Omicron and S‐Gene Target Failure Cases in the Highest COVID‐19 Case Rate Region in Canada — December 2021

The Omicron B.1.1.529 SARS-CoV-2 variant was first detected in late November 2021 and has since spread to multiple countries worldwide. We model the potential consequences of the Omicron variant on SARS-CoV-2 transmission and health outcomes in England between December 2021 and April 2022, using a deterministic compartmental model fitted to epidemiological data from March 2020 onwards. Because of uncertainty around the characteristics of Omicron, we explore scenarios varying the extent of Omicron's immune escape and the effectiveness of COVID-19 booster vaccinations against Omicron, assuming the level of Omicron's transmissibility relative to Delta to match the growth in observed S gene target failure data in England. We consider strategies for the re-introduction of control measures in response to projected surges in transmission, as well as scenarios varying the uptake and speed of COVID-19 booster vaccinations and the rate of Omicron's introduction into the population. These results suggest that Omicron has the potential to cause substantial surges in cases, hospital admissions and deaths in populations with high levels of immunity, including England. The reintroduction of additional non-pharmaceutical interventions may be required to prevent hospital admissions exceeding the levels seen in England during the previous peak in winter 2020-2021.

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

10.1101/2021.05.04.21256012 ◽

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.

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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

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.3.2100008 ◽

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.

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S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR

The Journal of Infectious Diseases ◽

10.1093/infdis/jiab082 ◽

2021 ◽

Author(s):

Michael Kidd ◽

Alex Richter ◽

Angus Best ◽

Nicola Cumley ◽

Jeremy Mirza ◽

...

Keyword(s):

Test Data ◽

Gene Target ◽

Viral Loads ◽

S Gene ◽

The Uk

Abstract A SARS-CoV-2 variant B1.1.7 containing a mutation Δ69/70 has spread rapidly in the UK and shows an identifiable profile in ThermoFisher TaqPath RTqPCR (S-gene target failure; SGTF). We analysed recent test data for trends and significance. Linked Ct values for respiratory samples showed that a low Ct for ORF1ab and N were clearly associated with SGTF. Significantly more SGTF samples had higher inferred viral loads between 1x10 7 and 1x10 8. Our conclusion is that patients whose samples exhibit the SGTF profile are more likely to have high viral loads, which may explain higher infectivity and rapidity of spread.

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Increased risk of infection with SARS-CoV-2 Omicron compared to Delta in vaccinated and previously infected individuals, the Netherlands, 22 November to 19 December 2021

10.1101/2021.12.20.21268121 ◽

2021 ◽

Author(s):

Dirk Eggink ◽

Stijn P. Andeweg ◽

Harry Vennema ◽

Noortje van Maarseveen ◽

Klaas Vermaas ◽

...

Keyword(s):

The Netherlands ◽

Confidence Interval ◽

Odds Ratio ◽

Substantial Decrease ◽

Risk Of Infection ◽

Gene Target ◽

S Gene ◽

Increased Risk ◽

Induced Immunity

Infections by the Omicron SARS-CoV-2 variant are rapidly increasing worldwide. Among 70,983 infected individuals (age ≥ 12 years), we observed an increased risk of S-gene target failure, predictive of the Omicron variant, in fully vaccinated (odds ratio: 5.0; 95% confidence interval: 4.0-6.1) and previously infected individuals (OR: 4.9: 95% CI: 3.1-7.7) compared with infected naive individuals. This suggests a substantial decrease in protection from vaccine- or infection-induced immunity against SARS-CoV-2 infections caused by the Omicron variant compared with the Delta variant.

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

10.1101/2021.07.03.21257942 ◽

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.

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Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.16.2100348 ◽

2021 ◽

Vol 26 (16) ◽

Author(s):

Tjede Funk ◽

Anastasia Pharris ◽

Gianfranco Spiteri ◽

Nick Bundle ◽

Angeliki Melidou ◽

...

Keyword(s):

Intensive Care ◽

Confidence Interval ◽

European Countries ◽

Odds Ratios ◽

Gene Target ◽

Intensive Care Admission ◽

S Gene

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0–2.9; B.1.351: 3.6, 95% CI: 2.1–6.2; P.1: 2.6, 95% CI: 1.4–4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4–3.5; P.1: 2.2, 95% CI: 1.7–2.8).

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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

10.1101/2021.12.14.21251883 ◽

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.

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Epidemiological Investigation of New SARS-CoV-2 Variant of Concern 202012/01 in England

10.1101/2021.01.14.21249386 ◽

2021 ◽

Author(s):

Alfredo Maria Gravagnuolo ◽

Layla Faqih ◽

Cara Cronshaw ◽

Jackie Wynn ◽

Lewis Burglin ◽

...

Keyword(s):

Target Detection ◽

Causative Agent ◽

Positive Test ◽

Test Results ◽

Epidemiological Investigation ◽

Gene Target ◽

S Gene ◽

New Variant ◽

Rapid Spread ◽

S Genes

AbstractLighthouse Labs network tests for the presence of RNA of SARS-CoV-2, the causative agent of COVID-19. The Thermofisher TaqPath assay targets three regions of SARS-CoV-2; ORF1ab, N and S-genes. The assay identified a drop in S-gene target detection among positive samples due to the circulation of a new SARS-CoV-2 Variant of Concern (VOC) designated as 202012/01. By end of December 2020, 60% of daily positive test results at Alderley Park Lighthouse Labs, were linked to the new Variant of Concern. This timeline view identifies the rapid spread of the variant across the country.

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Rapid Rise of S-Gene Target Failure and the UK variant B.1.1.7 among COVID-19 isolates in the Greater Toronto Area, Canada

10.1101/2021.02.09.21251225 ◽

2021 ◽

Cited By ~ 1

Author(s):

Kevin Antoine Brown ◽

Jonathan Gubbay ◽

Jessica Hopkins ◽

Samir Patel ◽

Sarah A Buchan ◽

...

Keyword(s):

Reproduction Number ◽

Early Warning Systems ◽

Warning Systems ◽

Gene Target ◽

Health Measures ◽

S Gene ◽

Greater Toronto Area ◽

The United Kingdom ◽

Novel Variant ◽

The Uk

A novel variant of SARS-CoV-2, B.1.1.7, originally discovered in the United Kingdom (UK), is rapidly overtaking other strains around the globe. In certain assays, absence of detection of the S-gene target, also known as S-gene target failure (SGTF) can be a sensitive surrogate of B.1.1.7. We analyzed daily counts of SGTF among samples from Dynacare Laboratory Ontario (which draws samples from the Greater Toronto Area) and resulted between December 16, 2020 and February 3, 2021. We identified 11,485 positive COVID-19 tests, of which 448 had SGTF (3.9%). The estimated prevalence of SGTF rose from 2.0% on December 16 to 15.2% on February 3 (1.8-fold weekly increase, 95%CI: 1.5, 2.2). The estimated reproduction number for SGTF cases was 1.17 (95%CI: 0.94 to 1.46), while the reproduction number for non-SGTF cases was 0.82 (95%CI: 0.65 to 1.01); the relative reproduction number was 1.44 (95%CI: 1.03, 1.99). 59 samples were sent for confirmatory testing, of which 53 (90%) were identified as B.1.1.7 using whole genome sequencing or found to have the N501Y mutation. In order to pre-emptively plan and implement public health measures to control COVID-19 now and through the spring, accurate and up-to-date early warning systems for new variants, including B.1.1.7, are essential across North America and the globe.

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