Population-Level SARS-CoV-2 RT–PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years

Viruses, Год журнала: 2025, Номер 17(1), С. 103 - 103

Опубликована: Янв. 14, 2025

This study investigates the relationship between SARS-CoV-2 RT-PCR cycle threshold (Ct) values and key COVID-19 transmission outcome metrics across five years of pandemic in Jalisco, Mexico. Utilizing a comprehensive time-series analysis, we evaluated weekly median Ct as proxies for viral load their temporal associations with positivity rates, reproduction numbers (Rt), hospitalizations, mortality. Cross-correlation lagged regression analyses revealed significant lead-lag relationships, declining consistently preceding surges rates particularly during early phases pandemic. Granger causality tests vector autoregressive modeling confirmed predictive utility values, highlighting potential warning indicators. The further observed weakening association later stages, likely influenced by emergence new variants, hybrid immunity, changes human behavior, diagnostic shifts. These findings underscore value scalable tools public health surveillance highlight importance contextualizing analysis within specific epidemiological frameworks. Integrating monitoring into systems could enhance preparedness, improve outbreak forecasting, strengthen modeling.

Язык: Английский

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4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection

Journal of Proteome Research, Год журнала: 2025, Номер 24(2), С. 499 - 514

Опубликована: Янв. 13, 2025

Since late 2021, Omicron variants have dominated the epidemiological scenario as most successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineages, driving new and breakthrough infections globally over past two years. In this study, we investigated for first time host salivary response of COVID-19 patients infected with (BA.1, BA.2, BA.4/5) by using an untargeted four-dimensional data-independent acquisition (4D-DIA)-based proteomics approach. We identified 137 proteins whose abundance levels differed between positive negative groups. Salivary signatures were mainly enriched in ribosomal proteins, linked to mRNAviral translation, protein synthesis processing, immune innate, antiapoptotic signaling. The higher 14-3-3 (YWHAG, YWHAQ, YWHAE, SFN) saliva, reported here, may be associated increased infectivity improved viral replicative fitness. also seven (ACTN1, H2AC2, GSN, NDKA, CD109, GGH, PCYOX) that yielded comprehension into infection performed outstandingly screening a hospital setting. This panel presented enhanced anti-COVID-19 anti-inflammatory signature, providing insights disease severity, supported comparisons other proteome data sets. signature provided valuable host's SARS-CoV-2 infection, shedding light on pathophysiology COVID-19, particularly cases mild disease. It underscores potential clinical applications saliva settings. Data are available via ProteomeXchange identifier PXD054133.

Язык: Английский

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Real-world accuracy of SARS-CoV-2 antigen detection compared with qPCR: A cross-sectional study in Toledo - PR, Brazil

The Brazilian Journal of Infectious Diseases, Год журнала: 2025, Номер 29(3), С. 104520 - 104520

Опубликована: Апрель 17, 2025

Язык: Английский

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Screening and diagnosis of respiratory diseases using metamaterial based sensitive terahertz impedance spectroscopy

Sensing and Bio-Sensing Research, Год журнала: 2024, Номер 44, С. 100639 - 100639

Опубликована: Март 19, 2024

Utilizing LC resonant metamaterials (MM) for terahertz (THz) impedance spectroscopy has opened new avenues detection of biomolecules and nanoparticles. A recent revelation highlights the pivotal role coupling between MM resonance Fabry-Pérot (FP) oscillations substrate. This interaction significantly influences observed spectral shift (ΔF), thereby enhancing overall sensitivity. In this work, we utilize FP-MM optical decoupling physics sensitivity enhancement to detect bio-particles at extremely low concentrations, overcoming particle limit. After implementing these innovations, discovered that technology can be leveraged screen patients infected with omicron variant SARS-CoV-2 other lung related diseases using exhaled breath from patients. Upon achieving excellent agreement simulations experimental spectroscopic data, have successfully detected screened multiple respiratory-related collected on metasurface in a breathalyzer configuration. We obtained significant ΔF even ultra-low concentrations demarcated ranges different do no overlap are not constrained by any limit detection. work reveals prospects diagnosis screening single prompt test.

Язык: Английский

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Identification of B-Cell Linear Epitopes in the Nucleocapsid (N) Protein B-Cell Linear Epitopes Conserved among the Main SARS-CoV-2 Variants

Viruses, Год журнала: 2023, Номер 15(4), С. 923 - 923

Опубликована: Апрель 6, 2023

The Nucleocapsid (N) protein is highlighted as the main target for COVID-19 diagnosis by antigen detection due to its abundance in circulation early during infection. However, effects of described mutations N epitopes and efficacy testing across SARS-CoV-2 variants remain controversial poorly understood. Here, we used immunoinformatics identify five (N(34–48), N(89–104), N(185–197), N(277–287), N(378–390)) validate their reactivity against samples from convalescent patients. All identified are fully conserved highly with SARS-CoV. Moreover, N(185–197) N(277–287) MERS-CoV, while N(34–48), N(378–390) lowly common cold coronaviruses (229E, NL63, OC43, HKU1). These data accordance observed conservation amino acids recognized antibodies 7R98, 7N0R, 7CR5, which variants, SARS-CoV MERS-CoV but coronaviruses. Therefore, support tests a scalable solution population-level SARS-CoV-2, highlight need verify cross-reactivity these

Язык: Английский

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Comparison of the analytical and clinical sensitivity of thirty-four rapid antigen tests with the most prevalent SARS-CoV-2 variants of concern during the COVID-19 pandemic in the UK

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июль 24, 2023

Abstract Background The continued emergence of SARS-CoV-2 variants concern (VOC) requires timely analytical and clinical evaluation antigen-based rapid diagnostic tests (Ag-RDTs) especially those that are recommended for at home use. Methods limit detection (LOD) 34 Ag-RDTs was evaluated using the most encountered VOC viral isolates (Alpha, Delta, Gamma, Omicron BA.1, BA.5) wild type (WT). Clinical sensitivity further five Ag-RDT utilising retrospective samples BA.1) one prospective (Delta BA.1). Findings For WT, Alpha, Gamma (BA.1) 22, 32, 29, 31 32 met World Health Organisations (WHO) target product profile (TPP), respectively. Of included BA.5 29 WHO TPP. Additionally, LODs spiked with were significantly lower than all other VOCs (p<0.001). In when comparing RNA copies/mL, detected Alpha more sensitively Delta VOC. Samples high RT-qPCR Cts (Ct>25) resulted in reduced test sensitivities across variants. We used linear regression to model 50% 95% LOD observed statistically similar results tests. samples, 71.9% (CI 53.3-86.6%) 84.4% (CI95% 75.3-91.2%). Interpretation Test performance differs between VOCs, achieved testing compared requirements. Continuous evaluations must be performed monitor performance. Funding This work funded as part FIND’s a co-convener diagnostics pillar Access COVID-19 Tools (ACT) Accelerator, including support from Unitaid (grant number 2019-32-FIND MDR), government Netherlands MINBUZA-2020.961444), UK Department International Development 300341-102). also obtained MRC RLB CGB. Facilitating Accelerated Evaluation Diagnostics (FALCON C-19) study by National Institute Care Research (NIHR).

Язык: Английский

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Comparing SARS-CoV-2 testing positivity rates and COVID-19 impact among different isolation strategies: a rapid systematic review and a modelling study

EClinicalMedicine, Год журнала: 2023, Номер 61, С. 102058 - 102058

Опубликована: Июнь 22, 2023

The optimal isolation duration for patients with COVID-19 remains unclear. To support an update of World Health Organization (WHO)'s Living Clinical management guidelines (https://www.who.int/publications/i/item/WHO-2019-nCoV-clinical-2022.2), this rapid systematic review and modelling study addresses the effects different periods preventing onward transmission leading to hospitalisation death among secondary cases.We searched WHO database studies up Feb 27, 2023. We included clinical any design confirmed by PCR test or antigen addressing impact strategy on spread COVID-19. There were no restrictions publication language, status, age patients, severity COVID-19, variants SARS-COV-2, comorbidity location, co-interventions. performed random-effects meta-analyses summarise testing rates persistent positivity after infection. pre-specified subgroup analyses symptom status meta-regression proportion fully vaccinated patients. developed a model compare three strategies death. (1) 5-day isolation, release; (2) removal based negative test; (3) 10-day release. incorporates estimates rates, effective reproduction number, adherence, false rate, case fatality rates. assess varying adherence testing, we conducted some sensitivity analyses. used Grading Recommendations Assessment, Development Evaluation approach certainty evidence. protocol is registered PROSPERO (CRD42022348626).Fifteen including 4188 proved eligible. Asymptomatic (27.1%, 95% CI: 15.8%-40.0%) had significantly lower positive rate than symptomatic (68.1%, 40.6%-90.3%) day 5. was 21.5% (95% 0-64.1%; moderate certainty) 10. Our suggested that risk difference (RD) asymptomatic between in hospitalisations (23 more cases per 10,000 isolated, uncertainty interval (UI) 14 33 more) mortality (5 UI 1 9 very small (very low certainty). For potential 5- versus much greater (RD 186 113 276 more; 41 11 73 may be little removing death, but average period (mean -3 days) will shorter (moderate certainty).5 days 10 result amount negligible mortality; however, level concerning lead high evidence is, uncertain.This work done collaboration WHO.

Язык: Английский

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Pipette‐free field‐deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses

Biotechnology Journal, Год журнала: 2024, Номер 19(2)

Опубликована: Фев. 1, 2024

Here, we developed a field-deployable molecular diagnostic kit for the detection of RNA viruses that operates in pipette-free manner. The is composed acrylic sticks, PCR tubes, and palm-sized three-dimensional(3D)-printed heaters operated by batteries. performs extraction, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), visual one kit. An stick was engraved with shallow deep cylindrical chamber at each end insertion an FTA card ethidium homodimer-1 (EthD-1), respectively, to perform extraction/purification bimodal target amplicons. First, intercalation EthD-1 into DNA initially produces fluorescence upon UV illumination. Next, addition strong oxidant, this case sodium (meta) periodate (NaIO

Язык: Английский

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Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants

Microbiology Spectrum, Год журнала: 2024, Номер 12(7)

Опубликована: Май 17, 2024

ABSTRACT Post-market surveillance of test performance is a critical function public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product quality, manufacturing processes over time, or the evolution new variants may impact performance. During COVID-19 pandemic, plethora point-of-care (POCTs) was released onto Canadian market. This study evaluated several most widely distributed POCTs Canada, including four rapid antigen (Abbott Panbio, BTNX Rapid Response, SD Biosensor, Quidel QuickVue) two molecular ID NOW Lucira Check IT). All were challenged with 149 SARS-CoV-2 positives, multiple up to Omicron XBB.1.5, as well 29 negatives. Results stratified based on whether isolate pre-Omicron by reverse transcriptase quantitative PCR Ct value. The each POCT consistent manufacturers' claims showed no significant decline against any tested. These findings provide continued confidence results these they continue be used support decentralized testing. work demonstrates essential role post-market ensuring reliability tools. IMPORTANCE ensure after especially context pandemic use became widespread. Our focused IT) across assessing using many variants, subvariant XBB.1.5. Overall, we found difference variant, reinforcing use. As concerns efficacy have been raised news outlets, particularly regarding this even more timely crucial. research offers insights into but also highlights necessity for surveillance.

Язык: Английский

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Development and characterization of monoclonal antibodies recognizing nucleocapsid protein of multiple SARS-CoV-2 variants

Heliyon, Год журнала: 2024, Номер 10(15), С. e35325 - e35325

Опубликована: Июль 27, 2024

Rapid antigen test (RAT) is widely used for SARS-CoV-2 infection diagnostics. However, sensitivity has decreased recently due to the emergence of Omicron variant and its sublineages. Here we developed a panel nucleocapsid protein (NP) specific mouse monoclonal antibodies (mAbs) assessed their specificity important variants. We identified seven mAbs that exhibited strong reactivity variants recombinant NP (rNP) by Western immunoblot or ELISA. Their was confirmed negative low rNPs from SARS-CoV-1, MERS, common human coronaviruses (HCoV-HKU1, HCoV-CO43, HCoV-NL63, HCoV-229E). These were further tested immunoplaque assay against selected concern (VOCs), including two sublineages, five (F461G13, F461G7, F459G7, F457G3, F461G6), showed reactions, warranting suitability testing development diagnostic assay.

Язык: Английский

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