Detecting and isolating false negatives of SARS-CoV-2 primers and probe sets among the Japanese Population: A laboratory testing methodology and study

[Objectives] In this study, a comparative study between primers from Japan's and US's disease control centers was conducted. As further investigation, virus sequence alignment with primers' oligonucleotide was analyzed. [Design or methods] 11,652 samples from Japanese population were tested for SARS-CoV-2 positive using recommended RT-PCR primer-probe sets from Japan National Institute of Infectious Disease (NIID) and US Centers for Disease Control and Prevention (CDC). [Results] Of the 102 positive samples, 17 samples (16.7% of total positives) showed inconsistent results when tested simultaneously for the following primers: JPN-N2, JPN-N1, CDC-N1, and CDC-N2. As a result, CDC recommended primer-probe sets showed relatively higher sensitivity and accuracy. Further virus sequence alignment analysis showed evidences for virus mutation happening at primer's binding sites. [Conclusions] The inconsistency in the RT-PCR results for JPN-N1, JPN-N2, CDC-N1, and CDC-N2 primer-probe sets could be attributed to differences in virus mutation at primers' binding site as observed in sequence analysis. The use of JPN-N2 combined with CDC-N2 primer produces the most effective result to reduce false negatives in Japan region. In addition, adding CDC-N1 will also help to detect false negatives.

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Recognition of another member of the malignant catarrhal fever virus group: an endemic gammaherpesvirus in domestic goats

Journal of General Virology ◽

10.1099/0022-1317-82-1-227 ◽

2001 ◽

Vol 82 (1) ◽

pp. 227-232 ◽

Cited By ~ 48

Author(s):

Hong Li ◽

Janice Keller ◽

Donald P. Knowles ◽

Timothy B. Crawford

Keyword(s):

Dna Polymerase ◽

Sequence Alignment ◽

Gene Sequence ◽

Homologous Sequence ◽

Malignant Catarrhal Fever ◽

Polymerase Gene ◽

Virus Sequence ◽

Herpesvirus 1 ◽

Alignment Analysis ◽

Recognition Of Another

A novel gammaherpesvirus in goats that is herein tentatively designated as caprine herpesvirus-2 was identified based on the sequence of a fragment from the herpesvirus DNA polymerase gene. Sequence alignment analysis revealed that the virus sequence isolated from goats was 67% identical to the homologous sequence from alcelaphine herpesvirus-1, 71% identical to ovine herpesvirus-2 and 73% identical to a recently recognized herpesvirus causing malignant catarrhal fever in white-tailed deer. Combined serological and PCR-survey data demonstrated that this virus is endemic in goats and its transmission pattern may be similar to that of ovine herpesvirus-2 in sheep.

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Review on Diagnostic Methods for SARS-CoV-2

Coronaviruses ◽

10.2174/2666796701999201211213517 ◽

2020 ◽

Vol 01 ◽

Author(s):

Chandrashekhar Chauriya ◽

Mahesh Sahu ◽

Anuj Kumar Singh ◽

Amita Verma

Keyword(s):

Disease Control ◽

Diagnostic Methods ◽

World Health ◽

Diagnostic Strategy ◽

Serological Testing ◽

Rt Pcr ◽

Number Of Patients ◽

Control And Prevention ◽

Antigen Tests ◽

Novel Coronavirus

Background: In December 2019, a large number of patients with a novel coronavirus were identified in Wuhan, China. The novel coronavirus (COVID-19) is highly contagious and increasing the rate of mortality day by day. The World Health Organization declared COVID-19 as a worldwide pandemic on March 11, 2020. Early diagnosis, of SARS-CoV-2, can restrict the COVID-19 pandemic. Objective: We aim to study the currently available diagnostic methods for COVID-19. Methods: World Health Organisation portal, Centre for Disease control and prevention portal, Indian Council of Medical Research portal, Chinese Centre for Disease Control and prevention portal, Science Direct, Google Scholar, Research Gate, etc. were searched for obtaining data. Results: Rapid diagnosis and prompt treatment can reduce the number of prospective cases. The diagnostic strategy encompasses the screening of virus with nucleic acid amplification test (NAAT) such as real-time reverse-transcription polymerase chain reaction (RT-PCR) assays. Serological testing is a diagnostic procedure used for identifying the presence of an immune responses. Radiological findings in individuals with COVID-19 were characterised by multiple areas of consolidation in chest. Rapid antigen tests are in- vitro diagnostics have been designed to give results within 10–20 min. Conclusion: Rapid, simple, and safe diagnosis of COVID-19 has a great impact on deciding clinical and epidemiological factors. RT-PCR results often require 5 to 6 hours. Diagnosis of by serological testing is not suitable but they are important epidemiologically. At present, the best radiological strategy remains undefined. Rapid antigen tests have limitations on sensitivity.

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A Two-Tube Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Sixteen Human Respiratory Virus Types/Subtypes

BioMed Research International ◽

10.1155/2013/327620 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 6

Author(s):

Jin Li ◽

Shunxiang Qi ◽

Chen Zhang ◽

Xiumei Hu ◽

Hongwei Shen ◽

...

Keyword(s):

Respiratory Virus ◽

Simultaneous Detection ◽

Rt Pcr ◽

Pcr Assay ◽

False Negatives ◽

Viral Pathogens ◽

Reverse Transcription Pcr ◽

Routine Surveillance ◽

Control And Prevention ◽

Respiratory Virus Infection

There is a need for the development of a rapid and sensitive diagnosis of respiratory viral pathogens. With an intended application in provincial Centers for Diseases Control and Prevention, in this study, we present a two-tube multiplex RT-PCR assay (two-tube assay) using automatic electrophoresis to simultaneously detect sixteen common respiratory viruses. The specificity and the sensitivity of the assay were tested. The assay could detect 20–200 copies per reaction when each viral type was assayed individually, 2000 copies with 9 premixed viral targets in the multiplexed assay in tube 1, and 200 copies with 8 premixed templates in tube 2. A total of 247 specimens were used to evaluate the two-tube assay, and the results were compared with those obtained from the Luminex xTAG RVP Fast assay. The discordant results were confirmed by sequencing or by the Seeplex RV15 ACE detection kit. There were no false positives, but six false negatives occurred with the two-tube assay. In conclusion, the two-tube assay is demonstrated to have great potential for routine surveillance of respiratory virus infection in China.

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The Speech-Language Pathologists' Role in Mild Traumatic Brain Injury for Middle and High School–Age Children: Viewpoints on Guidelines From the Centers for Disease Control and Prevention

American Journal of Speech-Language Pathology ◽

10.1044/2019_ajslp-18-0296 ◽

2019 ◽

Vol 28 (3) ◽

pp. 1363-1370 ◽

Cited By ~ 2

Author(s):

Jessica Brown ◽

Katy O'Brien ◽

Kelly Knollman-Porter ◽

Tracey Wallace

Keyword(s):

High School ◽

Traumatic Brain Injury ◽

Brain Injury ◽

Disease Control ◽

Mild Traumatic Brain Injury ◽

School Age Children ◽

School Age ◽

Speech Language Pathologists ◽

Control And Prevention ◽

Centers For Disease Control

Purpose The Centers for Disease Control and Prevention (CDC) recently released guidelines for rehabilitation professionals regarding the care of children with mild traumatic brain injury (mTBI). Given that mTBI impacts millions of children each year and can be particularly detrimental to children in middle and high school age groups, access to universal recommendations for management of postinjury symptoms is ideal. Method This viewpoint article examines the CDC guidelines and applies these recommendations directly to speech-language pathology practices. In particular, education, assessment, treatment, team management, and ongoing monitoring are discussed. In addition, suggested timelines regarding implementation of services by speech-language pathologists (SLPs) are provided. Specific focus is placed on adolescents (i.e., middle and high school–age children). Results SLPs are critical members of the rehabilitation team working with children with mTBI and should be involved in education, symptom monitoring, and assessment early in the recovery process. SLPs can also provide unique insight into the cognitive and linguistic challenges of these students and can serve to bridge the gap among rehabilitation and school-based professionals, the adolescent with brain injury, and their parents. Conclusion The guidelines provided by the CDC, along with evidence from the field of speech pathology, can guide SLPs to advocate for involvement in the care of adolescents with mTBI. More research is needed to enhance the evidence base for direct assessment and treatment with this population; however, SLPs can use their extensive knowledge and experience working with individuals with traumatic brain injury as a starting point for post-mTBI care.

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