scholarly journals Exploring secondary SARS-CoV-2 transmission from asymptomatic cases using contact tracing data

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Ko Nakajo ◽  
Hiroshi Nishiura
Keyword(s):  
Negative Binomial ◽  
Reproduction Number ◽  
Process Models ◽  
Contact Tracing ◽  
Primary Case ◽  
Binomial Distributions ◽  
Potential Association ◽  
Using Data ◽  
Asymptomatic Individuals ◽  
Asymptomatic Case

Abstract Background Individuals with asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can propagate the virus unknowingly and thus have been a focus of public health attentions since the early stages of the pandemic. Understanding viral transmissibility among asymptomatic individuals is critical for successful control of coronavirus disease 2019 (COVID-19). The present study aimed to understand SARS-CoV-2 transmissibility among young asymptomatic individuals and to assess whether symptomatology was associated with transmission of symptomatic vs. asymptomatic infections. Methods We analyzed one of the first-identified clusters of SARS-CoV-2 infections with multiple chains of transmission that occurred among university students in March 2020 in Kyoto prefecture, Japan, using discrete and two-type branching process models. Assuming that the number of secondary cases resulting from either primary symptomatic or asymptomatic cases independently followed negative binomial distributions, we estimated the relative reproduction numbers of an asymptomatic case compared with a symptomatic case. To explore the potential association between symptomatology and transmission of symptomatic vs. asymptomatic incident infections, we also estimated the proportion of secondary symptomatic cases produced by primary symptomatic and asymptomatic cases. Results The reproduction number for a symptomatic primary case was estimated at 1.14 (95% confidence interval [CI]: 0.61–2.09). The relative reproduction number for asymptomatic cases was estimated at 0.19 (95% CI: 0.03–0.66), indicating that asymptomatic primary cases did not result in sufficient numbers of secondary infections to maintain chains of transmission. There was no apparent tendency for symptomatic primary cases to preferentially produce symptomatic secondary cases. Conclusions Using data from a transmission network during the early epidemic in Japan, we successfully estimated the relative transmissibility of asymptomatic cases of SARS-CoV-2 infection at 0.22. These results suggest that contract tracing focusing on symptomatic index cases may be justified given limited testing capacity.

scholarly journals Reproduction number for an age of infection structured model

2021 ◽  
Author(s):  
Carles Barril ◽  
Àngel Calsina ◽  
Sílvia Cuadrado ◽  
Jordi Ripoll
Keyword(s):  
Reproduction Number ◽  
Limited Data ◽  
Epidemic Outbreak ◽  
Primary Case ◽  
Before And After ◽  
Asymptomatic Infections ◽  
A Chain ◽  
Asymptomatic Individuals ◽  
Virus Spreading ◽  
Fixed Period

We study the basic reproduction number ($R_0$) in an epidemic model where infected individuals are initially asymptomatic and structured by the time since infection. At the beginning of an epidemic outbreak the computation of $R_0$ relies on limited data based mostly on symptomatic cases, since asymptomatic infected individuals are not detected by the surveillance system. $R_0$ has been widely used as an indicator to assess the dissemination of infectious diseases. Asymptomatic individuals are assumed to either become symptomatic after a fixed period of time or they are removed (recovery or disease-related death).We determine $R_0$ , understood as the expected secondary symptomatic cases produced by a symptomatic primary case through a chain of asymptomatic infections. $R_0$ is computed directly by interpreting the model ingredients and also using a more systematic approach based on the next-generation operator. Reported Covid-19 cases data during the first wave of the pandemic in Spain are used to fit the model and obtain both values of $R_0$ before and after the severe lockdown imposed in March 2020. The results confirm that SARS-CoV-2 was expanding within the population before the lockdown whereas the virus spreading was controlled two weeks after the lockdown. p, li { white-space: pre-wrap; }

scholarly journals The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

2020 ◽  
Author(s):  
Sang Woo Park ◽  
Daniel M. Cornforth ◽  
Jonathan Dushoff ◽  
Joshua S. Weitz
Keyword(s):  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Mathematical Framework ◽  
Primary Case ◽  
Generation Interval ◽  
Temporal Course ◽  
Route Of Transmission ◽  
Asymptomatic Individuals ◽  
The Basic Reproduction Number

The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the implications of asymp- tomatic transmission on dynamics of disease. We use a mathematical framework to evaluate expected effects of asymptomatic transmission on the basic reproduction number ℛ0 (i.e., the expected number of secondary cases generated by an average primary case in a fully sus- ceptible population) and the fraction of new secondary cases attributable to asymptomatic individuals. If the generation-interval distribution of asymptomatic transmission differs from that of symptomatic transmission, then estimates of the basic reproduction number which do not explicitly account for asymptomatic cases may be systematically biased. Specifically, if asymptomatic cases have a shorter generation interval than symptomatic cases, ℛ0 will be over-estimated, and if they have a longer generation interval, ℛ0 will be under-estimated. Estimates of the realized proportion of asymptomatic transmission during the exponential phase also depend on asymptomatic generation intervals. Our analysis shows that understanding the temporal course of asymptomatic transmission can be important for assessing the importance of this route of transmission, and for disease dynamics. This provides an additional motivation for investigating both the importance and relative duration of asymptomatic transmission.

scholarly journals A reaction-diffusion system to better comprehend the unlockdown: Application of SEIR-type model with diffusion to the spatial spread of COVID-19 in France

2020 ◽  
Vol 8 (1) ◽  
pp. 102-113
Author(s):  
Youcef Mammeri
Keyword(s):  
Reproduction Number ◽  
Reaction Diffusion ◽  
Type Model ◽  
Spatial Spread ◽  
Daily Movement ◽  
Reaction Diffusion Model ◽  
The Mean ◽  
Using Data ◽  
Asymptomatic Individuals ◽  
Initial Spatial Distribution

AbstractWe wondered that if a reaction-diffusion model considering only the mean daily movement of susceptible, exposed and asymptomatic individuals was enough to describe the spread of the COVID-19 virus. The model was calibrated using data on the confirmed infection and death from France as well as their initial spatial distribution. First, the system of partial differential equations is studied, then the basic reproduction number, 𝒭0 is derived. Second, numerical simulations, based on a combination of level-set and finite differences, shown the spatial spread of COVID-19 from March 16 to June 16. Finally, scenarios of unlockdown are compared according to variation of distancing, or partially spatial lockdown.

scholarly journals Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February–March 2020

2021 ◽  
Vol 10 (11) ◽  
pp. 2392
Author(s):  
Andrei R. Akhmetzhanov ◽  
Kenji Mizumoto ◽  
Sung-Mok Jung ◽  
Natalie M. Linton ◽  
Ryosuke Omori ◽  
...  
Keyword(s):  
Cumulative Incidence ◽  
Surveillance System ◽  
Negative Binomial ◽  
Actual Number ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
Using Data ◽  
Insight Into ◽  
Actual Incidence

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382–7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0–4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

scholarly journals The Effect of Alcohol on Telomere Length: A Systematic Review of Epidemiological Evidence and a Pilot Study during Pregnancy

2021 ◽  
Vol 18 (9) ◽  
pp. 5038
Author(s):  
Andrea Maugeri ◽  
Martina Barchitta ◽  
Roberta Magnano San Lio ◽  
Maria Clara La Rosa ◽  
Claudia La Mastra ◽  
...  
Keyword(s):  
Systematic Review ◽  
Pilot Study ◽  
Alcohol Consumption ◽  
Telomere Length ◽  
Molecular Mechanisms ◽  
Epidemiological Studies ◽  
Potential Association ◽  
Significant Difference ◽  
Periconceptional Period ◽  
Using Data

Several studies—albeit with still inconclusive and limited findings—began to focus on the effect of drinking alcohol on telomere length (TL). Here, we present results from a systematic review of these epidemiological studies to investigate the potential association between alcohol consumption, alcohol-related disorders, and TL. The analysis of fourteen studies—selected from PubMed, Medline, and Web of Science databases—showed that people with alcohol-related disorders exhibited shorter TL, but also that alcohol consumption per se did not appear to affect TL in the absence of alcohol abuse or dependence. Our work also revealed a lack of studies in the periconceptional period, raising the need for evaluating this potential relationship during pregnancy. To fill this gap, we conducted a pilot study using data and samples form the Mamma & Bambino cohort. We compared five non-smoking but drinking women with ten non-smoking and non-drinking women, matched for maternal age, gestational age at recruitment, pregestational body mass index, and fetal sex. Interestingly, we detected a significant difference when analyzing relative TL of leukocyte DNA of cord blood samples from newborns. In particular, newborns from drinking women exhibited shorter relative TL than those born from non-drinking women (p = 0.024). Although these findings appeared promising, further research should be encouraged to test any dose–response relationship, to adjust for the effect of other exposures, and to understand the molecular mechanisms involved.

scholarly journals A Mathematical Model of Contact Tracing during the 2014–2016 West African Ebola Outbreak

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 608
Author(s):  
Danielle Burton ◽  
Suzanne Lenhart ◽  
Christina J. Edholm ◽  
Benjamin Levy ◽  
Michael L. Washington ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Disease Management ◽  
Ebola Virus ◽  
Virus Disease ◽  
Infected Individual ◽  
Vital Role ◽  
West African ◽  
Contact Tracing ◽  
The Novel ◽  
Using Data

The 2014–2016 West African outbreak of Ebola Virus Disease (EVD) was the largest and most deadly to date. Contact tracing, following up those who may have been infected through contact with an infected individual to prevent secondary spread, plays a vital role in controlling such outbreaks. Our aim in this work was to mechanistically represent the contact tracing process to illustrate potential areas of improvement in managing contact tracing efforts. We also explored the role contact tracing played in eventually ending the outbreak. We present a system of ordinary differential equations to model contact tracing in Sierra Leonne during the outbreak. Using data on cumulative cases and deaths, we estimate most of the parameters in our model. We include the novel features of counting the total number of people being traced and tying this directly to the number of tracers doing this work. Our work highlights the importance of incorporating changing behavior into one’s model as needed when indicated by the data and reported trends. Our results show that a larger contact tracing program would have reduced the death toll of the outbreak. Counting the total number of people being traced and including changes in behavior in our model led to better understanding of disease management.

scholarly journals Identifying Temporal Aggregation Effect on Crash-Frequency Modeling

2021 ◽  
Vol 13 (11) ◽  
pp. 6214
Author(s):  
Bumjoon Bae ◽  
Changju Lee ◽  
Tae-Young Pak ◽  
Sunghoon Lee
Keyword(s):  
Traffic Safety ◽  
Negative Binomial ◽  
Random Effect ◽  
Temporal Correlation ◽  
Negative Binomial Regression ◽  
Spatiotemporal Analysis ◽  
Parameter Estimates ◽  
Crash Frequency ◽  
Crash Frequency Modeling ◽  
Using Data

Aggregation of spatiotemporal data can encounter potential information loss or distort attributes via individual observation, which would influence modeling results and lead to an erroneous inference, named the ecological fallacy. Therefore, deciding spatial and temporal resolution is a fundamental consideration in a spatiotemporal analysis. The modifiable temporal unit problem (MTUP) occurs when using data that is temporally aggregated. While consideration of the spatial dimension has been increasingly studied, the counterpart, a temporal unit, is rarely considered, particularly in the traffic safety modeling field. The purpose of this research is to identify the MTUP effect in crash-frequency modeling using data with various temporal scales. A sensitivity analysis framework is adopted with four negative binomial regression models and four random effect negative binomial models having yearly, quarterly, monthly, and weekly temporal units. As the different temporal unit was applied, the result of the model estimation also changed in terms of the mean and significance of the parameter estimates. Increasing temporal correlation due to using the small temporal unit can be handled with the random effect models.

scholarly journals Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Setting-specific Transmission Rates: A Systematic Review and Meta-analysis

2021 ◽  
Author(s):  
Hayley A Thompson ◽  
Andria Mousa ◽  
Amy Dighe ◽  
Han Fu ◽  
Alberto Arnedo-Pena ◽  
...  
Keyword(s):  
Systematic Review ◽  
Severe Acute Respiratory Syndrome ◽  
Negative Binomial ◽  
Meta Analysis ◽  
Contact Tracing ◽  
Binomial Model ◽  
Transmission Potential ◽  
Transmission Rates ◽  
Symptom Status ◽  
Index Cases

Abstract Background Understanding the drivers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is crucial for control policies, but evidence of transmission rates in different settings remains limited. Methods We conducted a systematic review to estimate secondary attack rates (SARs) and observed reproduction numbers (Robs) in different settings exploring differences by age, symptom status, and duration of exposure. To account for additional study heterogeneity, we employed a beta-binomial model to pool SARs across studies and a negative-binomial model to estimate Robs. Results Households showed the highest transmission rates, with a pooled SAR of 21.1% (95% confidence interval [CI]:17.4–24.8). SARs were significantly higher where the duration of household exposure exceeded 5 days compared with exposure of ≤5 days. SARs related to contacts at social events with family and friends were higher than those for low-risk casual contacts (5.9% vs 1.2%). Estimates of SARs and Robs for asymptomatic index cases were approximately one-seventh, and for presymptomatic two-thirds of those for symptomatic index cases. We found some evidence for reduced transmission potential both from and to individuals younger than 20 years of age in the household context, which is more limited when examining all settings. Conclusions Our results suggest that exposure in settings with familiar contacts increases SARS-CoV-2 transmission potential. Additionally, the differences observed in transmissibility by index case symptom status and duration of exposure have important implications for control strategies, such as contact tracing, testing, and rapid isolation of cases. There were limited data to explore transmission patterns in workplaces, schools, and care homes, highlighting the need for further research in such settings.

scholarly journals Relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals: a rapid scoping review

BMJ Open ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. e042354
Author(s):  
David McEvoy ◽  
Conor McAloon ◽  
Aine Collins ◽  
Kevin Hunt ◽  
Francis Butler ◽  
...  
Keyword(s):  
Scoping Review ◽  
Quantitative Measure ◽  
Contact Tracing ◽  
Cochrane Library ◽  
International Studies ◽  
Screening Process ◽  
Modelling Studies ◽  
Asymptomatic Individuals ◽  
Definition Of ◽  
The Cochrane Library

ObjectivesThe aim of this study was to determine the relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals based on a scoping review of available literature.DesignRapid scoping review of peer-reviewed literature from 1 January to 5 December 2020 using the LitCovid database and the Cochrane library.SettingInternational studies on the infectiousness of individuals infected with SARS-CoV-2.ParticipantsStudies were selected for inclusion if they defined asymptomatics as a separate cohort distinct from presymptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics relative to symptomatics.Primary outcome measuresPCR result (PCR studies), the rate of infection (mathematical modelling studies) and secondary attack rate (contact tracing studies) - in each case from asymptomatic in comparison with symptomatic individuals.ResultsThere are only a limited number of published studies that report estimates of relative infectiousness of asymptomatic compared with symptomatic individuals. 12 studies were included after the screening process. Significant differences exist in the definition of infectiousness. PCR studies in general show no difference in shedding levels between symptomatic and asymptomatic individuals; however, the number of study subjects is generally limited. Two modelling studies estimate relative infectiousness to be 0.43 and 0.57, but both of these were more reflective of the infectiousness of undocumented rather than asymptomatic cases. The results from contact tracing studies include estimates of relative infectiousness of 0, but with insufficient evidence to conclude that it is significantly different from 1.ConclusionsThere is considerable heterogeneity in estimates of relative infectiousness highlighting the need for further investigation of this important parameter. It is not possible to provide any conclusive estimate of relative infectiousness, as the estimates from the reviewed studies varied between 0 and 1.

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