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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 145,822 papers from 617,318 authors.

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in category epidemiology

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21: Suppression of COVID-19 outbreak in the municipality of Vo, Italy
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Posted 18 Apr 2020

Suppression of COVID-19 outbreak in the municipality of Vo, Italy
62,319 downloads medRxiv epidemiology

Enrico Lavezzo, Elisa Franchin, Constanze Ciavarella, Gina Cuomo-Dannenburg, Luisa Barzon, Claudia Del Vecchio, Lucia Rossi, Riccardo Manganelli, Arianna Loregian, Nicolò Navarin, Davide Abate, Manuela Sciro, Stefano Merigliano, Ettore Decanale, Maria Cristina Vanuzzo, Francesca Saluzzo, Francesco Onelia, Monia Pacenti, Saverio Parisi, Giovanni Carretta, Daniele Donato, Luciano Flor, Silvia Cocchio, Giulia Masi, Alessandro Sperduti, Lorenzo Cattarino, Renato Salvador, Katy A.M. Gaythorpe, Imperial College London COVID-19 Response Team, Alessandra R. Brazzale, Stefano Toppo, Marta Trevisan, Vincenzo Baldo, Christl A Donnelly, Neil M Ferguson, Ilaria Dorigatti, Andrea Crisanti

On the 21st of February 2020 a resident of the municipality of Vo, a small town near Padua, died of pneumonia due to SARS-CoV-2 infection. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI 0.8-1.8%). Notably, 43.2% (95% CI 32.2-54.7%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic. The mean serial interval was 6.9 days (95% CI 2.6-13.4). We found no statistically significant difference in the viral load (as measured by genome equivalents inferred from cycle threshold data) of symptomatic versus asymptomatic infections (p-values 0.6 and 0.2 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). Contact tracing of the newly infected cases and transmission chain reconstruction revealed that most new infections in the second survey were infected in the community before the lockdown or from asymptomatic infections living in the same household. This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection and their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics, the duration of viral load detectability and the efficacy of the implemented control measures.

22: Selection into shift work is influenced by educational attainment and body mass index: A Mendelian randomization study
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Posted 13 Mar 2020

Selection into shift work is influenced by educational attainment and body mass index: A Mendelian randomization study
61,489 downloads medRxiv epidemiology

Iyas Daghlas, Rebecca C Richmond, Jacqueline M. Lane, Hassan S Dashti, Hanna M Ollila, Eva S. Schernhammer, George Davey Smith, Martin K Rutter, Richa Saxena, Céline Vetter

BackgroundShift work is associated with increased cardiometabolic disease risk, but whether this association is influenced by cardiometabolic risk factors driving selection into shift work is currently unclear. We addressed this question using Mendelian randomization (MR) in the UK Biobank. MethodsWe created genetic risk scores (GRS) associating with nine cardiometabolic risk factors (including education, body mass index [BMI], smoking, and alcohol consumption), and tested associations of each GRS with self-reported current frequency of shift work and night shift work amongst employed UKB participants of European ancestry (n=190,573). We used summary-level MR sensitivity analyses and multivariable MR to probe robustness of the identified effects, and tested whether effects were mediated through sleep timing preference. ResultsGenetically instrumented lower educational attainment and higher body mass index increased odds of reporting frequent shift work (odds ratio [OR] per 3.6 years [1-SD] decrease in educational attainment=2.40, 95% confidence interval [CI]=2.22-2.59, p=4.84 x 10-20; OR per 4.7kg/m2 [1-SD] increase in BMI=1.30, 95%CI=1.14-1.47, p=5.85 x 10-05). Results were unchanged in sensitivity analyses allowing for different assumptions regarding horizontal pleiotropy, and the effects of education and BMI were independent in multivariable MR. No causal effects were evident for the remaining factors, nor for any exposures on selection out of shift work. Sleep timing preference did not mediate any causal effects. ConclusionsEducational attainment and BMI may influence selection into shift work, which may have implications for epidemiologic associations of shift work with cardiometabolic disease. Key messagesO_LIAlthough it has been hypothesized that cardiometabolic risk factors and diseases may influence selection into shift work, little evidence for such an effect is currently available. C_LIO_LIUsing Mendelian randomization, we assessed whether cardiometabolic risk factors and diseases influenced selection into or out of shift work in the UK Biobank. C_LIO_LIOur results were consistent with a causal effect of both higher BMI and lower educational attainment on selection into current shift work, with stronger effects seen for shift work that is more frequent and includes more night shifts. C_LIO_LIUsing multivariable Mendelian randomization, we found that effects of higher BMI and lower education were independent. Sleep timing preference had a null effect on shift work selection and therefore did not mediate these effects. C_LIO_LISelection through education and BMI may bias the relationship of shift work with cardiometabolic disease. Social mechanisms underlying these effects warrant further investigation. C_LI

23: Fundamental principles of epidemic spread highlight the immediate need for large-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic
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Posted 26 Mar 2020

Fundamental principles of epidemic spread highlight the immediate need for large-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic
59,527 downloads medRxiv epidemiology

Jose Lourenco, Robert Paton, Craig Thompson, Paul Klenerman, Sunetra Gupta

The spread of a novel pathogenic infectious agent eliciting protective immunity is typically characterised by three distinct phases: (I) an initial phase of slow accumulation of new infections (often undetectable), (II) a second phase of rapid growth in cases of infection, disease and death, and (III) an eventual slow down of transmission due to the depletion of susceptible individuals, typically leading to the termination of the (first) epidemic wave. Before the implementation of control measures (e.g. social distancing, travel bans, etc) and under the assumption that infection elicits protective immunity, epidemiological theory indicates that the ongoing epidemic of SARS-CoV-2 will conform to this pattern. Here, we calibrate a susceptible-infected-recovered (SIR) model to data on cumulative reported SARS-CoV-2 associated deaths from the United Kingdom (UK) and Italy under the assumption that such deaths are well reported events that occur only in a vulnerable fraction of the population. We focus on model solutions which take into consideration previous estimates of critical epidemiological parameters such as the basic reproduction number (R0), probability of death in the vulnerable fraction of the population, infectious period and time from infection to death, with the intention of exploring the sensitivity of the system to the actual fraction of the population vulnerable to severe disease and death. Our simulations are in agreement with other studies that the current epidemic wave in the UK and Italy in the absence of interventions should have an approximate duration of 2-3 months, with numbers of deaths lagging behind in time relative to overall infections. Importantly, the results we present here suggest the ongoing epidemics in the UK and Italy started at least a month before the first reported death and have already led to the accumulation of significant levels of herd immunity in both countries. There is an inverse relationship between the proportion currently immune and the fraction of the population vulnerable to severe disease. This relationship can be used to determine how many people will require hospitalisation (and possibly die) in the coming weeks if we are able to accurately determine current levels of herd immunity. There is thus an urgent need for investment in technologies such as virus (or viral pseudotype) neutralization assays and other robust assays which provide reliable read-outs of protective immunity, and for the provision of open access to valuable data sources such as blood banks and paired samples of acute and convalescent sera from confirmed cases of SARS-CoV-2 to validate these. Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data. These data will be critical to the proper assessment of the effects of social distancing and other measures currently being adopted to slow down the case incidence and for informing future policy direction. Disclaimer(a) This material is not final and is subject to be updated any time. (b) Code used will be made available as soon as possible. (c) Contact for press enquiries: Cairbre Sugrue, cairbre@sugruecomms.com, +44 (0)7502 203 769.

24: Estimates of the severity of COVID-19 disease
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Posted 13 Mar 2020

Estimates of the severity of COVID-19 disease
57,654 downloads medRxiv epidemiology

Robert Verity, Lucy C Okell, Ilaria Dorigatti, Peter Winskill, Charles Whittaker, Natsuko Imai, Gina Cuomo-Dannenburg, Hayley Thompson, Patrick G T Walker, Han Fu, Amy Dighe, Jamie T Griffin, Marc Baguelin, Sangeeta Bhatia, Adhiratha Boonyasiri, Anne Cori, Zulma M Cucunuba, Rich FitzJohn, Katy Gaythorpe, Will Green, Arran Hamlet, Wes Hinsley, Daniel Laydon, Gemma Nedjati-Gilani, Steven Riley, Sabine van Elsland, Erik Volz, Haowei Wang, Yuanrong Wang, Xiaoyue Xi, Christl A Donnelly, Azra C Ghani, Neil M Ferguson

BackgroundA range of case fatality ratio (CFR) estimates for COVID-19 have been produced that differ substantially in magnitude. MethodsWe used individual-case data from mainland China and cases detected outside mainland China to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the CFR by relating the aggregate distribution of cases by dates of onset to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for the demography of the population, and age- and location-based under-ascertainment. We additionally estimated the CFR from individual line-list data on 1,334 cases identified outside mainland China. We used data on the PCR prevalence in international residents repatriated from China at the end of January 2020 to obtain age-stratified estimates of the infection fatality ratio (IFR). Using data on age-stratified severity in a subset of 3,665 cases from China, we estimated the proportion of infections that will likely require hospitalisation. FindingsWe estimate the mean duration from onset-of-symptoms to death to be 17.8 days (95% credible interval, crI 16.9-19.2 days) and from onset-of-symptoms to hospital discharge to be 22.6 days (95% crI 21.1-24.4 days). We estimate a crude CFR of 3.67% (95% crI 3.56%-3.80%) in cases from mainland China. Adjusting for demography and under-ascertainment of milder cases in Wuhan relative to the rest of China, we obtain a best estimate of the CFR in China of 1.38% (95% crI 1.23%-1.53%) with substantially higher values in older ages. Our estimate of the CFR from international cases stratified by age (under 60 / 60 and above) are consistent with these estimates from China. We obtain an overall IFR estimate for China of 0.66% (0.39%-1.33%), again with an increasing profile with age. InterpretationThese early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and demonstrate a strong age-gradient in risk.

25: Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity
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Posted 15 Apr 2020

Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity
55,930 downloads medRxiv epidemiology

Jasmine M Gardner, Lander Willem, Wouter van der Wijngaart, Shina Caroline Lynn Kamerlin, Nele Brusselaers, Peter M Kasson

Objectives: During March 2020, the COVID-19 pandemic has rapidly spread globally, and non-pharmaceutical interventions are being used to reduce both the load on the healthcare system as well as overall mortality. Design: Individual-based transmission modelling using Swedish demographic and Geographical Information System data and conservative COVID-19 epidemiological parameters. Setting: Sweden Participants: A model to simulate all 10.09 million Swedish residents. Interventions: 5 different non-pharmaceutical public-health interventions including the mitigation strategy of the Swedish government as of 10 April; isolation of the entire household of confirmed cases; closure of schools and non-essential businesses with or without strict social distancing; and strict social distancing with closure of schools and non-essential businesses. Main outcome measures: Estimated acute care and intensive care hospitalisations, COVID-19 attributable deaths, and infections among healthcare workers from 10 April until 29 June. Findings: Our model for Sweden shows that, under conservative epidemiological parameter estimates, the current Swedish public-health strategy will result in a peak intensive-care load in May that exceeds pre-pandemic capacity by over 40-fold, with a median mortality of 96,000 (95% CI 52,000 to 183,000). The most stringent public-health measures examined are predicted to reduce mortality by approximately three-fold. Intensive-care load at the peak could be reduced by over two-fold with a shorter period at peak pandemic capacity. Conclusions: Our results predict that, under conservative epidemiological parameter estimates, current measures in Sweden will result in at least 40-fold over-subscription of pre-pandemic Swedish intensive care capacity, with 15.8 percent of Swedish healthcare workers unable to work at the pandemic peak. Modifications to ICU admission criteria from international norms would further increase mortality.

26: Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship
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Posted 08 Mar 2020

Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship
53,626 downloads medRxiv epidemiology

Timothy W Russell, Joel Hellewell, Christopher I Jarvis, Kevin van Zandvoort, Sam Abbott, Ruwan Ratnayake, CMMID COVID-19 working group, Stefan Flasche, Rosalind M Eggo, W. John Edmunds, Adam J. Kucharski

Adjusting for delay from confirmation-to-death, we estimated case and infection fatality ratios (CFR, IFR) for COVID-19 on the Diamond Princess ship as 2.3% (0.75%-5.3%) and 1.2% (0.38-2.7%). Comparing deaths onboard with expected deaths based on naive CFR estimates using China data, we estimate IFR and CFR in China to be 0.5% (95% CI: 0.2-1.2%) and 1.1% (95% CI: 0.3-2.4%) respectively. AimTo estimate the infection and case fatality ratio of COVID-19, using data from passengers of the Diamond Princess cruise ship while correcting for delays between confirmation-and-death, and age-structure of the population.

27: Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China
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Posted 11 Feb 2020

Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China
51,351 downloads medRxiv epidemiology

Yang Yang, Qing-Bin Lu, Ming-Jin Liu, Yi-Xing Wang, An-Ran Zhang, Neda Jalali, Natalie E Dean, Ira M Longini, M. Elizabeth Halloran, Bo Xu, Xiao-Ai Zhang, Li-Ping Wang, Wei Liu, Li-Qun Fang

Our manuscript was based on surveillance cases of COVID-19 identified before January 26, 2020. As of February 20, 2020, the total number of confirmed cases in mainland China has reached 18 times of the number in our manuscript. While the methods and the main conclusions in our original analyses remain solid, we decided to withdraw this preprint for the time being, and will replace it with a more up-to-date version shortly. Should you have any comments or suggestions, please feel free to contact the corresponding author.

28: Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China
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Posted 06 Mar 2020

Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China
50,868 downloads medRxiv epidemiology

Chaolong Wang, Li Liu, Xingjie Hao, Huan Guo, Qi Wang, Jiao Huang, Na He, Hongjie Yu, Xihong Lin, An Pan, Sheng Wei, Tangchun Wu

BACKGROUNDWe described the epidemiological features of the coronavirus disease 2019 (Covid-19) outbreak, and evaluated the impact of non-pharmaceutical interventions on the epidemic in Wuhan, China. METHODSIndividual-level data on 25,961 laboratory-confirmed Covid-19 cases reported through February 18, 2020 were extracted from the municipal Notifiable Disease Report System. Based on key events and interventions, we divided the epidemic into four periods: before January 11, January 11-22, January 23 - February 1, and February 2-18. We compared epidemiological characteristics across periods and different demographic groups. We developed a susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions. RESULTSThe median age of the cases was 57 years and 50.3% were women. The attack rate peaked in the third period and substantially declined afterwards across geographic regions, sex and age groups, except for children (age <20) whose attack rate continued to increase. Healthcare workers and elderly people had higher attack rates and severity risk increased with age. The effective reproductive number dropped from 3.86 (95% credible interval 3.74 to 3.97) before interventions to 0.32 (0.28 to 0.37) post interventions. The interventions were estimated to prevent 94.5% (93.7 to 95.2%) infections till February 18. We found that at least 59% of infected cases were unascertained in Wuhan, potentially including asymptomatic and mild-symptomatic cases. CONCLUSIONSConsiderable countermeasures have effectively controlled the Covid-19 outbreak in Wuhan. Special efforts are needed to protect vulnerable populations, including healthcare workers, elderly and children. Estimation of unascertained cases has important implications on continuing surveillance and interventions.

29: An international comparison of the second derivative of COVID-19 deaths after implementation of social distancing measures
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Posted 25 Mar 2020

An international comparison of the second derivative of COVID-19 deaths after implementation of social distancing measures
50,432 downloads medRxiv epidemiology

W. T. Pike, V. Saini

This work compares deaths for confirmed COVID-19 cases in China to eight other countries, Italy, Spain, France, USA, UK, Germany, Netherlands and South Korea. After implementing varying intensities and timing of social distancing measures, several appear to be converging onto the decline in the daily growth rate of deaths, or relative second derivative of total deaths, seen in China after the implementation an aggressive social distancing policy. By calculating future trajectories in these countries based on the observed Chinese fatality statistics, an estimate of the total deaths and maximum daily death rates over a defined period of time is made. Our lower bound estimate for the United Kingdom based on the real data approximates the lower bound estimate of the recent modelling study of Ferguson et al. [1]. These results suggest there may be a threshold of effective public health intervention. Our method of viewing the data may be helpful in monitoring the course of the epidemic, judging the effectiveness of implementation, and monitoring the relaxation of social distancing.

30: Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals
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Posted 09 Apr 2021

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals
50,289 downloads medRxiv epidemiology

Talia Kustin, Noam Harel, Uriah Finkel, Shay Perchik, Sheri Harari, Maayan Tahor, Itamar Caspi, Rachel Levy, Michael Leschinsky, Shifra Ken Dror, Galit Bergerzon, Hala Gadban, Faten Gadban, Eti Eliassian, Orit Shimron, Loulou Saleh, Haim Ben-Zvi, Doron Amichay, Anat Ben-Dor, Dana Sagas, Merav Strauss, Yonat Shemer Avni, Amit Huppert, Eldad Kepten, Ran D. Balicer, Doron Nezer, Shay Ben-Shachar, Adi Stern

The SARS-CoV-2 pandemic has been raging for over a year, creating global detrimental impact. The BNT162b2 mRNA vaccine has demonstrated high protection levels, yet apprehension exists that several variants of concerns (VOCs) can surmount the immune defenses generated by the vaccines. Neutralization assays have revealed some reduction in neutralization of VOCs B.1.1.7 and B.1.351, but the relevance of these assays in real life remains unclear. Here, we performed a case-control study that examined whether BNT162b2 vaccinees with documented SARS-CoV-2 infection were more likely to become infected with B.1.1.7 or B.1.351 compared with unvaccinated individuals. Vaccinees infected at least a week after the second dose were disproportionally infected with B.1.351 (odds ratio of 8:1). Those infected between two weeks after the first dose and one week after the second dose, were disproportionally infected by B.1.1.7 (odds ratio of 26:10), suggesting reduced vaccine effectiveness against both VOCs under different dosage/timing conditions. Nevertheless, the B.1.351 incidence in Israel to-date remains low and vaccine effectiveness remains high against B.1.1.7, among those fully vaccinated. These results overall suggest that vaccine breakthrough infection is more frequent with both VOCs, yet a combination of mass-vaccination with two doses coupled with non-pharmaceutical interventions control and contain their spread.

31: Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
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Posted 16 Mar 2020

Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate
50,009 downloads medRxiv epidemiology

Miguel B. Araújo, Babak Naimi

As new cases of COVID-19 are being confirmed pressure is mounting to increase understanding of the factors underlying the spread the disease. Using data on local transmissions until the 23rd of March 2020, we develop an ensemble of 200 ecological niche models to project monthly variation in climate suitability for spread of SARS-CoV-2 throughout a typical climatological year. Although cases of COVID-19 are reported all over the world, most outbreaks display a pattern of clustering in relatively cool and dry areas. The predecessor SARS-CoV-1 was linked to similar climate conditions. Should the spread of SARS CoV-2 continue to follow current trends, asynchronous seasonal global outbreaks could be expected. According to the models, temperate warm and cold climates are more favorable to spread of the virus, whereas arid and tropical climates are less favorable. However, model uncertainties are still high across much of sub-Saharan Africa, Latin America and South East Asia. While models of epidemic spread utilize human demography and mobility as predictors, climate can also help constrain the virus. This is because the environment can mediate human-to-human transmission of SARS-CoV-2, and unsuitable climates can cause the virus to destabilize quickly, hence reducing its capacity to become epidemic.

32: The impact of host resistance on cumulative mortality and the threshold of herd immunity for SARS-CoV-2
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Posted 16 Jul 2020

The impact of host resistance on cumulative mortality and the threshold of herd immunity for SARS-CoV-2
49,771 downloads medRxiv epidemiology

Jose Lourenco, Francesco Pinotti, Craig Thompson, Sunetra Gupta

The risk of severe disease and death from COVID-19 is not uniformly distributed across all age classes, with the bulk of deaths occurring among older ages and those with comorbidities. Evidence is also mounting that some individuals have pre-existing immune responses to SARS-CoV-2 which may confer resistance to infection. We present a general mathematical framework which can be used to systematically explore the impact of variation in resistance to severe disease and infection by SARS-CoV-2 on its epidemiology. We find that the herd immunity threshold (HIT) can be lowered by the existence of a fraction of the population who are unable to transmit the virus, whether they are effectively segregated from the general population or mix randomly. These results help to explain the wide variation observed globally in seroprevalence and cumulative deaths and raise the possibility that the proportion exposed may have already exceeded HIT in certain regions.

33: Exposure to air pollution and COVID-19 mortality in the United States
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Posted 07 Apr 2020

Exposure to air pollution and COVID-19 mortality in the United States
46,670 downloads medRxiv epidemiology

Xiao Wu, Rachel C Nethery, Benjamin M. Sabath, Danielle Braun, Francesca Dominici

BackgroundUnited States government scientists estimate that COVID-19 may kill between 100,000 and 240,000 Americans. The majority of the pre-existing conditions that increase the risk of death for COVID-19 are the same diseases that are affected by long-term exposure to air pollution. We investigate whether long-term average exposure to fine particulate matter (PM2.5) increases the risk of COVID-19 deaths in the United States. MethodsData was collected for approximately 3,000 counties in the United States (98% of the population) up to April 04, 2020. We fit zero-inflated negative binomial mixed models using county level COVID-19 deaths as the outcome and county level long-term average of PM2.5 as the exposure. We adjust by population size, hospital beds, number of individuals tested, weather, and socioeconomic and behavioral variables including, but not limited to obesity and smoking. We include a random intercept by state to account for potential correlation in counties within the same state. ResultsWe found that an increase of only 1 {micro}g/m3 in PM2.5 is associated with a 15% increase in the COVID-19 death rate, 95% confidence interval (CI) (5%, 25%). Results are statistically significant and robust to secondary and sensitivity analyses. ConclusionsA small increase in long-term exposure to PM2.5 leads to a large increase in COVID-19 death rate, with the magnitude of increase 20 times that observed for PM2.5 and all-cause mortality. The study results underscore the importance of continuing to enforce existing air pollution regulations to protect human health both during and after the COVID-19 crisis. The data and code are publicly available.

34: The Risk of Indoor Sports and Culture Events for the Transmission of COVID-19 (Restart-19)
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Posted 30 Oct 2020

The Risk of Indoor Sports and Culture Events for the Transmission of COVID-19 (Restart-19)
44,887 downloads medRxiv epidemiology

Stefan Moritz, Cornelia Gottschick, Johannes Horn, Mario Popp, Susan Langer, Bianca Klee, Oliver Purschke, Michael Gekle, Angelika Ihling, Rafael Mikolajczyk

Nearly all mass gathering events (MGEs) worldwide have been banned since the outbreak of SARS-CoV-2 as they are supposed to pose a considerable risk for transmission of COVID-19. We investigated transmission risk of SARS-CoV-2 by droplets and aerosols during an experimental indoor MGE (using N95 masks and contact tracing devices) and conducted a simulation study to estimate the resulting burden of disease under conditions of controlled epidemics. The number of exposed contacts was <10 for scenarios with hygiene concept and good ventilation, but substantially higher otherwise. Of subsequent cases, 0%-23% were attributable to MGEs. Overall, the expected additional effect of indoor MGEs on burden of infections is low if hygiene concepts are applied and adequate ventilation exists. One Sentence SummarySeated indoor events, when conducted under hygiene precautions and with adequate ventilation, have small effects on the spread of COVID-19.

35: Herd immunity thresholds for SARS-CoV-2 estimated from unfolding epidemics
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Posted 24 Jul 2020

Herd immunity thresholds for SARS-CoV-2 estimated from unfolding epidemics
44,464 downloads medRxiv epidemiology

Ricardo Águas, Rodrigo M. Corder, Jessica G. King, Guilherme Gonçalves, Marcelo U Ferreira, M. Gabriela M. Gomes

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads, the susceptible subpopulation declines causing the rate at which new infections occur to slow down. Variation in individual susceptibility or exposure to infection exacerbates this effect. Individuals that are more susceptible or more exposed tend to be infected and removed from the susceptible subpopulation earlier. This selective depletion of susceptibles intensifies the deceleration in incidence. Eventually, susceptible numbers become low enough to prevent epidemic growth or, in other words, the herd immunity threshold is reached. Here we fit epidemiological models with inbuilt distributions of susceptibility or exposure to SARS-CoV-2 outbreaks to estimate basic reproduction numbers (R0) alongside coefficients of individual variation (CV) and the effects of containment strategies. Herd immunity thresholds are then calculated as 1 - (1/R0)1/(1+CV2) or 1 - (1/R0)1/(1+2CV2), depending on whether variation is on susceptibility or exposure. Our inferences result in herd immunity thresholds around 10-20%, considerably lower than the minimum coverage needed to interrupt transmission by random vaccination, which for R0 higher than 2.5 is estimated above 60%. We emphasize that the classical formula, 1 - 1/R0, remains applicable to describe herd immunity thresholds for random vaccination, but not for immunity induced by infection which is naturally selective. These findings have profound consequences for the governance of the current pandemic given that some populations may be close to achieving herd immunity despite being under more or less strict social distancing measures.

36: CoVID-19 in Japan: What could happen in the future?
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Posted 23 Feb 2020

CoVID-19 in Japan: What could happen in the future?
44,077 downloads medRxiv epidemiology

Nian Shao, Yan Xuan, Hanshuang Pan, Shufen Wang, Weijia Li, Yue Yan, Xingjie Li, Christopher Y. Shen, Xu Chen, Xinyue Luo, Yu Chen, Boxi Xu, Keji Liu, Min Zhong, Xiang Xu, Yu Jiang, Shuai Lu, Guanghong Ding, Jin Cheng, Wenbin Chen

COVID-19 has been impacting on the whole world critically and constantly Since December 2019. We have independently developed a novel statistical time delay dynamic model on the basis of the distribution models from CCDC. Based only on the numbers of confirmed cases in different regions in China, the model can clearly reveal that the containment of the epidemic highly depends on early and effective isolation. We apply the model on the epidemic in Japan and conclude that there could be a rapid outbreak in Japan if no effective quarantine measures are carried out immediately.

37: Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
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Posted 24 Apr 2021

Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
43,986 downloads medRxiv epidemiology

Yair Goldberg, Micha Mandel, Yonatan Woodbridge, Ronen Fluss, Ilya Novikov, Rami Yaari, Arnona Ziv, Laurence Freedman, Amit Huppert

Worldwide shortage of vaccination against SARS-CoV-2 infection while the pandemic is still uncontrolled leads many states to the dilemma whether or not to vaccinate previously infected persons. Understanding the level of protection of previous infection compared to that of vaccination is critical for policy making. We analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with COVID-19, severe disease, and death due to COVID-19. Vaccination was highly effective with overall estimated efficacy for documented infection of 92.8% (CI: [92.6, 93.0]); hospitalization 94.2% (CI: [93.6, 94.7]); severe illness 94.4% (CI: [93.6, 95.0]); and death 93.7% (CI: [92.5, 94.7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection for documented infection is 94.8% (CI: [94.4, 95.1]); hospitalization 94.1% (CI: [91.9, 95.7]); and severe illness 96.4% (CI: [92.5, 98.3]). Our results question the need to vaccinate previously-infected individuals.

38: Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period
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Posted 06 Mar 2020

Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period
39,316 downloads medRxiv epidemiology

Stephen Kissler, Christine Tedijanto, Edward M. Goldstein, Yonatan Grad, Marc Lipsitch

There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission of human betacoronaviruses HCoV-OC43 and HCoV-HKU1. We then built a mathematical model to simulate transmission of SARS-CoV-2 through the year 2025. We project that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after an initial pandemic wave. We summarize the full range of plausible transmission scenarios and identify key data still needed to distinguish between them, most importantly longitudinal serological studies to determine the duration of immunity to SARS-CoV-2.

39: Epidemiology of post-COVID syndrome following hospitalisation with coronavirus: a retrospective cohort study
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Posted 15 Jan 2021

Epidemiology of post-COVID syndrome following hospitalisation with coronavirus: a retrospective cohort study
38,970 downloads medRxiv epidemiology

Daniel Ayoubkhani, Kamlesh Khunti, Vahé Nafilyan, Thomas Maddox, Ben Humberstone, Ian Diamond, Amitava Banerjee

Objectives: The epidemiology of post-COVID syndrome (PCS) is currently undefined. We quantified rates of organ-specific impairment following recovery from COVID-19 hospitalisation compared with those in a matched control group, and how the rate ratio (RR) varies by age, sex, and ethnicity. Design: Observational, retrospective, matched cohort study. Setting: NHS hospitals in England. Participants: 47,780 individuals (mean age 65 years, 55% male) in hospital with COVID-19 and discharged alive by 31 August 2020, matched to controls on demographic and clinical characteristics. Outcome measures: Rates of hospital readmission, all-cause mortality, and diagnoses of respiratory, cardiovascular, metabolic, kidney and liver diseases until 30 September 2020. Results: Mean follow-up time was 140 days for COVID-19 cases and 153 days for controls. 766 (95% confidence interval: 753 to 779) readmissions and 320 (312 to 328) deaths per 1,000 person-years were observed in COVID-19 cases, 3.5 (3.4 to 3.6) and 7.7 (7.2 to 8.3) times greater, respectively, than in controls. Rates of respiratory, diabetes and cardiovascular events were also significantly elevated in COVID-19 cases, at 770 (758 to 783), 127 (122 to 132) and 126 (121 to 131) events per 1,000 person-years, respectively. RRs were greater for individuals aged <70 than [&ge;]70 years, and in ethnic minority groups than the White population, with the biggest differences observed for respiratory disease: 10.5 [9.7 to 11.4] for <70 years versus 4.6 [4.3 to 4.8] for [&ge;]70 years, and 11.4 (9.8 to 13.3) for Non-White versus 5.2 (5.0 to 5.5) for White. Conclusions: Individuals discharged from hospital following COVID-19 face elevated rates of multi-organ dysfunction compared with background levels, and the increase in risk is neither confined to the elderly nor uniform across ethnicities. The diagnosis, treatment and prevention of PCS require integrated rather than organ- or disease-specific approaches. Urgent research is required to establish risk factors for PCS.

40: A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates
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Posted 06 May 2020

A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates
36,623 downloads medRxiv epidemiology

Gideon Meyerowitz-Katz, Lea Merone

An important unknown during the COVID-19 pandemic has been the infection-fatality rate (IFR). This differs from the case-fatality rate (CFR) as an estimate of the number of deaths as a proportion of the total number of cases, including those who are mild and asymptomatic. While the CFR is extremely valuable for experts, IFR is increasingly being called for by policy-makers and the lay public as an estimate of the overall mortality from COVID-19. Methods Pubmed, Medline, SSRN, and Medrxiv were searched using a set of terms and Boolean operators on 25/04/2020 and re-searched 14/05/2020, 21/05/2020, and 16/06/2020. Articles were screened for inclusion by both authors. Meta-analysis was performed in Stata 15.1 using the metan command, based on IFR and confidence intervals extracted from each study. Google/Google Scholar was used to assess the grey literature relating to government reports. Results After exclusions, there were 26 estimates of IFR included in the final meta-analysis, from a wide range of countries, published between February and June 2020. The meta-analysis demonstrated a point-estimate of IFR of 0.68% (0.53-0.82%) with high heterogeneity (p<0.001). Conclusion Based on a systematic review and meta-analysis of published evidence on COVID-19 until May, 2020, the IFR of the disease across populations is 0.68% (0.53-0.82%). However, due to very high heterogeneity in the meta-analysis, it is difficult to know if this represents the true point estimate. It is likely that, due to age and perhaps underlying comorbidities in the population, different places will experience different IFRs due to the disease. Given issues with mortality recording, it is also likely that this represents an underestimate of the true IFR figure. More research looking at age-stratified IFR is urgently needed to inform policy-making on this front.

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