In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT‐qPCR assays for SARS‐CoV‐2 detection using whole genome sequencing

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Oct. 20, 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC) Omicron (B.1.1.529) has rapidly spread around the world, presenting a new threat to global public human health. Due large number mutations accumulated by SARS-CoV-2 Omicron, concerns have emerged over potentially reduced diagnostic accuracy reverse-transcription polymerase chain reaction (RT-qPCR), gold standard test for diagnosing disease 2019 (COVID-19). Thus, we aimed assess impact currently endemic sublineages BA.4 and BA.5 on integrity sensitivity RT-qPCR assays used (COVID-19) diagnosis via in silico analysis. We employed whole genome sequencing data evaluated potential false negatives or failure due mismatches between primers/probes VoC viral genome.In 12 tests (containing 30 primers probe sets) developed detection reported World Health Organization (WHO) available literature, was assessed specifically detecting sublineages, obtained after removing redundancy from publicly genomes National Center Biotechnology Information (NCBI) Global Initiative Sharing Avian Influenza Data (GISAID) databases. Mismatches amplicon regions sets were evaluated, clustering analysis corresponding sequences carried out.From 1164 representative sublineage analyzed, substitution first five nucleotides (C T) amplicon's 3'-end observed all samples resulting 0% HKUnivRdRp/Hel (mismatch reverse primer) CoremCharite N both forward primers). mismatch primer's 5'-end (3-nucleotide substitution, GGG AAC), ChinaCDC assay at 0.69%. The 10 nucleotide primer resulted 0.09% Thai assay. Of 1926 genomes, also had sensitivity. A 3.06% because AAC). Similarly, primer, assay's low 0.21% BA.5. Further, eight retained high (more than 97%) 9 more 99% sensitivity.We four (HKUnivRdRp/Hel, N, N) that could result negative results VoCs sublineages. Interestingly, Voc but 99.53% In addition, 66.67% 75% additional along with be modification development

Language: Английский

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Detection of SARS-CoV-2 Based on Nucleic Acid Amplification Tests (NAATs) and Its Integration into Nanomedicine and Microfluidic Devices as Point-of-Care Testing (POCT)

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(12), P. 10233 - 10233

Published: June 16, 2023

The coronavirus SARS-CoV-2 has highlighted the criticality of an accurate and rapid diagnosis in order to contain spread virus. Knowledge viral structure its genome is essential for development. virus still quickly evolving global scenario could easily change. Thus, a greater range diagnostic options face this threat public health. In response demand, there been advancement understanding current methods. fact, innovative approaches have emerged, leveraging benefits nanomedicine microfluidic technologies. Although development incredibly fast, several key areas require further investigation optimization, such as sample collection preparation, assay optimization sensitivity, cost effectiveness, scalability device miniaturization, portability integration with smartphones. Addressing these gaps knowledge technological challenges will contribute reliable, sensitive, user-friendly NAAT-based POCTs other infectious diseases, facilitating effective patient management. This review aims provide overview detection methods based on nucleic acid tests (NAATs). Additionally, it explores promising that combine devices high sensitivity relatively fast ‘time answer’ into point-of-care testing (POCT).

Language: Английский

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Long-term humoral and cellular immunity against vaccine strains and Omicron subvariants (BQ.1.1, BN.1, XBB.1, and EG.5) after bivalent COVID-19 vaccination

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: May 2, 2024

Background The assessment of long-term humoral and cellular immunity post-vaccination is crucial for establishing an optimal vaccination strategy. Methods This prospective cohort study evaluated adults (≥18 years) who received a BA.4/5 bivalent vaccine. We measured the anti-receptor binding domain immunoglobulin G antibody neutralizing antibodies (NAb) against wild-type Omicron subvariants (BA.5, BQ.1.1, BN.1, XBB.1 EG.5) up to 9 months post-vaccination. T-cell immune responses were before 4 weeks after vaccination. Results A total 108 (28 SARS-CoV-2-naïve 80 previously infected) participants enrolled. Anti-receptor (U/mL) levels higher at than baseline in SAR-CoV-2-naïve individuals (8,339 vs. 1,834, p<0.001). NAb titers significantly both groups, whereas EG.5 was negligible all time points. response (median spot forming unit/10 6 cells) highly cross-reactive (wild-type/BA.5/XBB.1.5, 38.3/52.5/45.0 individuals; 51.6/54.9/54.9 SARS-CoV-2-infected individuals) post-vaccination, with insignificant boosting Conclusion Remarkable neutralization observed vaccination, but not EG.5. cross-reactive.

Language: Английский

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Insights into Omicron: Genomic Characterization and Inpatient Risk Assessment at Single Tertiary Hospital in Indonesia

Journal of Multidisciplinary Healthcare, Journal Year: 2025, Volume and Issue: Volume 18, P. 71 - 81

Published: Jan. 1, 2025

Purpose: Omicron is a variant with the highest number of mutations among all Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) viruses, making whole genome sequencing (WGS) an essential tool for public health surveillance and molecular epidemiology. It important to note that data can provide insights into virus evolution disease control. This study aims overview WGS results SARS-CoV-2 Variant at Hasan Sadikin General Hospital Bandung. Patients Methods: was conducted using analytical observational method. Data collected retrospectively from medical records, reverse transcriptase polymerase chain reaction (RT-PCR) results, patients Bandung July December 2022, who met inclusion criteria. The lineage trends, mutation profiles, characteristics differences, factors influencing hospitalization were also described. Results: Among 239 subjects, 50 lineages identified, BA.5.2 (28%) XBB.1 (19.2%) dominating since October respectively. spike gene had frequency, accounting 28.8% out 532 types identified. In lineage, 97.01, 92.53, 100% L452R mutation, F486V H69/V70 deletion, R346T N460K mutations, no deletion observed. associated 5.49 times greater risk inpatient treatment (95% CI: 1.73– 17.38) compared BA.5.2, while adjusted odds ratio (aOR) vaccinations 0.45 0.29– 0.7). Conclusion: dominated infections most occurring in gene. Inpatient influenced by type showing higher risk. A significantly reduced this risk, emphasizing protective role vaccination. Keywords: SARS-CoV-2, variant,

Language: Английский

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Spatiotemporal prevalence of COVID-19 and SARS-CoV-2 variants in Africa

Frontiers in Public Health, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 20, 2025

The coronavirus disease 2019 (COVID-19) pandemic has caused significant public health and socioeconomic crises across Africa; however, the prevalent patterns of COVID-19 circulating characteristics severe acute respiratory syndrome 2 (SARS-CoV-2) variants in continent remain insufficiently documented. In this study, national data on case numbers, infection incidences, mortality rates, circulation SARS-CoV-2 variants, key indexes were collected from various official professional sources between January 2020 December 2023 analyzed with SaTScan geographically weighted regression (GWR). profiles features African continent, including its five regions all countries, analyzed. Four major waves epidemic observed. first wave was closely associated introduction early strain while subsequent linked to emergence specific concern (VOCs) Alpha, Beta, interest (VOIs) Eta (second wave), VOC Delta (third Omicron (fourth wave). analysis identified four large spatiotemporal clusters that affected countries. A number countries (50 out 56) reported their cases during February March 2020, predominantly involving individuals confirmed cross-continental travel histories, mainly Europe. total, 12 distinct VOCs VOIs identified, most being Omicron, Delta, VOI Eta. Unlike dominance third fourth wave, Alpha relatively rare Southern but more common other regions. At same time, Beta predominated region Western second wave. Additionally, higher incidences mortalities Northern Spearman rank correlation (GWR) analyses against 52 indicate expenditures better personnel tended report incidences. This study offers a detailed overview Africa. Strengthening capacity institutions is essential for timely detection new and, consequently, preparedness future pandemics potentially infectious outbreaks.

Language: Английский

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Comparative analysis of ACE2 mutations and their impact on SARS-CoV-2 susceptibility within diverse ethnic groups

Journal of Biomolecular Structure and Dynamics, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 14

Published: March 10, 2025

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted on global public health and economies. Emerging from China, virus generated diverse variants with varying infectivity drug resistance profiles. SARS-COV-2 requires an ACE-2 receptor for its adhesion, genetic analyses have identified multiple single-nucleotide variations in ACE2 across different human populations. We hypothesized that polymorphisms influence susceptibility to infection altering binding affinity between Spike protein. This study aimed explore of five ethnic regions (Africa, America, East Asia, Europe, South Asia) employing silico techniques. By introducing twenty-point mutations into a reference structure, we conducted molecular dynamics (MD) simulations utilized MM/GBSA method analyze impact these ACE2's interaction viral spike Our investigation revealed spectrum effects: 11 out 20 variations, predominantly found Asian population, were classified as deleterious, resulting diminished virus. Additionally, six African ethnicities, categorized potentially potential decrease affinity. Interestingly, two sourced European American groups considered neutral or enhancing, maintaining unaffected Conversely, one point mutation population exhibited increased affinity, indicating vulnerability attachment. These findings offer insights design targeted therapeutics at modulating ACE2-spike protein interaction, thereby mitigating entry infection.

Language: Английский

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Determinants and dynamics of the seroprevalence of anti‐SARS‐CoV‐2 antibodies in Poland

Advances in Medical Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Journal Year: 2023, Volume and Issue: 1870(2), P. 166959 - 166959

Published: Nov. 13, 2023

Language: Английский

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Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(12), P. 6338 - 6338

Published: June 7, 2024

Mutations have driven the evolution and development of new variants severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity vaccine escape among others. Genome sequencing is a technique that allows scientists to read genetic code an organism has become powerful tool studying emerging infectious diseases. Here, we conducted cross-sectional study in selected districts Eastern Province Zambia, from November 2021 February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total 4097 mutations were identified 69 genomes 47% (1925/4097) occurring spike protein. 83 unique amino acid protein seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 XT). Of these, 43.4% (36/83) present receptor binding domain, while 14.5% (12/83) motif. While recombinant XT strain, highly transmissible BA.2 sublineage was more predominant (40.8%). observed substitution other strain Province. This work shows importance pandemic preparedness need monitor general population.

Language: Английский

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SARS-CoV-2 infectivity and antigenic evasion: spotlight on isolated Omicron sub-lineages

Frontiers in Medicine, Journal Year: 2024, Volume and Issue: 11

Published: Aug. 29, 2024

Since the SARS-CoV-2 outbreak in 2019, a diversity of viral genomic variants has emerged and spread globally due to increased transmissibility, pathogenicity, immune evasion. By first trimester 2023 Chile, as most countries, BQ XBB were predominant circulating sub-lineages Omicron. The molecular antigenic characteristics these have been mainly determined using non-authentic spike pseudoviruses, which is often described limitation. Additionally, few comparative studies isolates from recent Omicron conducted. In this study, we isolated clinical samples, including ancestral B.1.1, Delta, BA.1, BA.2 BA.5. We assessed their infectivity through cell culture infections antibody evasion neutralization assays. observed variations plaque size, morphology, cytotoxicity upon infection Vero E6-TMPRSS2 cells for each variant compared B.1.1 virus. BA.2-derived sub-variants, such XBB.1.5, showed attenuated replication, while BA.5-derived variants, BQ.1.1, exhibited replication rates similar Similar trends intestinal Caco-2 cells, except Delta. Antibody experiments sera individuals infected during COVID-19 wave (FWI) consistent but moderate reduction against sub-lineages. Interestingly, despite being less prevalent, BQ.1.1 6.1-fold greater escape than XBB.1.5. Neutralization patterns when tested vaccinated with 3xBNT162b2 (PPP) or Coronavac-Coronavac-BNT162b2 (CCP) schedules. However, CCP 2.3-fold higher XBB.1.5 FWI PPP sera. This study provides new insights into differences between leading eventual outcompetition. Our analysis offers important evidence regarding balance that drives evolution second-generation population.

Language: Английский

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