Rapid Shift from SARS-CoV-2 Delta to Omicron Sub-Variants within a Dynamic Southern U.S. Borderplex

Viruses, Journal Year: 2023, Volume and Issue: 15(3), P. 658 - 658

Published: Feb. 28, 2023

COVID-19, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), remains an ongoing global health challenge. This study analyzed 3641 SARS-CoV-2 positive samples from El Paso, Texas, community and hospitalized patients over 48 weeks Fall 2021 to Summer 2022. The binational along U.S. southern border was predominantly Delta variant (B.1.617.2) for a 5-week period September January 2022 quickly transitioned Omicron (B.1.1.529), which first detected at end of December 2021. replaced as predominant detectable in associated with sharp increase COVID-19 positivity rate, related hospitalizations, newly reported cases. In this study, BA.1, BA.4, BA.5 variants were overwhelmingly S-gene dropout qRT-PCR analysis unlike BA.2 variants. reveals that dominant variant, like Delta, can be rapidly more transmissible Omicron, within dynamic metropolitan city, necessitating enhanced monitoring, readiness, response public officials healthcare workers.

Language: Английский

---

S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5

Microorganisms, Journal Year: 2024, Volume and Issue: 12(2), P. 321 - 321

Published: Feb. 3, 2024

During the SARS-CoV-2 pandemic, Dr. Risch medical group employed multiplex TaqPathTM COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and principality of Liechtenstein. The TaqPath is a widely used assay targeting three genes (i.e., ORF1AB, N, S). With emergence B.1.1.7 (Alpha) variant, flaw became apparent as amplification S-gene target was absent these samples due to deletion (ΔH69/V70) Alpha variant genome. This failure (SGTF) earliest indication new emerging also observed subsequent variants such Omicron BA.1 BA4/BA.5. Delta BA.2 did not present with SGTF. From September 2020 November 2022, we investigated applicability SGTF surrogate marker B.1.1.7, B.1.617.2 (Delta), BA.1, BA.2, BA.4/BA.5 cycle threshold (Ct) values < 30. Next true SGTF-positive SGTF-negative samples, there were presenting delayed-type (higher Ct value than ORF1ab gene). Among these, difference 3.8 between S- found best distinguish “true” variability assay. Samples above cutoff subsequently termed partial (pSGTF). Variant confirmation performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) among 240,896 positives variant-confirmed, resulting an overall sensitivity specificity 93.2% [92.7%, 93.7%] 99.3% [99.2%, 99.5%], respectively. Sensitivity increased 98.2% [97.9% 98.4%] lowered 98.9% [98.6% 99.1%] when pSGTF included. Furthermore, weekly logistic growth rates (α) sigmoid’s midpoint (t0) calculated based on data significantly differ from calculations comprehensive GISAID. therefore allowed valid real-time estimate introduction all dominant

Language: Английский

---

Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis

Diagnostics, Journal Year: 2023, Volume and Issue: 13(9), P. 1573 - 1573

Published: April 27, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology considered gold standard for monitoring known and new SARS-CoV-2 However, complexity this renders approach impracticable in laboratories located areas limited resources. We analyzed capability ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) Seegene Novaplex Variant assay (Novaplex) to detect Omicron variants; Allplex VariantII (Allplex) was also evaluated Delta Sanger sequencing (SaS) reference method. The results obtained n = 355 nasopharyngeal samples were: negative TaqPath, although positive other qualitative molecular assays (n 35); undetermined 40) both assays; ∆69/70 mutation confirmed as variant via SaS 100); BA.1 80); typed BA.2 80). 27.5% 11.4% 100% were subtypes. In total, 99/100 a per cent agreement (PPA) 98% compared SaS. As undermined showed RdRp median Ct values (Ct 35.4) statistically higher than those (median value 22.0; p < 0.0001, Mann–Whitney test), inability establish variants probably linked low viral load. No amplification among all 35 samples. Overall, 20% which or them, twelve not even SaS, but they instead correctly identified Novaplex. Although full-genome remains elected method characterize strains, our data show high ability SNP-based identify VOCs, resolving TaqPath.

Language: Английский

---

Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS‐CoV‐2 variants

Immunity Inflammation and Disease, Journal Year: 2022, Volume and Issue: 10(6)

Published: May 11, 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, limit viral community spread. SARS-CoV-2 variants concern (VOCs) such as Alpha Omicron, show increased transmissibility immune evasion, rapidly became dominant VOCs worldwide. Our objective was develop an evidenced-based genomic algorithm, combining reverse transcription polymerase chain reaction (RT-PCR) sequencing technologies quickly identify highly contagious VOCs, before cases accumulate exponentially. Deidentified data were obtained from 508,969 patients tested for disease 2019 (COVID-19) with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA-certified clinical laboratories Puerto Rico (n = 86,639) three United States 422,330). frequency S Gene Target Failure (SGTF) > 47% last week March 2021 both, US laboratories. monthly SGTF steadily exponentially 4% November 2020 2021. weekly rate samples high (>8%) late December early January then also through April (48%). exponential increase SGFT prevalence concurrent sharp among all sequences uploaded Global Influenza Surveillance Response System (GISAID) 461). variant <1% 51.5% collected According proposed evidence-based approximately 50% should be managed self-quarantine contact tracing protocols, while WGS confirms their lineage results suggest this workflow is useful tracking SGTF.

Language: Английский

---

Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 11, 2024

ABSTRACT The development of biosurveillance programs with strong analytical performance and economically accessible protocols is essential for monitoring viral pathogens. Throughout the COVID-19 pandemic, whole-genome sequencing (WGS) has been prevailing technology SARS-CoV-2 variant concern (VOC) detection. While WGS offers benefits, it a lengthy process, financially technically straining scalable tracking. aim this study was to compare economic feasibility PCR mutation panels distinguishing six known VOCs: Alpha (B.1.1.7 Q.4), Gamma (P.1), Delta (B.1.617.2 AY.4.2), Omicron. (B.1.1.529.1). In all, 78 SARS-CoV-2-positive samples were collected from April December 2021 at Northeastern University (Cabot Testing Site, Boston, MA, USA) genotyping analysis. MagMax Viral/Pathogen II Nucleic Acid Isolation TaqPath Combo Kits used RNA extraction confirmation. VOC discrimination assessed using two TaqMan single nucleotide polymorphism (SNP) assay layouts, Ion Torrent WGS. November 2021, panel demonstrated marked versatility by detecting emerging Omicron reported South Africa. SNP analysis yielded following identifications: B.1.1.7 ( N = 20), Q.4 3), P.1 1), B.1.617.2 30), AY.4.2 B.1.1.529.1 20) one undetermined 1) sample. Genotyping designated lineages in 77 samples, 46/78 confirmed WGS, while 32 failed lineage assignment. RT-PCR offer pronounced throughput sensitivity provide an advantageous technique biosurveillance. IMPORTANCE results presented our manuscript demonstrate how value simplistic reliable molecular assays coupled core scientific principle standardization can be overlooked charm more sophisticated instrumentation. This effect often amplified during tumultuous public health events, such as pandemic. By adapting standardized detect prominently circulating variants, we able better assess potential impacts rising positivity rates transmission clusters within population. several literature publications utilizing NGS have similar scope ours, many investigations lack sufficiently bioinformatics inclusionary/exclusionary criteria identification. Finally, benefits would allow global implementation biosurveillance, rather than reserving developed nations.

Language: Английский

---

To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant

Advances in Microbiology, Journal Year: 2024, Volume and Issue: 14(05), P. 247 - 255

Published: Jan. 1, 2024

Introduction: Omicron is a highly divergent variant of concern (VOCs) severe acute respiratory syndrome SARS-CoV-2. It carries high number mutations in its spike protein hence; it more transmissible the community by immune evasion mechanisms. Due to mutation within S gene, most variants have reported gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers screen Omicron. However, Whole Genome Sequencing (WGS) only gold standard approach confirm novel microorganisms at genetically level similar also found other that are circulating low frequencies worldwide. This Retrospective study aimed assess RT-PCR sensitivity detection comparison whole genome sequencing detect Methods: We analysed retrospective data SARS-CoV-2 positive samples for TaqPath COVID-19 Combo Kit (ThermoFisher) and combined technologies emerged pattern during third wave tertiary care centre, Surat. Results: From first day December 2021 till end February 2022, total 321,803 tests were performed, which 20,566 cases our centre an average cumulative positivity 6.39% over period three months. In month 21 characterized SGTF (70/129) suggestive being infected identified (B.1.1.529 lineage) when sequence. January, we subset (n = 618) (24%) without (76%) Ct values Conclusions: During pandemic, took almost than 15 days diagnose infection identify pathogen technology. contrast molecular assay provided quick identification help phenomenon 5 hours duration. strategy helps scientists health policymakers isolation clusters. That ultimately results decreased transmission among community.

Language: Английский

---

Evaluation of self‐collected nasal, urine, and saliva samples for molecular detection of SARS‐CoV‐2 using an EUA approved RT‐PCR assay and a laboratory developed LAMP SARS‐CoV‐2 test

Immunity Inflammation and Disease, Journal Year: 2024, Volume and Issue: 12(6)

Published: June 1, 2024

Abstract As the SARS‐CoV‐2 virus spread throughout world, millions of positive cases COVID‐19 were registered and, even though there are people already vaccinated against SARS‐CoV‐2, a large part global population remains vulnerable to contracting virus. Massive nasopharyngeal sample collection in Puerto Rico at beginning pandemic was limited by scarcity trained personnel and testing sites. To increase molecular availability, we evaluated diagnostic accuracy self‐collected nasal, saliva, urine samples using TaqPath reverse transcription polymerase chain reaction (RT‐PCR) kit detect SARS‐CoV‐2. We also created colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) as another strategy availability community‐based laboratories. Automated RNA extraction performed KingFisher Flex instrument, followed PCR quantification on 7500 Fast Dx RT‐PCR test. Data interpreted Interpretive Software from Applied Biosystems statistically analyzed with Cohen's kappa coefficient (k). (k) for paired nasal saliva showed moderate agreement (0.52). Saliva exhibited higher viral load. observed 90% concordance between LifeGene‐Biomarks' Rapid Colorimetric LAMP LDT Our results suggest that is superior testing. The rapid alternative tests detection This can be easily implemented clinics, hospitals, workplace, home; optimizing surveillance process, which helps mitigate public health socioeconomic upheaval caused airborne pandemics.

Language: Английский

---