scholarly journals Predicting COVID-19 Incidences from Patients’ Viral Load using Deep-Learning

2021 ◽  
Author(s):  
Athar Khalil ◽  
Khalil Al Handawi ◽  
Ibrahim Chamseddine ◽  
Zeina Mohsen ◽  
Afif Abdel Nour ◽  
...  
Keyword(s):  
Viral Load ◽  
Deep Neural Network ◽  
Viral Disease ◽  
Mean Square ◽  
Viral Dynamics ◽  
Viral Load Measurement ◽  
Cross Sectional ◽  
Post Vaccination ◽  
Early Testing ◽  
Testing Practices

AbstractThe transmission of the contagious COVID-19 is known to be highly dependent on individual viral dynamics. Since the cycle threshold (Ct) is the only semi-quantitative viral measurement that could reflect infectivity, we utilized Ct values to forecast COVID-19 incidences. Our COVID-19 cohort (n=9531), retrieved from a single representative cross-sectional virology test center in Lebanon, revealed that low daily mean Ct values are followed by an increase in the number of national positive COVID-19 cases. A subset of the data was used to develop a deep neural network model, tune its hyperparameters, and optimize the weights for minimal mean square error of prediction. The final model’s accuracy is reported by comparing its predictions with an unseen dataset. Our model was the first to capture the interaction of the previously reported Ct values with the upcoming number of COVID-19 cases and any temporal effects that arise from population dynamics. Our model was deployed as a publicly available and easy-to-use estimator to facilitate prospective validation. Our model has potential application in predicting COVID-19 incidences in other countries and in assessing post-vaccination policies. Aside from emphasizing patient responsibility in adopting early testing practices, this study proposed and validated viral load measurement as a rigid input that can enhance outcomes and precision of viral disease predicting models.

scholarly journals Estimating epidemiologic dynamics from single cross-sectional viral load distributions

2020 ◽  
Author(s):  
James A. Hay ◽  
Lee Kennedy-Shaffer ◽  
Sanjat Kanjilal ◽  
Marc Lipsitch ◽  
Michael J. Mina
Keyword(s):  
Public Health ◽  
Growth Rate ◽  
Viral Load ◽  
Population Level ◽  
Accurate Estimation ◽  
Cross Sectional ◽  
Individual Level ◽  
Viral Loads ◽  
Single Cross ◽  
Testing Practices

AbstractVirologic testing for SARS-CoV-2 has been central to the COVID-19 pandemic response, but interpreting changes in incidence and fraction of positive tests towards understanding the epidemic trajectory is confounded by changes in testing practices. Here, we show that the distribution of viral loads, in the form of Cycle thresholds (Ct), from positive surveillance samples at a single point in time can provide accurate estimation of an epidemic’s trajectory, subverting the need for repeated case count measurements which are frequently obscured by changes in testing capacity. We identify a relationship between the population-level cross-sectional distribution of Ct values and the growth rate of the epidemic, demonstrating how the skewness and median of detectable Ct values change purely as a mathematical epidemiologic rule without any change in individual level viral load kinetics or testing. Although at the individual level measurement variation can complicate interpretation of Ct values for clinical use, we show that population-level properties reflect underlying epidemic dynamics. In support of these theoretical findings, we observe a strong relationship between the time-varying effective reproductive number, R(t), and the distribution of Cts among positive surveillance specimens, including median and skewness, measured in Massachusetts over time. We use the observed relationships to derive a novel method that allows accurate inference of epidemic growth rate using the distribution of Ct values observed at a single cross-section in time, which, unlike estimates based on case counts, is less susceptible to biases from delays in test results and from changing testing practices. Our findings suggest that instead of discarding individual Ct values from positive specimens, incorporation of viral loads into public health data streams offers a new approach for real-time resource allocation and assessment of outbreak mitigation strategies, even where repeat incidence data is not available. Ct values or similar viral load data should be regularly reported to public health officials by testing centers and incorporated into monitoring programs.

Access of Key Population to Available HIV and TB Services in Nepal: A Cross Section Study

2019 ◽  
Vol 17 (1) ◽  
pp. 17-23
Author(s):  
B.B. Subba ◽  
N. Rimal ◽  
B.M. Shrestha
Keyword(s):  
Viral Load ◽  
Cross Section ◽  
General Knowledge ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Key Population ◽  
Mdr Tb ◽  
Study Population ◽  
Control And Management ◽  
Structured Questionnaire

Introduction: TB is considered one of the opportunistic infection among PLHIV. The increasing burden of HIV/TB co-infection among key population cause problem to maintain adherence to ART and DOTS services. The emergence of MDR-TB is one of the greatest challenge to control and management of both diseases. However, having knowledge and information of both diseases are important role to access the available HIV/TB services. Methods: A cross-sectional survey was conducted among key population who had HIV/TB co-infection in two-epidemic zone of Nepal. A pretested semi-structured questionnaire was used to collect data. ANOVA test was done to analyze the collected data by using SPSS version 20.0. Results: A total of 343 HIV/TB co-infected individuals were enrolled to the study. Most of participants were from ART and DOTS clients. Therefore, the study found that there was significance difference found between knowledge about TB (F=4.400, p= 0.005), causative agent of TB (F=3.160, p=0.025), risk of TB illness among PLHIV (F=8.491, p=0.001) and among key affected population. Moreover, there was significance difference found between access to OI treatment (F=5.113, p=0.002) and access to viral load (F=4.642, p=0.003) among key study population. In gender perspective, there was no significance difference to use and access to available HIV/TB services. Conclusion: The general knowledge on HIV/TB co-infection was significant association with key population. The knowledge on HIV/TB and access to NGOs’ help can significant effect to access the available HIV and TB services.

Factors associated with HIV care and treatment cascade in Rio Grande do Sul, Brazil, 2014–2017: A cross-sectional study

2021 ◽  
pp. 095646242097594
Author(s):  
Guilherme B Shimocomaqui ◽  
Craig S Meyer ◽  
Maria L Ikeda ◽  
Elson Romeu Farias ◽  
Tonantzin R Gonçalves ◽  
...  
Keyword(s):  
Viral Load ◽  
Rio Grande ◽  
Undetectable Viral Load ◽  
Cross Sectional Study ◽  
Hiv Care ◽  
Rio Grande Do Sul ◽  
Sectional Study ◽  
Cross Sectional ◽  
Treatment Cascade ◽  
Care And Treatment

In 2018, Rio Grande do Sul (RS) had some of the highest HIV/AIDS rates in Brazil, and we did not find any studies about the HIV care and treatment cascade (HCTC) related to this state. We aimed to estimate the indicators of HCTC of RS, Brazil, and associated factors. A cross-sectional study with all people living with HIV (PLWH) in RS between 1 January 2014 and 31 December 2017 was conducted using a national database which registers all HIV notifications, CD4 and viral load laboratory data and antiretroviral therapy (ART) usage in the public health system. We considered sex, age, education, race, year of HIV diagnosis, and health region as predictor factors, and defined linkage to care, retention to care, being on ART, and having undetectable viral load as the HCTC indicators. Descriptive analysis and multivariable logistic regression were performed using Stata 15.2. A total of 116,121 PLWH were diagnosed, 79,959 were linked to care, 72,117 retained in care, 69,219 on ART, and 54,857 had undetectable viral load from 2014 to 2017. We observed greatest attrition for younger age, non-white, and lower education in all HCTC indicators. Women are more likely to have undetectable viral load (OR = 1.04, 95% CI: 1.01–1.07), even though they are less likely to be retained to care (OR = 0.92; 95% CI: 0.89–0.96) and on ART (OR = 0.82; 95% CI: 0.78–0.86). Although all HCTC indicators have increased over the period and the “test and treat” policy indicates improvements in ART and in undetectable viral load outcomes, evidence suggests specific attrition and disparities such as those related to HIV healthcare facilities should be addressed. These findings may be used by researchers, health professionals, and policymakers in order to investigate and implement interventions to better engage PLWH across the HCTC.

scholarly journals Peste des Petits Ruminants Virus Infection at the Wildlife–Livestock Interface in the Greater Serengeti Ecosystem, 2015–2019

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 838
Author(s):  
Bryony A. Jones ◽  
Mana Mahapatra ◽  
Daniel Mdetele ◽  
Julius Keyyu ◽  
Francis Gakuya ◽  
...  
Keyword(s):  
Small Ruminants ◽  
Viral Disease ◽  
Global Strategy ◽  
Enzyme Linked Immunosorbent Assay ◽  
Weighted Estimate ◽  
Peste Des Petits Ruminants ◽  
African Buffalo ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Serengeti Ecosystem

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015–2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant’s gazelle, impala, Thomson’s gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018–2019, a cross-sectional survey of randomly selected African buffalo and Grant’s gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant’s gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife–livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson’s gazelle and wildebeest.

scholarly journals The Effect of Prophylactic HPV Vaccines on Oral and Oropharyngeal HPV Infection—A Systematic Review

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1339
Author(s):  
Kristoffer Juul Nielsen ◽  
Kathrine Kronberg Jakobsen ◽  
Jakob Schmidt Jensen ◽  
Christian Grønhøj ◽  
Christian Von Buchwald
Keyword(s):  
Cohort Study ◽  
Oropharyngeal Cancer ◽  
Hpv Infection ◽  
Case Control ◽  
Igg Antibodies ◽  
Hpv Vaccines ◽  
Case Control Studies ◽  
Cross Sectional ◽  
Post Vaccination ◽  
Cross Sectional Studies

Human papillomavirus (HPV) imposes an increased risk of developing cervical, anal and oropharyngeal cancer. In the Western world, HPV infection is currently the major cause of oropharyngeal cancer. The effectiveness of HPV vaccines for oral or oropharyngeal HPV infection is yet to be determined. This study conducted a systematic literature search in Pubmed and Embase. Studies investigating the impact of HPV vaccines on oral or oropharyngeal HPV infection were enrolled. This review reports the relative prevention percentage (RPP), including a risk of bias assessment as well as a quality assessment study. Nine studies were included (48,777 participants): five cross-sectional studies; one randomized community trial study (RCT); one longitudinal cohort study; and two case-control studies. A significant mean RPP of 83.9% (66.6–97.8%) was calculated from the cross-sectional studies, 82.4% in the included RCT and 83% in the longitudinal cohort study. Further, two case-control studies that measured antibody response in participants immunized with HPV vaccines were included. Respectively, 100% and 93.2% of participants developed HPV-16 Immunoglobulin G (IgG) antibodies in oral fluids post-vaccination. Analysis of the studies identified a significant decrease in vaccine-type oral or oropharyngeal HPV infections in study participants immunized with HPV vaccines across study designs and heterogenous populations. Further, a significant percentage of participants developed IgG antibodies in oral fluid post-vaccination.

The relationships among personal accomplishment, resilience and teachers’ experience of teaching multiple school subjects role conflict

2020 ◽  
pp. 1356336X2098077
Author(s):  
Cassandra Iannucci ◽  
K Andrew R Richards ◽  
Ann MacPhail
Keyword(s):  
Root Mean Square ◽  
Role Conflict ◽  
Structural Equation ◽  
Maslach Burnout Inventory ◽  
Personal Accomplishment ◽  
Mean Square ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
School Subjects ◽  
Fit Index

This study develops an understanding of the relationships among personal accomplishment, resilience, and teaching multiple school subjects role conflict (TMSS-RC) among Irish post-primary, multi-subject teachers. A theoretically informed conceptual framework was developed to explain the relationships among personal accomplishment, resilience, and the sub-domains of TMSS-RC: status conflict, schedule conflict, and energy expenditure. Participants included 259 post-primary teachers across Ireland who were responsible for teaching physical education and at least one other school subject concurrently. Participants completed a 46-item, cross-sectional survey consisting of a demographics questionnaire, the TMSS-RC scale, the personal accomplishment subscale from the Maslach Burnout Inventory–Educators Survey, and the 10-item version of the Connor–Davidson Resilience Scale. Concurrent confirmatory factor analysis was first used to confirm the psychometric quality of the hypothesised factor structure. Results indicated that the hypothesised model was a good fit for the data. Structural equation modelling was then used to examine and verify the hypothesised relationships of the conceptual model. Results supported the model with mediation, which showed good model fit: C3(129) = 174.97, p = 0.004, χ 2/df = 1.36; root mean square error of approximation = 0.044 (90% confidence interval = 0.031, 0.057; p = 0.770), standardised root mean square residual = 0.058; non-normed fit index = 0.974; comparitive-fit index (CFI) = 0.978. Collectively, results indicate that as teachers’ levels of personal accomplishment and resilience increase, their experiences of TMSS-RC decrease. This suggests that stress as a result of teaching multiple school subjects concurrently can be reduced with an increase in teachers’ perceived levels of personal accomplishment and resiliency.

scholarly journals Orthorexia nervosa and disordered eating attitudes among Lebanese adults: Assessing psychometric proprieties of the ORTO-R in a population-based sample

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0254948
Author(s):  
Souheil Hallit ◽  
Anna Brytek-Matera ◽  
Sahar Obeid
Keyword(s):  
Disordered Eating ◽  
Factor Structure ◽  
Population Based ◽  
Eating Attitudes ◽  
Orthorexia Nervosa ◽  
Arabic Version ◽  
Mean Square ◽  
Cross Sectional ◽  
Eat 26 ◽  
Disordered Eating Attitudes

Background Previous research demonstrated a relationship between ON and disordered eating symptoms (eating concern, restraint, cognitive preoccupations about body shape and weight) and disordered eating attitudes (DEA). Since screening for orthorexia nervosa is now part of clinical practice, the measurement instruments to be used must be clinically significant, reliable, valid and sensitive to our target population. The main objective of the present study was to confirm the factor structure of the Arabic version of the ORTO-R using a first sample of Lebanese adults and confirm those results on another sample. The secondary objective was to assess sex differences in terms of ON and DEA, as well as to examine whether symptoms of ON were related to DEA in Lebanese adults. Methods A total of 783 Lebanese adults was selected to participate in this cross-sectional study (January-May 2018) using a proportionate random sample from all Lebanese governorates. Results The mean age of the total sample was 27.78 ± 11.60 years (Min. 18 –Max. 84) (33.5% females) and their mean BMI was 24.36 ± 5.31 kg/m2. All items of the ORTO-R were extracted during the factor analysis and yielded a two-factor solution with Eigenvalues > 1 (variance explained  =  50.07%; KMO = 0.570; Bartlett’s sphericity test p<0.001; αCronbach = 0.755). This factor structure was confirmed by a confirmatory factor analysis; the Maximum Likelihood Chi-Square  =  26.894 and Degrees of Freedom  =  8, which gave a χ2/df  =  3.36. The Tucker Lewis Index (TLI) value was 0.914, whereas the standardized root mean square residual (SRMR) value was 0.032. The root mean square error of approximation (RMSEA) value was 0.077 [95% CI 0.046–0.111] (pclose = 0.07) and comparative fit index (CFI) value was 0.967 respectively, indicating a good fit of the model. There was also no measurement invariance between genders. Female gender was significantly associated with lower ORTO-R scores (more orthorexia nervosa) compared to males (B = -0.65; p = 0.026, 95% CI -1.22- -0.08; ɳ2 = 0.006). However, no significant difference was found between genders in terms of EAT-26 scores (B = 0.23; p = 0.813, 95% CI -1.66–2.12; ɳ2 = 0.0001). Higher ORTO-R scores (lower/ less pathological ON tendencies and behaviors) were significantly related to higher EAT-26 total scores (higher levels of DEA) as well as higher dieting, bulimia and oral control scores in both females (from a weak to a moderate positive correlation) and males (a weak positive correlation). Conclusion This cross-sectional population-based study confirmed the factor structure of the Arabic version of the ORTO-R, demonstrated an association between ON and DEA and revealed more ON among females compared to males.

scholarly journals Analysis of Community’s Knowledge of Hepatitis A Disease and Vaccines in Indonesia

2020 ◽  
Author(s):  
Dwi Endarti ◽  
Irfan Ahmad ◽  
Tri Murti Andayani
Keyword(s):  
Hepatitis A ◽  
Knowledge Score ◽  
Viral Disease ◽  
National Immunization Program ◽  
Immunization Program ◽  
Cross Sectional ◽  
National Immunization ◽  
The Mean ◽  
The Government ◽  
Central Sulawesi

Hepatitis A is a viral disease with a high potential for morbidity and mortality which is also the second highest incidence in Indonesia after hepatitis B. The purpose of this research is to measure knowledge of Indonesian community about hepatitis A disease and vaccine and to analyze the factors related to knowledge. This study used an observational survey research design applying a cross-sectional multi-center approach. The number of sample was 500 respondents located in 5 provinces in Indonesia, namely DIY, Lampung, West Java, North Kalimantan, and Central Sulawesi. Data collection was carried out using a questionnaire that was modified from the questionnaire in a similar study before. The results showed that the mean of knowledge score obtained was 75.2% ± 12.2% with a median of 76.9%. There are 2 items of knowledge that were lack understood by respondents, namely treatment of hepatitis A that cannot be treated with antibiotics and immunizations and hepatitis A is not included yet in the national immunization program in Indonesia. Statistical analysis using Mann-Whitney test showed that there were significant differences score of knowledge between groups on the characteristics of the number of dependents (p=0,000), experience of hearing a disease (p=0,000), experience of hearing a vaccine (p=0,000) and the experience of the child being vaccinated (p=0,000). It is recommended that the government conducts education programs for the community of Indonesia to improve knowledge related to hepatitis A diseases and the benefits of using hepatitis Avaccine.

scholarly journals Analisis Tingkat Pengetahuan Masyarakat Terhadap Penyakit dan Vaksin Hepatitis A di Indonesia

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Irfan Ahmad ◽  
Dwi Endarti ◽  
Tri Murti Andayani
Keyword(s):  
Hepatitis A ◽  
Knowledge Score ◽  
Viral Disease ◽  
Public Knowledge ◽  
Immunization Program ◽  
Cross Sectional ◽  
National Immunization ◽  
The Mean ◽  
The Government ◽  
Central Sulawesi

Hepatitis A is a viral disease with a high potential for morbidity and mortality. It is also the second highest viral disease in Indonesia after hepatitis B. Community’s knowledge regarding Hepatitis A disease dan vaccine is required to support such program for eradication of Hepatitis A. The aims of this study was to measure the knowledge of Indonesian community about hepatitis A disease and its vaccine indicated from knowledge score of correct answer towards questionnaire, as well as to analyze the factors that can influence it indicated from difference of mean of knowledge scores among groups of respondents characteristics. This study used an observational survey research design applying a cross-sectional multi-center approach. The number of sample was 500 respondents located in 5 provinces in Indonesia, namely DIY, Lampung, West Java, Central Kalimantan, and Central Sulawesi. Data collection was carried out using a questionnaire that was modified from the questionnaire in a similar previous study. The results showed that public knowledge related to diseases and hepatitis A vaccine in Indonesia was considered sufficient with the mean score obtained was 75.2% ± 12.2%. Statistical analysis using Mann-Whitney test showed that there were significant differences in score of knowledge between groups on the characteristics of experience of hearing a disease (p=0,000), experience of hearing a vaccine (p=0,000) and the experience of the child being vaccinated (p=0,000). There are 2 items of knowledge that werelack understood by respondents, namely treatment of hepatitis A that cannot be treated with antibiotics and immunizations and hepatitis A is not included yet in the national immunization program in Indonesia. It is concluded that community knowledge regarding hepatitis A disease and vaccine was fair (mean knowledge score between 65 – 80%). However, the government still needs to conduct educational programs for the Indonesian community about disease prevention through the vaccination process and provide counseling about the types of vaccines that are not included in the national health insurance program in Indonesia.

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