疫情共知貼吧 Covid-19 Fact Check

[theagora]

貼吧活動：(請查閱 SARS-CoV-2 Timeline by 2020.02.21, by Nathan ☁️ )

• Collaborators to WRITE DOWN links or texts in the comments.
• Others to CLICK-n-POST emoji votes 👍 or 👎 as credits.
• Assignees to MANAGE the whole issue.

✧【外聞貼報】@theagora
✧【微信截圖】@lavieti
✧【學術前哨】medRxiv • bioRxiv • The Lancet

✧【社區討論】 https://agora-republic.slack.com ➡️ #covid-19 | 邀請鏈接

[theagora]

【按需貼報】 On-demand News

Repo	URL
agorahub/news0	https://agorahub.github.io/news0/

[demosisto]

Covid-19 Communities

Name	URL
COVID-19 (r/nCoV)	https://www.reddit.com/r/ncov
COVID-19 (r/COVID19)	https://www.reddit.com/r/covid19

[demosisto]

香港区议会通过动议：邓炳强率警赴武汉抗疫
【阿波罗新闻网 2020-02-12 讯】

武汉疫情迅猛扩散。继香港元朗区议会促请警队“一哥”邓炳强率警队到武汉抗疫后，11日，西贡区议会亦一致通过动议，要求警队往武汉支援抗疫。有区议员表示，警队应北上抗疫，发挥“忠诚勇毅”的精神。

[demosisto]

The Novel Coronavirus, 2019-nCoV, is Highly Contagious and More Infectious Than Initially Estimated
7 Feb, 2020 | Pre-Peer Review / Pre-Print
Steven Sanche, Yen Ting Lin, Chonggang Xu, Ethan Romero-Severson, Nick Hengartner, View ORCID ProfileRuian Ke

Abstract
The novel coronavirus (2019-nCoV) is a recently emerged human pathogen that has spread widely since January 2020. Initially, the basic reproductive number, R0, was estimated to be 2.2 to 2.7. Here we provide a new estimate of this quantity. We collected extensive individual case reports and estimated key epidemiology parameters, including the incubation period. Integrating these estimates and high-resolution real-time human travel and infection data with mathematical models, we estimated that the number of infected individuals during early epidemic double every 2.4 days, and the R0 value is likely to be between 4.7 and 6.6. We further show that quarantine and contact tracing of symptomatic individuals alone may not be effective and early, strong control measures are needed to stop transmission of the virus.

[theagora]

【患者求助】信息列表及更新

站名	鏈接	备注
武汉·人间	www.wuhancrisis.com	2020.2.3 ~ 微博超話 肺炎患者求助

[demosisto]

Understanding the present status and forecasting of COVID-19 in Wuhan
13 Feb, 2020 | Pre-Peer Review / Pre-Print
Toshihisa Tomie

Abstract
The present status of COVID-19 is analyzed and the end of the disease is forecasted. The peak of the epidemic is different in three regions, Wuhan, Hubei province except Wuhan, and mainland China except Hubei. In two regions except Wuhan, the peak of the epidemic passed ten days ago. If the trend until February 11 does not change, the disease may end by the end of February. In Wuhan, the epidemic reached a peak but the reported number of newly infected patients fluctuates largely. We need to know the reason for the big fluctuation to forecast the end of the disease.

[demosisto]

Restore Censored WeChat Articles

Name	URL	Remarks
WeChatSCOPE	https://wechatscope.jmsc.hku.hk	2018.7.6 ~
分流備份站點	下架文章列表及搜索 | 遞交公衆號	2018.7.6 ~

[demosisto]

Early dynamics of transmission and control of COVID-19: a mathematical modelling study
31 Jan, 2020 | Pre-Peer Review / Pre-Print
Adam J Kucharski, Timothy W Russell, Charlie Diamond, Yang Liu, CMMID nCoV working group, John Edmunds, View ORCID ProfileSebastian Funk, Rosalind M Eggo

Abstract
Background: An outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. Methods: We combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. Findings: We estimated that the median daily reproduction number, Rt , declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. Interpretation: Our results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.

[demosisto]

COVID-19 Global Cases

Dashboard by JHU CSSE | Mobile Version

[theagora]

COVID-19 Global Cases

Dashboard by JHU CSSE | Mobile Version

武漢肺炎-香港最新情況 | Covid-19 in Hong Kong

[demosisto]

Estimating number of global importations of COVID-19 from Wuhan, risk of transmission outside mainland China and COVID-19 introduction index between countries outside mainland China
17 Feb, 2020 | Pre-Peer Review / Pre-Print
Haoyang Sun, Borame Lee Dickens, Mark Chen, Alex Richard Cook, Hannah Eleanor Clapham

Abstract
Background The emergence of a novel coronavirus (SARS-CoV-2) in Wuhan, China in early December 2019 has caused widespread transmission within the country, with over 1,000 deaths reported to date. Other countries have since reported coronavirus disease 2019 (COVID-19) importation from China, with some experiencing local transmission and even case importation from countries outside China. We aim to estimate the number of cases imported from Wuhan to each country or territory outside mainland China, and with these estimates assess the risk of onward local transmission and the relative potential of case importation between countries outside China. Methods We used the reported number of cases imported from Wuhan and flight data to generate an uncertainty distribution for the estimated number of imported cases from Wuhan to each location outside mainland China. This uncertainty was propagated to quantify the local outbreak risk using a branching process model. A COVID-19 introduction index was derived for each pair of donor and recipient countries, accounting for the local outbreak risk in the donor country and the between-country connectivity. Results We identified 13 countries or territories outside mainland China that may have under-detected COVID-19 importation from Wuhan, such as Thailand and Indonesia. In addition, 16 countries had a local outbreak risk estimate exceeding 50%, including four outside Asia. The COVID-19 introduction index highlights potential locations outside mainland China from which cases may be imported to each recipient country. Conclusions As SARS-CoV-2 continues to spread globally, more epicentres may emerge outside China. Hence, it is important for countries to remain alert for the possibilities of viral introduction from other countries outside China, even before local transmission in a source country becomes known.

[demosisto]

Fractal kinetics of COVID-19 pandemic
17 Feb, 2020 | Pre-Peer Review / Pre-Print
Robert M. Ziff, Anna L. Ziff

Abstract
The novel coronavirus (COVID-19) continues to grow rapidly in China and is spreading in other parts of the world. The classic epidemiological approach in studying this growth is to quantify a reproduction number and infection time, and this is the approach followed by many studies on the epidemiology of this disease. However, this assumption leads to exponential growth, and while the growth rate is high, it is not following exponential behavior. One approach that is being used is to simply keep adjusting the reproduction number to match the dynamics. Other approaches use rate equations such as the SEIR and logistical models. Here we show that the current growth closely follows power-law kinetics, indicative of an underlying fractal or small-world network of connections between susceptible and infected individuals. Positive deviations from this growth law might indicate either a failure of the current containment efforts while negative deviations might indicate the beginnings of the end of the pandemic. We cannot predict the ultimate extent of the pandemic but can get an estimate of the growth of the disease.

[demosisto]

Transmission potential of COVID-19 in South Korea
27 Feb, 2020 | Pre-Peer Review / Pre-Print
Eunha Shim, Amna Tariq, Wongyeong Choi, Yiseul Lee, Gerardo Chowell

Abstract
Since the first identified individual of 2019 novel coronavirus (COVID-19) infection on Jan 20, 2020 in South Korea, the number of confirmed cases rapidly increased. As of Feb 26, 2020, 1,261 cases of COVID-19 including 12 deaths were confirmed in South Korea. Using the incidence data of COVID-19, we estimate the reproduction number at 1.5 (95% CI: 1.4-1.6), which indicates sustained transmission and support the implementation of social distancing measures to rapidly control the outbreak.

[demosisto]

Transmission potential of COVID-19 in Iran
8 Mar, 2020 | Pre-Peer Review / Pre-Print
Kamalich Muniz-Rodriguez, Isaac Chun-Hai Fung, Shayesterh R. Ferdosi, Sylvia K. Ofori, Yiseul Lee, Amna Tariq, Gerardo Chowell

Abstract
We computed reproduction number of COVID-19 epidemic in Iran using two different methods. We estimated R0 at 3.6 (95% CI, 3.2, 4.2) (generalized growth model) and at 3.58 (95% CI, 1.29, 8.46) (estimated epidemic doubling time of 1.20 (95% CI, 1.05, 1.44) days) respectively. Immediate social distancing measures are recommended.

[demosisto]

Direct RNA sequencing and early evolution of SARS-CoV-2
5 Mar, 2020 | Pre-Peer Review / Pre-Print
George Taiaroa, Daniel Rawlinson, Leo Featherstone, Miranda Pitt, Leon Caly, Julian Druce, Damian Purcell, Leigh Harty, Thomas Tran, Jason Roberts, Mike Catton, Deborah Williamson, Lachlan Coin, Sebastian Duchene

Abstract
The rapid sharing of sequence information as seen throughout the current SARS-CoV-2 epidemic, represents an inflection point for genomic epidemiology. Here we describe aspects of coronavirus evolutionary genetics revealed from these data, and provide the first direct RNA sequence of SARS-CoV-2, detailing coronaviral subgenome-length mRNA architecture.

[theagora]

Airborne Nitrogen Dioxide Plummets Over China
March 1, 2020

NASA and European Space Agency (ESA) pollution monitoring satellites have detected significant decreases in nitrogen dioxide (NO2) over China. There is evidence that the change is at least partly related to the economic slowdown following the outbreak of coronavirus.
...

[demosisto]

武漢肺炎-香港民間資訊
https://wars.vote4.hk/

COVID-19 Global Cases

Dashboard by JHU CSSE | Mobile Version

武漢肺炎-香港最新情況 | Covid-19 in Hong Kong

[demosisto]

東京都COVID-19対策 | English | 中文版 | Github

COVID-19 Global Cases

Dashboard by JHU CSSE | Mobile Version

武漢肺炎-香港最新情況 | Covid-19 in Hong Kong

[demosisto]

台灣COVID-19資料站-皮丘版 | English | Github

COVID-19 Global Cases

Dashboard by JHU CSSE | Mobile Version

武漢肺炎-香港最新情況 | Covid-19 in Hong Kong

[demosisto]

一山還比一山高
鬧市無市靜悄悄
栽樹無木有共田
田中無物多逍遙
四張桌子腿鋸掉

猜五個字！

[demosisto]

为什么说中国的数字完全不可信
5 Apr, 2020 | QmfXAwxPPCqyD7pSvkhhsGBmz1gZvX1rDdfgjfeDji3454
Mischievous Physicsit (@MeBeingADonut) from Matters

我作为一个物理博士生，对于疫病传播的发展习惯利用模型，去研究现在发展到哪一步了，什么地方应该怎么做，做没做好，导致的后果是什么。这就需要数据库大量的公开数据判断来更正模型，细微调整参数。我所依赖于的模型原型，就是可以在任何疫病传播中必定会讨论到的SEIR模型，比如这个：https://www.sciencedirect.com/science/article/pii/S0022247X14007586#tl0010 。有时也会用Gamma分布去估算验证模型的符合程度。

[theagora]

出門戴口罩

一山還比一山高
鬧市無市靜悄悄
栽樹無木有共田
田中無物多逍遙
四張桌子腿鋸掉

猜五個字！

[theagora]

Possible association of vitamin D status with lung involvement and outcome in patients with COVID-19: a retrospective study
Alireza Abrishami, Nooshin Dalili, et al. | 30 October 2020
Abstract
Purpose - Vitamin D deficiency has been reported as a key factor in the development of infectious diseases such as respiratory tract infections and inflammatory processes like acute respiratory distress syndrome. However, the impact of vitamin D on the severity and outcome of COVID-19 is still not fully known. Herein, we aimed to evaluate the prognostic role of serum vitamin D concentration on the extent of lung involvement and final outcome in patients with COVID-19.
Methods - Seventy-three subjects with confirmed diagnosis of COVID-19 were investigated in this study. The patients had been admitted to our academic hospital from February 28, 2020 to April 19, 2020. Demographic and clinical data, serum 25(OH)D levels, and findings of initial chest computed tomography were recorded. Linear and binary logistic regression, cox regression and ROC curve tests were used for statistical analysis.
Results - The mean age of patients was 55.18 ± 14.98 years old; 46.4% were male. Mean serum 25(OH)D concentration was significantly lower in the deceased (13.83 ± 12.53 ng/ mL compared with discharged patients (38.41 ± 18.51 ng/mL) (P < 0.001). Higher levels of 25(OH)D were associated with significantly less extent of total lung involvement (β = − 0.10, P = 0.004). In addition, vitamin D deficiency [25(OH) D < 25 ng/mL] was associated with a significant increase in the risk of mortality (hazard ratio = 4.15, P = 0.04).
Conclusion - This study suggests that serum vitamin D status might provide useful information regarding the clinical course, extent of lung involvement and outcome of patients with COVID-19. However, further studies with larger sample size are needed to confirm these findings.

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[theagora]

Transmission of SARS-COV-2 Infections in Households — Tennessee and Wisconsin, April–September 2020
Carlos G. Grijalva, Melissa A. Rolfes, et al. | 30 October 2020
Summary
What is already known about this topic?
Transmission of SARS-CoV-2 occurs within households; however, transmission estimates vary widely and the data on transmission from children are limited.
What is added by this report?
Findings from a prospective household study with intensive daily observation for ≥7 consecutive days indicate that transmission of SARS-CoV-2 among household members was frequent from either children or adults.
What are the implications for public health practice?
Household transmission of SARS-CoV-2 is common and occurs early after illness onset. Persons should self-isolate immediately at the onset of COVID-like symptoms, at the time of testing as a result of a high risk exposure, or at time of a positive test result, whichever comes first. All household members, including the index case, should wear masks within shared spaces in the household.

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[theagora]

Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2
Alexandra C. Walls, Brooke Fiala, et al. | 30 October 2020
Highlights

• Two-component nanoparticle platform enabled rapid generation of SARS-CoV-2 vaccines
• The RBD-nanoparticle vaccines elicit potent neutralizing antibody responses
• Nanoparticle vaccine-elicited antibodies target multiple non-overlapping epitopes
• The lead nanoparticle vaccine candidate is being manufactured for clinical trials

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[theagora]

Slovakia to test all adults for SARS-CoV-2
Ed Holt | 31 October 2020

Slovakia plans to be the first country to test its whole population for SARS-CoV-2, but experts warn of logistical and technical challenges. Ed Holt reports from Bratislava.

Slovakia has begun a massive operation to test its entire adult population for SARS-CoV-2 in a bid to halt what its government has said is an alarming acceleration of the spread of the virus in the country.
......

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[theagora]

Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis
Silvia NunesSzente Fonseca, Anastasio Queiroz de Sousa, et al. | 31 October 2020
Abstract
Background - For the past few months, HMOs have faced crowded emergency rooms and insufficient hospital and intensive-care-unit beds, all from the worst pandemic of this century, COVID-19.
Methods - In a large HMO in Brazil, our approach was to allow treating physicians to prescribe antiviral medications immediately at presentation, and prednisone starting on day-6 of symptoms to treat pulmonary inflammation. We implemented this COVID-19 protocol for outpatients and studied 717 consecutive SARS-CoV-2-positive patients age 40 years or older presenting at our emergency rooms.
Results - Use of hydroxychloroquine (HCQ), prednisone or both significantly reduced hospitalization risk by 50-60%. Ivermectin, azithromycin and oseltamivir did not substantially reduce risk further. Hospitalization risk was doubled for people with type-2 diabetes or obesity, increased by two-thirds for people with heart disease, and by 75% for each decade of age over age 40. Similar magnitudes of reduced risk with HCQ and prednisone use were seen for mortality risk, though were not significant because of only 11 deaths among the 717 patients. No cardiac arrhythmias requiring medication termination were observed for any of the medications.
Conclusions - This work adds to the growing literature of studies that have found substantial benefit for use of HCQ combined with other agents in the early outpatient treatment of COVID-19, and adds the possibility of steroid use to enhance treatment efficacy.

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[demosisto]

COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning
29 Oct, 2020 | Pre-Print
Hagit Achdout, Anthony Aimon, et al.

Abstract
Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. Our approach uniquely combines crowdsourced medicinal chemistry insights with high throughput crystallography, exascale computational chemistry infrastructure for simulations, and machine learning in triaging designs and predicting synthetic routes. This manuscript describes our methodologies leading to both covalent and non-covalent inhibitors displaying protease IC50 values under 150 nM and viral inhibition under 5 uM in multiple different viral replication assays. Furthermore, we provide over 200 crystal structures of fragment-like and lead-like molecules in complex with the main protease. Over 1000 synthesized and ordered compounds are also reported with the corresponding activity in Mpro enzymatic assays using two different experimental setups. The data referenced in this document will be continually updated to reflect the current experimental progress of the COVID Moonshot project, and serves as a citable reference for ensuing publications. All of the generated data is open to other researchers who may find it of use.

[demosisto]

Amino acid transporter B0AT1 influence on ADAM17 interactions with SARS-CoV-2 receptor ACE2 putatively expressed in intestine, kidney, and cardiomyocytes
30 Oct, 2020 | Pre-Print
Jacob T. Andring, Robert McKenna, et al.

Abstract
SARS-CoV-2 exhibits significant experimental and clinical gastrointestinal, renal, and cardiac muscle tropisms responsible for local tissue-specific and systemic pathophysiology capriciously occurring in about half of COVID-19 patients. The underlying COVID-19 mechanisms engaged by these extra-pulmonary organ systems are largely unknown. We approached this knowledge gap by recognizing that neutral amino acid transporter B0AT1 (alternately called NBB, B, B0 in the literature) is a common denominator expressed nearly exclusively by three particular cell types: intestinal epithelia, renal proximal tubule epithelium, and cardiomyocytes. B0AT1 provides uptake of glutamine and tryptophan. The gut is the main depot expressing over 90% of the body's entire pool of SARS-CoV-2 receptor angiotensin converting enzyme-2 (ACE2) and B0AT1. Recent cryo-EM studies established that ACE2 forms a thermodynamically favored dimer-of-heterodimers complex with B0AT1 assembled in the form of a dimer of two ACE2:B0AT1 heterodimers anchored in plasma membranes. Prior epithelial cell studies demonstrated ACE2 chaperone trafficking of B0AT1. This contrasts with monomeric expression of ACE2 in lung pneumocytes, in which B0AT1 is undetectable. The cell types in question also express a disintegrin and metalloproteinase-17 (ADAM17) known to cleave and shed the ectodomain of monomeric ACE2 from the cell surface, thereby relinquishing protection against unchecked renin-angiotensin-system (RAS) events of COVID 19. The present study employed molecular docking modeling to examine the interplaying assemblage of ACE2, ADAM17 and B0AT1. We report that in the monomer form of ACE2, neck region residues R652-N718 provide unimpeded access to ADAM17 active site pocket, but notably R708 and S709 remained >10-15 Å distant. In contrast, interference of ADAM17 docking to ACE2 in a dimer-of-heterodimers arrangement was directly correlated with the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of the 2ACE2:2B0AT1 dimer of heterodimers, representing the expression pattern putatively exclusive to intestinal, renal and cardiomyocyte cell types. The monomer and dimer-of-heterodimers docking models were not influenced by the presence of SARS-CoV-2 receptor binding domain (RBD) complexed to ACE2. The results collectively provide the underpinnings for understanding the role of B0AT1 involvement in COVID-19 and the role of ADAM17 steering ACE2 events in intestinal and renal epithelial cells and cardiomyocytes, with implications useful for consideration in pandemic public hygiene policy and drug development.

[demosisto]

Brilacidin, a COVID-19 Drug Candidate, Exhibits Potent In Vitro Antiviral Activity Against SARS-CoV-2
29 Oct, 2020 | Pre-Print
Alison Bakovic, Kenneth Risner, et al.

Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the newly emergent causative agent of coronavirus disease-19 (COVID-19), has resulted in more than one million deaths worldwide since it was first detected in 2019. There is a critical global need for therapeutic intervention strategies that can be deployed to safely treat COVID-19 disease and reduce associated morbidity and mortality. Increasing evidence shows that both natural and synthetic antimicrobial peptides (AMPs), also referred to as Host Defense Proteins/Peptides (HDPs), can inhibit SARS-CoV-2, paving the way for the potential clinical use of these molecules as therapeutic options. In this manuscript, we describe the potent antiviral activity exerted by brilacidin−a de novo designed synthetic small molecule that captures the biological properties of HDPs−on SARS-CoV-2 in a human lung cell line (Calu-3) and a monkey cell line (Vero). These data suggest that SARS-CoV-2 inhibition in these cell culture models is primarily a result of the impact of brilacidin on viral entry and its disruption of viral integrity. Brilacidin has demonstrated synergistic antiviral activity when combined with remdesivir. Collectively, our data demonstrate that brilacidin exerts potent inhibition of SARS-CoV-2 and thus supports brilacidin as a promising COVID-19 drug candidate. Highlights: Brilacidin potently inhibits SARS-CoV-2 in an ACE2 positive human lung cell line. Brilacidin achieved a high Selectivity Index of 426 (CC50=241µM/IC50=0.565µM). Brilacidin's main mechanism appears to disrupt viral integrity and impact viral entry. Brilacidin and remdesivir exhibit excellent synergistic activity against SARS-CoV-2. Significance Statement: SARS-CoV-2, the emergent novel coronavirus, has led to the current global COVID-19 pandemic, characterized by extreme contagiousness and high mortality rates. There is an urgent need for effective therapeutic strategies to safely and effectively treat SARS-CoV-2 infection. We demonstrate that brilacidin, a synthetic small molecule with peptide-like properties, is capable of exerting potent in vitro antiviral activity against SARS-CoV-2, both as a standalone treatment and in combination with remdesivir, which is currently the only FDA-approved drug for the treatment of COVID-19.

[demosisto]

PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2
30 Oct, 2020 | Pre-Print
Saumyabrata Mazumder, Ruchir Rastogi, et al.

Abstract
The rapid development of safe and effective vaccines against SARS CoV−2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK−03202, the world′s first triple antigen VLP vaccine candidate in a highly characterized S. cerevisiae−based D−Crypt™ platform, which induced SARS CoV−2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK−03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK−03202, showed lymphocyte proliferation and elevated IFN-γ levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)−biased cellular immune responses. These data support the clinical development and testing of PRAK−03202 for use in humans.

[demosisto]

A Bayesian estimate of the COVID-19 infection fatality rate in Brazil based on a random seroprevalence survey
18 Aug, 2020 | Pre-Print v2
Valerio Marra, Miguel Quartin

Abstract
We infer the infection fatality rate (IFR) of SARS-CoV-2 in Brazil by combining three datasets. We compute the prevalence via the population-based seroprevalence survey EPICOVID19-BR, which tested 89000 people in 3 stages over a period of 5 weeks. This randomized survey selected people of 133 cities (accounting for 35.5% of the Brazilian population) and tested them for IgM/IgG antibodies making use of a rapid test. We estimate the time delay between the development of antibodies and subsequent fatality using the public SIVEP-Gripe dataset. The number of fatalities is obtained using the public Painel Coronavírus dataset. We obtain the IFR via Bayesian inference for each survey stage and 27 federal states. In particular, we include the effect of fading IgG levels by marginalizing over the time T after contagion at which the test gives a negative result. We adopt a flat broad prior on the interval [40, 80] days. We infer a country-wide average IFR of 0.85% (95% CI: 0.76–0.99%).

[demosisto]

Hyper-Exponential Growth of COVID-19 during Resurgence of the Disease in Russia
26 Oct, 2020 | Pre-Print
Hemanta K. Baruah

Abstract
In Russia, COVID-19 has currently been growing hyper-exponentially. This type of a spread pattern was not seen during the first wave of the pandemic the world over. Indeed when the disease had first appeared, in the accelerating stage the spread pattern was observed to have followed a highly nonlinear pattern that could be said to be approximately exponential or sub-exponential. As to why in the resurgence the growth has become hyper-exponential is another matter. But this has been happening in Europe and how long this would continue cannot be predicted. It may so happen that in the countries in which retardation has already been taking place, there may be resurgence of the disease. It was observed that in the World as a whole, retardation was on the threshold during the second half of September. But if the resurgence happens to follow the hyper-exponential growth pattern in different countries, there may be resurgence in the World as a whole.

[demosisto]

The Risk of Indoor Sports and Culture Events for the Transmission of COVID-19 (Restart-19)
28 Oct, 2020 | Pre-Print
Stefan Moritz, Cornelia Gottschick, et al.

Abstract
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.

[theagora]

COVID-19 Artificial Intelligence Diagnosis using only Cough Recordings
Jordi Laguarta, Ferran Hueto, et al. | 30 September 2020
Abstract
Goal: We hypothesized that COVID-19 subjects, especially including asymptomatics, could be accurately discriminated only from a forced-cough cell phone recording using Artificial Intelligence. To train our MIT Open Voice model we built a data collection pipeline of COVID-19 cough recordings through our website (opensigma.mit.edu) between April and May 2020 and created the largest audio COVID-19 cough balanced dataset reported to date with 5,320 subjects.
Methods: We developed an AI speech processing framework that leverages acoustic biomarker feature extractors to pre-screen for COVID-19 from cough recordings, and provide a personalized patient saliency map to longitudinally monitor patients in real-time, non-invasively, and at essentially zero variable cost. Cough recordings are transformed with Mel Frequency Cepstral Coefficient and inputted into a Convolutional Neural Network (CNN) based architecture made up of one Poisson biomarker layer and 3 pre-trained ResNet50’s in parallel, outputting a binary pre-screening diagnostic. Our CNN-based models have been trained on 4256 subjects and tested on the remaining 1064 subjects of our dataset. Transfer learning was used to learn biomarker features on larger datasets, previously successfully tested in our Lab on Alzheimer’s, which significantly improves the COVID-19 discrimination accuracy of our architecture.
Results: When validated with subjects diagnosed using an official test, the model achieves COVID-19 sensitivity of 98.5% with a specificity of 94.2% (AUC: 0.97). For asymptomatic subjects it achieves sensitivity of 100% with a specificity of 83.2%.
Conclusions: AI techniques can produce a free, non-invasive, real-time, any-time, instantly distributable, large-scale COVID-19 asymptomatic screening tool to augment current approaches in containing the spread of COVID-19. Practical use cases could be for daily screening of students, workers, and public as schools, jobs, and transport reopen, or for pool testing to quickly alert of outbreaks in groups.

[theagora]

From Cold to Killer: How SARS-CoV-2 Evolved without Hemagglutinin Esterase to Agglutinate, Then Clot Blood Cells in Pulmonary and Systemic Microvasculature
David Scheim | 12 October 2020
Abstract
Human betacoronaviruses, both those causing the common cold and the lethal strains, attach to sialic acid (SA) glycoconjugate receptors on host cells prior to fusion and replication. SARS-CoV-2, in particular, binds to SA and also to CD147 receptors, which in turn contain SA. The human host, reciprocally, mounts a blood-based antiviral defense spearheaded by trillions of red blood cells (RBCs), each presenting millions of SA surface molecules. This virus-host entanglement is simulated in the classic viral hemagglutination assay, refined by Jonas Salk in 1944, in which viruses mix with RBCs to form a hemagglutinated sheet. But for viruses that express hemagglutinin esterase (HE), which cleaves SA, that sheet subsequently collapses as HE disintegrates SA receptors on RBCs.
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Prediction of survival odds in COVID-19 by zinc, age and selenoprotein P as composite biomarker
Raban Arved Heller, Qian Sun, et al. | 20 October 2020
Abstract
SARS-CoV-2 infections cause the current coronavirus disease (COVID-19) pandemic and challenge the immune system with ongoing inflammation. Several redox-relevant micronutrients are known to contribute to an adequate immune response, including the essential trace elements zinc (Zn) and selenium (Se). In this study, we tested the hypothesis that COVID-19 patients are characterised by Zn deficiency and that Zn status provides prognostic information. Serum Zn was determined in serum samples (n = 171) collected consecutively from patients surviving COVID-19 (n = 29) or non-survivors (n = 6). Data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study were used for comparison. Zn concentrations in patient samples were low as compared to healthy subjects (mean ± SD; 717.4 ± 246.2 vs 975.7 ± 294.0 μg/L, P < 0.0001). The majority of serum samples collected at different time points from the non-survivors (25/34, i.e., 73.5%) and almost half of the samples collected from the survivors (56/137, i.e., 40.9%) were below the threshold for Zn deficiency, i.e., below 638.7 μg/L (the 2.5th percentile in the EPIC cohort). In view that the Se status biomarker and Se transporter selenoprotein P (SELENOP) is also particularly low in COVID-19, we tested the prevalence of a combined deficit, i.e., serum Zn below 638.7 μg/L and serum SELENOP below 2.56 mg/L. This combined deficit was observed in 0.15% of samples in the EPIC cohort of healthy subjects, in 19.7% of the samples collected from the surviving COVID-19 patients and in 50.0% of samples from the non-survivors. Accordingly, the composite biomarker (SELENOP and Zn with age) proved as a reliable indicator of survival in COVID-19 by receiver operating characteristic (ROC) curve analysis, yielding an area under the curve (AUC) of 94.42%. We conclude that Zn and SELENOP status within the reference ranges indicate high survival odds in COVID-19, and assume that correcting a diagnostically proven deficit in Se and/or Zn by a personalised supplementation may support convalescence.

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Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA
Fan-Yun Lan, Christian Suharlim, et al. | 30 October 2020
Abstract
Objectives - To investigate SARS-CoV-2 (the virus causing COVID-19) infection and exposure risks among grocery retail workers, and to investigate their mental health state during the pandemic.
Methods - This cross-sectional study was conducted in May 2020 in a single grocery retail store in Massachusetts, USA. We assessed workers’ personal/occupational history and perception of COVID-19 by questionnaire. The health outcomes were measured by nasopharyngeal SARS-CoV-2 reverse transcriptase PCR (RT-PCR) results, General Anxiety Disorder-7 (GAD-7) and Patient Health Questionnaire-9 (PHQ-9).
Results - Among 104 workers tested, 21 (20%) had positive viral assays. Seventy-six per cent positive cases were asymptomatic. Employees with direct customer exposure had an odds of 5.1 (95% CI 1.1 to 24.8) being tested positive for SARS-CoV-2 after adjustments. As to mental health, the prevalence of anxiety and depression (ie, GAD-7 score >4 or PHQ-9 score >4) was 24% and 8%, respectively. After adjusting for potential confounders, those able to practice social distancing consistently at work had odds of 0.3 (95% CI 0.1 to 0.9) and 0.2 (95% CI 0.03 to 0.99) screening positive for anxiety and depression, respectively. Workers commuting by foot, bike or private cars were less likely to screen positive for depression (OR 0.1, 95% CI 0.02 to 0.7).
Conclusions - In this single store sample, we found a considerable asymptomatic SARS-CoV-2 infection rate among grocery workers. Employees with direct customer exposure were five times more likely to test positive for SARS-CoV-2. Those able to practice social distancing consistently at work had significantly lower risk of anxiety or depression.

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SARS-CoV-2 viral load is associated with increased disease severity and mortality
Jesse Fajnzylber, James Regan, et al. | 30 October 2020
Abstract
The relationship between SARS-CoV-2 viral load and risk of disease progression remains largely undefined in coronavirus disease 2019 (COVID-19). Here, we quantify SARS-CoV-2 viral load from participants with a diverse range of COVID-19 disease severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. We detected SARS-CoV-2 plasma RNA in 27% of hospitalized participants, and 13% of outpatients diagnosed with COVID-19. Amongst the participants hospitalized with COVID-19, we report that a higher prevalence of detectable SARS-CoV-2 plasma viral load is associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. SARS-CoV-2 viral loads, especially plasma viremia, are associated with increased risk of mortality. Our data show that SARS-CoV-2 viral loads may aid in the risk stratification of patients with COVID-19, and therefore its role in disease pathogenesis should be further explored.

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COVID-19 Ahead-of-Print Subject Collection
JABFM | February 2021 Issue

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Campaign moved to agorahub/blog0#2.
Webpage: https://agora0.gitlab.io/blog/covid.