SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction–based assays in Addis Ababa, Ethiopia

IJID Regions, Journal Year: 2024, Volume and Issue: 11, P. 100363 - 100363

Published: March 30, 2024

This study aimed to determine the SARS-CoV-2 variants in first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection Addis Ababa, Ethiopia.

Language: Английский

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Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples

Journal of Virological Methods, Journal Year: 2024, Volume and Issue: 328, P. 114956 - 114956

Published: May 23, 2024

Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed quantitative detection RNA from wastewater samples, but little is known on their performance. In this study we compared three based Reverse Transcription Real Time-PCR (RT-PCR) and one Droplet Digital PCR (ddPCR) 35 samples. Overall, was detected by at least method in 85.7% while 51.4%, 22.8% 8.6% resulted positive with two, or all four methods, respectively. Protocols commercial RT-PCR assays showed an overall higher sensitivity vs. in-house assay. The use more than system, targeting different genes, could helpful increase sensitivity.

Language: Английский

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Molecular Amplification and Cell Culturing Efficiency for Enteroviruses’ Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis

Viruses, Journal Year: 2024, Volume and Issue: 16(2), P. 170 - 170

Published: Jan. 23, 2024

Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results EV infections. Herein, we evaluated the efficiency detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging patients suspected have meningitis in northern Algeria collected, anonymously numbered from subjected above-mentioned detection. Using RT-PCR, 34 CSF revealed be positive origin (68%). Thirteen them when RT-PCR was used (26%), only three gave culture technique (6%). Surprisingly, two culture-positive samples, namely, 31 39, negative using directly original samples. However, they turned amplification carried out their corresponding supernatant. The cell-cultured isolates then identified by sequencing genome’s VP1 regions. All belong echovirus 27 strain. This investigation demonstrates that are often more sensitive, accurate much faster, providing reliable within clinically acceptable timeframe. cultures remains crucial enough load serological tests or even avoid rare, but existing, false PCR.

Language: Английский

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Past, Present and Future of Wastewater-Based Surveillance in Public Health Monitoring

Published: Jan. 1, 2024

Language: Английский

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Mutations affect the quantification of SARS-CoV-2 in wastewater: observations, mechanisms, and recommendations

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 22, 2023

Abstract Wastewater surveillance is an effective tool for monitoring community spread of covid-19 and other diseases. Quantitative PCR (qPCR) analysis wastewater more susceptible than binary clinical to mutations in target genome regions. The SARS-CoV-2 concentrations estimated by N1 N2 qPCR assays started diverge around July 2022 data from different sampling sites, analytical methods, laboratories Japan. On the basis genomic experimental data, we demonstrate that divergence due two probe region, which can cause underestimation viral concentrations. We further show this inaccuracy be alleviated if are analyzed with second derivative method or Cy0 instead crossing point method.

Language: Английский

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Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(2)

Published: Jan. 8, 2024

ABSTRACT The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing early detection of severe acute respiratory syndrome 2 (SARS-CoV-2). Although has ended, assays are still needed to monitor viral spread at national levels and beyond through population wastewater surveillance. To enhance detection, SARS-CoV-2 should have high accuracy be validated assure results. Three distinct were evaluated with clinical samples using VALCOR (VALidation SARS-CORona Virus-2 assays) framework, TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We sensitivity, specificity, limit (LOD), overall concordance between comparator three index Allplex (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance LOD assessed dilution series synthetic sequence reference materials (RMs). Ninety positives 90 negatives tested. All had 100.0% sensitivity (95%CI = 95.9%–100.0%). Allplex-SC2 97.8% specificity 92.3%–99.7%) 98.9% [ κ 0.978 0.947–1.000)]. showed 95.9%–100.0%) 1.000 1.000–1.000)]. assessment revealed down 2.61 × 10 copies/mL in samples, while analytical was 9.00 copies/mL. In conclusion, evaluation Seegene an good low RM even slightly lower samples. Non-overlapping target gene sequences RMs emphasize aligning targeted RMs. IMPORTANCE significant impact on global public health, economies, societies. As shown first phases pandemic, timely diagnosis is crucial control, prevention, monitoring. Though phase (SARS-CoV-2) concluded, remain demand individual patient level, regionally, nationally, well infectious preparedness instrument any new dissemination across borders anticipation by WHO central health care policy entities such Center Disease Control, EMA, multiple authorities that will reside endemic years come. key strategic consideration hence shifting from combating situation number patients instead allowing precise diagnostics suspected intention correct management low-prevalence setting.

Language: Английский

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Development of New Rt-Pcr Assays for the Specific Detection of Ba.2.86 Sars-Cov-2 and its Descendent Sublineages

Published: Jan. 1, 2024

The SARS-CoV-2 BA.2.86 variant, also known as Pirola, has acquired over 30 amino acid changes in the Spike protein, evolving into more than 150 sublineages within ten months of its emergence. Among these, JN.1, been rapidly increasing globally becoming most prevalent variant. To facilitate identification sublineages, we designed PiroMet-1 and PiroMet-2 assays silico validated them using viral RNA clinical samples to ascertain analytical specificity sensitivity. were then applied a digital RT-PCR format wastewater samples, combined with OmMet assay (which identifies Omicron except descendants) JRC-UCE can universally recognize all variants), quantify proportion samples. Our results confirmed that both PiroMet are highly specific, sensitivity about 0.7 copies/µl. In conjunction JRC-CoV-UCE.2 assays, accurately quantified findings support integration these routine surveillance timely cost-effective complement sequencing for monitoring prevalence spread communities.

Language: Английский

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A Dual Loci Quality Assurance and Control Framework for Real-Time Evaluation of Signal Accuracy in Wastewater Surveillance of Pathogens with High Rates of Mutation

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 15, 2023

Abstract Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity RT-qPCR has been achieved, part, by monitoring two or more genomic loci SARS-CoV-2. Ontario, Canada, the provincial Surveillance Initiative reports average copies CDC N1 N2 normalized fecal biomarker pepper mild mottle virus. November 2021, emergence Omicron variant concern, harboring a C28311T mutation within probe region, challenged accuracy consensus between measurements this study, we developed applied novel real-time dual quality assurance control framework based on relative difference City Ottawa dataset identify loss assay period from July 10, 2022 January 31, 2023. Further analysis via sequencing allele-specific revealed high proportion mutations C28312T A28330G during study period, both across province. It is hypothesized that nucleotide especially A28330G, led inefficient annealing, resulting reduction assay. This highlights importance implementing criteria continually evaluate, near real-time, signal produced rely detection pathogens whose genomes undergo rates mutation.

Language: Английский

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Impact of sampling site on diagnostic test accuracy of RT-PCR in diagnosing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection since the emergence of omicron: a systematic review and meta-analysis

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 9, 2023

Abstract Nasopharyngeal sampling (NP) is the routine standard for SASR-CoV-2 detection using reverse transcription polymerase chain reaction (RT-PCR). In this systematic review, we assessed diagnostic test accuracy of alternative sites compared to NP RT-PCR testing Omicron (sub)-variants. We systematically searched studies from January 2022 until February 2023 investigating any type respiratory sample in people with suspected, known, or known absence SARS-CoV-2 infection. Data were pooled each comparison bivariate model, sensitivity and specificity was estimated 95% confidence intervals (CIs). Risk bias QUADAS-2 tool, certainty evidence GRADE. included three cohort-type cross-sectional (1,003 participants). Saliva versus showed a 92% (95% CI 87% 96%) 94% 83% 98%). AN one study 90% 82% 95%) 99% 100%). Certainty both comparisons low very low. Based on current low- low-certainty evidence, are uncertain about different RT-PCR.

Language: Английский

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EU surveys insights: analytical tools, future directions, and the essential requirement for reference materials in wastewater monitoring of SARS-CoV-2, antimicrobial resistance and beyond

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 19, 2024

Abstract Background Wastewater surveillance (WWS) acts as a vigilant sentinel system for communities, analysing sewage to protect public health by detecting outbreaks and monitoring trends in pathogens contaminants. To achieve thorough comprehension of present upcoming practices WWS, two EU surveys were conducted targeting WWS laboratories across Europe other regions. The first survey explored diverse range activities currently undertaken or planned laboratories. second specifically targeted methods quality controls utilised SARS-CoV-2 surveillance. Results findings the provide comprehensive insight into procedures methodologies applied WWS. In Europe, primarily focuses on with 99% participants dedicated this virus. However, responses highlighted lack standardisation employed SARS-CoV-2. pathogens, including antimicrobial resistance, is fragmented only limited number Notably, these are anticipated expand future. Survey replies emphasize collective recognition need enhance accuracy results practices, reflecting shared commitment advancing precision effectiveness methodologies. Conclusions These identified standards reference materials reliability addition, it important broaden efforts beyond include emerging resistance ensure approach protecting health.

Language: Английский

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