scholarly journals Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

2021 ◽  
Vol 26 (3) ◽  
Author(s):  
Antonin Bal ◽  
Gregory Destras ◽  
Alexandre Gaymard ◽  
Karl Stefic ◽  
Julien Marlet ◽  
...  
Keyword(s):  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
S Gene

We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

scholarly journals Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya

2021 ◽  
Author(s):  
Inas M Alhudiri ◽  
Ahmad M Ramadan ◽  
Khaled Ibrahim Ibrahim ◽  
Mouna Eljilani ◽  
Adel Abdalla Aboud ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Drop Out ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
Specific Identification ◽  
S Gene ◽  
The Uk

A cluster-5 variant was detected in September 2020 in minks and humans in Denmark and currently classified as Alpha or B.1.1.7 strain. This variant presents several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The national center for disease control (NCDC) announced on 24th February 2021 the discovery of B.1.1.7 strain in Libya using a reverse-transcriptase PCR assay for S-gene target failure (SGTF) and reported that 25% of the tested samples were UK variant. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes S gene drop out in RT-PCR; characteristic of the UK variant (B.1.1.7). This letter discusses our whole genome sequencing results of positive SARS-COV-2 samples with SGTF collected between 25th February - 4th March 2021 in Libya.

scholarly journals S Gene Target Failure (SGTF) in Commercial Multiplex RT-PCR assay as indicator to detect SARS-CoV-2 VOC B.1.1.7 lineage in Tamil Nadu, India

2021 ◽  
Author(s):  
Vidhya N M ◽  
Kumaresan A ◽  
Kalaivani V ◽  
Rajesh Kumar A ◽  
Gurunathan Subramanian ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tamil Nadu ◽  
Immune Escape ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
S Gene ◽  
Significant Public Health

Emergence of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) Variants of Concern (VOC) possessing improved virulence, transmissibility and/or immune-escape capabilities has raised significant public health concerns. In order to identify VOCs, WHO recommends Whole-Genome Sequencing approach, which is costly and involves longer completion time. Hence, potential role of commercial multiplex RT-PCR kit to screen variants rapidly is being attempted in this study. A total of 1200 suspected COVID samples from different districts of Tamil Nadu State (India) were screened with Thermo TaqPath RT-PCR kit and Altona Realstar RT-PCR Assay kit. Among 1200 screened, S-gene target failure (SGTF) phenomenon were identified in 112 samples while testing with TaqPath RT-PCR Kit. 100% concordant results were observed between SGTF phenomenon and whole-genome sequencing (WGS) results in detecting SARS-CoV-2 VOC B.1.1.7. TaqPath RT-PCR assay testing can be utilized by laboratories to screen rapidly the VOC B.1.1.7 variants, thus enabling early detection of B.1.1.7 variant infection and transmission in population. This in turn will pave way to implement suitable preventive measures by appropriate authorities to control the transmission of the viral variant.

scholarly journals Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants.

2021 ◽  
Author(s):  
Rafael Guerrero-Preston ◽  
Vanessa Rivera Amill ◽  
Karem Caraballo ◽  
Andrea Arias Garcia ◽  
Raphael Sanchez Torres ◽  
...  
Keyword(s):  
Puerto Rico ◽  
The United States ◽  
Contact Tracing ◽  
Rt Pcr ◽  
Surveillance Network ◽  
Gene Target ◽  
S Gene ◽  
Sequencing Technologies ◽  
Clinical Laboratories ◽  
Exponential Increase

Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. Deidentified data were obtained from 508,969 patients tested for COVID-19 with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA certified clinical laboratories in Puerto Rico (n=86,639) and in three CLIA certified clinical laboratories in the US (n=422,330). TaqPath data revealed a frequency of S Gene Target Failure (SGTF) >47% for the last week of March 2021, in both Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021.The weekly SGTF rate in US samples was high (>8%) from late December to early January, and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico is concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to GISAID (n=461). B.1.1.7 frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021. The exponential increase in SGTF and B.1.1.7 prevalence in Puerto Rico and US requires an urgent response. According to the proposed evidence-based algorithm, approximately 50% of all positive samples should be managed as potential B.1.1.7 carriers with VOC quarantine and contact tracing protocols while their lineage is confirmed by WGS in surveillance laboratories. Patients infected with VOCs should be effectively triaged for isolation, contact tracing and follow-up treatment purposes.

scholarly journals Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

2021 ◽  
Author(s):  
Zain Mushtaq ◽  
Sadia Shakoor ◽  
Akbar Kanji ◽  
Najma Shaheen ◽  
Asghar Nasir ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
Missed Opportunities ◽  
Spike Gene ◽  
Diagnostic Assays ◽  
Additional Testing ◽  
Pcr Assays ◽  
Possible Cause

Abstract Objective: To investigate the possible cause of discrepancy between clinical and RT-PCR based diagnosis of patients with COVID-19.Results: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested using the Roche SARS-CoV-2 Cobas assay and were found to be negative. Further investigation for other viral causes of pneumonia was conducted using the Filmarray RP2.1 assay, which identified SARS-CoV-2 as the pathogen in all ten cases. To investigate whether this could be due to discrepancies between PCR assay, additional testing was conducted using the TaqPath TM COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, could be due to variation in the primer binding sites. The identification of strains with SGTF identify the possible presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.

scholarly journals Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70, Lyon, France, August to December 2020

2020 ◽  
Author(s):  
Antonin Bal ◽  
Gregory Destras ◽  
Alexandre Gaymard ◽  
Hadrien Regue ◽  
Quentin Semanas ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
False Negative ◽  
False Negative Result ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Large Scale Screening

AbstractThe spike deletion H69-V70 (ΔH69/ΔV70) has been recently detected in a SARS-CoV-2 variant under investigation in England (VUI 202012/01) as well as in cluter-5 variant detected both in minks and humans in Denmark. Herein we report the implementation of a two-step strategy enabling to detect SARS-CoV-2 variants carrying H69-V70 deletion. We found that this deletion resulted in a false negative result for the spike target of a three-target RT-PCR assay (TaqPath kit). From August 3rd to December 20th, 59/9,266 (0.6%) of positive tests displayed a S negative profile (negative for S target and positive for N & ORF1ab targets). Among the 59 samples without detection of the S target, 36 were available for whole genome sequencing (WGS). The most frequent S mutations co-occurring with ΔH69/ΔV70 were S477N & D614G (21/36 samples). The co-occurrence of N439K and D614G mutations was found in 10/36 samples. The complete combination of S mutations detected in VUI 202012/01 or in cluster-5 variant was not found. The data presented herein emphasize that the TaqPath RT-PCR assay enables a rapid, large-scale screening of ΔH69/ΔV70 variants. Samples with S negative profiles should be further addressed to national referral laboratories for SARS-CoV-2 WGS. This 2-step strategy is currently being reinforced in France as national diagnostic platforms have mainly implemented the TaqPath RT-PCR kit.

scholarly journals Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assay

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 491 ◽  
Author(s):  
Dóra Tombácz ◽  
Judit S Tóth ◽  
Pál Petrovszki ◽  
Zsolt Boldogkői
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Genome Analysis ◽  
Pseudorabies Virus ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Whole Genome Analysis ◽  
Virus Gene ◽  
Virus Gene Expression

1089: Prognostic Value of Molecular Staging of Bladder Cancer with RT -PCR Assay for KRT20: Results at 5 Year-Follow-up

2007 ◽  
Vol 177 (4S) ◽  
pp. 360-360
Author(s):  
Ana Agud ◽  
Maria J. Ribal ◽  
Lourdes Mengual ◽  
Mercedes Marin-Aguilera ◽  
Laura Izquierdo ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Prognostic Value ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Molecular Staging

Phylogeny of 2019-nCoVs and SARS-like CoVs of Human, Bat and Pangolin Origin

2020 ◽  
Keyword(s):  
N Gene ◽  
Whole Genome ◽  
Human Origin ◽  
Gene Sequences ◽  
M Gene ◽  
S Gene ◽  
Shared Identity ◽  
Novel Coronavirus ◽  
S Genes

A novel coronavirus first broke out in Wuhan, China in December, 2019 has been declared a pandemic by WHO on March, 2020. This work aimed to search for probable ancestor of the virus, phylogeny of 2019-nCoVs and similar SL-CoVs based on the whole genome, M, N, ORF1ab, orf3a, and S gene sequences (n=84) obtained from GenBank using BLASTn software in the NCBI was done. Nucleotides of ORF3a and S-genes among 2019-nCoVs are identical, whereas its similar on the whole genome (99.9-100%), M-gene (99.7-100%), N-gene (99.9-100%) and ORF1ab-gene (99.7-100%). nCoVs are similar to bat CoV/RaTG13 on the whole genome (96.2%), M-gene (95.0%), N-gene (97%), ORF1ab-gene (95.3%), ORF3a-gene (99.1%) and S-gene (90.7%). Likewise, nCoVs exhibited homology to bat-CoVZXC21 on M-gene (93.2%), N-gene (91.5%), ORF1ab-gene (93.1%) and ORF3a-gene (94.4%). The emergent viruses shared identity to bat-CoVZC45 on N-gene (91.3%), ORF1ab-gene (92.8%) and ORF3a-gene (94.0%). In addition, pangolin-CoV/MP789 exhibited common sequences on M-gene (91.0%), N-gene (96.3%) and ORF3a-gene (93.3%) to nCoV. Furthermore, pangolin-CoV/MP789 is analogous to bat CoV/RaTG13 (91.3%) and bat-SL-CoVZXC21 (92.2%) on M-gene and to bat CoV/RaTG13 (94.8%) on N-gene. Nevertheless, nCoVs are distinct from the previously identified SL-CoVs of human origin. The present analysis indicates that nCoVs may have transmitted from bats, pangolin and/or unidentified hosts.

Polymerase chain reaction amplification and typing of rotavirus in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 371-374 ◽  
Author(s):  
R. Gajardo ◽  
R. M. Pintó ◽  
A. Bosch
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Polymerase Chain Reaction Amplification ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Group A ◽  
Reaction Amplification ◽  
Stool Specimens ◽  
Polymerase Chain

A reverse transcription polymerase chain reaction (RT-PCR) assay is described that has been developed for the detection and serotyping of group A rotavirus in stool specimens and concentrated and non-concentrated sewage specimens.

Scoring System for the Diagnosis of COVID-19

2020 ◽  
Vol 13 (1) ◽  
pp. 413-414 ◽  
Author(s):  
Mohamed Farouk Allam
Keyword(s):  
Scoring System ◽  
Clinical Symptoms ◽  
False Negative ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Negative Results ◽  
False Negative Results ◽  
Symptoms And Signs

Due to the international spread of COVID-19, the difficulty of collecting nasopharyngeal swab specimen from all suspected patients, the costs of RT-PCR and CT, and the false negative results of RT-PCR assay in 41% of COVID-19 patients, a scoring system is needed to classify the suspected patients in order to determine the need for follow-up, home isolation, quarantine or the conduction of further investigations. A scoring system is proposed as a diagnostic tool for suspected patients. It includes Epidemiological Evidence of Exposure, Clinical Symptoms and Signs, and Investigations (if available). This scoring system is simple, could be calculated in a few minutes, and incorporates the main possible data/findings of any patient.

Sign in / Sign up

Export Citation Format

Share Document