scholarly journals Smart investment of virus RNA testing resources to enhance Covid-19 mitigation

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259018
Author(s):  
Hossein Gorji ◽  
Markus Arnoldini ◽  
David F. Jenny ◽  
Wolf-Dietrich Hardt ◽  
Patrick Jenny
Keyword(s):  
Selection Procedure ◽  
Virus Antigen ◽  
Economic Life ◽  
Mitigation Strategies ◽  
Viral Rna ◽  
Disease Spread ◽  
Two Stage ◽  
Social Distancing ◽  
Virus Rna ◽  
Antigen Tests

A variety of mitigation strategies have been employed against the Covid-19 pandemic. Social distancing is still one of the main methods to reduce spread, but it entails a high toll on personal freedom and economic life. Alternative mitigation strategies that do not come with the same problems but are effective at preventing disease spread are therefore needed. Repetitive mass-testing using PCR assays for viral RNA has been suggested, but as a stand-alone strategy this would be prohibitively resource intensive. Here, we suggest a strategy that aims at targeting the limited resources available for viral RNA testing to subgroups that are more likely than the average population to yield a positive test result. Importantly, these pre-selected subgroups include symptom-free people. By testing everyone in these subgroups, in addition to symptomatic cases, large fractions of pre- and asymptomatic people can be identified, which is only possible by testing-based mitigation. We call this strategy smart testing (ST). In principle, pre-selected subgroups can be found in different ways, but for the purpose of this study we analyze a pre-selection procedure based on cheap and fast virus antigen tests. We quantify the potential reduction of the epidemic reproduction number by such a two-stage ST strategy. In addition to a scenario where such a strategy is available to the whole population, we analyze local applications, e.g. in a country, company, or school, where the tested subgroups are also in exchange with the untested population. Our results suggest that a two-stage ST strategy can be effective to curb pandemic spread, at costs that are clearly outweighed by the economic benefit. It is technically and logistically feasible to employ such a strategy, and our model predicts that it is even effective when applied only within local groups. We therefore recommend adding two-stage ST to the portfolio of available mitigation strategies, which allow easing social distancing measures without compromising public health.

scholarly journals Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation

2020 ◽  
Author(s):  
Hossein Gorji ◽  
Markus Arnoldini ◽  
David F. Jenny ◽  
Wolf-Dietrich Hardt ◽  
Patrick Jenny
Keyword(s):  
Reproduction Number ◽  
Economic Cost ◽  
Virus Antigen ◽  
Mitigation Strategies ◽  
Contact Tracing ◽  
Model Parameters ◽  
Two Stage ◽  
Social Distancing ◽  
Virus Rna ◽  
High Prevalence

AbstractCovid-19 mitigation commonly involves contact tracing (CT) and social distancing. Due to its high economic toll and its impact on personal freedom, we need to ease social distancing and deploy alternative measures, while preventing further waves of infections. While reliable mass testing (for virus RNA) would require too many resources to be effective, CT, which focuses on isolating symptomatic cases and their contacts, has been implemented in many countries. However, the latter approach has reduced efficiency when high numbers of positive patients are burdening the tracing centers. Moreover, CT misses transmissions by asymptomatic cases. Therefore, its effect in reducing the reproduction number has a theoretical limit.To improve effectiveness of contact tracing, we propose to complement it with a strategy relying on identifying and testing symptom free subgroups with a significantly higher than average virus prevalence. We call this smart testing (ST). By testing everybody in these subgroups, in addition to symptomatic cases, also large fractions of pre- and asymptomatic persons can be identified, which enhances the effectiveness of contact tracing. High prevalence subgroups can be found in different ways, which are discussed in this paper. A particularly efficient way is via preselection using cheap and fast virus antigen tests, as proposed recently. Mathematical modeling quantifies the potential reduction of the reproduction number by such a two-stage ST strategy. In addition to global scenarios, also more realistic local applications of two-stage ST have been investigated, that is, within counties, institutions, schools, companies, etc., where members have internal as well as external contacts. All involved model parameters have been varied within realistic ranges and results are presented with probabilities. Even with the most pessimistic parameter set, these results suggest that the effect of two-stage ST on the reproduction number would clearly outweigh its economic cost. Two-stage ST is technically and logistically feasible. Further, it is locally effective also when only applied within small local subpopulations. Thereby, two-stage ST efficiently complements the portfolio of mitigation strategies, which allow easing social distancing without compromising public health.Single Sentence SummaryIdentification of high prevalence groups within subpopulations to enhance detection rate of Covid-19 infections by virus RNA tests combined with subsequent isolation.

scholarly journals Addressing the COVID-19 transmission in inner Brazil by a mathematical model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
G. B. Almeida ◽  
T. N. Vilches ◽  
C. P. Ferreira ◽  
C. M. C. B. Fortaleza
Keyword(s):  
Mathematical Model ◽  
Disease Transmission ◽  
Abiotic Factors ◽  
Severe Pneumonia ◽  
Mitigation Strategies ◽  
Social Distancing ◽  
Control Disease ◽  
Set Up ◽  
Novel Coronavirus ◽  
Public Health Strategies

AbstractIn 2020, the world experienced its very first pandemic of the globalized era. A novel coronavirus, SARS-CoV-2, is the causative agent of severe pneumonia and has rapidly spread through many nations, crashing health systems and leading a large number of people to death. In Brazil, the emergence of local epidemics in major metropolitan areas has always been a concern. In a vast and heterogeneous country, with regional disparities and climate diversity, several factors can modulate the dynamics of COVID-19. What should be the scenario for inner Brazil, and what can we do to control infection transmission in each of these locations? Here, a mathematical model is proposed to simulate disease transmission among individuals in several scenarios, differing by abiotic factors, social-economic factors, and effectiveness of mitigation strategies. The disease control relies on keeping all individuals’ social distancing and detecting, followed by isolating, infected ones. The model reinforces social distancing as the most efficient method to control disease transmission. Moreover, it also shows that improving the detection and isolation of infected individuals can loosen this mitigation strategy. Finally, the effectiveness of control may be different across the country, and understanding it can help set up public health strategies.

scholarly journals Effects of Gag Mutation and Processing on Retroviral Dimeric RNA Maturation

2006 ◽  
Vol 80 (3) ◽  
pp. 1242-1249 ◽  
Author(s):  
William Fu ◽  
Que Dang ◽  
Kunio Nagashima ◽  
Eric O. Freed ◽  
Vinay K. Pathak ◽  
...  
Keyword(s):  
Viral Protein ◽  
Leukemia Virus ◽  
Viral Rna ◽  
Host Cells ◽  
Protein Cleavage ◽  
Rna Packaging ◽  
Virus Rna ◽  
Rna Dimer ◽  
Rna Maturation ◽  
Hiv 1

ABSTRACT After their release from host cells, most retroviral particles undergo a maturation process, which includes viral protein cleavage, core condensation, and increased stability of the viral RNA dimer. Inactivating the viral protease prevents protein cleavage; the resulting virions lack condensed cores and contain fragile RNA dimers. Therefore, protein cleavage is linked to virion morphological change and increased stability of the RNA dimer. However, it is unclear whether protein cleavage is sufficient for mediating virus RNA maturation. We have observed a novel phenotype in a murine leukemia virus capsid mutant, which has normal virion production, viral protein cleavage, and RNA packaging. However, this mutant also has immature virion morphology and contains a fragile RNA dimer, which is reminiscent of protease-deficient mutants. To our knowledge, this mutant provides the first evidence that Gag cleavage alone is not sufficient to promote RNA dimer maturation. To extend our study further, we examined a well-defined human immunodeficiency virus type 1 (HIV-1) Gag mutant that lacks a functional PTAP motif and produces immature virions without major defects in viral protein cleavage. We found that the viral RNA dimer in the PTAP mutant is more fragile and unstable compared with those from wild-type HIV-1. Based on the results of experiments using two different Gag mutants from two distinct retroviruses, we conclude that Gag cleavage is not sufficient for promoting RNA dimer maturation, and we propose that there is a link between the maturation of virion morphology and the viral RNA dimer.

scholarly journals Differential Roles of Viral RNA and cRNA in Functional Modulation of the Influenza Virus RNA Polymerase

2001 ◽  
Vol 276 (33) ◽  
pp. 31179-31185 ◽  
Author(s):  
Ayae Honda ◽  
Atsushi Endo ◽  
Kiyohisa Mizumoto ◽  
Akira Ishihama
Keyword(s):  
Influenza Virus ◽  
Rna Polymerase ◽  
Viral Rna ◽  
Virus Rna ◽  
Functional Modulation

A Two-Stage Hybrid Algorithm for Flexible Job-Shop Scheduling

2011 ◽  
Vol 268-270 ◽  
pp. 476-481
Author(s):  
Li Gao ◽  
Ke Lin Xu ◽  
Wei Zhu ◽  
Na Na Yang
Keyword(s):  
Genetic Algorithm ◽  
Hybrid Algorithm ◽  
Job Shop ◽  
Flow Shop ◽  
Job Shop Scheduling ◽  
Selection Procedure ◽  
Dynamic Programming Method ◽  
Two Stage ◽  
Simulated Annealing Genetic Algorithm ◽  
Mutation Operators

A mathematical model was constructed with two objectives. A two-stage hybrid algorithm was developed for solving this problem. At first, the man-hour optimization based on genetic algorithm and dynamic programming method, the model decomposes the flow shop into two layers: sub-layer and patrilineal layer. On the basis of the man-hour optimization，A simulated annealing genetic algorithm was proposed to optimize the sequence of operations. A new selection procedure was proposed and hybrid crossover operators and mutation operators were adopted. A benchmark problem solving result indicates that the proposed algorithm is effective.

scholarly journals Detection of Schmallenberg Virus RNA in Bull Semen in Poland

2016 ◽  
Vol 19 (3) ◽  
pp. 655-657 ◽  
Author(s):  
J. Kęsik-Maliszewska ◽  
M. Larska
Keyword(s):  
Extraction Method ◽  
Rna Extraction ◽  
Viral Rna ◽  
Schmallenberg Virus ◽  
Rt Pcr ◽  
Bovine Semen ◽  
Bull Semen ◽  
Virus Rna ◽  
Virus Excretion ◽  
Venereal Transmission

Abstract The detection of Schmallenberg virus (SBV) in the breeding bull semen raised the question of the possibility of venereal transmission of SBV which could result in cost-intensive restrictions in the trade of bovine semen. In order to evaluate the presence of SBV RNA in bovine semen, 131 bull semen samples from four locations in Poland collected between 2013 and 2015 were analysed by RT-PCR for viral RNA. SBV RNA was detected in 5.3% of the samples. The study has revealed that application of an appropriate RNA extraction method is crucial to detect virus excretion via semen.

Disparity and Dynamics of Social Distancing Behaviors in Japan: An Investigation of mobile phone mobility data (Preprint)

2021 ◽  
Author(s):  
Zeyu Lyu ◽  
Hiroki Takikawa
Keyword(s):  
Large Scale ◽  
Age Groups ◽  
Mitigation Strategies ◽  
Social Distancing ◽  
Demographic Groups ◽  
Fine Grained ◽  
Mobility Data ◽  
The Social ◽  
The Government ◽  
Over Time

BACKGROUND The availability of large-scale and fine-grained aggregated mobility data has allowed researchers to observe the dynamic of social distancing behaviors at high spatial and temporal resolutions. Despite the increasing attentions paid to this research agenda, limited studies have focused on the demographic factors related to mobility and the dynamics of social distancing behaviors has not been fully investigated. OBJECTIVE This study aims to assist in the design and implementation of public health policies by exploring the social distancing behaviors among various demographic groups over time. METHODS We combined several data sources, including mobile tracking data and geographical statistics, to estimate visiting population of entertainment venues across demographic groups, which can be considered as the proxy of social distancing behaviors. Then, we employed time series analyze methods to investigate how voluntary and policy-induced social distancing behaviors shift over time across demographic groups. RESULTS Our findings demonstrate distinct patterns of social distancing behaviors and their dynamics across age groups. The population in the entertainment venues comprised mainly of individuals aged 20–40 years, while according to the dynamics of the mobility index and the policy-induced behavior, among the age groups, the extent of reduction of the frequency of visiting entertainment venues during the pandemic was generally the highest among younger individuals. Also, our results indicate the importance of implementing the social distancing policy promptly to limit the spread of the COVID-19 infection. However, it should be noticed that although the policy intervention during the second wave in Japan appeared to increase the awareness of the severity of the pandemic and concerns regarding COVID-19, its direct impact has been largely decreased could only last for a short time. CONCLUSIONS At the time we wrote this paper, in Japan, the number of daily confirmed cases was continuously increasing. Thus, this study provides a timely reference for decision makers about the current situation of policy-induced compliance behaviors. On the one hand, age-dependent disparity requires target mitigation strategies to increase the intention of elderly individuals to adopt mobility restriction behaviors. On the other hand, considering the decreasing impact of self-restriction recommendations, the government should employ policy interventions that limit the resurgence of cases, especially by imposing stronger, stricter social distancing interventions, as they are necessary to promote social distancing behaviors and mitigate the transmission of COVID-19. CLINICALTRIAL None

The Potential for Transmission of Coronaviruses via Sports Equipment; A Cricket Case Study

2021 ◽  
Author(s):  
Rory England ◽  
Nicholas Peirce ◽  
Joseph Torresi ◽  
Sean Mitchell ◽  
Andy Harland
Keyword(s):  
Viral Load ◽  
Mitigation Strategies ◽  
Infected Person ◽  
Review Of Literature ◽  
Airborne Transmission ◽  
Social Distancing ◽  
Transmission Pathways ◽  
Respiratory Droplets

AbstractA review of literature on the role of fomites in transmission of coronaviruses informed the development of a framework which was used to qualitatively analyse a cricket case study, where equipment is shared and passed around, and identify potential mitigation strategies. A range of pathways were identified that might in theory allow coronavirus transmission from an infected person to a non-infected person via communal or personal equipment fomites or both. Eighteen percent of potential fomite based interactions were found to be non-essential to play including all contact with another persons equipment. Six opportunities to interrupt the transmission pathway were identified, including the recommendation to screen participants for symptoms prior to play. Social distancing between participants and avoiding unnecessary surface contact provides two opportunities; firstly to avoid equipment exposure to infected respiratory droplets and secondly to avoid uninfected participants touching potential fomites. Hand sanitisation and equipment sanitisation provide two further opportunities by directly inactivating coronavirus. Preventing players from touching their mucosal membranes with their hands represents the sixth potential interruption. Whilst potential fomite transmission pathways were identified, evidence suggests that viral load will be substantially reduced during surface transfer. Mitigation strategies could further reduce potential fomites, suggesting that by comparison, direct airborne transmission presents the greater risk in cricket.

scholarly journals A new subclass of exoribonuclease resistant RNA found in multiple Flaviviridae genera

2020 ◽  
Author(s):  
Matthew J. Szucs ◽  
Parker J. Nichols ◽  
Rachel A. Jones ◽  
Quentin Vicens ◽  
Jeffrey S. Kieft
Keyword(s):  
Rna Structure ◽  
Three Dimensional ◽  
Viral Rna ◽  
Human Pathogens ◽  
Virus Family ◽  
Innovative Strategies ◽  
Virus Rna ◽  
High Resolution Structure ◽  
Cellular Machinery ◽  
Rna Maturation

ABSTRACTViruses have developed innovative strategies to exploit the cellular machinery and overcome the host antiviral defenses, often using specifically structured RNA elements. Examples are found in flaviviruses; during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5’ to 3’ exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease resistant RNA structure (xrRNA) located in the viral genome’s 3’untranslated region (UTR). Although known to exist in several Flaviviridae genera the full distribution and diversity of xRNAs in this virus family was unknown. Using the recent high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNA in the Pegivirus, Pestivirus, and Hepacivirus genera. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Our findings thus require adjustments of previous xrRNA classification schemes and expand on the previously known distribution of the xrRNA in Flaviviridae, indicating their widespread distribution and illustrating their importance.IMPORTANCEThe Flaviviridae comprise one of the largest families of positive sense single stranded (+ssRNA) and it is divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika Virus, Dengue Virus, and Powassan Virus. In these, a part of the virus’s RNA twists up into a very special three-dimensional shape called an xrRNA that blocks the ability of the cell to “chew up” the viral RNA. Hence, part of the virus’ RNA remains intact, and this protected part is important for viral infection. This was known to occur in Flaviviruses but whether it existed in the other members of the family was not known. In this study, we not only identified a new subclass of xrRNA found in Flavivirus but also in the remaining three genera. The fact that this process of viral RNA maturation exists throughout the entire Flaviviridae family makes it clear that this is an important but underappreciated part of the infection strategy of these diverse human pathogens.

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