scholarly journals Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

2020 ◽  
Author(s):  
Danielle Miller ◽  
Michael A Martin ◽  
Noam Harel ◽  
Talia Kustin ◽  
Omer Tirosh ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Full Genome ◽  
Viral Pathogens ◽  
Social Distancing ◽  
Viral Spread ◽  
Geographic Spread ◽  
Secondary Infections ◽  
Viral Sequences ◽  
Phylodynamic Analysis ◽  
Local Transmission

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread.

scholarly journals Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Danielle Miller ◽  
Michael A. Martin ◽  
Noam Harel ◽  
Omer Tirosh ◽  
Talia Kustin ◽  
...  
Keyword(s):  
Reproduction Number ◽  
The United States ◽  
Full Genome ◽  
Viral Pathogens ◽  
Social Distancing ◽  
Viral Spread ◽  
Geographic Spread ◽  
Secondary Infections ◽  
Viral Sequences ◽  
Phylodynamic Analysis

Abstract Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

scholarly journals Real-Time Estimation of Rt for Supporting Public-Health Policies Against COVID-19

2020 ◽  
Vol 8 ◽  
Author(s):  
Sebastián Contreras ◽  
H. Andrés Villavicencio ◽  
David Medina-Ortiz ◽  
Claudia P. Saavedra ◽  
Álvaro Olivera-Nappa
Keyword(s):  
Public Health ◽  
Real Time ◽  
Reproduction Number ◽  
Case Reports ◽  
Mathematical Formulation ◽  
Time Estimation ◽  
Consensus Protocol ◽  
Viral Spread ◽  
Effective Interventions ◽  
Secondary Infections

In the absence of a consensus protocol to slow down the spread of SARS-CoV-2, policymakers need real-time indicators to support decisions in public health matters. The Effective Reproduction Number (Rt) represents the number of secondary infections generated per each case and can be dramatically modified by applying effective interventions. However, current methodologies to calculate Rt from data remain somewhat cumbersome, thus raising a barrier between its timely calculation and application by policymakers. In this work, we provide a simple mathematical formulation for obtaining the effective reproduction number in real-time using only and directly daily official case reports, obtained by modifying the equations describing the viral spread. We numerically explore the accuracy and limitations of the proposed methodology, which was demonstrated to provide accurate, timely, and intuitive results. We illustrate the use of our methodology to study the evolution of the pandemic in different iconic countries, and to assess the efficacy and promptness of different public health interventions.

Are social networking platforms the key to effective social distancing for COVID-19? (Preprint)

2020 ◽  
Author(s):  
Viknesh Sounderajah ◽  
Hutan Ashrafian ◽  
Sheraz Markar ◽  
Ara Darzi
Keyword(s):  
Operating System ◽  
Social Networking ◽  
Contact Tracing ◽  
Text Data ◽  
Social Distancing ◽  
Web Mapping ◽  
Viral Spread ◽  
Behavioural Insights ◽  
Mapping Software ◽  
Incidence And Mortality

UNSTRUCTURED If health systems are to effectively employ social distancing measures to in response to further COVID-19 peaks, they must adopt new behavioural metrics that can supplement traditional downstream measures, such as incidence and mortality. Access to mobile digital innovations may dynamically quantify compliance to social distancing (e.g. web mapping software) as well as establish personalised real-time contact tracing of viral spread (e.g. mobile operating system infrastructure through Google-Apple partnership). In particular, text data from social networking platforms can be mined for unique behavioural insights, such as symptom tracking and perception monitoring. Platforms, such as Twitter, have shown significant promise in tracking communicable pandemics. As such, it is critical that social networking companies collaborate with each other in order to (1) enrich the data that is available for analysis, (2) promote the creation of open access datasets for researchers and (3) cultivate relationships with governments in order to affect positive change.

scholarly journals Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katherine F. Jarvis ◽  
Joshua B. Kelley
Keyword(s):  
Viral Load ◽  
Temporal Dynamics ◽  
Reproduction Number ◽  
False Negative ◽  
False Negative Rate ◽  
Agent Based Model ◽  
Agent Based ◽  
Viral Spread ◽  
Negative Rate

AbstractColleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID-19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~ 17 to ~ 48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.

scholarly journals Public Compliance With Social Distancing Measures and SARS-CoV-2 Spread

2021 ◽  
pp. 003335492110112
Author(s):  
Hongjie Liu ◽  
Chang Chen ◽  
Raul Cruz-Cano ◽  
Jennifer L. Guida ◽  
Minha Lee
Keyword(s):  
Growth Rate ◽  
Reproduction Number ◽  
Early Stage ◽  
Human Mobility ◽  
The United States ◽  
Density Change ◽  
Regression Coefficients ◽  
Daily Growth Rate ◽  
Daily Growth ◽  
Social Distancing

Objective We quantified the association between public compliance with social distancing measures and the spread of SARS-CoV-2 during the first wave of the epidemic (March–May 2020) in 5 states that accounted for half of the total number of COVID-19 cases in the United States. Methods We used data on mobility and number of COVID-19 cases to longitudinally estimate associations between public compliance, as measured by human mobility, and the daily reproduction number and daily growth rate during the first wave of the COVID-19 epidemic in California, Illinois, Massachusetts, New Jersey, and New York. Results The 5 states mandated social distancing directives during March 19-24, 2020, and public compliance with mandates started to decrease in mid-April 2020. As of May 31, 2020, the daily reproduction number decreased from 2.41-5.21 to 0.72-1.19, and the daily growth rate decreased from 0.22-0.77 to –0.04 to 0.05 in the 5 states. The level of public compliance, as measured by the social distancing index (SDI) and daily encounter-density change, was high at the early stage of implementation but decreased in the 5 states. The SDI was negatively associated with the daily reproduction number (regression coefficients range, –0.04 to –0.01) and the daily growth rate (from –0.009 to –0.01). The daily encounter-density change was positively associated with the daily reproduction number (regression coefficients range, 0.24 to 1.02) and the daily growth rate (from 0.05 to 0.26). Conclusions Social distancing is an effective strategy to reduce the incidence of COVID-19 and illustrates the role of public compliance with social distancing measures to achieve public health benefits.

scholarly journals COVID-19 in comparison with other emerging viral diseases: risk of geographic spread via travel

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
A. Wilder-Smith
Keyword(s):  
Reproduction Number ◽  
Emerging Infectious Diseases ◽  
Case Fatality ◽  
The Elderly ◽  
Air Travel ◽  
Viral Diseases ◽  
Fatality Rate ◽  
The Past ◽  
Geographic Spread ◽  
Emerging Viral Diseases

Abstract Purpose of review The COVID-19 pandemic poses a major global health threat. The rapid spread was facilitated by air travel although rigorous travel bans and lockdowns were able to slow down the spread. How does COVID-19 compare with other emerging viral diseases of the past two decades? Recent findings Viral outbreaks differ in many ways, such as the individuals most at risk e.g. pregnant women for Zika and the elderly for COVID-19, their vectors of transmission, their fatality rate, and their transmissibility often measured as basic reproduction number. The risk of geographic spread via air travel differs significantly between emerging infectious diseases. Summary COVID-19 is not associated with the highest case fatality rate compared with other emerging viral diseases such as SARS and Ebola, but the combination of a high reproduction number, superspreading events and a globally immunologically naïve population has led to the highest global number of deaths in the past 20 decade compared to any other pandemic.

scholarly journals Impact of early detection and vaccination strategy in COVID-19 eradication program in Jakarta, Indonesia

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dipo Aldila ◽  
Brenda M. Samiadji ◽  
Gracia M. Simorangkir ◽  
Sarbaz H. A. Khosnaw ◽  
Muhammad Shahzad
Keyword(s):  
Mathematical Model ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Vaccination Strategy ◽  
Vaccination Rate ◽  
Rapid Testing ◽  
Social Distancing ◽  
Rapid Spread ◽  
Vaccine Potential ◽  
The Basic Reproduction Number

Abstract Objective Several essential factors have played a crucial role in the spreading mechanism of COVID-19 (Coronavirus disease 2019) in the human population. These factors include undetected cases, asymptomatic cases, and several non-pharmaceutical interventions. Because of the rapid spread of COVID-19 worldwide, understanding the significance of these factors is crucial in determining whether COVID-19 will be eradicated or persist in the population. Hence, in this study, we establish a new mathematical model to predict the spread of COVID-19 considering mentioned factors. Results Infection detection and vaccination have the potential to eradicate COVID-19 from Jakarta. From the sensitivity analysis, we find that rapid testing is crucial in reducing the basic reproduction number when COVID-19 is endemic in the population rather than contact trace. Furthermore, our results indicate that a vaccination strategy has the potential to relax social distancing rules, while maintaining the basic reproduction number at the minimum possible, and also eradicate COVID-19 from the population with a higher vaccination rate. In conclusion, our model proposed a mathematical model that can be used by Jakarta’s government to relax social distancing policy by relying on future COVID-19 vaccine potential.

scholarly journals SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marta Giovanetti ◽  
Eleonora Cella ◽  
Francesca Benedetti ◽  
Brittany Rife Magalis ◽  
Vagner Fonseca ◽  
...  
Keyword(s):  
Public Health ◽  
Epidemiological Data ◽  
Health Interventions ◽  
Transmission Dynamics ◽  
Public Health Interventions ◽  
Viral Spread ◽  
Three Phase ◽  
Phylodynamic Analysis ◽  
Epidemic Wave ◽  
Over Time

AbstractWe investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as “hidden reservoirs” during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

scholarly journals Examining the interplay between face mask usage, asymptomatic transmission, and social distancing on the spread of COVID-19

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adam Catching ◽  
Sara Capponi ◽  
Ming Te Yeh ◽  
Simone Bianco ◽  
Raul Andino
Keyword(s):  
Social Distance ◽  
Large Fraction ◽  
Real Life ◽  
Virus Transmission ◽  
Face Mask ◽  
Social Distancing ◽  
Viral Spread ◽  
The Face ◽  
Asymptomatic Individuals ◽  
High Virus

AbstractCOVID-19’s high virus transmission rates have caused a pandemic that is exacerbated by the high rates of asymptomatic and presymptomatic infections. These factors suggest that face masks and social distance could be paramount in containing the pandemic. We examined the efficacy of each measure and the combination of both measures using an agent-based model within a closed space that approximated real-life interactions. By explicitly considering different fractions of asymptomatic individuals, as well as a realistic hypothesis of face masks protection during inhaling and exhaling, our simulations demonstrate that a synergistic use of face masks and social distancing is the most effective intervention to curb the infection spread. To control the pandemic, our models suggest that high adherence to social distance is necessary to curb the spread of the disease, and that wearing face masks provides optimal protection even if only a small portion of the population comply with social distance. Finally, the face mask effectiveness in curbing the viral spread is not reduced if a large fraction of population is asymptomatic. Our findings have important implications for policies that dictate the reopening of social gatherings.

scholarly journals The challenges of containing SARS-CoV-2 via test-trace-and-isolate

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sebastian Contreras ◽  
Jonas Dehning ◽  
Matthias Loidolt ◽  
Johannes Zierenberg ◽  
F. Paul Spitzner ◽  
...  
Keyword(s):  
Analytical Model ◽  
Reproduction Number ◽  
Tipping Points ◽  
Social Distancing ◽  
Promising Tool

AbstractWithout a cure, vaccine, or proven long-term immunity against SARS-CoV-2, test-trace-and-isolate (TTI) strategies present a promising tool to contain its spread. For any TTI strategy, however, mitigation is challenged by pre- and asymptomatic transmission, TTI-avoiders, and undetected spreaders, which strongly contribute to ”hidden" infection chains. Here, we study a semi-analytical model and identify two tipping points between controlled and uncontrolled spread: (1) the behavior-driven reproduction number $${R}_{t}^{H}$$ R t H of the hidden chains becomes too large to be compensated by the TTI capabilities, and (2) the number of new infections exceeds the tracing capacity. Both trigger a self-accelerating spread. We investigate how these tipping points depend on challenges like limited cooperation, missing contacts, and imperfect isolation. Our results suggest that TTI alone is insufficient to contain an otherwise unhindered spread of SARS-CoV-2, implying that complementary measures like social distancing and improved hygiene remain necessary.

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