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 :cloud: )

• Collaborators to WRITE DOWN links or texts in the comments.
• Others to CLICK-n-POST emoji votes :+1: or :-1: 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~

[demosisto]

Estimating population immunity without serological testing 23 Apr, 2020 | Pre-Peer Review / Pre-Print Andrew Lesniewski

Abstract We propose an approximate methodology for estimating the overall level of immunity against COVID-19 in a population that has been affected by the recent epidemic. The methodology relies on the currently available mortality data and utilizes the properties of the SIR model. We illustrate the application of the method by estimating the recent levels of immunity in 10 US states with highest case numbers of COVID-19.

[theagora]

港大研究：新冠病毒可倉鼠間空氣傳播　破壞嗅覺神經元致失嗅覺可復元 【明報港聞】2020年5月14日

港大醫學院公共衛生學院及病理學系，利用金倉鼠研究發現，新型冠狀病毒可在倉鼠之間，透過直接接觸或空氣傳播，但透過受污染鼠籠傳播的效率較低。研究又發現，新冠病毒會損害倉鼠鼻黏膜中的嗅覺神經元，但嗅覺神經元所受破壞只屬暫時性質，之後會快速修復，相信這可解釋為何部分確診者會暫時失去嗅覺。研究結果已在學術期刊《自然》發表。 研究團隊在港大醫學院的三級生物安全水平實驗室進行一系列實驗，發現新型冠狀病毒可在倉鼠的呼吸道和腸道複製，導致肺炎和體重明顯下降。 研究又發現，受感染倉鼠的鼻腔或糞便，可連續最少14日檢測到新冠病毒核糖核酸（RNA），但只在感染後首6日檢測出具傳染力的病毒，證明病毒在倉鼠的有效傳播期少於6日。這顯示即使可持續數星期在受感染動物或患者體內驗出病毒RNA，但在病徵出現一星期後，通常已無法檢測出具傳染力的病毒，即受感染動物或患者不再具傳播能力。帶領研究的港大醫學院公共衛生學院副教授嚴慧玲認為，研究結果與衛生署上周更新的確診者終止隔離準則脗合。

[theagora]

世衛指或成風土病 料4至5年方受控 2020年5月15日

【明報專訊】各國相繼放寬限制和考慮重啟經濟活動之際，世界衛生組織（WHO）周三（13日）警告，新型冠狀病毒或會成為風土病（endemic），可能像愛滋病毒（HIV）不會消失，即使疫苗面世，仍要付出「巨大努力」控制病毒傳播。世衛首席科學家預料可能需4至5年才能控制疫情。衛生防護中心傳染病處主任張竹君承認各地疫情嚴重，難以斷尾，要有心理準備與病毒共存。 ……

[theagora]

Leaked Chinese Virus Database Covers 230 Cities, 640,000 Updates 12 May 2020 | Foreign Policy Isaac Stone Fish, Maria Krol Sinclair

New information may offer insight into the honesty of China’s coronavirus numbers.

Beijing claims that since the coronavirus pandemic began at the end of last year, there have been only 82,919 confirmed cases and 4,633 deaths in mainland China. Those numbers could be roughly accurate, and in that case a detailed account would be an important tool in judging the spread of the virus. But it’s also possible that the numbers presented to the rest of the world are vastly understated compared to Beijing’s private figures. The opaqueness and mistrust of outsiders in the Chinese Communist Party’s system makes it hard to judge—but learning more about the coronavirus data used directly by Chinese officials is invaluable for governments elsewhere. A dataset of coronavirus cases and deaths from the military’s National University of Defense Technology, leaked to Foreign Policy, offers insight into how Beijing has gathered coronavirus data on its population. The source of the leak, who asked to remain anonymous because of the sensitivity of sharing Chinese military data, said that the data came from the university. The school publishes a data tracker for the coronavirus: The online version matches with the leaked information, except it is far less detailed—it shows just the map of cases, not the distinct data.

The dataset, though it contains inconsistencies—and though it may not be comprehensive enough to contradict Beijing’s official numbers—is the most extensive dataset proved to exist about coronavirus cases in China. But more importantly, it can serve as a valuable trove of information for epidemiologists and public health experts around the globe—a dataset that Beijing has almost certainly not shared with U.S. officials or doctors. (The World Health Organization and the U.S. Centers for Disease Control and Prevention did not immediately respond to requests for comment.)

While not fully comprehensive, the data is incredibly rich: There are more than 640,000 updates of information, covering at least 230 cities—in other words, 640,000 rows purporting to show the number of cases in a specific location at the time the data was gathered.

While not fully comprehensive, the data is incredibly rich: There are more than 640,000 updates of information, covering at least 230 cities—in other words, 640,000 rows purporting to show the number of cases in a specific location at the time the data was gathered.

Each update includes the latitude, longitude, and “confirmed” number of cases at the location, for dates ranging from early February to late April. ......

[demosisto]

Establishment of an African green monkey model for COVID-19 17 May, 2020 | Pre-Peer Review / Pre-Print Courtney B. Woolsey, Viktoriya Borisevich, Abhishek N Prasad, Krystle N. Agans, Daniel J. Deer, Natalie S. Dobias, John C. Heymann, Stephanie L. Foster, Corri B. Levine, Liana Medina, Kevin Melody, Joan B. Geisbert, Karla A. Fenton, Thomas W. Geisbert, Robert W. Cross

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for an unprecedented global pandemic of COVID-19. Animal models are urgently needed to study the pathogenesis of COVID-19 and to screen candidate vaccines and treatments. Nonhuman primates (NHP) are considered the gold standard model for many infectious pathogens as they usually best reflect the human condition. Here, we show that African green monkeys support a high level of SARS-CoV-2 replication and develop pronounced respiratory disease that may be more substantial than reported for other NHP species including cynomolgus and rhesus macaques. In addition, SARS-CoV-2 was detected in mucosal samples of all animals including feces of several animals as late as 15 days after virus exposure. Importantly, we show that virus replication and respiratory disease can be produced in African green monkeys using a much lower and more natural dose of SARS-CoV-2 than has been employed in other NHP studies.

[demosisto]

SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics 15 May, 2020 | Pre-Peer Review / Pre-Print Ruchir Gupta, Jacob Charron, Cynthia Stenger, Jared Painter, Hunter Steward, Taylor Cook, William Faber, Austin Frisch, Eric Lind, Jacob Bauss, Xiaopeng Li, Olivia Sirpilla, Xavier Soehnlen, Adam Underwood, David Hinds, Michele Morris, Neil Lamb, Joseph Carcillo, Caleb Bupp, Bruce Uhal, Surender Rajasekaran, Jeremy W Prokop

Abstract The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.

[demosisto]

Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence 12 May, 2020 | Pre-Peer Review / Pre-Print Thanh Thi Nguyen, Mohamed Abdelrazek, Dung Tien Nguyen, Sunil Aryal, Duc Thanh Nguyen, Amin Khatami

Abstract Origin of the COVID-19 virus has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the original hosts for the virus based on comparative studies using its genomic sequences. This paper investigates the COVID-19 virus origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined COVID-19 virus genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidences strongly supporting scientific hypotheses that bats and pangolins are probable hosts for the COVID-19 virus. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.

[demosisto]

Superspreaders help covid-19 elimination 19 Apr, 2020 | Pre-Peer Review / Pre-Print David Abraham Kault

Abstract There seems to be widespread pessimism regarding the ability of a nation to eliminate covid. One factor in this pessimism seems to be concern that covid might always be able to re-emerge because of the ongoing presence of unrecognised asymptomatic cases. However, it is shown here that it should be possible to eliminate covid more easily than anticipated, for a reason that at first glance seems paradoxical - the presence of superspreaders. If superspreaders are responsible for most of the spread, then, with the average number of secondary cases fixed at say R0=2.5, we have to conclude that superspreaders are relatively rare. When towards the end of an elimination program, there are very few infected people, whether symptomatic or asymptomatic, that small number of people may well not include any superspreaders. As a result, chance effects may make extinction likely. Nevertheless it is clear an attempt at elimination will require a rather onerous lockdown. In this paper we use a branching processes model to look at the tradeoff between risk of disease re-emergence and the length of lockdown required after a program of elimination has dropped the number of symptomatic cases in a region to just one.

[demosisto]

Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19 23 May, 2020 | Pre-Peer Review / Pre-Print Anna A. Valyaeva, Anastasia A. Zharikova, Artem S. Kasianov, Yegor S. Vassetzky, Eugene V. Sheval

Abstract SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be infected by SARS-CoV-2, which can lead to defects in regeneration capacity and account for the severity of SARS-CoV-2 infection and its consequences.

[theagora]

失憶之國：為何中國如此迅速地遺忘了新冠這場災難 2020年5月28日 袁莉

整個國家能多快忘記一場災難？ 在陳冠中2009年的反烏托邦小說《盛世》中，中國經歷了一場巨大的虛構危機。兩年後，似乎就沒有人記得這件事了。

實際上，陳冠中意識到，讓許多中國人不再提他們在新型冠狀病毒危機期間的憤怒和絕望，以及政府早期的糟糕響應，只用了不到兩個月的時間。今天，他們對中國戰勝了疫情信以為真。

「好像之前什麼都沒有發生過一樣，」陳冠中在接受採訪時說。「這次我都嚇了一跳，為什麼這個轉彎這麼快？」 陳冠中的《盛世》是一個警世故事。今天，這個故事中的一切似乎都太真實。災難帶來痛苦和死亡。集體失憶開始出現。災難讓共產黨顯得比以往任何時候都更加強大。 在中國以外的地方，讀者求助於捕捉了當下情緒的書籍，比如阿爾貝·加繆(Albert Camus)的《鼠疫》。《盛世》並未享有同樣的復興。首先，這本書在中國被禁。書的盜版曾轟動一時，但那是十年前的事情。很多年輕讀者不知道有這本書。 然而，那些現在讀它的人，讀完後會心緒不寧。一位年輕的白領告訴我，她感覺像是在讀過去幾個月的事情。書中的一個角色——一名年輕的民族主義者，讓她想起一個親戚，這讓她不寒而慄。 我有點好奇，想知道陳冠中看到自己想像出來的東西變成了現實是怎樣的感覺。我也想知道為什麼他的無憂無慮的反烏托邦小說——這本書更像《美麗新世界》，而不是《1984》——沒有預測到當今中國更嚴酷的現實。 67歲的陳冠中在上海出生、香港長大，在華語世界的新聞、電影和文學領域享有聲譽。幾十年來，他一直留著中分齊肩長頭，頭髮現已灰白。 ……

[demosisto]

Preprinting a pandemic: the role of preprints in the COVID-19 pandemic 22 May, 2020 | Pre-Peer Review / Pre-Print Nicholas Fraser, Liam Brierley, Gautam Dey, Jessica K Polka, Máté Pálfy, Jonathon Alexis Coates

Abstract The world continues to face an ongoing viral pandemic that presents a serious threat to human health. The virus underlying the COVID-19 disease, SARS-CoV-2, has caused over 3.2 million confirmed cases and 220,000 deaths between January and April 2020. Although the last pandemic of respiratory disease of viral origin swept the globe only a decade ago, the way science operates and responds to current events has experienced a paradigm shift in the interim. The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 16,000 COVID-19 related scientific articles within 4 months of the first confirmed case, of which at least 6,000 were hosted by preprint servers. We focused our analysis on bioRxiv and medRxiv, two growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, characteristics of their sharing on online platforms, and the relationship between preprints and their published articles. Our data provides evidence for increased scientific and public engagement (COVID-19 preprints are accessed and distributed at least 15 times more than non-COVID-19 preprints) and changes in journalistic practice with reference to preprints. We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter, with fewer panels and tables, and reviewed faster. Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science, and the likely long-term impact of the pandemic on the scientific publishing landscape.

[theagora]

《刺針》等撤回質疑抗瘧疾藥物對新冠病毒療效研究 2020年6月5日

【Now新聞台】國際醫學期刊《刺針》和《新英倫醫學雜誌》，先後撤回指抗瘧疾藥物羥氯喹對治療新型冠狀病毒沒用的研究報告。

研究報告的撰寫人指，提供新冠患者數據的美國公司Surgisphere拒絕讓他們接觸所有數據，用作獨立核查，鑑於無法保證數據的準確性，決定撤回研究報告，並為造成不便致歉。

有份撰寫報告的其中一人，Surgisphere的行政總裁德賽就拒絕評論事件。

被撤回的研究報告指，新冠患者服用羥氯喹沒益處，並可能增加出現心血管問題及死亡的風險，但外界質疑該公司如何在短時間內，取得多個國家和地區的龐大數據，近二百名醫生發聯署信質疑數據的真確性。

世界衛生組織早前曾因應有關的研究報告，取消在全球進行羥氯喹臨床試驗，但其後已宣布重啟測試。

[theagora]

新加坡研發可穿戴追蹤裝置 將分發予所有國民 05.06.2020 13:28

新加坡政府正研發可穿戴的裝置，用作追蹤曾經接觸新型冠狀病毒確診者。外交部長維文表示成功研發後會派發給全國570萬人，相信能更好地保障國民健康。當局早前已經研發一個手機應用程式，對曾接觸過患者的人作出警示和追蹤，維文指由於程序不能在所有手機上應用，因此不考慮強制下載，改為研發可穿戴的追蹤裝置。

[theagora]

歐盟點名中俄散播假訊息 2020/06/11

【有線新聞】歐盟指控中國和俄羅斯在疫情期間，散播不實訊息。

歐盟外交與安全政策高級代表博雷利稱：「新型冠狀病毒大流行伴隨大規模假資訊，我們目睹一系列虛假和誤導訊息、騙局和陰謀論，以及外國人員的針對性行動，部分旨在損害歐盟及其成員國，試圖間中侵蝕我們的民主、歐盟和國際組織的信譽。」

歐盟委員會副主席堯羅娃表示，必須採取行動，又呼籲Facebook和Twitter等社交平台加強對付假消息。

歐洲多國下星期起就陸續重開邊境，德國下星期一起，取消對瑞士、法國、奧地利和丹麥實施的邊境管制，由這些國家入境德國的人，毋須隔離檢疫。奧地利下星期二起亦會向31個歐洲國家開放邊境，但不包括西班牙、葡萄牙、瑞典和英國。希臘下星期會讓遊客飛到首都雅典，和第二大城市塞薩洛尼基。

_{View in Slack}

[theagora]

海上滯留逾百日 中國船員歸國無期? 2020/06/10

一名滯留在英國多佛爾對開海面郵輪的中國船員，近日在網上發文求助。她表示在海上已經漂泊100多天，至今仍不能下船，在郵輪上同一遭遇的還有超過300多名中國船員。該船員表示，他們工作的郵輪3月中去到美國邁阿密，因疫情而暫停服務，遊客全部落船離去，但中國籍船員一直無人安排離開，只好留在船上，她形容「感覺在坐牢」。

文中指，船公司分別在3月尾及5月中，兩次安排包機打算送中國船員回國，不過包機最終取消了。郵輪去到英國的多佛爾，公司再安排一班包機準備在6月9日起飛，但最終都要取消。多次包機都不能成事原因只有一個，就是中國方面沒有發出降落許可。

求助的不止她一人，隨著內地疫情逐漸緩和，滯留海上的中國船員，都心急何時才可以回家。有滯留菲律賓海域的船員，指船上剛剛傳出有人確診，但他們連口罩等防護物資都沒有，致電大使館得到的回覆是「幫不了」，覺得海員似是被忽視。

內地傳媒《第一財經》報道，截至3月底，有約8萬名中國船員仍然在國際航行船舶上工作，當中近1萬名船員的勞工合約在5月底到期。交通運輸部及外交部等6個部門在4月底曾發表通告，要求駐外使領館做好領事保護工作，研究以適當方式安排身處困境的中國籍船員回國。

_{View in Slack}

[demosisto]

The impact of super-spreaders in COVID-19: mapping genome variation worldwide 19 May, 2020 | Pre-Peer Review / Pre-Print Alberto Gomez-Carballa, Xabier Bello, Jacobo Pardo-Seco, Federico Martinon-Torres, Antonio Salas

Abstract The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effects, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent.

[demosisto]

COVID-19 Deaths: Which Explanatory Variables Matter the Most? 11 Jun, 2020 | Pre-Peer Review / Pre-Print Pete Riley, Allison Riley, James Turtle, Michal Ben-Nun

Abstract As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spreads around the World, many questions about the disease are being answered; however, many more remain poorly understood. Although the situation is rapidly evolving, with datasets being continually corrected or updated, it is crucial to understand what factors may be driving transmission through different populations. While studies are beginning to highlight specific parameters that may be playing a role, few have attempted to thoroughly estimate the relative importance of these disparate variables that likely include: climate, population demographics, and imposed state interventions. In this report, we compiled a database of more than 28 potentially explanatory variables for each of the 50 U.S. states through early May 2020. Using a combination of traditional statistical and modern machine learning approaches, we identified those variables that were the most statistically significant, and, those that were the most important. These variables were chosen to be fiduciaries of a range of possible drivers for COVID-19 deaths in the USA. We found that population-weighted density (PWD), some "stay at home" metrics, monthly temperature and precipitation, race/ethnicity, and chronic low respiratory death rate, were all statistically significant. Of these, PWD and mobility metrics dominated. This suggests that the biggest impact on COVID-19 deaths was, at least initially, a function of where you lived, and not what you did. However, clearly, increasing social distancing has the net effect of (at least temporarily) reducing the effective PWD. Our results strongly support the idea that the loosening of "lock-down" orders should be tailored to the local PWD. In contrast to these variables, while still statistically significant, race/ethnicity, health, and climate effects could only account for a few percent of the variability in deaths. Where associations were anticipated but were not found, we discuss how limitations in the parameters chosen may mask a contribution that might otherwise be present.

[demosisto]

Asymptomatic and presymptomatic transmission of SARS-CoV-2: A systematic review 11 Jun, 2020 | Pre-Peer Review / Pre-Print Christina Savvides, Robert Siegel

Abstract Many of the statutes comprising the shelter-in-place and phased-reopening orders are centered around minimizing asymptomatic and presymptomatic transmission. Assumptions about the presence and relative importance of asymptomatic and presymptomatic transmission are based on case reports, the failing of quarantine measures aimed at sequestering ill patients, viral dynamic studies suggesting SARS-CoV-2 production peaks before symptoms appear, and modeling evidence that calculates serial interval between successive generations of infection. In aggregate, these data offer compelling evidence of presymptomatic and asymptomatic transmission, but individually these studies have notable shortcomings that undermine their conclusions. Conducting high quality studies with the aim of understanding the relative role of presymptomatic and asymptomatic transmission is instrumental to developing the most informed policies on reopening our cities, states, and countries. To that end, the purpose of this systemic review is to discuss the literature of asymptomatic and presymptomatic transmission, highlight limitations of recent studies, and propose experiments that, if conducted, would provide a more definitive analysis of the relative role of presymptomatic and asymptomatic transmission in the ongoing SARS-CoV-2 pandemic.

[theagora]

Coronavirus: Chinese activists held for posting censored articles to face trial on criminal charges

by Guo Rui, SCMP, 14 Jun, 2020

• Chen Mei and Cai Wei have been in detention since April but case is expected to go to court soon
• Activists ran online project that published material about sensitive issues like #MeToo movement, eviction of migrant workers in Beijing

Two Chinese activists who have been detained for almost two months for sharing censored material about the early days of the coronavirus outbreak are set to face trial on criminal charges, a family member said. ......

_{View in Slack}

[theagora]

British scientists bypass drug giants to sell potential coronavirus vaccine

by Sarah Shearman, Thomson Reuters Foundation, 9 Jun, 2020

LONDON, June 8 (Thomson Reuters Foundation) - A team of British scientists developing a coronavirus vaccine has set up a special company to distribute it if they are successful, rather than partnering with a big pharmaceutical company, to ensure access for the world’s poorest.

The scientists from London’s Imperial College hope to bring a low-cost vaccine to the world early next year via a social enterprise — a company that seeks to do good as well as making a profit. ......

_{View in Slack}

[theagora]

習近平指會以疫苗援助非洲國家 2020/06/18

【有線新聞】習近平在中非團結抗疫特別峰會上，表示會提前在今年內動工興建非洲疾控中心總部，加快中非友好醫院建設，和中非對口醫院合作，承諾新型肺炎疫苗研發完成，並投入使用後率先惠及非洲國家。

習近平指中方會免除非洲國家，截至2020年底到期的對華無息貸款債務。同國際社會一齊，對疫情特別重、壓力特別大的非洲國家，進一步延長緩債期限。

外交學院國際關係研究所教授周永生表示今次峰會並非要修補之前抗疫期間，廣州當局收取非洲人護照而引發的非洲國家抗議。「因為初期對於那些不按規定來做，違犯防疫制度的非洲人，收取他們的護照，最後很快廣州地方當局，把暫時扣押的護照還給他們了。不用修補(關係)，那事件並不大，規模也很小，只不過被媒體炒作起來，講得好像影響比較大。」

[theagora]

中疾控：疫情已受控 2020/06/18

【有線新聞】北京疫情自上周四開始反彈後，每日持續出現多宗新增個案，截至周三已累計有158例，但中國疾控中心專家認為這次疫情已經受到控制：「每天新診斷的報告病例不等於是新感染的。周三確診的21個人基本上都是在6月12號前感染，初步估計高峰是發生在6月13號。疫情控制住了，不是說明天就不會報告新增病例，這些報告病例都是對既往感染病例的檢測發現過程。」

他指中疾控經初步分析，發現來自新發地市場的病例中，賣水產的檔主數量最多，發病時間亦為最早，環境採樣結果亦顯示水產大廳污染比較嚴重。他提出去年疫情同樣是最先於武漢華南海鮮市場發生，雖然當時將矛頭放在野生動物，但這次北京的分析結果為病毒來源提供新的方向。至於為甚麼海鮮市場會產生可能的傳染源頭，他估計有機會源於海鮮涉及到水和冰凍，溫度較低，濕度較高，比較適合病毒存活，但實際的基理尚要再進一步研究。

而為防疫情擴散，北京市進一步嚴格管控，禁止確診、疑似病例、密切接觸者和自5月30日以來曾去過新發地市場的人離開及進入北京，但強調不是封城。入境進京人員亦會繼續實行閉環管理，14天集中和居家觀察，賓館酒店亦禁止接待14天內從屬於中高風險的外省市區返京的人員入住。

住在西城區的唐先生，是北京這波疫情的第一個確診者，但他沒有被責難，反而大獲官方好評。原因是他可以明確講出過去2周中所接觸的每一個人，提供了一份38人的詳細名單，又準確列出此前10天去過哪些地方，網民稱他是「最強大腦」。

北京社區衛生首席專家吳浩就說，他發現徵狀後，主動地騎車醫療機構就診，是保護易感人群的一個重要手段，再配合大數據分析，成功找出相關的風險人群。他說，唐先生幫助他們快速收窄病毒源頭，並鎖定在新發地市場，為疫情響起第一聲警報。

[demosisto]

Germany completely open sourced their decentralised Coronavirus Tracing App for anyone to analyse and improve.	Website	Github
coronawarn.app	github.com/corona-warn-app

[demosisto]

A FRACTAL VIEWPOINT TO COVID-19 INFECTION 3 Jun, 2020 | Pre-Peer Review / Pre-Print Oscar Sotolongo-Costa, José Weberszpil, Oscar Sotolongo-Grau

Abstract One of the central tools to control the COVID-19 pandemics is the knowledge of its spreading dynamics. Here we develop a fractal model capable of describe this dynamics, in term of daily new cases, and provide quantitative criteria for some predictions. We propose a fractal dynamical model using conformed derivative and fractal time scale. A Burr-XII shaped solution of the fractal-like equation is obtained. The model is tested using data from several countries, showing that a single function is able to describe very different shapes of the outbreak. The diverse behavior of the outbreak on those countries is presented and discussed. Moreover, a criterion to determine the existence of the pandemic peak and a expression to find the time to reach herd immunity are also obtained.

[demosisto]

On Reliability of the COVID-19 Forecasts 1 Jun, 2020 | Pre-Peer Review / Pre-Print Hemanta Kumar Baruah

Abstract In this expository article, we are aiming to show with an example that even short term forecasts regarding the COVID-19 spread pattern may sometimes not be very reliable. We have studied data published by Worldometers.info to get numerically an approximate formula of the spread pattern for a short period. We have observed that in the United States of America, there was a nearly exponential spread pattern for a very short period from May 3 to May 8, 2020. From May 9 to May 13, the nearly exponential character of the spread was found to be absent. Hence it can be concluded that the COVID-19 spread pattern, even after more than four months from the start of the outbreak, is not quite predictable. Therefore even short term forecasts regarding the spread may not be very reliable. We have found that forecasts using the assumption of an exponential pattern of spread may actually lead to overestimation.

[demosisto]

Early epidemic spread, percolation and Covid-19 11 Jun, 2020 | Pre-Print Goncalo Oliveira

Abstract Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between individuals, the vertices. This article attempts to account for the case when each individual entails in different kinds of interactions which have therefore different probabilities of transmitting the disease. The majority of these results can be also stated in the language of percolation theory. The main contributions of the article are: (1) Extend to this setting some results which were previously known in the case when each individual has only one kind of interactions. (2) Find an explicit formula for the basic reproduction number $R_0$ which depends only on the probabilities of transmitting the disease along the different edges and the first two moments of the degree distributions of the associated graphs. (3) Motivated by the recent Covid-19 pandemic, we use the framework developed to compute the $R_0$ of a model disease spreading in populations whose trees and degree distributions are adjusted to several different countries. In this setting, we shall also compute the probability that the outbreak will not lead to an epidemic. In all cases we find such probability to be very low if no interventions are put in place.

[theagora]

Trial of Oxford COVID-19 vaccine in South Africa begins 23 Jun, 2020, University of Oxford

The first clinical trial in South Africa and on the continent for a COVID-19 vaccine was announced today, 23 June, at a virtual press conference hosted by the University of the Witwatersrand, Johannesburg (Wits).

Wits University is collaborating with the University of Oxford and the Oxford Vaccine Group on the South African trial. The South African Ox1Cov-19 Vaccine VIDA-Trial aims to find a vaccine that will prevent infection by SARS-CoV-2, the virus that causes COVID-19. The technical name of the vaccine is ChAdOx1 nCoV-19, as it is made from a virus called ChAdOx1, which is a weakened and non-replicating version of a common cold virus (adenovirus). The vaccine has been engineered to express the SARS-CoV-2 spike protein.

The vaccine was developed at the University of Oxford’s Oxford Jenner Institute and is currently on trial in the UK, where over 4,000 participants are already enrolled into the clinical trial and enrolment of an additional 10, 000 participants is planned. ......

_{View in Slack}

[theagora]

七一遊行遭警反對　區議員徐子見：恐歷史寫「國安法在無遊行反對下通過」 【明報港聞】2020年6月26日

一批民主派區議員發起下周日（28日）或7月1日（下周三）遊行，反對「港區國安法」，計劃由銅鑼灣遊行至中環遮打花園。警方今早（26日）向有份發起遊行的東區區議員徐子見發出反對通知書，兩日遊行的申請均遭反對。徐子見對此表示憤怒，「國安法通過前無人搞遊行，若國安法在七一前通過，恐怕歷史上會寫『國安法在無遊行反對下獲得通過』。」他表明一定會上訴，希望爭取七一前成功舉辦遊行。

徐子見向本報表示，警方以兩大理由反對舉辦遊行，包括新型冠狀病毒疫情和「限聚令」；以及過去遊行及他們申請的遊行路線、例如灣仔地鐵站，過去曾出現暴力情況。

徐子見昨日（25日）表示，今次舉辦的是和平遊行，知道限聚令仍然生效，申請時已告知警方，遊行會以35人一組，每35秒才放行一組，大會亦會提供口罩及搓手液予遊行參加者。

_{View in Slack}

[theagora]

美國疾控中心推算全國實際感染人數或逾二千萬 2020/06/26 【Now新聞台】美國新冠病毒單日新增病例數目再創新高，多個州的疫情反彈，其中得州暫停進一步重啟經濟，疾病控制及預防中心推算全國實際感染人數，可能比累計確診個案多十倍，即有二千多萬人已受感染。 綜合美國各州衞生部門統計，全國周四再多三萬九千多人確診感染新型冠狀病毒，是單日新增紀錄新高。多個州都增幅顯著，包括率先重啟經濟的得州，連續三日錄得逾五千宗新增病例，留院人數連日刷新紀錄。 為減慢病毒傳播，州長阿博特宣布暫停進一步重啟經濟，已獲准重開的企業，可以在現有客流限制下繼續營業。他又要求部分地區的醫院推遲非緊急的手術，騰出醫療資源，並要求民眾戴口罩及保持社交距離。 佛羅里達州亦錄得逾五千宗新增病例，州長德桑蒂斯表示患者例包括不少年輕人，呼籲民眾要戴口罩。 亞利桑那州過去一周有近四分一接受病毒檢測的人，結果呈陽性。 美國目前約有250萬人確診，但疾病控制及預防中心根據在全國進行的新冠病毒抗體測試結果，推算實際感染人數可能比目前累計個案多十倍，即有二千多萬人曾感染病毒，不過只佔全國人口約百分之六，又遠遠未達致群體免疫。 美國政府轄下監察機構政府問責局發表報告，指特朗普政府在應對新冠疫情和相應的經濟危機方面準備不足，並且缺乏完整而連貫的病毒檢測數據，導致疫情防控更困難，亦令地方難以下決定是否重開經濟。 白宮經濟顧問庫德洛就表明，不會再因為疫情而停止經濟活動。

_{View in Slack}

[theagora]

Modeling herd immunity H. Holden Thorp, Valda Vinson, and Caroline Ash | 23 June, 2020

Today, Science published a study by Britton et al. that incorporates population heterogeneity into modeling the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—that is, it accounts for the fact that members of a population may have differential exposure and susceptibility to infection. In this model, the authors vary the extent of mobility and the susceptibility to infection by age. These heterogeneities lead to a decrease in the percentage of the population that must be infected to achieve herd immunity, the condition in which a threshold proportion of immune individuals should lead to a decline in the incidence of infection. The authors are very careful to point out that this is just a model that is highly dependent on their assumptions.

The prevailing assumption in the public discourse is that herd immunity will require 60% of the population to be infected. This estimate is based on the reproductive number (R0), which is the number of cases, on average, that an infected person will cause during their infection period. It is calculated as 1 – 1/R0, and for SARS-CoV-2, the authors use a value of R0 = 2.5. Using the parameters that Britton et al. put in their model, the effective herd immunity threshold is reduced to 43%. The last sentence of the abstract is worth emphasizing: “Our estimates should be interpreted as an illustration of how population heterogeneity affects herd immunity, rather than an exact value or even a best estimate.” ......

_{View in Slack}

[theagora]

An Open Letter from Daniel O’Day, Chairman & CEO, Gilead Sciences Daniel O’Day | June 22, 2020

After receiving the green light from the FDA to move forward, Gilead is about to start trials of an inhaled version of remdesivir. We will screen healthy volunteers for Phase 1 trials this week and hope to begin studies in patients with COVID-19 in August. If the trials are successful, this could represent important progress. Remdesivir, our investigational antiviral medicine, is currently given to patients intravenously through daily infusions in the hospital. An inhaled formulation would be given through a nebulizer, which could potentially allow for easier administration outside the hospital, at earlier stages of disease. That could have significant implications in helping to stem the tide of the pandemic. ......

_{View in Slack}

[demosisto]

Behavioral changes before lockdown, and decreased retail and recreation mobility during lockdown, contributed most to the successful control of the COVID-19 epidemic in 35 Western countries 20 Jun, 2020 | Pre-Print Koen Deforche, Jurgen Vercauteren, Viktor Müller, Anne-Mieke Vandamme

Abstract The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus. This resulted in curbing the epidemic by reducing the time-varying basic reproduction number (Rt) to below one. Governments are looking for evidence to balance the demand of their citizens to ease some of the restriction, against the fear of a second peak in infections. More details on the specific circumstances that promote exponential spread (i.e. Rt>1) and the measures that contributed most to a reduction in Rt are needed. Here we show that in 33 of 35 Western countries (32 European, plus Israel, USA and Canada), Rt fell to around or below one during lockdown (March - May 2020). One third of the effect happened already on average 6 days before the lockdown, with lockdown itself causing another major drop in transmission. Country-wide compulsory usage of masks was implemented only in Slovakia 10 days into lockdown, and on its own reduced transmission by half. During lockdown, decreased mobility in retail and recreation was an independent predictor of lower Rt during lockdown, while changes in other types of mobility were not. These results are consistent with anecdotal evidence that large recreational gatherings are super-spreading events, and may even suggest that infections during day-to-day contact at work are not sufficient to spark exponential growth. Our data suggest measures that will contribute to avoiding a second peak include a tight control on circumstances that facilitate massive spread such as large gatherings especially indoors, physical distancing, and mask use.

[demosisto]

Citizen Scientists Create an Exascale Computer to Combat COVID-19 27 Jun 2020 | Pre-Print Maxwell I. Zimmerman, et al.

Abstract The SARS-CoV-2/COVID-19 pandemic continues to threaten global health and socioeconomic stability. Experiments have revealed snapshots of many of the viral components but remain blind to moving parts of these molecular machines. To capture these essential processes, over a million citizen scientists have banded together through the Folding@home distributed computing project to create the worlds first Exascale computer and simulate protein dynamics. An unprecedented 0.1 seconds of simulation of the viral proteome reveal how the spike complex uses conformational masking to evade an immune response, conformational changes implicated in the function of other viral proteins, and "cryptic" pockets that are absent in experimental snapshots. These structures and mechanistic insights present new targets for the design of therapeutics. This living document will be updated as we perform further analysis and make the data publicly accessible.

[theagora]

How can airborne transmission of COVID-19 indoors be minimised? Lidia Morawska, et al. | 27 May 2020 Abstract During the rapid rise in COVID-19 illnesses and deaths globally, and notwithstanding recommended precautions, questions are voiced about routes of transmission for this pandemic disease. Inhaling small airborne droplets is probable as a third route of infection, in addition to more widely recognized transmission via larger respiratory droplets and direct contact with infected people or contaminated surfaces. While uncertainties remain regarding the relative contributions of the different transmission pathways, we argue that existing evidence is sufficiently strong to warrant engineering controls targeting airborne transmission as part of an overall strategy to limit infection risk indoors. Appropriate building engineering controls include sufficient and effective ventilation, possibly enhanced by particle filtration and air disinfection, avoiding air recirculation and avoiding overcrowding. Often, such measures can be easily implemented and without much cost, but if only they are recognised as significant in contributing to infection control goals. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public.

_{View in Slack}

[theagora]

China found Covid-like virus in 2013 and kept it stored in Wuhan lab

As World Health Organisation scientists prepare to enter China on the trail of the coronavirus, an Insight investigation reveals that an almost identical virus had been stored in a Wuhan lab since 2013

The world’s closest known match to the Covid-19 virus was found seven years ago by Chinese scientists in an abandoned mine where it was linked to deaths caused by a coronavirus-type respiratory illness.

An investigation by The Sunday Times has found evidence that China has failed to publicly share this crucial information about the sister virus to Covid-19, even though it is the strongest lead in the hunt for the origin of the pandemic.

The “new strain” of coronavirus, which was discovered in the mine in 2013, has been stored for years at a virology lab in the Chinese city of Wuhan, where the Covid-19 pandemic started at the end of last year. ...

_{View in Slack}

[demosisto]

An Epidemic Model SIPHERD and its application for prediction of the spread of COVID-19 infection in India 25 Jun, 2020 | Pre-Print Ashutosh Mahajan, Ravi Solanki, Namitha Sivadas

Abstract After originating from Wuhan, China, in late 2019, with a gradual spread in the last few months, COVID-19 has become a pandemic crossing 9 million confirmed positive cases and 450 thousand deaths. India is not only an overpopulated country but has a high population density as well, and at present, a high-risk nation where COVID-19 infection can go out of control. In this paper, we employ a compartmental epidemic model SIPHERD for COVID-19 and predict the total number of confirmed, active and death cases, and daily new cases. We analyze the impact of lockdown and the number of tests conducted per day on the prediction and bring out the scenarios in which the infection can be controlled faster. Our findings indicate that increasing the tests per day at a rapid pace (10k per day increase), stringent measures on social-distancing for the coming months and strict lockdown in the month of July all have a significant impact on the disease spread.

[theagora]

Trial of Oxford COVID-19 vaccine in South Africa begins 23 Jun, 2020, University of Oxford

Trial of Oxford COVID-19 vaccine starts in Brazil 26 Jun, 2020, University of Oxford

Volunteers have begun taking part in Latin America’s first clinical trial for a vaccine against COVID-19.

Volunteers in Brazil have begun receiving a trial vaccine against COVID-19, in Latin America’s first phase 3 COVID-19 clinical trial.

The trial officially began on Saturday 20th June and will enrol 5,000 volunteers across the country. Vaccinations will take place in Sao Paulo, Rio de Janeiro and a site in the Northeast of Brazil.

The Brazilian Health Regulatory Agency (ANVISA) approved the inclusion of Brazil in the clinical trials on 2nd June, which are being conducted in partnership with AstraZeneca. The trial is being sponsored entirely by Brazilian entrepreneurs. ......

[theagora]

Your Mask Cuts Own Risk by 65 Percent Rick Kushman, UC Davis | July 6, 2020

Scientific evidence is clear: Social distancing and wearing masks help prevent people from spreading COVID-19, and masks also protect those who wear them, two UC Davis Health experts said on UC Davis LIVE: COVID-19.

A range of new research on face coverings shows that the risk of infection to the wearer is decreased by 65 percent, said Dean Blumberg, chief of pediatric infectious diseases at UC Davis Children’s Hospital. ...... Transmission by droplets There are two primary methods of transmission, they said. The first is via droplets a carrier expels, which are about one-third the size of a human hair but still large enough that we can see them. Masks create an effective barrier against droplets. ...... Transmission by aerosol particles The second major transmission method is via the aerosol particles we expel when we talk. Those are about 1/100th the size of a human hair and are more difficult to defend against. Social distancing and staying outdoors, where there is more air flow, are helpful, Blumberg and Ristenpart said. ......

_{View in Slack}

[theagora]

Working memory capacity predicts individual differences in social-distancing compliance during the COVID-19 pandemic in the United States Weizhen Xie, Stephen Campbell, Weiwei Zhang | July 10, 2020 Abstract Noncompliance with social distancing during the early stage of the coronavirus disease 2019 (COVID-19) pandemic poses a great challenge to the public health system. These noncompliance behaviors partly reflect people’s concerns for the inherent costs of social distancing while discounting its public health benefits. We propose that this oversight may be associated with the limitation in one’s mental capacity to simultaneously retain multiple pieces of information in working memory (WM) for rational decision making that leads to social-distancing compliance. We tested this hypothesis in 850 United States residents during the first 2 wk following the presidential declaration of national emergency because of the COVID-19 pandemic. We found that participants’ social-distancing compliance at this initial stage could be predicted by individual differences in WM capacity, partly due to increased awareness of benefits over costs of social distancing among higher WM capacity individuals. Critically, the unique contribution of WM capacity to the individual differences in social-distancing compliance could not be explained by other psychological and socioeconomic factors (e.g., moods, personality, education, and income levels). Furthermore, the critical role of WM capacity in social-distancing compliance can be generalized to the compliance with another set of rules for social interactions, namely the fairness norm, in Western cultures. Collectively, our data reveal contributions of a core cognitive process underlying social-distancing compliance during the early stage of the COVID-19 pandemic, highlighting a potential cognitive venue for developing strategies to mitigate a public health crisis.

_{View in Slack}

[theagora]

Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19) W. Joost Wiersinga, et al. | July 10, 2020 Abstract SARS-CoV-2 is spread primarily via respiratory droplets during close face-to-face contact. Infection can be spread by asymptomatic, presymptomatic, and symptomatic carriers. The average time from exposure to symptom onset is 5 days, and 97.5% of people who develop symptoms do so within 11.5 days. The most common symptoms are fever, dry cough, and shortness of breath. Radiographic and laboratory abnormalities, such as lymphopenia and elevated lactate dehydrogenase, are common, but nonspecific. Diagnosis is made by detection of SARS-CoV-2 via reverse transcription polymerase chain reaction testing, although false-negative test results may occur in up to 20% to 67% of patients; however, this is dependent on the quality and timing of testing. Manifestations of COVID-19 include asymptomatic carriers and fulminant disease characterized by sepsis and acute respiratory failure. Approximately 5% of patients with COVID-19, and 20% of those hospitalized, experience severe symptoms necessitating intensive care. More than 75% of patients hospitalized with COVID-19 require supplemental oxygen. Treatment for individuals with COVID-19 includes best practices for supportive management of acute hypoxic respiratory failure. Emerging data indicate that dexamethasone therapy reduces 28-day mortality in patients requiring supplemental oxygen compared with usual care (21.6% vs 24.6%; age-adjusted rate ratio, 0.83 [95% CI, 0.74-0.92]) and that remdesivir improves time to recovery (hospital discharge or no supplemental oxygen requirement) from 15 to 11 days. In a randomized trial of 103 patients with COVID-19, convalescent plasma did not shorten time to recovery. Ongoing trials are testing antiviral therapies, immune modulators, and anticoagulants. The case-fatality rate for COVID-19 varies markedly by age, ranging from 0.3 deaths per 1000 cases among patients aged 5 to 17 years to 304.9 deaths per 1000 cases among patients aged 85 years or older in the US. Among patients hospitalized in the intensive care unit, the case fatality is up to 40%. At least 120 SARS-CoV-2 vaccines are under development. Until an effective vaccine is available, the primary methods to reduce spread are face masks, social distancing, and contact tracing. Monoclonal antibodies and hyperimmune globulin may provide additional preventive strategies.

_{View in Slack}

[demosisto]

A seven-day cycle in COVID-19 infection and mortality rates: Are inter-generational social interactions on the weekends killing susceptible people? 3 May, 2020 | Pre-Print Itay Ricon-Becker, et al.

Abstract We observed a significant seven-day cycle in (i) reported COVID-19 new cases (in 7/12 countries), and in (ii) reported COVID-19 deaths (in 7/12 countries), based on data from the 12 developed North-American and European countries that reported more than 1,000 deaths by April 28th (Spain, Italy and Switzerland, Belgium, Canada and the USA, Germany, the Netherlands, Sweden and the UK). Daily reported numbers (March 29th to April 28th) are based on Our World in Data database (derived from the European Center for Disease Control and Prevention, ECDC). In all seven countries, numbers of new cases peaked on Thursday-Friday, five days after the weekend, corresponding with a reported ~5-day lag between contact with an infected person and the manifestation of clinical symptoms. Death tolls peaked on Wednesday-Thursday in all seven countries, ~12-14 days following a weekend, corresponding with the reported median of 14-day hospitalization before death. One may suspect that the weekend restricts the availability of testing or reporting of new cases, that are eventually reported during the following week. However, to completely account for both observations, this artifact should occur uniformly in all the above-mentioned countries and consistently along the entire month studied. Moreover, deaths are defined events and seems less likely to be recorded or reported inaccurately, at least for the vast majority of cases. Thus, we hypothesize that an increase in inter-generational social interactions occurs during the weekend, which facilitates transfer of COVID-19 from younger people to older vulnerable individuals. These and additional infected older people account for most recognized COVID-19 cases and deaths, which may occur at regular time intervals, specifically in this vulnerable population. Additional explanations may include weekly rhythms in immune functions, hospital care quality, or other various health-related behaviors. Our hypotheses should be re-tested and refined based on databases that accurately report events times when these will become available.

[demosisto]

SARS-CoV-2 transmission chains from genetic data: a Danish case study 29 May, 2020 | Pre-Print Andreas Bluhm, et al.

Abstract Background The COVID-19 pandemic caused by the SARS-CoV-2 virus started in China in December 2019 and has since spread globally. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Denmark is currently opening up after a lockdown in mid-March. Methods We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries. Result Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark and in at least one case find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes is stable after lockdown. Conclusion Our work shows how genetic data can be used to identify routes of introduction of a virus into a region and provide alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission chains suggesting that Denmark was part of a network of countries among which the virus was being transmitted; thus challenging the common narrative that Denmark only got infected from abroad. Our analysis does not indicate that the major haplotypes appearing in Denmark have a different degree of virality. Our methods can be applied to other countries, regions or even highly localised outbreaks. When used in real-time, we believe they can serve to identify transmission events and supplement traditional methods such as contact tracing.

[theagora]

Children and COVID-19 July 2, 2020

Worldwide, relatively few children have been reported with COVID-19, the disease caused by the novel coronavirus. Data from the Netherlands also confirms the current understanding: that children play a minor role in the spread of the novel coronavirus. The virus is mainly spread between adults and from adult family members to children. The spread of COVID-19 among children or from children to adults is less common.

Since children play a minor role in the spread of the virus, the 1.5 metre measure is less strict for young children:

• Children up to and including 12 years of age do not have to keep 1.5 metres apart from each other and from adults. This also applies to childcare and primary education.
• Young people aged 13 until 18 years old (i.e. 17 years old and younger) do not have to stay 1.5 metres apart from each other. In secondary schools, this applies to all pupils, regardless of their age.
• In secondary vocational education (MBO) and higher education, all students should stay 1.5 metres apart, regardless of their age
• Since adults play a greater role in the spread of the novel coronavirus, teachers need to stay 1.5 metres apart from others as often as possible.

Younger children with nasal colds symptoms are allowed to attend childcare and primary school Children aged 0 to 4 years old with cold symptoms (runny nose, nasal cold, sneezing and sore throat) are allowed to go to the childcare centre or host parent, as long as they do not have a fever. Similarly, children in group 1 or 2 of primary school with cold symptoms may go to school and to after-school childcare, as long as they do not have a fever. ......

_{View in Slack}

[theagora]

Hypothesis to explain the severe form of COVID-19 in Northern Italy Luca Cegolon, et al. | June, 2020

Summary

What is already known about this subject?

• Human coronaviruses are known to cause respiratory re-infections, regardless of pre-existing humoural immunity.
• There is evidence suggesting that severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) had been circulating in Italy before the first COVID-19 case was detected in the country.

What are the new findings?

• Prior infections with SARS-CoV-2 (or other viruses/coronaviruses) may arguably predispose to more severe forms of the disease following re-infection with SARS-CoV-2, with an immunological mechanism known as Antibody-Dependent-Enhancement, already observed with infections sustained by other coronaviruses (MERS-CoV and SARS-CoV) or other viruses such as the West Nile Virus and Dengue.

What are the recommendations for policy and practice?

• If confirmed by in vivo studies, this hypothesis may have relevant implications for the treatment of severe forms of COVID-19, yet the possibility to produce an effective vaccine against SARS-CoV-2 might be hampered.

_{View in Slack}

[theagora]

COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? Antonio De Maio and Lawrence E. Hightower | May 18, 2020 ...... The first SARS virus, SARS-CoV, also appeared in China and spread to at least 29 countries during 2002–2003. The most frequent cause of death from this virus was respiratory insufficiency with subsequent respiratory failure. What little we know about SARS-CoV-2 is based mainly on SARS-CoV and a small number of other animal coronaviruses. These viruses cause damage to tissues and organs of the infected host by direct infection of target cells or indirectly by prolonged activation of host defense responses. The virus has been detected in the lungs and immune cells of patients who have succumbed to the infection, consistent with direct injury to the pulmonary tissue and activation of the immune response. Activation of the innate immune system stimulates the production of chemokines and cytokines as part of the inflammatory defense response. As a result, neutrophils and macrophages, among other immune system cells, are drawn to infected tissues. Macrophage activation is accompanied by the release of more chemokines creating a two-edged sword capable of both killing virus-infected cells and damaging normal host tissues (reviewed in Perlman and Dandekar 2005). If these activated leukocytes remained at the site of lung infection, the lethality of SARS-CoV-2 virus likely would be lower, but unfortunately, both the chemokine/cytokine “storm” and infected/activated leukocytes released into the circulation by damaged lung tissue affect several organs, of which the brain, kidneys, and heart are particularly susceptible (Huang et al. 2005). Leukocyte extravasation has drug targets that should be explored for COVID-19 patients. As we will discuss in more detail, proteins of the infecting coronavirus interfere with these host responses, possibly causing imbalances that result in immunopathogenesis. ......

_{View in Slack}

[theagora]

What is the evidence to support the 2-metre social distancing rule to reduce COVID-19 transmission? Zeshan Qureshi, et al. | June 22, 2020 VERDICT

• The 2-metre social distancing rule assumes that the dominant routes of transmission of SARS-CoV-2 are via respiratory large droplets falling on others or surfaces.
• A one-size-fits-all 2-metre social distancing rule is not consistent with the underlying science of exhalations and indoor air. Such rules are based on an over-simplistic picture of viral transfer, which assume a clear dichotomy between large droplets and small airborne droplets emitted in isolation without accounting for the exhaled air. The reality involves a continuum of droplet sizes and an important role of the exhaled air that carries them.
• Smaller airborne droplets laden with SARS-CoV-2 may spread up to 8 metres concentrated in exhaled air from infected individuals, even without background ventilation or airflow. Whilst there is limited direct evidence that live SARS-CoV-2 is significantly spread via this route, there is no direct evidence that it is not spread this way.
• The risk of SARS-CoV-2 transmission falls as physical distance between people increases, so relaxing the distancing rules, particularly for indoor settings, might therefore risk an increase in infection rates. In some settings, even 2 metres may be too close.
• Safe transmission mitigation measures depend on multiple factors related to both the individual and the environment, including viral load, duration of exposure, number of individuals, indoor versus outdoor settings, level of ventilation and whether face coverings are worn.
• Social distancing should be adapted and used alongside other strategies to reduce transmission, such as air hygiene, involving in part maximizing and adapting ventilation to specific indoor spaces, effective hand washing, regular surface cleaning, face coverings where appropriate and prompt isolation of affected individuals.

  _{View in Slack}

[theagora]

The pandemic virus is slowly mutating. But is it getting more dangerous? Kai Kupferschmidt | July 14, 2020

It’s only a tiny change. At some point early in the pandemic, one of the 30,000 letters in the genome of SARS-CoV-2 changed from an A to a G. Today, that mutation, at position 23,403, has spread around the world. It is found in the vast majority of newly sequenced viruses and has become the center of a burning scientific question: Has the mutation become so common because it helps the virus spread faster? Or is it just coincidence?

More than 6 months into the pandemic, the virus’ potential to evolve in a nastier direction—or, if we’re lucky, become more benign—is unclear. In part that’s because it changes more slowly than most other viruses, giving virologists fewer mutations to study. But some virologists also raise an intriguing possibility: that SARS-CoV-2 was already well adapted to humans when it burst onto the world stage at the end of 2019, having quietly honed its ability to infect people beforehand.

On average, the coronavirus accumulates about two changes per month in its genome. Sequencing SARS-CoV-2 genomes helps researchers follow how the virus spreads. Most of the changes don’t affect how the virus behaves, but a few may change the disease’s transmissibility or severity.

One of the earliest candidates was the wholesale deletion of 382 base pairs in a gene called ORF8, whose function is unknown. First reported by Linfa Wang and others at the Duke-NUS Medical School in Singapore in a March preprint, the deletion has since been reported from Taiwan as well. A deletion in the same gene occurred early in the 2003 severe acute respiratory syndrome (SARS) outbreak, caused by a closely related coronavirus; lab experiments later showed that variant replicates less efficiently than its parent, suggesting the mutation may have slowed the SARS epidemic. Cell culture experiments suggest the mutation does not have the same benign effect in SARS-CoV-2, Wang says, “but there are indications that it may cause milder disease in patients.”

Weak evidence of a moderate effect ......

_{View in Slack}

[demosisto]

Detecting Emerging COVID-19 Community Outbreaks at High Spatiotemporal Resolution - New York City, June 2020 18 Jul, 2020 | Pre-Print Sharon K. Greene, Eric R. Peterson, et al.

Abstract To quickly detect hotspots, the New York City Health Department launched a SARS-CoV-2 percent positivity cluster detection system using census tract resolution and the SaTScan prospective Poisson-based space-time scan statistic. Soon after implementation, this system prompted an investigation identifying a gathering with inadequate social distancing where viral transmission likely occurred.

[demosisto]

Recurrent SARS-CoV-2 RNA positivity after COVID-19: A systematic review and meta analysis 19 Jul, 2020 | Pre-Print Mahalul Azam, Rina Sulistana, et al.

Abstract Background: Previous studies reported recurrent SARS CoV2 RNA positivity in individuals who had recovered from COVID 19 infections. However, little is known regarding the systematic review of recurrent SARS-CoV-2 RNA positivity. The current study conducted a systematic review and meta-analysis, aimed to estimate the incidence of recurrent SARS CoV 2 RNA positivity after recovery from COVID 19 and to determine the factors associated with recurrent positivity. Methods: We searched the PubMed, MedRxiv, BioRxiv, the Cochrane Library, ClinicalTrials.gov, and the World Health Organization International Clinical Trials Registry for studies published to June 12, 2020. Studies were reviewed to determine the risk of bias. A random-effects model was used to pool results. Heterogeneity was assessed using I2. Results: Fourteen studies of 2,568 individuals were included. The incidence of recurrent SARS-CoV-2 positivity was 14.81% (95% confidence interval [CI]: 11.44-18.19%). The pooled estimate of the interval from disease onset to recurrence was 35.44 days (95% CI: 32.65-38.24 days), and from the last negative to recurrent positive result was 9.76 days (95% CI: 7.31-12.22 days). Patients with younger age (mean difference [MD]=-2.27, 95% CI: -2.95 to -1.80) and a longer initial illness (MD=8.24 days; 95% CI: 7.54-8.95; I2=98.9%) were more likely to experience recurrent SARS-CoV-2 positivity, while patients with diabetes (RR=0.52; 95% CI: 0.30-0.90; I2=53%), severe disease (RR=0.54; 95% CI: 0.35-0.84; I2=70%), and a low lymphocyte count (RR=0.58; 95% CI: 0.39-0.86; I2=48%) were less likely to experience recurrent SARS CoV 2 positivity. Conclusions: The incidence of recurrent SARS CoV 2 positivity was 14.81%. The estimated interval from disease onset to repeat positivity was 35.44 days, and the estimated interval from the last negative result to recurrent positive result duration was 9.76 days.

[demosisto]

Humoral Response Dynamics Following Infection with SARS-CoV-2 16 Jul, 2020 | Pre-Print Louis Grandjean, Anja Saso, et al.

Abstract Objectives: To understand humoral dynamics following SARS-CoV-2 infection Design Prospective Cohort Study Setting Great Ormond Street Hospital (Central London Paediatric Hospital) Participants 67 healthcare workers aged >18 years who provided monthly serial serological samples from 29th April 2020 until 30th June 2020. Main outcome measures The change in monthly serial antibody titers to SARS-CoV-2 nucleoprotein (N), spike protein and the receptor binding domain of the spike protein. Results The mean estimated half-life of the nucleoprotein antibody was 52 days (95% CI 42-65). The spike and RBD antibody had significantly longer mean half-lives of 81 days (95% CI 61-111) and 83 days (95% CI 55-137) respectively. An ACE-2 receptor competition assay demonstrated significant correlation between the spike and RBD antibody titers and ACE2 receptor blocking in-vitro. The time to a negative nucleoprotein antibody test for 50% of the seropositive population was predicted to be 195 days (95% CI 163-236). Conclusions After SARS-CoV-2 infection, the predicted half-life of nucleoprotein antibody was 52 days with 50% of seropositives becoming seronegative to this antibody at 195 days. Widely used serological tests including the Public Health England endorsed assay that depend on the nucleoprotein antibody will therefore underestimate the true prevalence of infection within a year following the majority of infections.