A simple but complex enough  si4.svg -SIR type model to be used with COVID-19 real data. Application to the case of Italy

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Abstract

Since the start of the COVID-19 pandemic in China many models have appeared in the literature, trying to simulate its dynamics. Focusing on modeling the biological and sociological mechanisms which influence the disease spread, the basic reference example is the SIR model. However, it is too simple to be able to model those mechanisms (including the three main type of control measures: social distancing, contact tracing and health system measures) to fit real data and to simulate possible future scenarios. A question, then, arises: how much and how do we need to complexify a SIR model? We develop a $θ$ -SEIHQRD model, which may be the simplest one satisfying the mentioned requirements for arbitrary territories and can be simplified in particular cases. We show its very good performance in the Italian case and study different future scenarios.

Highlights

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Mathematical model for coronavirus disease (COVID-19).
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New $θ$ -SEIHQRD model taking into account quarantine and undetected infections.
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Validation of the model with the reported data for Italy.
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New formula for the effective reproduction number.
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Different scenarios to show the impact of undetected cases and control measures.

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Most cited references 63

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Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2)

Ruiyun Li, Sen Pei, Bin Chen … (2020)

Estimation of the prevalence and contagiousness of undocumented novel coronavirus (SARS-CoV2) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Here we use observations of reported infection within China, in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with SARS-CoV2, including the fraction of undocumented infections and their contagiousness. We estimate 86% of all infections were undocumented (95% CI: [82%–90%]) prior to 23 January 2020 travel restrictions. Per person, the transmission rate of undocumented infections was 55% of documented infections ([46%–62%]), yet, due to their greater numbers, undocumented infections were the infection source for 79% of documented cases. These findings explain the rapid geographic spread of SARS-CoV2 and indicate containment of this virus will be particularly challenging.

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COVID-19 and Italy: what next?

Andrea Remuzzi, Giuseppe Remuzzi (2020)

Summary The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks. A global response to prepare health systems worldwide is imperative. Although containment measures in China have reduced new cases by more than 90%, this reduction is not the case elsewhere, and Italy has been particularly affected. There is now grave concern regarding the Italian national health system's capacity to effectively respond to the needs of patients who are infected and require intensive care for SARS-CoV-2 pneumonia. The percentage of patients in intensive care reported daily in Italy between March 1 and March 11, 2020, has consistently been between 9% and 11% of patients who are actively infected. The number of patients infected since Feb 21 in Italy closely follows an exponential trend. If this trend continues for 1 more week, there will be 30 000 infected patients. Intensive care units will then be at maximum capacity; up to 4000 hospital beds will be needed by mid-April, 2020. Our analysis might help political leaders and health authorities to allocate enough resources, including personnel, beds, and intensive care facilities, to manage the situation in the next few days and weeks. If the Italian outbreak follows a similar trend as in Hubei province, China, the number of newly infected patients could start to decrease within 3–4 days, departing from the exponential trend. However, this cannot currently be predicted because of differences between social distancing measures and the capacity to quickly build dedicated facilities in China.

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Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Melissa M. Arons, Kelly Hatfield, Sujan Reddy … (2020)

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can spread rapidly within skilled nursing facilities. After identification of a case of Covid-19 in a skilled nursing facility, we assessed transmission and evaluated the adequacy of symptom-based screening to identify infections in residents. Methods We conducted two serial point-prevalence surveys, 1 week apart, in which assenting residents of the facility underwent nasopharyngeal and oropharyngeal testing for SARS-CoV-2, including real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), viral culture, and sequencing. Symptoms that had been present during the preceding 14 days were recorded. Asymptomatic residents who tested positive were reassessed 7 days later. Residents with SARS-CoV-2 infection were categorized as symptomatic with typical symptoms (fever, cough, or shortness of breath), symptomatic with only atypical symptoms, presymptomatic, or asymptomatic. Results Twenty-three days after the first positive test result in a resident at this skilled nursing facility, 57 of 89 residents (64%) tested positive for SARS-CoV-2. Among 76 residents who participated in point-prevalence surveys, 48 (63%) tested positive. Of these 48 residents, 27 (56%) were asymptomatic at the time of testing; 24 subsequently developed symptoms (median time to onset, 4 days). Samples from these 24 presymptomatic residents had a median rRT-PCR cycle threshold value of 23.1, and viable virus was recovered from 17 residents. As of April 3, of the 57 residents with SARS-CoV-2 infection, 11 had been hospitalized (3 in the intensive care unit) and 15 had died (mortality, 26%). Of the 34 residents whose specimens were sequenced, 27 (79%) had sequences that fit into two clusters with a difference of one nucleotide. Conclusions Rapid and widespread transmission of SARS-CoV-2 was demonstrated in this skilled nursing facility. More than half of residents with positive test results were asymptomatic at the time of testing and most likely contributed to transmission. Infection-control strategies focused solely on symptomatic residents were not sufficient to prevent transmission after SARS-CoV-2 introduction into this facility.

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Author and article information

Journal

Journal ID (nlm-ta): Physica D

Journal ID (iso-abbrev): Physica D

Title: Physica D. Nonlinear Phenomena

Publisher: Elsevier B.V.

ISSN (Print): 0167-2789

ISSN (Electronic): 0167-2789

Publication date PMC-release: 1 January 2021

Publication date (Electronic): 1 January 2021

Electronic Location Identifier: 132839

Affiliations

[a ]MOMAT Research Group, Interdisciplinary Mathematics Institute, Complutense University of Madrid, Spain

[b ]Department of Computer Science, University of Almería, Spain

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[* ]Corresponding author.

Article

Publisher Item ID: S0167-2789(20)30840-X Publisher ID: 132839

DOI: 10.1016/j.physd.2020.132839

PMC ID: 7775262

PubMed ID: 33424064

SO-VID: a39d57b5-4cad-488e-8b40-aabe4e32fcc7

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Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

A simple but complex enough θ-SIR type model to be used with COVID-19 real data. Application to the case of Italy

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Novel Coronavirus Disease COVID-19

Most cited references 63

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2)

COVID-19 and Italy: what next?

Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

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