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  1. Article ; Online: MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread.

    De-Leon, Hilla / Aran, Dvir

    Journal of biomedical informatics

    2023  Volume 141, Page(s) 104364

    Abstract: In the three years since SARS-CoV-2 was first detected in China, hundreds of millions of people have been infected and millions have died. Along with the immediate need for treatment solutions, the COVID-19 epidemic has reinforced the need for ... ...

    Abstract In the three years since SARS-CoV-2 was first detected in China, hundreds of millions of people have been infected and millions have died. Along with the immediate need for treatment solutions, the COVID-19 epidemic has reinforced the need for mathematical models that can predict the spread of the pandemic in an ever-changing environment. The susceptible-infectious-removed (SIR) model has been widely used to model COVID-19 transmission, however, with limited success. Here, we present a novel, dynamic Monte-Carlo Agent-based Model (MAM), which is based on the basic principles of statistical physics. Using public aggregative data from Israel on three major outbreaks, we compare predictions made by SIR and MAM, and show that MAM outperforms SIR in all aspects. Furthermore, MAM is a flexible model and allows to accurately examine the effects of vaccinations in different subgroups, and the effects of the introduction of new variants.
    MeSH term(s) Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Models, Statistical ; Models, Theoretical ; Disease Outbreaks
    Language English
    Publishing date 2023-04-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2023.104364
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Statistical mechanics study of the introduction of a vaccine against COVID-19 disease.

    De-Leon, Hilla / Pederiva, Francesco

    Physical review. E

    2021  Volume 104, Issue 1-1, Page(s) 14132

    Abstract: By the end of 2020, a year since the first cases of infection by the Covid-19 virus have been reported; several pharmaceutical companies made significant progress in developing effective vaccines against the Covid-19 virus that has claimed the lives of ... ...

    Abstract By the end of 2020, a year since the first cases of infection by the Covid-19 virus have been reported; several pharmaceutical companies made significant progress in developing effective vaccines against the Covid-19 virus that has claimed the lives of more than 10^{6} people over the world. On the other hand, there is growing evidence of re-infection by the virus, which can cause further outbreaks. In this paper, we apply statistical physics tools to examine theoretically the vaccination rate required to control the pandemic for three different vaccine efficiency scenarios and five different vaccination rates. Also, we study the effect of temporal restrictions or reliefs on the pandemic's outbreak, assuming that re-infection is possible. When examining the efficiency of the vaccination rate of the general population in preventing an additional outbreak of the disease, we find that a high vaccination rate (where 0.3% of the population is vaccinated daily, which is equivalent to ≈10^{6} vaccine doses in the United States daily) is required to gain control over the spread of the virus without further restrictions.
    MeSH term(s) Biophysics ; COVID-19 Vaccines ; Humans ; Pandemics ; Vaccination/statistics & numerical data
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2021-09-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.104.014132
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Particle modeling of the spreading of coronavirus disease (COVID-19).

    De-Leon, Hilla / Pederiva, Francesco

    Physics of fluids (Woodbury, N.Y. : 1994)

    2020  Volume 32, Issue 8, Page(s) 87113

    Abstract: By the end of July 2020, the COVID-19 pandemic had infected more than 17 × ... ...

    Abstract By the end of July 2020, the COVID-19 pandemic had infected more than 17 × 10
    Keywords covid19
    Language English
    Publishing date 2020-08-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1472743-2
    ISSN 1089-7666 ; 1070-6631
    ISSN (online) 1089-7666
    ISSN 1070-6631
    DOI 10.1063/5.0020565
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: MAM: Flexible Monte-Carlo Agent-based Model for Modelling COVID-19 Spread

    De-Leon, Hilla / Aran, Dvir

    medRxiv

    Abstract: In the two and half years since SARS-CoV-2 was first detected in China, hundreds of millions of people have been infected and millions have died. Along with the immediate need for treatment solutions, the COVID-19 pandemic has reinforced the need for ... ...

    Abstract In the two and half years since SARS-CoV-2 was first detected in China, hundreds of millions of people have been infected and millions have died. Along with the immediate need for treatment solutions, the COVID-19 pandemic has reinforced the need for mathematical models that can predict the spread of the pandemic in an ever-changing environment. The susceptible-infectious-removed (SIR) model has been widely used to model COVID-19 transmission, however, with limited success. Here, we present a novel, dynamic Monte-Carlo Agent-based Model (MAM), which is based on the basic principles of statistical physics. Using data from Israel on three major outbreaks, we compare predictions made by SIR and MAM, and show that MAM outperforms SIR in all aspects. Furthermore, MAM is a flexible model and allows to accurately examine the effects of vaccinations in different subgroups, and the effects of the introduction of new variants
    Keywords covid19
    Language English
    Publishing date 2022-09-12
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2022.09.11.22279815
    Database COVID19

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  5. Book ; Online: Using a physical model and aggregate data to estimate the spreading of Covid-19 in Israel in the presence of waning immunity and competing variants

    De-Leon, Hilla / Pederiva, Francesco

    2022  

    Abstract: In more than two years since the COVID-19 virus was first detected in China, hundreds of millions of individuals have been infected, and millions have died. Aside from the immediate need for medical solutions (such as vaccines and medications) to treat ... ...

    Abstract In more than two years since the COVID-19 virus was first detected in China, hundreds of millions of individuals have been infected, and millions have died. Aside from the immediate need for medical solutions (such as vaccines and medications) to treat the epidemic, the Corona pandemic has strengthened the demand for mathematical models that can predict the spread of the pandemic in an ever-changing reality. Here, we present a novel, dynamic particle model based on the basic principles of statistical physics that enables the prediction of the spreading of Covid-19 in the presence of effective vaccines. This particle model enables us to accurately examine the effects of the vaccine on different subgroups of the vaccinated population and the entire population and to identify the vaccine waning. Furthermore, a particle model can predict the prevalence of two competing variants over time and their associated morbidity.

    Comment: 9 pages 8 figures
    Keywords Quantitative Biology - Populations and Evolution
    Publishing date 2022-05-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: What pushed Israel out of herd immunity? Modeling COVID-19 spread of Delta and Waning immunity

    De-Leon, Hilla / Aran, Dvir

    medRxiv

    Abstract: Following a successful vaccination campaign at the beginning of 2021 in Israel, where approximately 60% of the population were vaccinated with an mRNA BNT162b2 vaccine, it seemed that Israel had crossed the herd immunity threshold (HIT). Nonetheless, ... ...

    Abstract Following a successful vaccination campaign at the beginning of 2021 in Israel, where approximately 60% of the population were vaccinated with an mRNA BNT162b2 vaccine, it seemed that Israel had crossed the herd immunity threshold (HIT). Nonetheless, Israel has seen a steady rise in COVID-19 morbidity since June 2021, reaching over 1,000 cases per million by August. This outbreak is attributed to several events that came together: the temporal decline of the vaccine9s efficacy (VE); lower efficacy of the vaccine against the current Delta (B.1.617.2) variant; highly infectiousness of Delta; and temporary halt of mandated NPIs (non-pharmaceutical interventions) or any combination of the above. Using a novel spatial-dynamic model and recent aggregate data from Israel, we examine the extent of the impact of the Delta variant on morbidity and whether it can solely explain the outbreak. We conclude that both Delta infectiousness and waning immunity could have been able to push Israel above the HIT independently, and thus, to mitigate the outbreak effective NPIs are required. Our analysis cautions countries that once vaccines9 will wane a highly infectious spread is expected, and therefore, the expected decline in the vaccine9s effectiveness in those countries should be accompanied by another vaccination campaign and effective NPIs
    Keywords covid19
    Language English
    Publishing date 2021-09-15
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.09.12.21263451
    Database COVID19

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  7. Article ; Online: Using a physical model and aggregate data from Israel to estimate the current (July 2021 ) efficacy of the Pfizer-BioNTech vaccine

    De-Leon, Hilla / Pederiva, Francesco

    medRxiv

    Abstract: From the end of June 2021, the state of Israel, where ~60\% of the population is vaccinated with an mRNA BNT162b2 vaccine, has an increase in the daily morbidity. This increase may be a result of different events: a temporal decline of the vaccine9s ... ...

    Abstract From the end of June 2021, the state of Israel, where ~60\% of the population is vaccinated with an mRNA BNT162b2 vaccine, has an increase in the daily morbidity. This increase may be a result of different events: a temporal decline of the vaccine9s efficacy; Lower efficacy of the vaccine against the current Delta ( (B.1.617.2) variant (which is now the dominant strain in Israel); A result of lack of social restrictions, a highly contagious variant, or any combination of the above. We found, by using a novel spatial-dynamic model and recent {aggregate} data from Israel, that this new surge of cases is partiality due to a decline in the shielding of those who were vaccinated about six months ago. Also, we found a decrease in the vaccine9s efficacy against severe morbidity for the early elderly population compared to the rest of the vaccinated population. These results, which are consistent with recent studies, emphasize the high ability of the model in evaluating the time- and age-dependent efficacy of the vaccine for different age groups and enables to predict the spread of the pandemic as a function of such efficacy.
    Keywords covid19
    Language English
    Publishing date 2021-08-11
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.08.10.21261856
    Database COVID19

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  8. Article ; Online: Particle modeling of the spreading of coronavirus disease (COVID-19)

    De-Leon, Hilla / Pederiva, Francesco

    Physics of Fluids

    2020  Volume 32, Issue 8, Page(s) 87113

    Keywords Condensed Matter Physics ; covid19
    Language English
    Publisher AIP Publishing
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1472743-2
    ISSN 1089-7666 ; 1070-6631
    ISSN (online) 1089-7666
    ISSN 1070-6631
    DOI 10.1063/5.0020565
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Particle modeling of the spreading of coronavirus disease (COVID-19)

    De-Leon, Hilla / Pederiva, Francesco

    Physics of fluids (Woodbury, N.Y. : 1994)

    Abstract: ... banning public events, and forcing social distancing, including local and national lockdowns In our work ... lockdown models and eight various combinations of constraints, which allow us to examine the efficiency ... restriction/lockdown patterns This model's main prediction is that a cyclic schedule of no-restrictions ...

    Abstract By the end of July 2020, the COVID-19 pandemic had infected more than 17 × 10(6) people and had spread to almost all countries worldwide In response, many countries all over the world have used different methods to reduce the infection rate, such as case isolation, closure of schools and universities, banning public events, and forcing social distancing, including local and national lockdowns In our work, we use a Monte Carlo based algorithm to predict the virus infection rate for different population densities using the most recent epidemic data We test the spread of the coronavirus using three different lockdown models and eight various combinations of constraints, which allow us to examine the efficiency of each model and constraint In this paper, we have tested three different time-cyclic patterns of no-restriction/lockdown patterns This model's main prediction is that a cyclic schedule of no-restrictions/lockdowns that contains at least ten days of lockdown for each time cycle can help control the virus infection In particular, this model reduces the infection rate when accompanied by social distancing and complete isolation of symptomatic patients
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #733466
    Database COVID19

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  10. Book ; Online: Particle modeling of the spreading of Coronavirus Disease (COVID-19)

    De-Leon, Hilla / Pederiva, Francesco

    2020  

    Abstract: ... lockdowns. We use a Monte-Carlo (MC) based algorithm to predict the virus infection rate for different ... different lockdown models, and eight various combinations of constraints, which allow us to examine ... of no-restrictions/lockdown patterns. This model's main prediction is that a cyclic schedule of no ...

    Abstract By the end of July 2020, the COVID-19 pandemic had infected more than seventeen million people and had spread to almost all countries worldwide. In response, many countries all over the world have used different methods to reduce the infection rate, such as including case isolation, the closure of schools and universities, banning public events, and mostly forcing social distancing, including local and national lockdowns. We use a Monte-Carlo (MC) based algorithm to predict the virus infection rate for different population densities using the most recent epidemic data in our work. We test the spread of the Coronavirus using three different lockdown models, and eight various combinations of constraints, which allow us to examine the efficiency of each model and constraint. In this paper, we have tested three different time-cyclic patterns of no-restrictions/lockdown patterns. This model's main prediction is that a cyclic schedule of no-restrictions/lockdown that contains at least ten days of lockdown for each time cycle can help control the virus infection. In particular, this model reduces the infection rate when accompanied by social distancing and complete isolation of symptomatic patients.

    Comment: 8 pages, 5 figures
    Keywords Physics - Physics and Society ; Quantitative Biology - Populations and Evolution ; covid19
    Publishing date 2020-05-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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