scholarly journals Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar

2021 ◽  
Author(s):  
Soa Fy Andriamandimby ◽  
Cara E. Brook ◽  
Norosoa H Razanajatovo ◽  
Jean-Marius Rakotondramanga ◽  
Fidisoa Rasambainarivo ◽  
...  
Keyword(s):  
Growth Rates ◽  
Population Level ◽  
Additive Models ◽  
Reference Laboratory ◽  
Viral Kinetics ◽  
Cross Sectional ◽  
Cycle Threshold ◽  
Incidence Data ◽  
Ct Value ◽  
Epidemic Wave

As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.

scholarly journals Spectrum of Primary Cancer Diagnoses Among Patients at Uganda Cancer Institute in 2015 and 2016

2018 ◽  
Vol 4 (Supplement 2) ◽  
pp. 80s-80s
Author(s):  
B.S. Angucia ◽  
M. Nabwana ◽  
J. Asasira ◽  
Y. Mulumba ◽  
I. Mutyaba ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Colorectal Cancer ◽  
Wilms Tumor ◽  
Kaposi Sarcoma ◽  
Population Level ◽  
Cross Sectional Study ◽  
Quality Of Data ◽  
Cross Sectional ◽  
Incidence Data ◽  
Cancer Registry Data

Background: Most recent cancer registry data suggests a change in cancer occurrence in Uganda with a decrease in incidence of Kaposi sarcoma (KS) but an increase in cervical, prostate and breast cancer. Anecdotal data suggest that KS, non-Hodgkin's lymphoma and breast cancer were the most common cancers among patients at Uganda Cancer Institute (UCI) by 2006. Aim: To describe the spectrum of cancer diagnoses among new patients that presented for care at UCI over the past 2-years. Methods: We conducted a cross sectional study of patients admitted into care at UCI with a histologic or clinical diagnosis of cancer from January 2015 to December 2016. Cancer diagnoses were reported as proportions by gender and age - children (0-14 years) and adults (above 14 years). Results: Overall, 8279 new patients were registered during the study period but only 7588 (92%) were recorded in the electronic database and had information on cancer diagnosis. Of these, 53% were admitted in 2015, and 55% were females. Median age was 48 years (IQR: 34-62). Among 2997 female adults, 30% had cervical, 17% breast, 5% Kaposi sarcoma (KS), 4% leukemia and 3.9% esophageal cancer. Among 2136 male adults, 17% had KS, 12% prostate, 10% esophageal, 6% leukemia and 4% colorectal cancer. Among the 486 children, 17% had leukemia, 16.7% nephroblastoma (Wilms tumor), 15.9% Burkitt lymphoma (BL), 8% rhabdomyosarcoma, and 6% Kaposi sarcoma. Conclusion: The distribution of cancer diagnoses among patients seen at UCI reflects the population level cancer incidence with cervical, breast, KS, prostate, esophageal, and colorectal cancer in adults, and nephroblastoma in children as the leading cause of cancer related morbidity. The overrepresentation of leukemia may be due to referral bias but warrants further study. The correlation of our findings with incidence data suggests that missing information did not significantly skew our findings. However more investments are needed to improve the quality of data captured electronically.

scholarly journals Investigation of Viral Load Cycle Threshold Values in Patients with SARS-CoV-2 Associated Pneumonia with Real-Time PCR Method

2021 ◽  
Vol 15 (10) ◽  
pp. 1408-1414
Author(s):  
Ayfer Bakir ◽  
Tugrul Hosbul ◽  
Ferhat Cuce ◽  
Cumhur Artuk ◽  
Gurhan Taskin ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Load Cycle ◽  
Cross Sectional Study ◽  
Chest Ct ◽  
Upper Respiratory Tract ◽  
Cross Sectional ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Ct Value

Introduction: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. Methodology: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. Results: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson’s r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. Conclusions: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.

scholarly journals 1171. Measles and Rubella Seroprevalence among HIV-infected and uninfected Children and Adults in Zambia

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S676-S677
Author(s):  
Yangyupei Yang ◽  
Simon Mutembo ◽  
Andrea Carcelen ◽  
Kyla Hayford ◽  
Francis Mwansa ◽  
...  
Keyword(s):  
Control Strategies ◽  
Generalized Additive Models ◽  
Additive Model ◽  
Population Level ◽  
Dried Blood Spots ◽  
Cross Sectional Study ◽  
Additive Models ◽  
Sub Saharan Africa ◽  
Cross Sectional ◽  
Significant Difference

Abstract Background Despite the availability of safe and effective vaccines, measles and congenital rubella syndrome remain important causes of morbidity and mortality. HIV-infected individuals may be more vulnerable to measles because of poor immune responses to vaccination. Population-level estimates and comparisons of measles and rubella seroprevalence between HIV-infected and uninfected children and adults in sub-Saharan Africa are needed to guide vaccination policy and control strategies. Methods This cross-sectional study was performed by analysing a selected and weighted subsample from the Zambia Population HIV Impact Assessment survey (ZAMPHIA). ZAMPHIA was conducted in 2016 to estimate national HIV incidence and prevalence in Zambia. Dried blood spots and plasma samples were tested for IgG antibodies to measles and rubella viruses using a commercial enzyme immunoassay. We estimated national age-specific measles and rubella seroprevalence by HIV infection status using hierarchical generalized additive models. Results Specimens from 9521 HIV-uninfected (3840 children age under 10 years, 3981 youth age 10-19 years, and 1700 adults age 20-49 years) and 331 HIV-infected (53, 107, and 171 respectively) individuals were included in the study. Measles seroprevalence was lower among HIV-infected children (46.4%) compared to HIV-uninfected children (76.4%, p < 0.001). In both HIV-uninfected and HIV-infected individuals, measles seroprevalence increased steadily with age but more rapidly in the HIV-infected until about the age of 20 years when the seroprevalence was similar between the two groups. Above 20 years, measles seroprevalence was similar between HIV-infected and uninfected adults. There was no significant difference in rubella seroprevalence between HIV-infected and HIV-uninfected individuals. Figure 1. Measles and Rubella Age-specific Seroprevalence The lines represent generalized additive model fits for the mean (solid) and 95% confidence intervals (dashed). Data are grouped by age in years and year 0 includes only specimens from children 9-11 months. Rubella-containing vaccine was not available in the public sector prior to the serosurvey. Conclusion Measles seroprevalence was lower among HIV-infected than uninfected children and youth. HIV-infected children would likely benefit from revaccination. Many children were susceptible to rubella before the introduction of the combined measles and rubella vaccine in Zambia. Disclosures Kyla Hayford, PhD, MA, Pfizer, Inc. (Other Financial or Material Support, KH conducted the study and analyses while working at the Johns Hopkins School of Public Health but is an employee at Pfizer, Inc. as of 26 October 2020.)

scholarly journals Viral loads observed under competing strain dynamics

2021 ◽  
Author(s):  
James A Hay ◽  
Lee Kennedy-Shaffer ◽  
Michael J Mina
Keyword(s):  
Growth Rates ◽  
Population Distribution ◽  
Surveillance Systems ◽  
Sample Collection ◽  
Viral Kinetics ◽  
Cross Sectional ◽  
Viral Loads ◽  
Epidemic Dynamics ◽  
Routine Surveillance ◽  
Plausible Mechanism

A plausible mechanism for the increased transmissibility of SARS-CoV-2 variants of concern (VOCs) results from VOC infections causing higher viral loads in infected hosts. However, investigating this hypothesis using routine RT-qPCR testing data is challenging because the population-distribution of viral loads changes depending on the epidemic growth rate; lower cycle threshold (Ct) values for a VOC lineage may simply reflect increasing incidence relative to preexisting lineages. To understand the extent to which viral loads observed under routine surveillance systems reflect viral kinetics or population dynamics, we used a mathematical model of competing strain dynamics and simulated Ct values for variants with different viral kinetics. We found that comparisons of Ct values obtained under random cross-sectional surveillance were highly biased unless samples were obtained at times when the variants had comparable growth rates. Conversely, comparing Ct values from symptom-based testing was largely unaffected by epidemic dynamics, and accounting for the time between symptom onset and sample collection date further reduced the risk of statistical errors. Finally, we show how a single cross-sectional sample of Ct values can be used to jointly estimate differences in viral kinetics and epidemic growth rates between variants. Epidemic dynamics should be accounted for when investigating strain-specific viral kinetics using virologic surveillance data, and findings should be corroborated with longitudinal viral kinetics studies.

scholarly journals Incidence Correction Factors for Moderate and Severe Acute Child Malnutrition From 2 Longitudinal Cohorts in Mali and Burkina Faso

2020 ◽  
Vol 189 (12) ◽  
pp. 1623-1627
Author(s):  
Francisco M Barba ◽  
Lieven Huybregts ◽  
Jef L Leroy
Keyword(s):  
Burkina Faso ◽  
Low Income ◽  
Severe Acute Malnutrition ◽  
Acute Malnutrition ◽  
Cross Sectional ◽  
Incidence Data ◽  
Moderate Acute Malnutrition ◽  
Cluster Randomized ◽  
Definition Of ◽  
Mid Upper Arm Circumference

Abstract Child acute malnutrition (AM) is an important cause of child mortality. Accurately estimating its burden requires cumulative incidence data from longitudinal studies, which are rarely available in low-income settings. In the absence of such data, the AM burden is approximated using prevalence estimates from cross-sectional surveys and the incidence correction factor $K$, obtained from the few available cohorts that measured AM. We estimated $K$ factors for severe acute malnutrition (SAM) and moderate acute malnutrition (MAM) from AM incidence and prevalence using representative cross-sectional baseline and longitudinal data from 2 cluster-randomized controlled trials (Innovative Approaches for the Prevention of Childhood Malnutrition—PROMIS) conducted between 2014 and 2017 in Burkina Faso and Mali. We compared K estimates using complete (weight-for-length z score, mid-upper arm circumference (MUAC), and edema) and partial (MUAC, edema) definitions of SAM and MAM. $K$ estimates for SAM were 9.4 and 5.7 in Burkina Faso and in Mali, respectively; K estimates for MAM were 4.7 in Burkina Faso and 5.1 in Mali. The MUAC and edema–based definition of AM did not lead to different $K$ estimates. Our results suggest that $K$ can be reliably estimated when only MUAC and edema-based data are available. Additional studies, however, are required to confirm this finding in different settings.

scholarly journals Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1091
Author(s):  
Ali A. Rabaan ◽  
Raghavendra Tirupathi ◽  
Anupam A Sule ◽  
Jehad Aldali ◽  
Abbas Al Mutair ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Disease Severity ◽  
False Negative ◽  
Influential Factors ◽  
Confirmatory Test ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Viral Kinetics ◽  
Ct Value

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

scholarly journals 414. Association of SARS-CoV-2 Genomic Load Trends with Clinical Status in COVID-19:A Retrospective Analysis from an Academic Hospital Center in New York City

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S275-S275
Author(s):  
Ioannis Zacharioudakis ◽  
Fainareti Zervou ◽  
Prithiv Prasad ◽  
Yongzhao Shao ◽  
Atreyee Basu ◽  
...  
Keyword(s):  
New York ◽  
Sofa Score ◽  
Research Question ◽  
Clinical Status ◽  
Inverse Correlation ◽  
Duration Of Symptoms ◽  
Cycle Threshold ◽  
Ct Value ◽  
Failure Assessment ◽  
Polymerase Chain

Abstract Background The Infectious Diseases Society of America has identified the potential use of SARS-CoV-2 genomic load for prognostication purposes as a key research question. Methods We designed a retrospective cohort study that included adult patients with COVID-19 pneumonia who had at least 2 positive nasopharyngeal tests at least 24 hours apart to study the correlation between the change in the genomic load of SARS-CoV-2 in nasopharyngeal samples, as reflected by the Cycle threshold (Ct) value of the real-time Polymerase Chain Reaction (PCR) assay, with change in clinical status. The Sequential Organ Failure Assessment (SOFA) score was used as a surrogate for patients’ clinical status. A linear mixed-effects regression analysis was performed. Results Among 457 patients who presented to the emergency department between 3/31/2020- 4/10/2020, we identified 42 patients who met the inclusion criteria. The median initial SOFA score was 2 (IQR 2–3). 20 out of 42 patients had a lower SOFA score on their subsequent tests. We identified a statistically significant inverse correlation between the change in SOFA score and change in the Ct value with a decrease in SOFA score by 0.05 (SE 0.02; p < 0.05) for an increase in Ct values by 1. This correlation was independent of the duration of symptoms. Flow chart A graph of the Cycle Threshold (Ct) values of the of Cepheid Xpert® Xpress SARS-CoV-2 assay measured on repeat screening of the 42 included patients. Graph of the fitted SOFA scores based on the Cycle Threshold values per patient. Conclusion Our findings suggest that an increasing Ct value in sequential tests may be of prognostic value for patients diagnosed with COVID-19 pneumonia. Before repeat testing can be recommended routinely in clinical practice as a predictor of disease outcomes, prospective studies with a standardized interval between repeat tests should confirm our findings. Disclosures All Authors: No reported disclosures

scholarly journals Modeling Hearing Loss Progression and Asymmetry in the Older Old: A National Population-Based Survey

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 214-215
Author(s):  
Rahul Sharma ◽  
Anil Lalwani ◽  
Justin Golub
Keyword(s):  
Hearing Loss ◽  
Pure Tone ◽  
Population Level ◽  
Population Based ◽  
National Database ◽  
Cross Sectional ◽  
Adult Lifespan ◽  
Pure Tone Average ◽  
Age Related ◽  
Public Datasets

Abstract The progression and asymmetry of age-related hearing loss has not been well characterized in those 80 years of age and older because public datasets mask upper extremes of age to protect anonymity. We aimed to model the progression and asymmetry of hearing loss in the older old using a representative, national database. This was a cross-sectional, multicentered US epidemiologic analysis using the National Health and Nutrition Examination Study (NHANES) 2005-2006, 2009-2010, and 2011-2012 cycles. Subjects included non-institutionalized, civilian adults 80 years and older (n=621). Federal security clearance was granted to access publicly-restricted age data. Outcome measures included pure-tone average air conduction thresholds and the 4-frequency pure tone average (PTA). 621 subjects were 80 years old or older (mean=84.2 years, range=80-104 years), representing 10,600,197 Americans. Hearing loss exhibited constant acceleration across the adult lifespan at a rate of 0.0052 dB/year2 (95% CI = 0.0049, 0.0055). Compounded over a lifetime, the velocity of hearing loss would increase five-fold, from 0.2 dB loss/year at age 20 to 1 dB loss/year at age 100. This model predicted mean PTA within 2 dB of accuracy for most ages between 20 and 100 years. There was no change in the asymmetry of hearing loss with increasing age over 80 years (linear regression coefficient of asymmetry over age=0.07 (95% CI=-0.01, 0.24). In conclusion, hearing loss steadily and predictably accelerates across the adult lifespan to at least age 100, becoming near-universal. These population-level statistics will guide treatment and policy recommendations for hearing health in the older old.

scholarly journals Recall of government healthy eating campaigns by consumers in five countries

2021 ◽  
pp. 1-31
Author(s):  
Samantha Goodman ◽  
Gabriela Armendariz ◽  
Adele Corkum ◽  
Laura Arellano ◽  
Alejandra Jáuregui ◽  
...  
Keyword(s):  
Healthy Eating ◽  
Fruits And Vegetables ◽  
Food Policy ◽  
Logistic Models ◽  
Population Level ◽  
Policy Study ◽  
Cross Sectional ◽  
Sugary Drinks ◽  
Income Adequacy ◽  
Low Education

ABSTRACT Objective: To examine awareness and recall of healthy eating public education campaigns in five countries. Design: Data were cross-sectional and collected as part of the 2018 International Food Policy Study. Respondents were asked whether they had seen government healthy eating campaigns in the past year; if yes (awareness), they were asked to describe the campaign. Open-ended descriptions were coded to indicate recall of specific campaigns. Logistic models regressed awareness of healthy eating campaigns on participant country, age, sex, ethnicity, education, income adequacy and BMI. Analyses were also stratified by country. Setting: Online surveys. Participants: Participants were Nielsen panelists aged ≥18 years in Australia, Canada, Mexico, UK and US (n=22,463). Results: Odds of campaign awareness were higher in Mexico (50.9%) than UK (18.2%), Australia (17.9%), US (13.0%) and Canada (10.2%) (P<0.001). Awareness was also higher in UK and Australia versus Canada and US, and US versus Canada (P<0.001). Overall, awareness was higher among males versus females and respondents with medium or high versus low education (P<0.001 for all). Similar results were found in stratified models, although no sex difference was observed in Australia or UK (P>0.05), and age was associated with campaign awareness in UK (P<0.001). Common key words in all countries included sugar/sugary drinks, fruits and vegetables, and physical activity. The top five campaigns recalled were Chécate, mídete, muévete (Mexico), PrevenIMSS (Mexico), Change4Life (UK), LiveLighter® (Australia), and Actívate, Vive Mejor (Mexico). Conclusions: In Mexico, UK and Australia, comprehensive campaigns to promote healthy lifestyles appear to have achieved broad, population-level reach.

Sign in / Sign up

Export Citation Format

Share Document