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 Estimating epidemiologic dynamics from cross-sectional viral load distributions

Science ◽  
2021 ◽  
pp. eabh0635
Author(s):  
James A. Hay ◽  
Lee Kennedy-Shaffer ◽  
Sanjat Kanjilal ◽  
Niall J. Lennon ◽  
Stacey B. Gabriel ◽  
...  
Keyword(s):  
Population Distribution ◽  
Quantitative Polymerase Chain Reaction ◽  
Cross Sectional ◽  
Outbreak Management ◽  
Viral Loads ◽  
Time Estimates ◽  
Load Distributions ◽  
Random Samples ◽  
Combining Data ◽  
Polymerase Chain

Estimating an epidemic’s trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values obtained from reverse-transcription quantitative polymerase chain reaction testing, changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic’s trajectory. Combining data from multiple such samples improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.

scholarly journals Evaluating the outcomes of enhanced adherence counselling intervention on clients with high viral loads in selected health facilities in Monze.

2021 ◽  
Author(s):  
Martha Kaira ◽  
Tresford Sikazwe ◽  
John Simwanza ◽  
Mowa Zambwe ◽  
Peter J. Chipimo
Keyword(s):  
Viral Load ◽  
High Viral Load ◽  
Cross Sectional Study ◽  
Health Facilities ◽  
Sample Collection ◽  
Viral Load Suppression ◽  
Cross Sectional ◽  
Viral Loads ◽  
Adherence Counselling ◽  
Counselling Intervention

To investigate the changes in Viral Load(VL) during Enhanced Adherence Counselling (EAC) sessions and its determinants among ART clients with unsuppressed VLs in Monze district. Method: A Cross-sectional study involving 616 HVL ART clients from 15 health facilities in Monze district which was conducted between October 1 2019 and March 30 2021. Results Out of 616 clients analysed, there was an improvement in viral load suppression following completion of EAC with a final outcome of 61% suppression. 28.7% remained unsuppressed. A total of 9.1% had no final viral load results documented and 0.2 % had been transferred out of their respective facilities and were not included in the study. Collection of repeat Viral loads was done on 84% of the clients with high viral load results while 16% had no record of sample collection. A total of 56 results were not received giving a result return of 89% from repeat samples collected. Females had a 40% likelihood of being unsuppressed at 95% CI (41% to 86%) compared to the males. Conclusion EAC improves the outcomes of HVLs and should be encouraged on all high viral clients. Programs should be developed to improve suppression in females on ART

Health Surveys

2021 ◽  
pp. 102-120
Author(s):  
J Patrick Vaughan ◽  
Cesar Victora ◽  
A Mushtaque R Chowdhury
Keyword(s):  
Health Surveys ◽  
Population Distribution ◽  
Survey Methods ◽  
Health Behaviours ◽  
Health Interventions ◽  
Local Health ◽  
Surveillance Systems ◽  
Cross Sectional ◽  
Longitudinal Surveys ◽  
Use Of Services

Surveys are used to collect data on the population distribution and frequency of health behaviours and use of services, health risks and diseases, as well as for the monitoring the implementation of health interventions, services, and programmes. Cross-sectional surveys collect prevalence data and longitudinal surveys collect mainly incidence information. Surveys can provide more accurate data than is available from local health information or surveillance systems. Survey methods are explained, such as on objectives, choice of variables, and sampling. Before undertaking surveys, local teams are advised to seek specialist advice and support.

scholarly journals Challenges in identifying the methodology to estimate the prevalence of infectious intestinal disease in Malta

2005 ◽  
Vol 134 (2) ◽  
pp. 393-399 ◽  
Author(s):  
C. GAUCI ◽  
H. GILLES ◽  
S. O'BRIEN ◽  
J. MAMO ◽  
I. STABILE ◽  
...  
Keyword(s):  
Large Scale ◽  
Intestinal Disease ◽  
International Studies ◽  
Surveillance Systems ◽  
Cross Sectional ◽  
Infectious Intestinal Disease ◽  
Participation Bias ◽  
Routine Surveillance ◽  
Sample Size Calculations ◽  
Stratified Sample

Routine surveillance systems capture only a fraction of infectious intestinal disease (IID) that is actually occurring in the community. Different methodologies utilized among various international studies in the field were reviewed in order to devise an appropriate survey to obtain current estimates of prevalence of IID in Malta. An age-stratified retrospective cross-sectional telephone study was selected for the study due to its feasibility in terms of limited resources necessary (funds, time and human). The disadvantages of this type of study include the inherent biases such as selection bias (sampling, ascertainment and participation bias) and information bias (recall and observer bias). A pilot study was carried out using a random age-stratified sample of 100 persons over a 3-month period. A total of 5·0% (95% CI ±4·27) of the population was estimated to have suffered from IID during that period. This estimate was used in order to assist in sample size calculations for a large-scale community study. It also served to test the survey instrument and methodology and to identify operational problems.

scholarly journals Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings

2021 ◽  
Vol 13 (589) ◽  
pp. eabf1568 ◽  
Author(s):  
Brian Cleary ◽  
James A. Hay ◽  
Brendan Blumenstiel ◽  
Maegan Harden ◽  
Michelle Cipicchio ◽  
...  
Keyword(s):  
Time Course ◽  
Resource Constraints ◽  
Group Testing ◽  
Individual Identification ◽  
Pooling Designs ◽  
Viral Kinetics ◽  
Viral Loads ◽  
Pooled Testing ◽  
Epidemic Dynamics ◽  
Resource Limited

Virological testing is central to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combined a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence and to ratify sensitivity losses against the time course of individual infections. We show that prevalence can be accurately estimated across a broad range, from 0.02 to 20%, using only a few dozen pooled tests and using up to 400 times fewer tests than would be needed for individual identification. We then exhaustively evaluated the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many true positives as individual testing with a given budget. Crucially, we confirmed that our theoretical results can be translated into practice using pooled human nasopharyngeal specimens by accurately estimating a 1% prevalence among 2304 samples using only 48 tests and through pooled sample identification in a panel of 960 samples. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.

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.

HUBUNGAN FAKTOR-FAKTOR INTERNAL PERAWAT DENGAN PENGETAHUAN PERAWAT TENTANG PENERAPAN STRATEGI PELAKSANAAN PADA PASIEN DENGAN GANGGUAN HALUSINASI

2018 ◽  
Vol 1 (1) ◽  
pp. 60
Author(s):  
Widya Arisandy
Keyword(s):  
Strategy Implementation ◽  
Analytic Approach ◽  
P Value ◽  
Sample Collection ◽  
Cross Sectional ◽  
Internal Factors ◽  
Is Research ◽  
Knowledge Strategy ◽  
Independent Variable ◽  
Research Nurses

Knowledge is the result of �know� and this is happening after they made a sensing towards an object certain .Sensing towards an object occur through panca human senses the sight , hearing , of smell , taste and touched with own .Knowledge about the implementation of the nurse strategy is obliged to understandable and in understand by a nurse soul .Many things can affect knowledge a nurse soul both internally and externally.Strategy the implementation of the act of nursing is a in made as a guide by a nurse if when interacting with disorder patients hallucinations.The purpose of research to know relations factors internal a nurse with knowledge nurse in the application of the implementation of the strategy in patients with disorder hallucinations in inpatient Rooms Hospital Ernaldi Bahar The Province Of South Sumatera 2017 . The kind of research done is research quantitative by using the method survey analytic approach in cross sectional .Technique the sample collection that is using a technique the sample collection total of sampling , the number of the sample are always 33 people .To research this independent variable consists of education , length of employment and the days of while dependent variable is knowledge nurse about strategy the implementation of the hallucinations . the results of this research was obtained one variable are associated than 3 variable internal factors researched namely working time with the results of p-value 0,011. Researchers hope from the results of this research , nurses can identify any factor that could affect the knowledge nurses and also can be used to understand the science of psychiatric Keywords : Nurses Knowledge, Strategy Implementation Hallucinations

Awareness of symptomatic differences Covid-19, SARS, Swine Flu, Common cold among dental students

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 1026-1033
Author(s):  
Nivedha Valliammai Mahalingam ◽  
Abilasha R ◽  
Kavitha S
Keyword(s):  
Infectious Diseases ◽  
Undergraduate Students ◽  
Common Cold ◽  
Emerging Infectious Diseases ◽  
Dental Students ◽  
Swine Flu ◽  
Viral Diseases ◽  
Surveillance Systems ◽  
Cross Sectional ◽  
The Impact

Enormous successes have been obtained against the control of major epidemic diseases, such as SARS, MERS, Ebola, Swine Flu in the past. Dynamic interplay of biological, socio-cultural and ecological factors, together with novel aspects of human-animal interphase, pose additional challenges with respect to the emergence of infectious diseases. The important challenges faced in the control and prevention of emerging and re-emerging infectious diseases range from understanding the impact of factors that are necessary for the emergence, to development of strengthened surveillance systems that can mitigate human suffering and death. The aim of the current study is to assess the awareness of symptomatic differences between viral diseases like COVID-19, SARS, Swine flu and common cold among dental students that support the prevention of emergence or re-emergence. Cross-sectional type of study conducted among the undergraduate students comprising 100 Subjects. A questionnaire comprising 15 questions in total were framed, and responses were collected in Google forms in SPSS Software statistical analysis. The study has concluded that dental students have an awareness of the symptomatic differences between infectious viral disease. The study concluded that the awareness of symptomatic differences between viral diseases like COVID-19, SARS, Swine flu, Common cold is good among the dental students who would pave the way for early diagnosis and avoid spreading of such diseases. A further awareness can be created by regular webinars, seminars and brainstorming sessions among these healthcare professionals.

scholarly journals Predictors of loss to follow-up in art experienced patients in Nigeria: a 13 year review (2004–2017)

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Ahmad Aliyu ◽  
Babatunde Adelekan ◽  
Nifarta Andrew ◽  
Eunice Ekong ◽  
Stephen Dapiap ◽  
...  
Keyword(s):  
Patient Adherence ◽  
Cross Sectional Study ◽  
Emergency Plan ◽  
Cross Sectional ◽  
Loss To Follow Up ◽  
Viral Loads ◽  
Review Period ◽  
Lost To Follow Up ◽  
Differentiated Care

Abstract Background Expanded access to antiretroviral therapy (ART) leads to improved HIV/AIDS treatment outcomes in Nigeria, however, increasing rates of loss to follow-up among those on ART is threatening optimal standard achievement. Therefore, this retrospective cross-sectional study is aimed at identifying correlates and predictors of loss to follow-up in patients commencing ART in a large HIV program in Nigeria. Methods Records of all patients from 432 US CDC Presidents Emergency Plan for AIDS Relief (PEPFAR) supported facilities across 10 States and FCT who started ART from 2004 to 2017 were used for this study. Bivariate and multivariate analysis of the demographic and clinical parameters of all patients was conducted using STATA version 14 to determine correlates and predictors of loss to follow-up. Results Within the review period, 245,257 patients were ever enrolled on anti-retroviral therapy. 150,191 (61.2%) remained on treatment, 10,960 (4.5%) were transferred out to other facilities, 6926 (2.8%) died, 2139 (0.9%) self-terminated treatment and 75,041 (30.6%) had a loss to follow-up event captured. Males (OR: 1.16), Non-pregnant female (OR: 4.55), Patients on ≥ 3-monthly ARV refills (OR: 1.32), Patients with un-suppressed viral loads on ART (OR: 4.52), patients on adult 2nd line regimen (OR: 1.23) or pediatric on 1st line regimen (OR: 1.70) were significantly more likely to be lost to follow-up. Conclusion Despite increasing access to anti-retroviral therapy, loss to follow-up is still a challenge in the HIV program in Nigeria. Differentiated care approaches that will focus on males, non-pregnant females and paediatrics is encouraged. Reducing months of Anti-retroviral drug refill to less than 3 months is advocated for increased patient adherence.

scholarly journals Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
B F Koel ◽  
R M Vigeveno ◽  
M Pater ◽  
S M Koekkoek ◽  
A X Han ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
De Novo ◽  
Diagnostic Testing ◽  
Influenza Viruses ◽  
Surface Proteins ◽  
H3n2 Virus ◽  
Virus Population ◽  
Sample Collection ◽  
Routine Surveillance ◽  
H3n2 Influenza

Abstract Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.

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