Tracing Emergence of SARS-CoV-2 Variants: Insights from Comprehensive Assessment Using Reverse Transcription Polymerase Chain Reaction and Whole Genome Sequencing

Microorganisms, Journal Year: 2025, Volume and Issue: 13(2), P. 311 - 311

Published: Jan. 31, 2025

The emergence and evolution of SARS-CoV-2 variants, such as Delta Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness reverse-transcription polymerase chain reaction (RT-PCR) whole-genome sequencing (WGS) in detecting characterizing variants using 624 samples collected South Korea from mid-2021 mid-2022. Two RT-PCR genotyping assays demonstrated a high concordance rate (90.4%) identifying variant during its dominance. In contrast, WGS revealed extensive genetic diversity among Omicron sub-lineages, 29 distinct including two Korea-specific (BA.1.1.5 BA.2.3.8). Clustering analysis data highlighted groupings BA.1, BA.2, BA.5 with overlap shared mutations suggesting evolutionary convergence. Sub-lineage expanded rapid transmission phases subsequently consolidated dominant lineages emerged. These findings highlight complementary strengths underscore importance integrating these methodologies for effective monitoring public health response.

Language: Английский

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Microbial genomics and genome sequencing approaches

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 3 - 20

Published: Jan. 1, 2025

Language: Английский

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Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern

Vaccines, Journal Year: 2025, Volume and Issue: 13(4), P. 424 - 424

Published: April 17, 2025

Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating severity clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have developed to this effect, including BioNTech-Pfizer Moderna’s mRNA vaccines, as well adenovirus vector-based such Oxford–AstraZeneca. However, emergence new variants subvariants SARS-CoV-2, characterized by enhanced transmissibility immune evasion, poses significant challenges efficacy current vaccination strategies. In review, we aim comprehensively outline landscape emerging concern (VOCs) sub-lineages that recently surfaced post-pandemic years. We assess effectiveness existing their booster doses, against these subvariants, BA.2-derived sub-lineages, XBB BA.2.86 (Pirola). Furthermore, discuss latest advancements vaccine technology, multivalent pan-coronavirus approaches, along development several next-generation coronavirus exosome-based, virus-like particle (VLP), mucosal, nanomaterial-based vaccines. Finally, highlight key critical areas for future research address evolving threat develop strategies combating viral threats, thereby improving preparedness pandemics.

Language: Английский

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Mapping mutational fitness effects across the coxsackievirus B3 proteome reveals distinct profiles of mutation tolerability

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002709 - e3002709

Published: July 16, 2024

RNA viruses have notoriously high mutation rates due to error-prone replication by their polymerase. However, natural selection concentrates variability in a few key viral proteins. To test whether this stems from different tolerance profiles among proteins, we measured the effect of >40,000 non-synonymous mutations across full proteome coxsackievirus B3 as well >97% all possible codon deletions nonstructural We find significant variation mutational within and between individual which correlated with both general protein-specific structural functional attributes. Furthermore, fitness effects remained stable cell lines, suggesting pressures are mostly conserved environments. In addition providing rich dataset for understanding virus biology evolution, our results illustrate that incorporation data into druggable pocket discovery can aid selecting targets barriers drug resistance.

Language: Английский

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Lessons identified for a future pandemic

Journal of Antimicrobial Chemotherapy, Journal Year: 2023, Volume and Issue: 78(Supplement_2), P. ii43 - ii49

Published: Nov. 1, 2023

Abstract Pandemics are complex events requiring a coordinated, global response. The response to the pandemic exposed vulnerabilities in system preparedness. Lessons arising from COVID-19 characterized by four broad themes: (i) investment public health and infrastructure, (ii) countermeasures (medical non-medical), (iii) risk communication measures (iv) people partnerships. Learning identifies an approach that focusses on capacities capabilities pathogen agnostic, ensuring we can respond diverse emerging infectious disease threats will be essential. lessons learned previous ongoing outbreaks should kept under constant review, line with technological scientific advances, improve our ability detect, mitigate new threats.

Language: Английский

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Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(9), P. 2383 - 2394

Published: Aug. 23, 2024

Language: Английский

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Combating Emerging Respiratory Viruses: Lessons and Future Antiviral Strategies

Vaccines, Journal Year: 2024, Volume and Issue: 12(11), P. 1220 - 1220

Published: Oct. 27, 2024

Emerging viral diseases, including seasonal illnesses and pandemics, pose significant global public health risks. Respiratory viruses, particularly coronaviruses influenza are associated with high morbidity mortality, imposing substantial socioeconomic burdens. This review focuses on the current landscape of respiratory SARS-CoV-2, their antiviral treatments. It also discusses potential for pandemics development new vaccines therapies, drawing lessons from past outbreaks to inform future strategies managing threats.

Language: Английский

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Mapping the mutational landscape of a full viral proteome reveals distinct profiles of mutation tolerability

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 7, 2024

SUMMARY RNA viruses have notoriously high mutation rates due to error-prone replication by their polymerase. However, natural selection concentrates variability in a few key viral proteins. To test whether this stems from different tolerance profiles among proteins, we measured the effect of >40,000 non-synonymous mutations across full proteome coxsackievirus B3 as well >97% all codon deletions non-structural We find significant variation mutational within and between individual which correlated with both general protein-specific structural functional attributes. Further, fitness effects remained largely constant cell lines, highlighting conserved pressures. In addition providing rich dataset for understanding virus biology evolution, our results illustrate that incorporation data into druggable pocket discovery can aid selecting targets barriers drug resistance.

Language: Английский

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Wastewater surveillance in post-omicron silent phase uncovers silent waves and cryptic transmission of SARS-CoV-2 variants; a yearlong study in Western India

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 955, P. 176833 - 176833

Published: Oct. 11, 2024

Language: Английский

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