scholarly journals Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

2021 ◽  
Vol 27 (9) ◽  
pp. 2361-2368
Author(s):  
Jordan Douglas ◽  
Jemma L. Geoghegan ◽  
James Hadfield ◽  
Remco Bouckaert ◽  
Matthew Storey ◽  
...  
Keyword(s):  
New Zealand ◽  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Virus Elimination

scholarly journals Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chukwunonso Onyilagha ◽  
Henna Mistry ◽  
Peter Marszal ◽  
Mathieu Pinette ◽  
Darwyn Kobasa ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Point Of Care ◽  
Middle Eastern ◽  
Turnaround Time ◽  
Cross Reactivity ◽  
Clinical Samples ◽  
Diarrhea Virus ◽  
Highly Sensitive ◽  
Transmissible Gastroenteritis

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), calls for prompt and accurate diagnosis and rapid turnaround time for test results to limit transmission. Here, we evaluated two independent molecular assays, the Biomeme SARS-CoV-2 test, and the Precision Biomonitoring TripleLock SARS-CoV-2 test on a field-deployable point-of-care real-time PCR instrument, Franklin three9, in combination with Biomeme M1 Sample Prep Cartridge Kit for RNA 2.0 (M1) manual extraction system for rapid, specific, and sensitive detection of SARS-COV-2 in cell culture, human, and animal clinical samples. The Biomeme SARS-CoV-2 assay, which simultaneously detects two viral targets, the orf1ab and S genes, and the Precision Biomonitoring TripleLock SARS-CoV-2 assay that targets the 5′ untranslated region (5′ UTR) and the envelope (E) gene of SARS-CoV-2 were highly sensitive and detected as low as 15 SARS-CoV-2 genome copies per reaction. In addition, the two assays were specific and showed no cross-reactivity with Middle Eastern respiratory syndrome coronavirus (MERS-CoV), infectious bronchitis virus (IBV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis (TGE) virus, and other common human respiratory viruses and bacterial pathogens. Also, both assays were highly reproducible across different operators and instruments. When used to test animal samples, both assays equally detected SARS-CoV-2 genetic materials in the swabs from SARS-CoV-2-infected hamsters. The M1 lysis buffer completely inactivated SARS-CoV-2 within 10 min at room temperature enabling safe handling of clinical samples. Collectively, these results show that the Biomeme and Precision Biomonitoring TripleLock SARS-CoV-2 mobile testing platforms could reliably and promptly detect SARS-CoV-2 in both human and animal clinical samples in approximately an hour and can be used in remote areas or health care settings not traditionally serviced by a microbiology laboratory.

scholarly journals RT-PCR for COVID-19: Diagnosis Made Easy

BioMedica ◽  
2020 ◽  
Vol 36 (2S) ◽  
pp. 115-120
Author(s):  
Osheen Sajjad ◽  
Aiman Shahzad ◽  
Saqib Mahmood
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Detection Method ◽  
Current Knowledge ◽  
Detection Methods ◽  
Rt Pcr ◽  
Corona Virus ◽  
Positive Sense ◽  
Affected Person ◽  
Sampling Procedures

<p>Coronavirus disease COVID-19, caused by Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV2), is highly contagious and has been a pandemic since March 2020. The SARS-CoV-2 is an enveloped, single-stranded, positive-sense RNA viruswhich spreadsthrough air droplets by sneezing and coughing from affected person. The diagnosis of the COVID-19 remains a challenge to the scientists since the genome of the SARS-CoV-2 was novel and varying. Various studies have reported the validated procedures for sampling and the detection method of SARS-CoV-2. This mini-review provides a brief introduction of the SARS-CoV-2 features and the current knowledge for the recommended COVID19 detection methods including sampling procedures and real time SARS-CoV-2 genome detection.</p>

Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽  
2022 ◽  
Author(s):  
Rochelle de Bruyn ◽  
Rachelle Bester ◽  
Glynnis Cook ◽  
Chanel Steyn ◽  
Johannes Hendrik Jacobus Breytenbach ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Real Time ◽  
South African ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Citrus Paradisi ◽  
Virus Elimination ◽  
Shoot Tip Grafting ◽  
Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

Qua pote quisque, in ea conterat arte diem: COVID-19 and Australian and New Zealand intensive care

2020 ◽  
Vol 22 (2) ◽  
pp. 103-104
Author(s):  
Andrew Udy ◽  
◽  
Keyword(s):  
Public Health ◽  
Health Care ◽  
Intensive Care Unit ◽  
Intensive Care ◽  
New Zealand ◽  
Severe Acute Respiratory Syndrome ◽  
Clinical Care ◽  
Public Health Emergency ◽  
Care Practice ◽  
Health Care Practice

The current global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has thrust intensive care medicine to the forefront of health care practice in Australia and New Zealand. Indeed, reports from other countries and jurisdictions convey highly confronting statistics about the scale of this public health emergency, particularly in terms of the demand on intensive care unit (ICU)services. Whether this occurs here remains to be seen, although if such a scenario does eventuate, it will represent an unprecedented challenge to our community. In parallel, these events offer the opportunity for greater coordination, improved communication, and innovation in clinical care, which are principles that in many ways define our specialty.

Real‐Time Earthquake Monitoring during the Second Phase of the Deep Fault Drilling Project, Alpine Fault, New Zealand

2017 ◽  
Vol 88 (6) ◽  
pp. 1443-1454 ◽  
Author(s):  
Calum J. Chamberlain ◽  
Carolin M. Boese ◽  
Jennifer D. Eccles ◽  
Martha K. Savage ◽  
Laura‐May Baratin ◽  
...  
Keyword(s):  
New Zealand ◽  
Real Time ◽  
Second Phase ◽  
Deep Fault ◽  
Alpine Fault ◽  
Earthquake Monitoring ◽  
Drilling Project

scholarly journals The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Alexander L. Greninger ◽  
Keith R. Jerome
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Real Time Pcr ◽  
Medical Center ◽  
Rt Pcr ◽  
University Of Washington ◽  
Clinical Laboratories ◽  
To Come ◽  
The Many ◽  
The University

ABSTRACT In early March 2020, the University of Washington Medical Center clinical virology laboratory became one of the first clinical laboratories to offer testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When we first began test development in mid-January, neither of us believed there would be more than 2 million confirmed SARS-CoV-2 infections nationwide or that we would have performed more than 150,000 real-time PCR (RT-PCR) tests, with many more to come. This article will be a chronological summary of how we rapidly validated tests for SARS-CoV-2, increased our testing capacity, and addressed the many problems that came up along the way.

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