H5N1

German COVID-19 outbreak traced to restaurant

Via DW Radio News: German COVID-19 outbreak traced to restaurant.

Health officials in the German state of Lower Saxony said Saturday they are investigating a COVID-19 outbreak traced to a restaurant where people allegedly failed to follow hygiene and distancing regulations.   

Authorities said at least 10 people, including the restaurant's owner, were infected with COVID-19 in the rural municipality of Moormerland in Germany's northwestern coastal region of East Frisia. None of the cases have been reported as serious.   

On May 15, the "Alte Scheune" restaurant was celebrating reopening following a year of renovations.  The restaurant's owner told the local newspaper Ostfriesen-Zeitung that he had invited around 40 people who had helped with the renovation to the restaurant, and that the occasion wasn't a party, but rather a "test run" for himself and his team before reopening to the public.   

Handshakes and no masks 

However, Lower Saxony's health minister, Carola Reimann, said Saturday that the "break out of infections at the location was not due to a normal restaurant visit. Instead, a private party was apparently celebrated there." 

Leer district counselor, Matthias Groote, said that "from the information we have, there are indications that coronavirus rules may have been violated on the evening of May 15."  

German media NDR reported statements from guests that night citing violations like people shaking hands, not wearing masks, and disregarding minimum distancing of 2 meters (7 feet) between guests.  

Health officials said that around 70 people who have been in contact with those infected are now in quarantine, and more tests are currently being done.  

COVID-19 is 'still here'  

The owner has maintained that distancing and hygiene regulations were followed, and that people could have been infected before or after the evening of May 15. He added he has closed the restaurant, but plans reopen after his quarantine is over on June 4, and "all the tests come out negative."  

Health minister Reimann said that people need to remain "very vigilant to not jeopardize that big progress of the previous weeks," while emphasizing that COVID-19 is "still here" and people need to "take the situation seriously" and "follow distancing and hygiene measures."

Lower Saxony allowed restaurants to reopen on May 11 under lower occupancy and strict hygiene and distancing guidelines. 

Singapore reports 548 new COVID-19 cases, including 3 Singaporeans or PRs

Via Channel NewsAsia: Singapore reports 548 new COVID-19 cases, including 3 Singaporeans or PRs.

SINGAPORE: Singapore reported 548 new COVID-19 cases as of noon on Sunday (May 24), taking its total number of coronavirus infections to 31,616.   

The vast majority of the new cases are foreign workers living in dormitories, the Ministry of Health (MOH) said in its preliminary daily update.   

Three of the new cases are Singaporeans or permanent residents, MOH said. READ: Inside the SuperStar Gemini cruise ship for foreign workers who've recovered from COVID-19 

MORE PRE-SCHOOL STAFF MEMBERS TEST POSITIVE  

On Saturday, two pre-school staff members were among the 11 community cases reported. One of them, a 24-year-old Filipino woman, works at PCF Sparkletots @ Gambas and the other is a 54-year-old Singaporean woman who works at Shaws Preschool @ Lorong Chuan.  

As of Sunday 12pm, seven pre-school staff members have tested positive for COVID-19, less than one per cent of the 15,300 who have been swabbed so far.     

The mass testing exercise, ahead of pre-schools reopening on Jun 2, is now at the halfway mark, said the Early Childhood Development Agency (ECDA) on Saturday.

COVID-19 conspiracy leak claims ‘pure fabrication’, Wuhan lab chief says

Via the South China Morning Post: Coronavirus conspiracy leak claims ‘pure fabrication’, Wuhan lab chief says. Excerpt:

The head of a top Chinese laboratory dogged by coronavirus conspiracy theories has again rejected suggestions that it leaked the pathogen, saying the institute “had never discovered or kept” the virus before it erupted in central China late last year. 

In an interview with state media on Saturday, Wang Yanyi, director of the Wuhan Institute of Virology, said it was “pure fabrication” that the coronavirus leaked from the lab, leading to the global pandemic. 

Wang said the institute first received a clinical sample of the then unknown pneumonia on December 30. After checking the pathogen, the researchers found it contained a new coronavirus, which is now called Sars-CoV-2, she said. 

“We didn’t have any knowledge before that, nor had we ever encountered, researched or kept the virus. In fact, like everyone else, we didn’t even know the virus existed. How could it have leaked from our lab when we never had it?” Wang told state broadcaster China Global Television Network. 

She also said the institute did not isolate or obtain the live virus of the RaTG-13 bat coronavirus, which shares 96.2 per cent of the genome of Sars-CoV-2. 

Senior American officials have accused the institute, the first in Asia equipped to handle Class 4 pathogens such as Ebola, of being the source of the coronavirus pandemic, which has killed more than 340,000 people around the world.  

US President Donald Trump and Secretary of State Mike Pompeo have both claimed that there is evidence the pathogen is connected to the lab in Wuhan – the city where the disease was first detected late last year.

But the World Health Organisation said Washington had offered no evidence to support the “speculative” claims. 

Some of the speculation is based on an article the institute published in Nature in April 2018, saying it discovered a novel coronavirus originating from bats. 

In February this year, it published another article in Nature saying another novel coronavirus from bats was discovered, and the similarity between this virus and the Sars-CoV-2 is up to 96.2 per cent. 

“Actually, the virus mentioned in the 2018 article wasn’t Sars-CoV-2. The virus in the article mainly causes diarrhoea and death among piglets. It was later named Sads. The genome sequence of Sads is only 50 per cent similar to that of Sars-CoV-2. It’s a rather big difference,” she said. 

The bat coronavirus that had a 96.2 per cent genomic similarity to Sars-CoV-2 was RaTG-13, she said. “From the perspective of many non-professionals, the similarity rate of 96.2 per cent is a very high number. But coronavirus is one of the RNA viruses that have the largest genomes. 

“Take the Sars-CoV-2 for example. Its entire genome contains about 30,000 bases. The difference of a percentage of 3.8 means the difference of over 1,100 nucleotide positions. In the natural world, it takes a long period of time for a virus to naturally evolve and mutate to become Sars-CoV-2.” 

Although the researchers identified the genome sequence of RaTG-13, they did not isolate nor obtain the live virus of RaTG-13. “Thus, there is no possibility of us leaking RaTG-13,” she said. 

Wang said that a team at the institute had been on the trail of the source of Sars – severe acute respiratory syndrome – for many years and had obtained some coronaviruses from bats. 

She said the institute now had three strains of live viruses, including one that was 96 per cent genomically similar to the Sars virus. But their highest similarity to Sars-CoV-2 was only 79.8 per cent, she said.

COVID-19 on Saturday night: 5,354,800 cases, 342,923 deaths

A screenshot from Covidly.com taken at 8:46 p.m. Pacific time: 5,354,800 Cases, 342,923 Deaths.

COVID-19: Cuba says 2 drugs have reduced its death toll

Via Globalnews.ca, a Reuters report: Coronavirus: Cuba says 2 drugs have reduced its death toll.

Communist-run Cuba said this week that use of two drugs produced by its biotech industry that reduce hyper-inflammation in seriously ill COVID-19 patients has sharply curbed its coronavirus-related death toll. 

Health authorities have reported just two virus-related deaths over the past nine days among more than 200 active cases on the Caribbean’s largest island, a sign they may have the worst of the outbreak under control.  

The government, which hopes to increase its biopharmaceutical exports, has touted various drugs it produces for helping prevent infection with the new coronavirus and treating the COVID-19 disease it causes. 

It ascribes the recent reduction in deaths of severely ill COVID-19 patients largely to the use beginning in April of two drugs that appear to help calm the “cytokine storm,” a dangerous overresponse by the immune system in which it attacks healthy tissue as well as the invading virus.

One is itolizumab, a monoclonal antibody produced in Cuba and elsewhere. The other is a peptide that Cuba says its biotech industry discovered and has been testing for rheumatoid arthritis in Phase II clinical trials.

“Some 80 per cent of patients who end up in critical condition are dying. In Cuba, with the use of these drugs, 80 per cent of those who end up in critical or serious condition are being saved,” President Miguel Diaz-Canel said on Thursday in a meeting shown on state television.

Scientists caution that large placebo-controlled studies are needed to assess the safety and efficacy of these drugs for treating COVID-19.  

But Cuba’s experimental treatments have helped it achieve an overall COVID-19 death rate of 4.2 per cent, compared with the regional and global averages of 5.9 per cent and 6.6 per cent, respectively, health authorities say.  

Fatality rates depend on many variables, including the rate of testing, quality of healthcare systems, and age and underlying health condition of the population. 

Official data suggests that Cuba, with universal healthcare and a well-staffed care system, has done well in containing its outbreak. It has registered less than 20 cases per day over the past week, down from a peak of 50 to 60 in mid-April. In total, Cuba has reported 1,916 cases for a population of 11 million and 81 death.

That translates to an infection rate 0.71 per 100,000 inhabitants, compared with about 29 per 100,000 for the United States, according to a John’s Hopkins University tally.

Swift action helped Cuba contain its outbreak. After closing borders, schools and public transportation in March, Cuba urged residents to stay home, made wearing of masks obligatory, and employed effective contact tracing to curb the virus spread.

Africa COVID-19 cases top 100,000

An email from WHO:

Brazzaville/Cairo, 22 May 2020 – The COVID-19 pandemic today reached a milestone in Africa, with more than 100 000 confirmed cases. The virus has now spread to every country in the continent since the first case was confirmed in the region 14 weeks ago.

Despite crossing this threshold, the pandemic, which has struck with such devastating force in much of the world, appears to be taking a different pathway in Africa. Case numbers have not grown at the same exponential rate as in other regions and so far Africa has not experienced the high mortality seen in some parts of the world. Today, there are 3100 confirmed deaths on the continent.

By comparison, when cases reached 100 000 in the World Health Organization (WHO) European region, deaths stood at more than 4900. Early analysis by WHO suggests that Africa’s lower mortality rate may be the result of demography and other possible factors. Africa is the youngest continent demographically with more than 60% of the population under the age of 25. Older adults have a significantly increased risk of developing a severe illness. In Europe nearly 95% of deaths occurred in those older than 60 years.

African governments have made difficult decisions and were quick to impose confinement measures, including physical and social distancing, which will have significant socio-economic costs. These measures, which along with contact tracing and isolation, expanded or increased hand washing have helped to slow down the spread of the virus.

“For now COVID-19 has made a soft landfall in Africa, and the continent has been spared the high numbers of deaths which have devastated other regions of the world,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. “It is possible our youth dividend is paying off and leading to fewer deaths. But we must not be lulled into complacency as our health systems are fragile and are less able to cope with a sudden increase in cases.”

The continent has made significant progress in testing with around 1.5 million COVID-19 tests conducted so far. However, testing rates remain low and many countries continue to require support to scale-up testing. There is a need to expand the testing capacity in urban, semi-urban and rural areas, and provide additional test kits.

Cases continue to rise in Africa and while overall it took 52 days to reach the first 10,000 cases, it took only 11 days to move from 30 000 to 50 000 cases. About half of the countries in Africa are experiencing community transmission. More than 3400 health care workers have been infected by COVID-19. It is important that health authorities prioritize the protection of healthcare workers from COVID-19 infection at medical facilities and communities. There is also a need to provide enough personal protective equipment to health care workers and raise their awareness as well as increase infection prevention and control in health facilities.

“Testing as many people as possible and protecting health workers who come into contact with suspected and confirmed cases are crucial aspects of this response. Despite global shortages, we are working hard to prioritize the delivery of testing kits and personal protective equipment to low- and middle-income countries that have the most vulnerable populations, based on the number of cases reported,” said Dr Ahmed Al Mandhari, WHO Regional Director for the Eastern Mediterranean.

Despite the relatively lower number of COVID-19 cases in Africa, the pandemic remains a major threat to the continent’s health systems. A new modelling study by WHO predicts that if containment measures fail, even with a lower number of cases requiring hospitalization than elsewhere, the medical capacity in much of Africa would be overwhelmed.

Now that countries are starting to ease their confinement measures, there is a possibility that cases could increase significantly, and it is critical that governments remain vigilant and ready to adjust measures in line with epidemiological data and proper risk assessment.

WHO has offices in every country on the continent and is working closely with the Africa Centres for Disease Control, Ministries of Health, United Nations agencies and other partners to support the scale-up of the response through coordination, technical expertise, the provision of much needed medical supplies and assisting with data collection and analysis. WHO has trained more than 7000 health workers, including 1000 district health teams to support the decentralization of the response. So far, more than 225 experts have been deployed to over 39 countries in Africa and over 900 staff have been repurposed at the regional and country level to support the response.

Brazil moves to #2 in COVID-19 ranking

Via Worldometer, a screenshot taken at 3:53 p.m. Pacific time: Coronavirus Update (Live): 5,295,753 Cases and 339,330 Deaths from COVID-19 Virus Pandemic.

With 330,890 cases (almost 20,000 of them registered in the past 24 hours), Brazil now has more cases than any other nation except the US.

Report 23 - State-level tracking of COVID-19 in the United States

Imperial College London has published Report 23 - State-level tracking of COVID-19 in the United States. The summary, with my bolding:

As of 20 May 2020, the US Centers for Disease Control and Prevention reported 91,664 confirmed or probable COVID-19-related deaths, more than twice the number of deaths reported in the next most severely impacted country. In order to control the spread of the epidemic and prevent health care systems from being overwhelmed, US states have implemented a suite of non-pharmaceutical interventions (NPIs), including “stay-at-home” orders, bans on gatherings, and business and school closures. 

We model the epidemics in the US at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the time-varying reproduction number (the average number of secondary infections caused by an infected person), the number of individuals that have been infected and the number of individuals that are currently infectious. We use changes in mobility as a proxy for the impact that NPIs and other behaviour changes have on the rate of transmission of SARS-CoV-2. We project the impact of future increases in mobility, assuming that the relationship between mobility and disease transmission remains constant. We do not address the potential effect of additional behavioural changes or interventions, such as increased mask-wearing or testing and tracing strategies. 

Nationally, our estimates show that the percentage of individuals that have been infected is 4.1% [3.7%-4.5%], with wide variation between states. For all states, even for the worst affected states, we estimate that less than a quarter of the population has been infected; in New York, for example, we estimate that 16.6% [12.8%-21.6%] of individuals have been infected to date. Our attack rates for New York are in line with those from recent serological studies broadly supporting our modelling choices.  

There is variation in the initial reproduction number, which is likely due to a range of factors; we find a strong association between the initial reproduction number with both population density (measured at the state level) and the chronological date when 10 cumulative deaths occurred (a crude estimate of the date of locally sustained transmission). 

Our estimates suggest that the epidemic is not under control in much of the US: as of 17 May 2020, the reproduction number is above the critical threshold (1.0) in 24 [95% CI: 20-30] states. Higher reproduction numbers are geographically clustered in the South and Midwest, where epidemics are still developing, while we estimate lower reproduction numbers in states that have already suffered high COVID-19 mortality (such as the Northeast). These estimates suggest that caution must be taken in loosening current restrictions if effective additional measures are not put in place.  

We predict that increased mobility following relaxation of social distancing will lead to resurgence of transmission, keeping all else constant. We predict that deaths over the next two-month period could exceed current cumulative deaths by greater than two-fold, if the relationship between mobility and transmission remains unchanged. Our results suggest that factors modulating transmission such as rapid testing, contact tracing and behavioural precautions are crucial to offset the rise of transmission associated with loosening of social distancing.  

Overall, we show that while all US states have substantially reduced their reproduction numbers, we find no evidence that any state is approaching herd immunity or that its epidemic is close to over.

ECDC launches new weekly COVID-19 surveillance report

ECDC has published ECDC launches new weekly COVID-19 surveillance report. Excerpt:

Trends in notification rates and deaths 

Based on data available to ECDC on 20 May 2020, 29 out of 31 countries (EU/EEA countries and the UK) showed consistently decreasing trends in COVID-19 14-day case notification rates compared to peaks that were observed 13–49 days earlier. The average rate for the EU/EEA and the UK was 68% lower than at the peak on 9 April 2020. There have been slight recent increases in 14-day notification rates in two countries. 

Many countries are facing challenges in collecting and submitting reliable syndromic and virological data from primary care sentinel surveillance for COVID-19 using the systems established for influenza. All countries that reported data observed decreasing trends in SARS-CoV-2 positivity among individuals with respiratory symptoms.  

The number of countries reporting moderate to extremely high excess all-cause mortality to EuroMOMO is decreasing. All-cause excess mortality is an objective measure of the pandemic’s impact, particularly during periods when competing drivers of excess mortality (influenza and high/low temperatures) are largely absent. 

Risk of severe outcome 

We estimate that overall 35% of COVID-19 cases to date in the EU/EEA and the UK were hospitalised. Among hospitalised patients, 9% required ICU and/or respiratory support and 21% died, although there is considerable variation between countries. 

The latest pooled analysis of data from countries participating in the EuroMOMO network showed all-cause excess mortality primarily affecting people aged 65 years and above, but also those aged 15–64 years. 

The risk of hospitalisation increased rapidly with age (from 30 years of age); the risk of death increased from 60 years of age. Hospitalised cases aged 70 years and above were less likely to be admitted to ICU or to receive mechanical respiratory support. Older males were particularly affected, being more likely than females of the same age to be hospitalised, require ICU/respiratory support, and die. The sex-difference in these severe outcomes increased with age. 

Limitations 

COVID-19 surveillance data reported so far by the EU/EEA and the UK provide relevant information for public health policymakers. However, further improvements are needed to reliably estimate indicators such as intensity, geographical spread, severity and impact of the disease. These can be obtained by establishing or strengthening population-based surveillance systems.  

The numbers of reported cases and deaths can be influenced by testing policies, the way in which deaths are defined, and the settings included in death reporting. All these factors can affect within-country trends and make it difficult to directly compare countries.

COVID-19: US has three months to rebuild medical supplies stockpile, Obama administration scientists warn

Via The Guardian: Exclusive: US has three months to rebuild medical supplies stockpile, Obama administration scientists warn. Excerpt:

Nine top scientists who advised Barack Obama in the White House are warning that the US has just three months to rebuild its national stockpile of emergency medical supplies or risk further drastic shortages of testing kits and protective gear should coronavirus strike again in the fall. 

The dramatic warning from Obama’s former science advisers contains an implicit criticism of Donald Trump’s handling of the pandemic. In a seven-page missive, the group says that federal government preparations for a possible resurgence of the disease must be triggered immediately if a repeat of the “extraordinary shortage of supplies” that was seen in March and April is to be avoided. 

“Preparation for a resurgence needs to be initiated now. It needs to be at a national level, in close collaboration and coordination with state and local officials,” the letter says. 

The nine authors, led by John Holdren, Obama’s White House science adviser throughout his two terms in office, criticise the Trump administration for failing to act on numerous studies urging replenishment of the Strategic National Stockpile (SNS) in preparation for just the kind of health emergency unfolding today. 

“The United States was unprepared for the supply needs of the spring 2020 Covid-19 pandemic,” the group says.  

The scientists add: “There has been a persistent shortage of ventilators, testing kits, masks and other PPE [personal protective equipment] … In recent years the nation has let down its guard.”  

The group of nine are among the most pre-eminent scientists in the country. In addition to Holdren, now at Harvard, they include Eric Lander of MIT and Harvard, Chris Chyba of Princeton and Susan Graham of UC Berkeley.  

All nine were members of the Council of Advisors on Science and Technology assembled by Obama at the start of his presidency. Between 2009 and 2016 they co-wrote six reports for the president that touched on viral pandemics.  

Though many other experts have offered advice on dealing with Covid-19, the connection between the nine and Obama sharpens their intervention. The former president is not responsible for any of the scientists’ findings, but he has been kept informed about the group’s progress since its inception.