The Mutational Landscape of SARS-CoV-2

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 9072 - 9072

Published: May 22, 2023

Mutation research is crucial for detecting and treating SARS-CoV-2 developing vaccines. Using over 5,300,000 sequences from genomes custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in genome has mutated at some time, substantial differences frequency regularity mutations warrant further examination. C>U are most common. They found largest number variants, pangolin lineages, countries, which indicates that they a driving force behind evolution Not all genes have same way. Fewer non-synonymous single variations encode proteins with critical role virus replication than ancillary roles. Some genes, such as spike (S) nucleocapsid (N), show more others. prevalence target regions COVID-19 diagnostic RT-qPCR tests generally low, cases, primers bind to N gene, it significant. Therefore, ongoing monitoring crucial. The Portal provides access database mutations.

Language: Английский

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An electrochemical genomagnetic assay for detection of SARS-CoV-2 and Influenza A viruses in saliva

Biosensors and Bioelectronics, Journal Year: 2024, Volume and Issue: 255, P. 116210 - 116210

Published: March 24, 2024

Language: Английский

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Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Feb. 14, 2024

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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Explaining the impact of mutations on quantification of SARS-CoV-2 in wastewater

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: May 30, 2024

Abstract Wastewater surveillance is an effective tool for monitoring community spread of COVID-19 and other diseases. Quantitative PCR (qPCR) analysis wastewater more susceptible to mutations in target genome regions than binary clinical surveillance. 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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Smartphone integrated handheld (SPEED) digital polymerase chain reaction device

Biosensors and Bioelectronics, Journal Year: 2023, Volume and Issue: 232, P. 115319 - 115319

Published: April 15, 2023

Language: Английский

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Phenol-free in-house kit for RNA extraction with applicability to SARS-CoV-2 genomic sequencing studies: A contribution to biotechnological sovereignty in Colombia

Journal of Virological Methods, Journal Year: 2025, Volume and Issue: unknown, P. 115116 - 115116

Published: Feb. 1, 2025

During the COVID-19 pandemic, reagents for SARS-CoV-2 detection were scarce or sold at high prices, particularly in Latin America. In this study, a significant step towards self-sufficiency was achieved through development of an in-house extraction kit detecting from nasopharyngeal swab samples. The purity and concentration RNA extracted using compared to those obtained GeneJET Purification Kit (Thermo-Scientific®) as reference. applicability evaluated four samples positive by NGS sequencing with Illumina®. There no differences between results commercial kit. These findings confirm that protocol demonstrated satisfactory diagnostic accuracy virus patients COVID-19. works effectively, providing optimal genomic characterization lineage assignment within analyzed. This phenol-free represents local design production achievement, offering effective solution swabs. data highlight essential contribution study health biotechnological sovereignty Colombia.

Language: Английский

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Validation and implementation of TaqMAMA RT-PCR for SARS-CoV-2 variant surveillance: experience from a high-volume setting

BMC Infectious Diseases, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 24, 2025

The genomic surveillance of SARS-CoV-2 is challenging in high-volume, resource-limited settings. Faster and less expensive methods are required for the prompt detection variants interest. This study aimed to validate implement TaqMAMA RT-PCR method variants. We developed From viral genomes obtained from GISAID database, fluorescent amplification probes oligonucleotides were designed detect two specific mutations each variant. consisted an assay validation phase comparing newly WGS COVID-19-positive samples, followed by a large-scale implementation calculate its performance. During phase, we included 232 samples analysis using WGS. identified 82.3% as positive, had sensitivities 82%, 100%, 50%, specificities 91%, 99%, with PPVs 75%, NPVs 20%, 100% Delta, Alpha, Gamma variants, respectively. For 1315 68% positive 97.5% delta. predicted performance Bayesian statistics was 95%, 55%, 0% 29%, 0%, < 1% negative delta, alpha, gamma diagnostic acceptable most prevalent offers cost time-saving alternative high-volume

Language: Английский

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Evaluating Interlaboratory Variability in Wastewater-Based COVID-19 Surveillance

Microorganisms, Journal Year: 2025, Volume and Issue: 13(3), P. 526 - 526

Published: Feb. 27, 2025

Wastewater-based environmental surveillance enables the monitoring of SARS-CoV-2 dynamics within populations, offering critical epidemiological insights. Numerous workflows for tracking have been developed globally, underscoring need interlaboratory comparisons to ensure data consistency and comparability. An inter-calibration test was conducted among laboratories network in wastewater samples across Lombardy region (Italy). The aimed evaluate reliability identify potential sources variability using robust statistical approaches. Three were analyzed parallel by four identical pre-analytical (PEG-8000-based centrifugation) analytical processes (qPCR targeting N1/N3 Orf-1ab). A two-way ANOVA framework Generalized Linear Models applied, multiple pairwise performed Bonferroni post hoc test. analysis revealed that primary source results associated with phase. This likely influenced differences standard curves used quantify concentrations, as well size treatment plants. findings this study highlight importance testing verifying determinations identifying key variation.

Language: Английский

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Gold nanoparticle-based immunochromatographic assay for the rapid detection of the SARS-CoV-2 Omicron variant

Materials Chemistry Frontiers, Journal Year: 2023, Volume and Issue: 7(18), P. 4063 - 4072

Published: Jan. 1, 2023

At present, the prevalent Omicron mutant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has characteristics high infectivity and strong concealment, leading to more asymptomatic infections.

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

Human Genomics, Journal Year: 2024, Volume and Issue: 18(1)

Published: June 27, 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 identify challenges opportunities standardisation improvement WWS methodologies, two EU surveys were conducted targeting over 750 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 employed SARS-CoV-2. pathogens, including antimicrobial resistance, is fragmented only limited number Notably, these are anticipated expand future. Survey replies emphasise collective recognition need enhance accuracy results practices, reflecting shared commitment advancing precision effectiveness methodologies. Conclusions These identified standardised common standards reference materials reliability addition, it important broaden efforts beyond include emerging resistance ensure approach protecting health.

Language: Английский

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