kazufumi Okada; Yoko Unoki; Yichi Yang; Tasuku Inao; Kentaro Sakamaki; Sumio Iwasaki; Kasumi Hayasaka; Junichi Sugita; Mutsumi Nishida; Shinichi Fujisawa; Takanori Teshima

    doi:10.1101/2020.08.13.20174078 Date: 2020-08-14 Source: medRxiv

    Background COVID-19 MESHD has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS MESHD and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Results In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence, 0.3%. In positive individuals, viral load was highly correlated between NPS MESHD and saliva. Conclusion Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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