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41: The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic
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Posted 29 Jan 2021

The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic
34,939 downloads medRxiv epidemiology

Ariel Karlinsky, Dmitry Kobak

Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported numbers of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the recent average, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no central, frequently-updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 77 countries, openly available as the regularly-updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in the worst-affected countries the annual mortality increased by over 50%, while in several other countries it decreased by over 5%, presumably due to lockdown measures decreasing the non-COVID mortality. Moreover, we found that while some countries have been reporting the COVID-19 deaths very accurately, many countries have been underreporting their COVID-19 deaths by an order of magnitude or more. Averaging across the entire dataset suggests that the world's COVID-19 death toll may be at least 1.6 times higher than the reported number of confirmed deaths.

42: Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
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Posted 07 Apr 2020

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
34,076 downloads medRxiv epidemiology

Paul S Wikramaratna, Robert Paton, Mahan Ghafari, Jose Lourenco

Reverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.

43: A surprising formula for the spread of Covid-19 under aggressive management
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Posted 02 May 2020

A surprising formula for the spread of Covid-19 under aggressive management
33,633 downloads medRxiv epidemiology

Ivan Cherednik

AO_SCPLOWBSTRACTC_SCPLOWWe propose an algebraic-type formula that describes with high accuracy the total number of detected infections for the Covid-19 pandemic in many countries. Our 2-phase formula can be used as a powerful forecasting tool. It is based on the authors new theory of momentum management of epidemics; Bessel functions are employed. Its 3 parameters are the initial transmission rate, reflecting the viral fitness and "normal" frequency of contacts in the infected areas, and the intensity of prevention measures at phases 1, 2. Austria, Brazil, Germany, Japan, India, Israel, Italy, the Netherlands, Sweden, Switzerland, UK, and the USA are considered, including the second wave in the latter. The forecasting software is provided as a supplement (any groups of countries).

44: Quantifying the effect of quarantine control in Covid-19 infectious spread using machine learning
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Posted 06 Apr 2020

Quantifying the effect of quarantine control in Covid-19 infectious spread using machine learning
33,122 downloads medRxiv epidemiology

Raj Dandekar, George Barbastathis

Since the first recording of what we now call Covid-19 infection in Wuhan, Hubei province, China on Dec 31, 2019 (CHP 2020), the disease has spread worldwide and met with a wide variety of social distancing and quarantine policies. The effectiveness of these responses is notoriously difficult to quantify as individuals travel, violate policies deliberately or inadvertently, and infect others without themselves being detected (Li et al. 2020a; Wu & Leung 2020; Wang et al. 2020; Chinazzi et al. 2020; Ferguson et al. 2020; Kraemer et al. 2020). Moreover, the publicly available data on infection rates are themselves unreliable due to limited testing and even possibly under-reporting (Li et al. 2020b). In this paper, we attempt to interpret and extrapolate from publicly available data using a mixed first-principles epidemiological equations and data-driven neural network model. Leveraging our neural network augmented model, we focus our analysis on four locales: Wuhan, Italy, South Korea and the United States of America, and compare the role played by the quarantine and isolation measures in each of these countries in controlling the effective reproduction number Rt of the virus. Our results unequivocally indicate that the countries in which rapid government interventions and strict public health measures for quarantine and isolation were implemented were successful in halting the spread of infection and prevent it from exploding exponentially. In the case of Wuhan especially, where the available data were earliest available, we have been able to test the predicting ability of our model by training it from data in the January 24th till March 3rd window, and then matching the predictions up to April 1st. Even for Italy and South Korea, we have a buffer window of one week (25 March - 1 April) to validate the predictions of our model. In the case of the US, our model captures well the current infected curve growth and predicts a halting of infection spread by 20 April 2020. We further demonstrate that relaxing or reversing quarantine measures right now will lead to an exponential explosion in the infected case count, thus nullifying the role played by all measures implemented in the US since mid March 2020.

45: Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
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Posted 22 Dec 2020

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
32,106 downloads medRxiv epidemiology

Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline I Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira

Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

46: The effectiveness and perceived burden of nonpharmaceutical interventions against COVID-19 transmission: a modelling study with 41 countries
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Posted 30 May 2020

The effectiveness and perceived burden of nonpharmaceutical interventions against COVID-19 transmission: a modelling study with 41 countries
30,783 downloads medRxiv epidemiology

Jan M. Brauner, Sören Mindermann, Mrinank Sharma, David Johnston, John Salvatier, Tomáš Gavenčiak, Anna B. Stephenson, Gavin Leech, George Altman, Vladimir Mikulik, Alexander John Norman, Joshua Teperowski Monrad, Tamay Besiroglu, Hong Ge, Meghan A. Hartwick, Yee Whye Teh, Leonid Chindelevitch, Yarin Gal, Jan Kulveit

Governments are attempting to control the COVID-19 pandemic with nonpharmaceutical interventions (NPIs). However, it is still largely unknown how effective different NPIs are at reducing transmission. Data-driven studies can estimate the effectiveness of NPIs while minimising assumptions, but existing analyses lack sufficient data and validation to robustly distinguish the effects of individual NPIs. We gather chronological data on NPIs in 41 countries between January and the end of May 2020, creating the largest public NPI dataset collected with independent double entry. We then estimate the effectiveness of 8 NPIs with a Bayesian hierarchical model by linking NPI implementation dates to national case and death counts. The results are supported by extensive empirical validation, including 11 sensitivity analyses with over 200 experimental conditions. We find that closing schools and universities was highly effective; that banning gatherings and closing high-risk businesses was effective, but closing most other businesses had limited further benefit; and that many countries may have been able to reduce R below 1 without issuing a stay-at-home order.

47: Understanding the effectiveness of government interventions in Europe's second wave of COVID-19
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Posted 26 Mar 2021

Understanding the effectiveness of government interventions in Europe's second wave of COVID-19
30,714 downloads medRxiv epidemiology

Mrinank Sharma, Sören Mindermann, Charlie Rogers-Smith, Gavin Leech, Benedict Snodin, Janvi Ahuja, Jonas B. Sandbrink, Joshua Teperowski Monrad, George Altman, Gurpreet Dhaliwal, Lukas Finnveden, Alexander John Norman, Sebastian B. Oehm, Julia Fabienne Sandkühler, Thomas Mellan, Jan Kulveit, Leonid Chindelevitch, Seth Flaxman, Yarin Gal, Swapnil Mishra, Jan Markus Brauner, Samir Bhatt

As European governments face resurging waves of COVID-19, non-pharmaceutical interventions (NPIs) continue to be the primary tool for infection control. However, updated estimates of their relative effectiveness have been absent for Europe's second wave, largely due to a lack of collated data that considers the increased subnational variation and diversity of NPIs. We collect the largest dataset of NPI implementation dates in Europe, spanning 114 subnational areas in 7 countries, with a systematic categorisation of interventions tailored to the second wave. Using a hierarchical Bayesian transmission model, we estimate the effectiveness of 17 NPIs from local case and death data. We manually validate the data, address limitations in modelling from previous studies, and extensively test the robustness of our estimates. The combined effect of all NPIs was smaller relative to estimates from the first half of 2020, indicating the strong influence of safety measures and individual protective behaviours--such as distancing--that persisted after the first wave. Closing specific businesses was highly effective. Gathering restrictions were highly effective but only for the strictest limits. We find smaller effects for closing educational institutions compared to the first wave, suggesting that safer operation of schools was possible with a set of stringent safety measures including testing and tracing, preventing mixing, and smaller classes. These results underscore that effectiveness estimates from the early stage of an epidemic are measured relative to pre-pandemic behaviour. Updated estimates are required to inform policy in an ongoing pandemic.

48: The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
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Posted 04 Dec 2020

The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
28,543 downloads medRxiv epidemiology

Martin Pavelka, Kevin van Zandvoort, Sam Abbott, Katharine Sherratt, Marek Majdan, CMMID COVID-19 working group, Inštitút Zdravotných Analýz, Pavol Jarčuška, Marek Krajčí, Stefan Flasche, Sebastian Funk

Slovakia conducted multiple rounds of population-wide rapid antigen testing for SARS-CoV-2 in late 2020, combined with a period of additional contact restrictions. Observed prevalence decreased by 58% (95% CI: 57-58%) within one week in the 45 counties that were subject to two rounds of mass testing, an estimate that remained robust when adjusting for multiple potential confounders. Adjusting for epidemic growth of 4.4% (1.1-6.9%) per day preceding the mass testing campaign, the estimated decrease in prevalence compared to a scenario of unmitigated growth was 70% (67-73%). Modelling suggests that this decrease cannot be explained solely by infection control measures, but requires the additional impact of isolation as well as quarantine of household members of those testing positive.

49: Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States
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Posted 03 Apr 2020

Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States
28,257 downloads medRxiv epidemiology

Justin D Silverman, Nathaniel Hupert, Alex D. Washburne

Detection of SARS-CoV-2 infections to date has relied on RT-PCR testing. However, a failure to identify early cases imported to a country, bottlenecks in RT-PCR testing, and the existence of infections which are asymptomatic, sub-clinical, or with an alternative presentation than the standard cough and fever have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how publicly available CDC influenza-like illness (ILI) outpatient surveillance data can be repurposed to estimate the detection rate of symptomatic SARS-CoV-2 infections. We find a surge of non-influenza ILI above the seasonal average and show that this surge is correlated with COVID case counts across states. By quantifying the number of excess ILI patients in March relative to previous years and comparing excess ILI to confirmed COVID case counts, we estimate the syndromic case detection rate of SARS-CoV-2 in the US to be approximately 1 our of 100. This corresponds to at least 28 million presumed symptomatic SARS-CoV-2 patients across the US during the three week period from March 8 to March 28. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to be doubling slower than every 3.5 days. Together these results suggest a conceptual model for the COVID epidemic in the US in which rapid spread across the US are combined with a large population of infected patients with presumably mild-to-moderate clinical symptoms. We emphasize the importance of testing these findings with seroprevalence data, and discuss the broader potential to use syndromic time series for early detection and understanding of emerging infectious diseases.

50: The role of absolute humidity on transmission rates of the COVID-19 outbreak
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Posted 17 Feb 2020

The role of absolute humidity on transmission rates of the COVID-19 outbreak
27,696 downloads medRxiv epidemiology

Wei Luo, Maimuna S Majumder, Diambo Liu, Canelle Poirier, Kenneth D Mandl, Marc Lipsitch, Mauricio Santillana

A novel coronavirus (COVID-19) was identified in Wuhan, Hubei Province, China, in December 2019 and has caused over 40,000 cases worldwide to date. Previous studies have supported an epidemiological hypothesis that cold and dry (low absolute humidity) environments facilitate the survival and spread of droplet-mediated viral diseases, and warm and humid (high absolute humidity) environments see attenuated viral transmission (i.e., influenza). How-ever, the role of absolute humidity in transmission of COVID-19 has not yet been established. Here, we examine province-level variability of the basic reproductive numbers of COVID-19 across China and find that changes in weather alone (i.e., increase of temperature and humidity as spring and summer months arrive in the North Hemisphere) will not necessarily lead to declines in COVID-19 case counts without the implementation of extensive public health interventions.

51: Total COVID-19 Mortality in Italy: Excess Mortality and Age Dependence through Time-Series Analysis
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Posted 20 Apr 2020

Total COVID-19 Mortality in Italy: Excess Mortality and Age Dependence through Time-Series Analysis
26,819 downloads medRxiv epidemiology

Chirag Modi, Vanessa Boehm, Simone Ferraro, George Stein, Uros Seljak

We perform a counterfactual time series analysis on 2020 mortality data from towns in Italy using data from the previous five years as control. We find an excess mortality that is correlated in time with the official COVID-19 death rate, but exceeds it by a factor of at least 1.5. Our analysis suggests that there is a large population of predominantly older people that are missing from the official fatality statistics. We estimate that the number of COVID-19 deaths in Italy is 49,000-53,000 as of May 9 2020, as compared to the official number of 33,000. The Population Fatality Rate (PFR) has reached 0.26% in the most affected region of Lombardia and 0.58% in the most affected province of Bergamo. These PFRs constitutes a lower bound to the Infection Fatality Rate (IFR). We combine the PFRs with the Test Positivity Ratio to derive a better lower bound of 0.61% on the IFR for Lombardia. We further estimate the IFR as a function of age and find a steeper age dependence than previous studies: we find 17% of COVID-related deaths are attributed to the age group above 90, 7.5% to 80-89, declining to 0.04% for age 40-49 and 0.01% for age 30-39, the latter more than an order of magnitude lower than previous estimates. We observe that the IFR traces the Yearly Mortality Rate (YMR) above ages of 60 years, which can be used as a model to estimate the IFR for other populations and thus other regions in the world. We predict an IFR lower bound of 0.5% for NYC and that 27% of the total COVID-19 fatalities in NYC should arise from the population below 65 years. This is in agreement with the official NYC data and three times higher than the percentage observed in Lombardia. Combining the PFR with the Princess Diamond cruise ship IFR for ages above 70 we estimate the infection rates (IR) for regions in Italy. These peak in Lombardia at 26% (13%-47%, 95% c.l.), and for provinces in Bergamo at 69% (35%- 100%, 95% c.l.). These estimates suggest that the number of infected people greatly exceeds the number of positive tests, e.g., by a factor of 35 in Lombardia.

52: Performance of fabrics for home-made masks against spread of respiratory infection through droplets: a quantitative mechanistic study
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Posted 24 Apr 2020

Performance of fabrics for home-made masks against spread of respiratory infection through droplets: a quantitative mechanistic study
26,372 downloads medRxiv epidemiology

Onur Aydin, Md Abul Bashar Emon, Shyuan Cheng, Liu Hong, Leonardo P. Chamorro, M Taher A Saif

Respiratory infections may spread through droplets, Respiratory infections may spread through droplets and aerosols released by infected individuals coughing, sneezing, or speaking. In the case of Coronavirus Disease 2019 (COVID-19), spread can occur from symptomatic, pre-symptomatic, and asymptomatic persons. Given the limited supply of professional face masks and respirators, the U.S. Centers for Disease Control and Prevention (CDC) has recommended home-made cloth face coverings for use by the general public in areas of significant community-based transmission. There is, however, little information on the effectiveness of cloth face coverings in reducing droplet dissemination. Here, we ascertained the performance of 11 household fabrics at blocking high-velocity droplets, using a commercial medical mask as a benchmark. We also assessed their breathability (air permeability), texture, fiber composition, and water absorption properties. We found that droplet blocking efficiency anti-correlates with breathability; less breathable fabrics being more effective in blocking. However, materials with high breathability are desirable for comfort and to reduce airflow through gaps between the mask and face. Our measurements indicate that 2 or 3 layers of highly permeable fabric, such as T-shirt cloth, may block droplets with an efficacy similar to that of medical masks, while still maintaining comparable breathability. Overall, our study suggests that cloth face coverings, especially with multiple layers, may help reduce droplet transmission of respiratory infections. Furthermore, face coverings made from biodegradable fabrics such as cotton allow washing and reusing, and can help reduce the adverse environmental effects of widespread use of commercial disposable and non-biodegradable facemasks.

53: Modeling the combined effect of digital exposure notification and non-pharmaceutical interventions on the COVID-19 epidemic in Washington state
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Posted 02 Sep 2020

Modeling the combined effect of digital exposure notification and non-pharmaceutical interventions on the COVID-19 epidemic in Washington state
26,359 downloads medRxiv epidemiology

Matthew Abueg, Robert Hinch, Neo Wu, Luyang Liu, William J M Probert, Austin Wu, Paul Eastham, Yusef Shafi, Matt Rosencrantz, Michael Dikovsky, Zhao Cheng, Anel Nurtay, Lucie Abeler-Dörner, David G Bonsall, Michael V McConnell, Shawn O'Banion, Christophe Fraser

Contact tracing is increasingly being used to combat COVID-19, and digital implementations are now being deployed, many of them based on Apple and Google's Exposure Notification System. These systems are new and are based on smartphone technology that has not traditionally been used for this purpose, presenting challenges in understanding possible outcomes. In this work, we use individual-based computational models to explore how digital exposure notifications can be used in conjunction with non-pharmaceutical interventions, such as traditional contact tracing and social distancing, to influence COVID-19 disease spread in a population. Specifically, we use a representative model of the household and occupational structure of three counties in the state of Washington together with a proposed digital exposure notifications deployment to quantify impacts under a range of scenarios of adoption, compliance, and mobility. In a model in which 15% of the population participated, we found that digital exposure notification systems could reduce infections and deaths by approximately 8% and 6%, effectively complementing traditional contact tracing. We believe this can serve as guidance to health authorities in Washington state and beyond on how exposure notification systems can complement traditional public health interventions to suppress the spread of COVID-19.

54: Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2
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Posted 27 Mar 2020

Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2
25,691 downloads medRxiv epidemiology

Yasuhiko Kamikubo, Atsushi Takahashi

The outbreak of SARS coronavirus 2 (SARS-CoV-2), which occurred in Wuhan, China in December 2019, has caused a worldwide pandemic of coronavirus disease 2019 (COVID-19). However, there is a lack of epidemiological tools to guide effective public policy development. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Analysis of regional disparities in incidence has revealed that a sharp decline in influenza epidemics is a useful surrogate indicator for the undocumented spread of SARS-CoV-2. The biggest concern in the world is knowing when herd immunity has been achieved and scheduling a time to regain the living activities of each country. This study provides a useful tool to guide the development of local policies to contain the virus.

55: Association of country-wide coronavirus mortality with demographics, testing, lockdowns, and public wearing of masks.
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Posted 25 May 2020

Association of country-wide coronavirus mortality with demographics, testing, lockdowns, and public wearing of masks.
24,703 downloads medRxiv epidemiology

Christopher T Leffler, Edsel B. Ing, Joseph D. Lykins, Matthew C Hogan, Craig A. McKeown, Andrzej Grzybowski

Purpose. To determine sources of variation between countries in per-capita mortality from COVID-19 (caused by the SARS-CoV-2 virus). Methods. Potential predictors of per-capita coronavirus-related mortality in 200 countries by May 9, 2020 were examined, including age, sex, obesity prevalence, temperature, urbanization, smoking, duration of infection, lockdowns, viral testing, contact tracing policies, and public mask-wearing norms and policies. Multivariable linear regression analysis was performed. Results. In univariate analyses, the prevalence of smoking, per-capita gross domestic product, urbanization, and colder average country temperature were positively associated with coronavirus-related mortality. In a multivariable analysis of 196 countries, the duration of infection in the country, and the proportion of the population 60 years of age or older were positively associated with per-capita mortality, while duration of mask-wearing by the public was negatively associated with mortality (all p<0.001). International travel restrictions and a lower prevalence of obesity were independently associated with mortality in a model which controlled for testing policy. Internal lockdown requirements and viral testing policies and levels were not associated with mortality. The association of contact tracing policy with mortality approached statistical significance (p=0.06). In countries with cultural norms or government policies supporting public mask-wearing, per-capita coronavirus mortality increased on average by just 15.8% each week, as compared with 62.1% each week in remaining countries. Conclusions. Societal norms and government policies supporting the wearing of masks by the public, as well as international travel controls, are independently associated with lower per-capita mortality from COVID-19.

56: Critical levels of mask efficiency and of mask adoption that theoretically extinguish respiratory virus epidemics
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Posted 15 May 2020

Critical levels of mask efficiency and of mask adoption that theoretically extinguish respiratory virus epidemics
24,665 downloads medRxiv epidemiology

Alan D Kot

Using a respiratory virus epidemiological model we derive equations for the critical levels of mask efficiency (fraction blocked) and mask adoption (fraction of population wearing masks) that lower the effective reproduction number to unity. The model extends a basic epidemiological model and assumes that a specified fraction of a population dons masks at a given initial number of infections. The model includes a contribution from the ocular (nasolacrimal duct) route, and does not include contributions from contact (fomite) routes. The model accommodates dose-response (probability of infection) functions that are linear or non-linear. Our motivation to study near-population-wide mask wearing arises from the concept that, between two mask wearers, the concentration of particles at inhalation should be the square of the mask penetration fraction. This combination, or team, of masks can provide a strong dose-lowering squaring effect, which enables the use of lower-efficiency, lower-cost, lower pressure-drop (easier breathing) masks. For an epidemic with basic reproduction number R0=2.5 and with a linear dose-response, the critical mask efficiency is calculated to be 0.5 for a mask adoption level of 0.8 of the population. Importantly, this efficiency is well below that of a N95 mask, and well above that of some fabric masks. Numerical solutions of the model at near-critical levels of mask efficiency and mask adoption demonstrate avoidance of epidemics. To be conservative we use mask efficiencies measured with the most-penetrating viral-particle sizes. The critical mask adoption level for surgical masks with an efficiency of 0.58 is computed to be 0.73. With surgical masks (or equally efficient substitutes) and 80% and 90% adoption levels, respiratory epidemics with R0 of about 3 and 4, respectively, would be theoretically extinguished.

57: A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing
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Posted 14 Feb 2020

A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing
24,425 downloads medRxiv epidemiology

Leon Danon, Ellen Brooks-Pollock, Mick Bailey, Matt J Keeling

BackgroundAn outbreak of a novel coronavirus, named CoVID-19, was first reported in China on 31 December 2019. As of 9 February 2020, cases have been reported in 25 countries, including probable cases of human-to-human transmission in England. MethodsWe adapted an existing national-scale metapopulation model to capture the spread of CoVID-19 in England and Wales. We used 2011 census data to capture population sizes and population movement, together with parameter estimates from the current outbreak in China. ResultsWe predict that a CoVID-19 outbreak will peak 126 to 147 days ([~]4 months) after the start of person-to-person transmission in England and Wales in the absence of controls, assuming biological parameters remain unchanged. Therefore, if person-to-person transmission persists from February, we predict the epidemic peak would occur in June. The starting location has minimal impact on peak timing, and model stochasticity varies peak timing by 10 days. Incorporating realistic parameter uncertainty leads to estimates of peak time ranging from 78 days to 241 days after person-to-person transmission has been established. Seasonal changes in transmission rate substantially impact the timing and size of the epidemic peak, as well as the total attack rate. DiscussionWe provide initial estimates of the potential course of CoVID-19 in England and Wales in the absence of control measures. These results can be refined with improved estimates of epidemiological parameters, and permit investigation of control measures and cost effectiveness analyses. Seasonal changes in transmission rate could shift the timing of the peak into winter months, which will have important implications for health-care capacity planning.

58: Prediction of survival for severe Covid-19 patients with three clinical features: development of a machine learning-based prognostic model with clinical data in Wuhan
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Posted 01 Mar 2020

Prediction of survival for severe Covid-19 patients with three clinical features: development of a machine learning-based prognostic model with clinical data in Wuhan
22,882 downloads medRxiv epidemiology

Li Yan, Hai-Tao Zhang, Jorge Goncalves, Yang Xiao, Maolin Wang, Yuqi Guo, Chuan Sun, Xiuchuan Tang, Liang Jin, Mingyang Zhang, Xiang Huang, Ying Xiao, Haosen Cao, Yanyan Chen, Tongxin Ren, Fang Wang, Yaru Xiao, Sufang Huang, Xi Tan, Niannian Huang, Bo Jiao, Yong Zhang, Ailin Luo, Laurent Mombaerts, Junyang Jin, Zhiguo Cao, Shusheng Li, Hui Xu, Ye Yuan

The sudden increase of COVID-19 cases is putting a high pressure on healthcare services worldwide. At the current stage, fast, accurate and early clinical assessment of the disease severity is vital. To support decision making and logistical planning in healthcare systems, this study leverages a database of blood samples from 404 infected patients in the region of Wuhan, China to identify crucial predictive biomarkers of disease severity. For this purpose, machine learning tools selected three biomarkers that predict the survival of individual patients with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). In particular, relatively high levels of LDH alone seem to play a crucial role in distinguishing the vast majority of cases that require immediate medical attention. This finding is consistent with current medical knowledge that high LDH levels are associated with tissue breakdown occurring in various diseases, including pulmonary disorders such as pneumonia. Overall, this paper suggests a simple and operable formula to quickly predict patients at the highest risk, allowing them to be prioritised and potentially reducing the mortality rate. FundingNone.

59: Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis
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Posted 07 Apr 2020

Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis
21,932 downloads medRxiv epidemiology

Mingming Liang, Liang Gao, Ce Cheng, Qin Zhou, John Patrick Uy, Kurt Heiner, Chenyu Sun

BackgroundConflicting recommendations exist related to whether masks have a protective effect on the spread of respiratory viruses. MethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement was consulted to report this systematic review. Relevant articles were retrieved from PubMed, Web of Science, ScienceDirect, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI), VIP (Chinese) database. ResultsA total of 21 studies met our inclusion criteria. Meta-analyses suggest that mask use provided a significant protective effect (OR = 0.35 and 95% CI = 0.24-0.51). Use of masks by healthcare workers (HCWs) and non-healthcare workers (Non-HCWs) can reduce the risk of respiratory virus infection by 80% (OR = 0.20, 95% CI = 0.11-0.37) and 47% (OR = 0.53, 95% CI = 0.36-0.79). The protective effect of wearing masks in Asia (OR = 0.31) appeared to be higher than that of Western countries (OR = 0.45). Masks had a protective effect against influenza viruses (OR = 0.55), SARS (OR = 0.26), and SARS-CoV-2 (OR = 0.04). In the subgroups based on different study designs, protective effects of wearing mask were significant in cluster randomized trials, case-control studies and retrospective studies. ConclusionsThis study adds additional evidence of the enhanced protective value of masks, we stress that the use masks serve as an adjunctive method regarding the COVID-19 outbreak.

60: Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study
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Posted 05 Feb 2020

Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study
20,371 downloads medRxiv epidemiology

Shengjie Lai, Isaac Bogoch, Nick W Ruktanonchai, Alexander Watts, Xin Lu, Weizhong Yang, Hongjie Yu, Kamran Khan, Andrew J Tatem

BackgroundA novel coronavirus (2019-nCoV) emerged in Wuhan City, China, at the end of 2019 and has caused an outbreak of human-to-human transmission with a Public Health Emergency of International Concern declared by the World Health Organization on January 30, 2020. AimWe aimed to estimate the potential risk and geographic range of Wuhan novel coronavirus (2019-nCoV) spread within and beyond China from January through to April, 2020. MethodsA series of domestic and international travel network-based connectivity and risk analyses were performed, by using de-identified and aggregated mobile phone data, air passenger itinerary data, and case reports. ResultsThe cordon sanitaire of Wuhan is likely to have occurred during the latter stages of peak population numbers leaving the city before Lunar New Year (LNY), with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% UI: 478 - 1349) had 2019-nCoV infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to Wuhans lockdown. The majority of these cities were in Asia, but major hubs in Europe, the US and Australia were also prominent, with strong correlation seen between predicted importation risks and reported cases. Because significant spread has already occurred, a large number of airline travellers (3.3 million under the scenario of 75% travel reduction from normal volumes) may be required to be screened at origin high-risk cities in China and destinations across the globe for the following three months of February to April, 2020 to effectively limit spread beyond its current extent. ConclusionFurther spread of 2019-nCoV within China and international exportation is likely to occur. All countries, especially vulnerable regions, should be prepared for efforts to contain the 2019-nCoV infection.

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