scholarly journals Detection of human Coronavirus 229E in nasal specimens in large scale studies using an RT-PCR hybridization assay

2004 ◽  
Vol 18 (2) ◽  
pp. 75-80 ◽  
Author(s):  
Sophie Vallet ◽  
Arnaud Gagneur ◽  
Pierre J Talbot ◽  
Marie-Christine Legrand ◽  
Jacques Sizun ◽  
...  
Keyword(s):  
Large Scale ◽  
Hybridization Assay ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
Human Coronavirus 229E

scholarly journals Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

2017 ◽  
Author(s):  
Alexander L. Greninger ◽  
Gregory Pepper ◽  
Ryan C. Shean ◽  
Anne Cent ◽  
Isabel Palileo ◽  
...  
Keyword(s):  
Large Scale ◽  
Hematopoietic Cell Transplantation ◽  
Rna Virus ◽  
Conditioning Regimen ◽  
Human Coronavirus ◽  
Genomic Deletions ◽  
Total Body ◽  
Orf4 Gene ◽  
Human Coronavirus 229E ◽  
Generation Sequencing

AbstractWe describe metagenomic next-generation sequencing (mNGS) of a human coronavirus 229E from a patient with AML and persistent upper respiratory symptoms, who underwent hematopoietic cell transplantation (HCT). mNGS revealed a 548-nucleotide deletion, which comprised the near entirety of the ORF4 gene, and no minor allele variants were detected to suggest a mixed infection. As part of her pre-HCT conditioning regimen, the patient received myeloablative treatment with cyclophosphamide and 12 Gy total body irradiation. Iterative sequencing and RT-PCR confirmation of 4 respiratory samples over the 4-week peritransplant period revealed that the pre-conditioning strain contained an intact ORF4 gene, while the deletion strain appeared just after conditioning and persisted over a 2.5-week period. This sequence represents one of the largest genomic deletions detected in a human RNA virus and describes large-scale viral mutation associated with myeloablation for HCT.

scholarly journals Quickly and simply detection for coronaviruses including SARS-CoV-2 on the mobile Real-Time PCR without treating RNA in advance

2020 ◽  
Author(s):  
Masaaki Muraoka ◽  
Yukiko Tanoi ◽  
Tetsutaro Tada ◽  
Mikio Mizukoshi ◽  
Osamu Kawaguchi
Keyword(s):  
Real Time ◽  
Correlation Coefficient ◽  
Real Time Pcr ◽  
Positive Control ◽  
List Type ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
One Step ◽  
Short Time ◽  
Human Coronavirus 229E

ABSTRACTSARS-CoV-2 was reported to the WHO as an outbreak in Wuhan City, China on end of 2019, afterwards pandemic on the worldwide in 2020. The SARS-CoV-2 virus is less deadly, but far more transmissible. Therefore, it needs to detect and monitor quickly and simply on site to prevent SARS-CoV-2.If detecting coronaviruses including SARS-CoV-2, the real-time RT-PCR method is sensitive and specific for the unique target, however, it must take long time and labour that RNA is treated in advance, transcribed and amplified. Therefore, referenced previously report, in this study, we modified various methods to prove hypotheses the followed.Firstly, we hypothesized that real-time RT-PCR could be finished in very short time by the mobile real-time PCR device and one-step RT-PCR reagent. Secondly, we hypothesized that it was possible to perform RT-PCR utilizing the reagent as the above without RNA treatment in advance so called “direct”.Firstly, it was able to detect the positive control RNA of SARS-CoV-2 for less than 13.5 minutes by primer-probe referring to the CDC. Moreover, each detection value varied in accordance with each concentration (This correlation coefficient R2 > 0.95). Secondary, it was possible to detect human coronavirus 229E with direct RT-PCR. Furthermore, each detection value varied in accordance with each titer (TCID50 / mL) of human coronavirus 229E (This correlation coefficient R2 > 0.95).Considering the above, causing by utilizing the mobile real-time PCR device and the one-step real-time PCR reagent simultaneously following as: 1) It was possible to detect SARS-CoV-2 in very short time as compared to conventional method; 2) It was possible to detect human coronavirus quickly and simply with “direct”. For these reasons, we hypothesized that it is possible to detect SARS-CoV-2 quickly and simply by utilizing methods the above without treating RNA in advance. This hypothesis is our next try.STRENGTHS AND LIMITATIONS OF THIS STUDY*This study developed it possible to detect the positive control RNA of SARS-CoV-2 more quickly than previously, however couldn’t try to detect the genetic RNA.*This study proved clearly that the human coronavirus instead of SARS-CoV-2 could be detected simply without treating RNA in advance by the same method above.*This study couldn’t try to utilize the human specimens because of our institution limited.*This study could utilize the device and the reagents commercial and not especial.

scholarly journals A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Andra Waagmeester ◽  
Egon L. Willighagen ◽  
Andrew I. Su ◽  
Martina Kutmon ◽  
Jose Emilio Labra Gayo ◽  
...  
Keyword(s):  
Common Ground ◽  
Knowledge Bases ◽  
Public Knowledge ◽  
Medical Problems ◽  
Human Coronavirus ◽  
Data Schema ◽  
Helping Others ◽  
Human Coronaviruses ◽  
The Right ◽  
Human Coronavirus 229E

Abstract Background Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons.” Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. Results As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Conclusions Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

scholarly journals Examining the persistence of human Coronavirus 229E on fresh produce

2021 ◽  
pp. 103780
Author(s):  
Madeleine Blondin-Brosseau ◽  
Jennifer Harlow ◽  
Tanushka Doctor ◽  
Neda Nasheri
Keyword(s):  
Fresh Produce ◽  
Human Coronavirus ◽  
Human Coronavirus 229E

Effect of pH and temperature on the infectivity of human coronavirus 229E

1989 ◽  
Vol 35 (10) ◽  
pp. 972-974 ◽  
Author(s):  
Alain Lamarre ◽  
Pierre J. Talbot
Keyword(s):  
Incubation Period ◽  
Storage Conditions ◽  
Viral Infectivity ◽  
Human Coronavirus ◽  
Virus Growth ◽  
The Stability ◽  
And Storage ◽  
Influence Of Ph ◽  
Human Coronavirus 229E

The stability of human coronavirus 229E infectivity was maximum at pH 6.0 when incubated at either 4 or 33 °C. However, the influence of pH was more pronounced at 33 °C. Viral infectivity was completely lost after a 14-day incubation period at 22, 33, or 37 °C but remained relatively constant at 4 °C for the same length of time. Finally, the infectious titer did not show any significant reduction when subjected to 25 cycles of thawing and freezing. These studies will contribute to optimize virus growth and storage conditions, which will facilitate the molecular characterization of this important pathogen.Key words: coronavirus, pH, temperature, infectivity, human coronavirus.

Development of a novel RT-PCR luminometric hybridization assay for hTERT active transcript in colorectal cancer tissues

2003 ◽  
Vol 124 (4) ◽  
pp. A423
Author(s):  
K. Angelopoulou ◽  
Dimitris Dimitroulopoulos ◽  
A. Spiropoulos ◽  
A. Stthopoulou ◽  
Klisthenis Tsamakidis ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Hybridization Assay ◽  
Rt Pcr ◽  
Cancer Tissues

Cross-contamination in molecular laboratories: A challenge to COVID-19 testing in Bangladesh

2021 ◽  
Vol 2 (5) ◽  
Author(s):  
Mohammad Jahidur Rahman Khan ◽  
◽  
Selim Reza ◽  
Farzana Mim ◽  
Md Abdullah Rumman ◽  
...  
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Diagnostic Errors ◽  
Laboratory Diagnosis ◽  
Cross Contamination ◽  
Rt Pcr ◽  
Public Health Response ◽  
Surveillance Programs ◽  
The Government

Rapid and accurate laboratory diagnosis of SARS-CoV-2 infection is crucial for the management of COVID-19 patients and control of the spread of the virus. At the start of the COVID-19 pandemic, Bangladesh had only one government molecular laboratory where real-time RT-PCR will be performed to diagnose SARS-CoV-2 infection. With the increasing number of suspected cases requiring confirmation diagnostic testing, there was a requirement to quickly expand capacity for large-scale testing. The government of Bangladesh established over 100 molecular laboratories within one year to test COVID-19. To fulfil the requirement for expanded testing, the government was compelled to recruit laboratory employees with inadequate experience, technical knowledge, and skills in molecular assays, particularly in processing specimens, interpreting results, recognizing errors, and troubleshooting. As a result, the risk of diagnostic errors, such as cross-contamination, is increased, as is that the risk of false-positive results, which might risk the patient’s health and undermine the efficacy of public health policies, public health response, surveillance programs, and restrictive measures aimed toward containing the outbreak. This review article aims to explain different sources of crosscontamination in the COVID-19 RT-PCR laboratories and the way to forestall them in efficient and practical ways.

scholarly journals Picornavirus-Like Cytopathic Effects on RD-18S Cell Lines Were Induced by Human Coronavirus 229E Not Picornaviruses

2015 ◽  
Vol 68 (1) ◽  
pp. 78-79 ◽  
Author(s):  
Yohei Matoba ◽  
Yoko Aoki ◽  
Shizuka Tanaka ◽  
Kazue Yahagi ◽  
Tsutomu Itagaki ◽  
...  
Keyword(s):  
Cell Lines ◽  
Human Coronavirus ◽  
Cytopathic Effects ◽  
Human Coronavirus 229E

scholarly journals High speed large scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled with high content screening

2020 ◽  
Author(s):  
Rania Francis ◽  
Marion Le Bideau ◽  
Priscilla Jardot ◽  
Clio Grimaldier ◽  
Didier Raoult ◽  
...  
Keyword(s):  
High Speed ◽  
Large Scale ◽  
Vaccine Development ◽  
Work Load ◽  
Drug Susceptibility Testing ◽  
High Content Screening ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Positive Elements

AbstractSARS-CoV-2, a novel coronavirus infecting humans, is responsible for the current COVID-19 global pandemic. If several strains could be isolated worldwide, especially for in-vitro drug susceptibility testing and vaccine development, few laboratories routinely isolate SARS-CoV-2. This is due to the fact that the current co-culture strategy is highly time consuming and requires working in a biosafety level 3 laboratory. In this work, we present a new strategy based on high content screening automated microscopy (HCS) allowing large scale isolation of SARS-CoV-2 from clinical samples in 1 week. A randomized panel of 104 samples, including 72 tested positive by RT-PCR and 32 tested negative, were processed with our HCS procedure and were compared to the classical isolation procedure. Isolation rate was 43 % with both strategies on RT-PCR positive samples, and was correlated with the initial RNA viral load in the samples, where we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with HCS strategy, where 80 % of the positive samples were recovered by the third day of co-culture, as compared to only 25 % with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive elements after 1 week of co-culture. This system allows rapid and automated screening of clinical samples with minimal operator work load, thus reducing the risks of contamination.

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