Nowcasting epidemic trends using hospital- and community-based virologic test data DOI Creative Commons
Tse Yang Lim, Sanjat Kanjilal, Shira Doron

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 2, 2024

Abstract Epidemiological surveillance typically relies on reported incidence of cases or hospitalizations, which can suffer significant reporting lags, biases and under-ascertainment. Here, we evaluated the potential viral loads measured by RT-qPCR cycle threshold (Ct) values to track epidemic trends. We used SARS-CoV-2 results from hospital testing in Massachusetts, USA, municipal California, simulations identify predictive models covariates that maximize short-term trend prediction accuracy. found Ct value distributions correlated with growth rates under real-world conditions. fitted generalized additive predict log rate direction case using features time-varying population distribution assessed models’ ability dynamics rolling two-week windows. Observed accurately predicted (growth RMSE ∼ 0.039-0.052) (AUC 0.72-0.78). Performance degraded during periods rapidly changing rate. Predictive were robust regimes sample sizes; accounting for immunity symptom status yielded no substantial improvement. Trimming outliers improved performance. These indicate analysis routine PCR tests help monitor trends, complementing traditional metrics.

Язык: Английский

Interplay of inflammatory markers and anti-SARS-CoV-2 antibodies in COVID-19 mortality: A prospective cohort study DOI Creative Commons
Sylvia Mink, Heinz Drexel, Andreas Leiherer

и другие.

International Journal of Infectious Diseases, Год журнала: 2024, Номер 143, С. 107016 - 107016

Опубликована: Март 22, 2024

Despite high global vaccination coverage, it remains unclear how and anti-SARS-CoV-2 antibodies affect immune responses inflammation levels in patients with COVID-19. It is further whether the inflammatory response differs depending on antibody combination of COVID-19 affects mortality rates.

Язык: Английский

Процитировано

2
Overestimation of Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission in Settings of High Community Transmission: Insights From an Informal Settlement Community in Salvador, Brazil DOI Creative Commons
Juan P. Aguilar Ticona, Nívison Nery, Matt D. T. Hitchings

и другие.

Open Forum Infectious Diseases, Год журнала: 2024, Номер 11(3)

Опубликована: Фев. 5, 2024

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread globally. However, the contribution of community versus household transmission to overall risk infection remains unclear. Between November 2021 and March 2022, we conducted an active case-finding study in urban informal settlement with biweekly visits across 1174 households 3364 residents. Individuals displaying disease 2019 (COVID-19)-related symptoms were identified, interviewed along contacts, defined as index secondary cases based on reverse-transcription polymerase chain reaction (RT-PCR) symptom onset. In 61 households, detected a total 94 RT-PCR-positive cases. Of 69 sequenced samples, 67 (97.1%) attributed BA.1* variant. Among 35 their attack rate was 50.0% (95% confidence interval [CI], 37.0%-63.0%). Women (relative [RR], 1.6 [95% CI, .9-2.7]), older individuals (median difference, 15 2-21] years), those reporting (RR, 1.73 1.0-3.0]) had significantly increased for SARS-CoV-2 infection. Genomic analysis revealed substantial acquisition viruses from even among other infections. After excluding acquisition, estimated 24.2% 11.9%-40.9%). These findings underscore ongoing current observed high necessitates swift booster vaccination, rapid testing availability, therapeutic options mitigate outcomes COVID-19.

Язык: Английский

Процитировано

0
Anti-SARS-CoV-2 Antibodies versus Vaccination Status in CAD Patients with COVID-19: A Prospective, Propensity Score-Matched Cohort Study DOI Creative Commons
Sylvia Mink, Heinz Drexel, Andreas Leiherer

и другие.

Vaccines, Год журнала: 2024, Номер 12(8), С. 855 - 855

Опубликована: Июль 30, 2024

Despite the currently prevailing, milder Omicron variant, coronary artery disease (CAD) patients constitute a major risk group in COVID-19, exhibiting 2.6 times mortality of non-CAD and representing over 22% non-survivors. No data are available on efficacy antibody levels CAD patients, nor relevance vaccination status versus for predicting severe courses COVID-19 mortality. Nor there definitive indicators to assess if individual sufficiently protected from adverse outcomes or determine necessity booster vaccinations.

Язык: Английский

Процитировано

0
Genetic diversity and genomic epidemiology of SARS-CoV-2 during the first 3 years of the pandemic in Morocco: comprehensive sequence analysis, including the unique lineage B.1.528 in Morocco DOI Creative Commons

Soulandi Djorwé,

Abderrahim Malki,

Néhémie Nzoyikorera

и другие.

Access Microbiology, Год журнала: 2024, Номер 6(10)

Опубликована: Окт. 1, 2024

During the 3 years following emergence of COVID-19 pandemic, African continent, like other regions world, was substantially impacted by COVID-19. In Morocco, pandemic has been marked and spread several SARS-CoV-2 variants, leading to a substantial increase in incidence infections deaths. Nevertheless, comprehensive understanding genetic diversity, evolution, epidemiology viral lineages remained limited Morocco. This study sought deepen genomic through retrospective analysis. The main objective this analyse diversity identify distinct lineages, as well assess their evolution during using approaches. Furthermore, key mutations functional proteins across different were highlighted along with an analysis relationships amongst these strains better understand evolutionary pathways. A total 2274 sequences isolated Morocco period 2020 2023, extracted from GISAID EpiCoV database subjected Lineages clades classified according nomenclature GISAID, Nextstrain, Pangolin. conducted reported accordance STROBE (Strengthening Reporting Observational Studies Epidemiology) guidelines. An exhaustive led identification 157 PANGO including notable such B.1, B.1.1, B.1.528, B.1.177, variants B.1.1.7, B.1.621, B.1.525, B.1.351, B.1.617.1, B.1.617.2, its sublineages AY.33, AY.72, AY.112, AY.121 that evolved over time before being supplanted Omicron December 2021. Among analysed, subvariants had prevalence 59.5%. most predominant 21K, 21L, 22B, which are respectively related phylogenetically BA.1, BA.2, BA.5. June 2022, rapidly observed recrudescence cases infection, concurrent coexistence clade 22B BA.5.2.20, BA.5, BA.5.1, BA.5.2.1, BF.5, supplanting BA.1 (clade display 21K) BA.2 21L), became marginal. However, XBB 22F) progeny XBB.1.5(23A), XBB.1.16(23B), CH.1.1(23C), XBB.1.9(23D), XBB.2.3(23E), EG.5.1(23F), XBB.1.5.70(23G) have sporadically. mutations, H69del/V70del, G142D, K417N, T478K, E484K, E484A, L452R, F486P, N501Y, Q613H, D614G, P681H/R, identified. Some known be involved increasing transmissibility, virulence, antibody escape. identified Moroccan isolates, trends. These findings provide robust basis for roles variation pathogenicity, antigenicity (immune evasion/reinfection). noteworthy number highlights importance maintaining continuous surveillance Moreover, expanding vaccination coverage would also help protect patients against more severe clinical disease.

Язык: Английский

Процитировано

0
Nowcasting epidemic trends using hospital- and community-based virologic test data DOI Creative Commons
Tse Yang Lim, Sanjat Kanjilal, Shira Doron

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 2, 2024

Abstract Epidemiological surveillance typically relies on reported incidence of cases or hospitalizations, which can suffer significant reporting lags, biases and under-ascertainment. Here, we evaluated the potential viral loads measured by RT-qPCR cycle threshold (Ct) values to track epidemic trends. We used SARS-CoV-2 results from hospital testing in Massachusetts, USA, municipal California, simulations identify predictive models covariates that maximize short-term trend prediction accuracy. found Ct value distributions correlated with growth rates under real-world conditions. fitted generalized additive predict log rate direction case using features time-varying population distribution assessed models’ ability dynamics rolling two-week windows. Observed accurately predicted (growth RMSE ∼ 0.039-0.052) (AUC 0.72-0.78). Performance degraded during periods rapidly changing rate. Predictive were robust regimes sample sizes; accounting for immunity symptom status yielded no substantial improvement. Trimming outliers improved performance. These indicate analysis routine PCR tests help monitor trends, complementing traditional metrics.

Язык: Английский

Процитировано

0