Coronavirus m in focus

Editor's Notes

1. The Los Angeles Times reported that two months before the virus spread through Wuhan, the Trump administration halted a $200 million early-warning program to train scientists in China and elsewhere to deal with a pandemic. The name of the program? “PREDICT.”
2. One of the biggest takeaway messages [from the viral sequences] is that there was a single introduction into humans and then human-to-human spread When the first 2019-nCoV sequence became available, researchers placed it on a family tree of known coronaviruses—which are abundant and infect many species—and found that it was most closely related to relatives found in bats. A team led by Shi Zheng-Li, a coronavirus specialist at the Wuhan Institute of Virology, reported on 23 January on bioRxiv that 2019-nCoV’s sequence was 96.2% similar to a bat virus and had 79.5% similarity to the coronavirus that causes severe acute respiratory syndrome (SARS), a disease whose initial outbreak was also in China more than 15 years ago. But the SARS coronavirus has a similarly close relationship to bat viruses, and sequence data make a powerful case that it jumped into people from a coronavirus in civets that differed from human SARS viruses by as few as 10 nucleotides. That’s one reason why many scientists suspect there’s an “intermediary” host species—or several—between bats and 2019-nCoV. The longer a virus circulates in a human populations, the more time it has to develop mutations that differentiate strains in infected people, and given that the 2019-nCoV sequences analyzed to date differ from each other by seven nucleotides at most, this suggests it jumped into humans very recently. But it remains a mystery which animal spread the virus to humans. “There’s a very large grey area between viruses detected in bats and the virus now isolated in humans,” says Vincent Munster, a virologist at the U.S. National Institute of Allergy and Infectious Diseases who studies coronaviruses in bats, camels, and others species.
3. A doctor in Wuhan has spoken out after seeing several of her colleagues die from the coronavirus, criticising hospital authorities for suppressing early warnings of the outbreak in an interview censors have been trying to erase from the internet. On 30 December, after seeing several patients with flu-like symptoms and resistant to usual treatment methods, Ai received the lab results of one case, which contained the word: “Sars coronavirus.” On 21 January, the day after Chinese officials finally confirmed there was human to human transmission of the virus, the number of sick residents coming to the emergency room had already reached 1,523 in a day – three times the normal volume.
4. attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct … That string of apparent gibberish is anything but: It’s a snippet of a DNA sequence from the viral pathogen, dubbed 2019 novel coronavirus (2019-nCoV), that is overwhelming China and frightening the entire world. Scientists are publicly sharing an ever-growing number of full sequences of the virus from patients—53 at last count in the Global Initiative on Sharing All Influenza Data database. These viral genomes are being intensely studied to try to understand the origin of 2019-nCoV and how it fits on the family tree of related viruses found in bats and other species. They have also given glimpses into what this newly discovered virus physically looks like, how it’s changing, and how it might be stopped. “One of the biggest takeaway messages [from the viral sequences] is that there was a single introduction into humans and then human-to-human spread,” says Trevor Bedford, a bioinformatics specialist at the University of Washington and Fred Hutchinson Cancer Research Center. The role of Huanan Seafood Wholesale Market in Wuhan, China, in spreading 2019-nCoV remains murky, though such sequencing, combined with sampling the market’s environment for the presence of the virus, is clarifying that it indeed had an important early role in amplifying the outbreak. The viral sequences, most researchers say, also knock down the idea the pathogen came from a virology institute in Wuhan.
5. Jonathan Mayer, professor emeritus at the University of Washington’s department of epidemiology, said it was “entirely conceivable” there were cases as early as mid-November. He said there were three possibilities: that cases weren’t detected at the time, that they were detected but not recognised as a new disease, or they were detected and recognised but reporting was suppressed. “I have no way of knowing which of these possibilities in fact happened,” Mayer told the Guardian. “We know that there are reports of early suppression of reports of cases, and the ‘whistleblowers’ dealt with rather severely. But in fairness, the signs and symptoms of C​ovid-19 are non-specific and even now, without confirmatory testing, it is easy to mistake this for another disease.” Mayer said it was highly improbably that patient zero would ever be identified. (Guardian Fri 13 Mar)
6. Some point in late 2019: The coronavirus jumps from some animal species to a human being. The best guess at this point is that it happened at a Chinese “wet market.” December 6: According to a study in The Lancet, the symptom onset date of the first patient identified was “Dec 1, 2019 . . . 5 days after illness onset, his wife, a 53-year-old woman who had no known history of exposure to the market, also presented with pneumonia and was hospitalized in the isolation ward.” In other words, as early as the second week of December, Wuhan doctors were finding cases that indicated the virus was spreading from one human to another. December 21: Wuhan doctors begin to notice a “cluster of pneumonia cases with an unknown cause.” December 25: Chinese medical staff in two hospitals in Wuhan are suspected of contracting viral pneumonia and are quarantined. This is additional strong evidence of human-to-human transmission. Sometime in “Late December”: Wuhan hospitals notice “an exponential increase” in the number of cases that cannot be linked back to the Huanan Seafood Wholesale Market, according to the New England Journal of Medicine. December 30: Dr. Li Wenliang sent a message to a group of other doctors warning them about a possible outbreak of an illness that resembled severe acute respiratory syndrome (SARS), urging them to take protective measures against infection. In December 2019, 27 of the first 41 people hospitalised (66%) passed through a market located in the heart of Wuhan city in Hubei province. But, according to a study conducted at Wuhan Hospital, the very first human case identified did not frequent this market. Instead, a molecular dating estimate based on the SARS-CoV-2 genomic sequences indicates an origin in November. This raises questions about the link between this COVID-19 epidemic and wildlife.Conversation.com these genomic comparisons suggest that the SARS-Cov-2 virus is the result of a recombination between two different viruses, one close to RaTG13 and the other closer to the pangolin virus. In other words, it is a chimera between two pre-existing viruses.
7. Symptoms vary from person to person and are non-specific.
8. Jan 22 President Trump, in an interview with CNBC at the World Economic Forum in Davos, Switzerland, declared, “We have it totally under control. It’s one person coming in from China. We have it under control. It’s going to be just fine.”
9. January 23: Chinese authorities announce their first steps for a quarantine of Wuhan. By this point, millions have already visited the city and left it during the Lunar New Year celebrations. Singapore and Vietnam report their first cases, and by now an unknown but significant number of Chinese citizens have travelled abroad as asymptomatic, oblivious carriers.
10. Wuhan under lockdown.
11. When Dr. Li Wenliang, a Chinese doctor, died on Feb. 7 after contracting the coronavirus, he was hailed as a hero by many for trying to ring early alarms that a cluster of infections could spin out of control. The death of Dr. Li Wenliang provoked anger at how the Chinese government handled the epidemic.Credit...Tyrone Siu/Reuters In early January, the authorities reprimanded him, and he was forced to sign a statement denouncing his warning as an unfounded and illegal rumor. Dr. Li’s death provoked anger and frustration at how the Chinese government mishandled the situation by not sharing information earlier and silencing whistle-blowers.
12. Feb. 11 The disease the virus causes got a new name. The World Health Organization on Feb. 11 proposed an official name for the disease the virus coronavirus causes: Covid-19, an acronym that stands for coronavirus disease 2019. The name makes no reference to any of the people, places, or animals associated with the coronavirus, given the goal to avoid stigma. By the next day, the death toll in China had reached 1,113 and the total number of confirmed cases rose to 44,653. There were 393 cases outside of China, in 24 countries.
13. Feb 23 Europe faced its first major outbreak as the number of reported cases in Italy grew from fewer than five to more than 150. In the Lombardy region, officials locked down 10 towns after a cluster of cases suddenly emerged in Codogno, southeast of Milan. As a result, schools closed and sporting and cultural events were canceled.
14. Feb 24. Iran emerges as a second focus point of the virus. Iran said it had 61 coronavirus cases and 12 deaths, more than any other country but China, and public health experts warned that Iran was a cause for worry — its borders are crossed each year by millions of religious pilgrims, migrant workers and others. Cases in Iraq, Afghanistan, Bahrain, Kuwait, Oman, Lebanon, the United Arab Emirates and one in Canada, have been traced back to Iran. As the number of coronavirus cases around the globe continued to climb, the Trump administration began preparing for the virus to arrive in the United States. The White House asked Congress to allocate $1.25 billion in new emergency funds to bolster its preparedness — a significant escalation in the administration’s response. At this point the United States, where Centers for Disease Control and Prevention officials warned of an almost certain outbreak, had 35 confirmed cases and no deaths.
15. From the first confirmed US case in Washington state on 20 January to Trump’s citing of Imperial’s 2.2 million projected deaths which he did for the first time just this week (Apr 3), he has kept up a relentlessly upbeat facade, downplaying the severity of the threat largely for the benefit of the New York stock exchange. “We have it totally under control,” he said two days after that first confirmed case and a day before China cut off Wuhan, a city of 11 million. “We only have five people, we pretty much shut it down coming from China,” he said on 30 January, the day the World Health Organization declared a global emergency. “It’s going to disappear. One day – it’s like a miracle – it will disappear,” he said on 27 February, the day before America mourned its first coronavirus death. A patient near Seattle became the first coronavirus patient to die in the United States on Feb. 28. As the number of global cases rose to nearly 87,000, the Trump administration issued its highest-level warning, known as a “do not travel” warning, for areas in Italy and South Korea most affected by the virus. The government also banned all travel to Iran and barred entry to any foreign citizen who had visited Iran in the previous 14 days.
16. A medical professional escorts a patient from an ambulance into hospital. Photograph: Daniel Leal-Olivas/AFP/Getty NHS England has now said that the earliest death occurred on 28 February, almost a week before the previously acknowledged date. Scotland’s first minister, Nicola Sturgeon, admitted on Thursday that the death toll in Scotland had been significantly under-reported because of delays in notifying the government of 40 Covid-19 fatalities earlier this week, which increased Scotland’s total by 31% in a day. Catherine Calderwood, Scotland’s chief medical officer, said every death meant there were roughly 1,000 coronavirus infections in the general population, implying that 40,000 more Scots may have been infected. It’s clear that a lack of testing is contributing to the lack of information, which is unacceptable.
17. Tues 3rd March – At a time when the WHO was encouraging countries to track and isolate cases and test, test, test, and stock, stock, stock, No 10 was saying that the time for urgent action was not yet upon us and that everything should be kept as normal as possible, and that we should wash our hands as often as possible.
18. Already by 6 March the absence of effective diagnostic testing – caused in part by the CDC’s botched rollout of its own Covid-19 test – was severely hampering efforts to track the spread of the disease in the hope of containing it before it overwhelmed the country. “Anybody that needs a test gets a test,” Trump told the gaggle of reporters in Atlanta. “They have the tests. And the tests are beautiful.” The tests were not beautiful, they were critically flawed. Anybody who needed them was not getting them. Mr. Trump officially declared a national emergency, and said he was making $50 billion in federal funds available to states and territories to combat the coronavirus. He also said he would give hospitals and doctors more flexibility to respond to the virus, including making it easier to treat people remotely. (NYTimes)
19. The WHO warning came as the death toll from the virus in Italy rose by 31% in 24 hours to 827, and the government there began considering imposing even tighter restrictions on daily life and announced billions of euros in financial relief to cushion against the economic shock.
20. This is now the official government response. History has been rewritten. This is what should have happened. There was a time when it seemed possible for the world to contain COVID-19—the disease caused by the new coronavirus. That time is over. What began as an outbreak in China has become a pandemic, and as a growing number of countries struggle to control the virus, talk of “flattening the curve” is increasing. That is, a lot of people are going to get sick, and delaying infections as much as possible is imperative, so that cases occur over a long period of time and health systems aren’t suddenly inundated. Almost every country is trying to achieve this goal through the standard arsenal of public health—testing people and tracing contacts—and through more restrictive measures that include instituting quarantines, closing public spaces, banning mass gatherings, and issuing strong advice about social distancing. But on Thursday (12th March), at a press conference, Boris Johnson seemingly revealed that the United Kingdom would adopt a different strategy. The government would no longer try to track and trace the contacts of every suspected case, and it would test only people who are admitted to hospitals. In lieu of any major social-distancing measures, Johnson instead offered a suite of soft advice—people with symptoms should stay home; no school trips abroad; people over 70 should avoid cruises. With the peak of the pandemic still weeks away, the time hadn’t come yet for stricter measures, Johnson and his advisers said. They worried about “behavioral fatigue”—if restrictions come into force too early, people could become increasingly uncooperative and less vigilant, just as the outbreak swings into high gear. (As of March 15th, the U.K. had identified 1,391 cases, although thousands more were likely undetected.) (The Atlantic)
21. And so the lampooning continued into April. …..
22. March 19 Italy has overtaken China as the country with the most coronavirus-related deaths in the world after reporting 3,405 fatalities from the Covid-19 pandemic. In a stark illustration of how Europe has become the new epicentre of the pandemic, Italian officials reported 427 additional deaths on the same day Wuhan, the Chinese city where the virus was first identified, recorded no new infections. UN and Italian health authorities have cited a variety of reasons for Italy's toll, most notably its large elderly population, which is the second oldest in the world. The vast majority of people who have died in Italy - 87 per cent, as of Thursday - have been older than 70 years old. Italy, with its population of 60 million people, has now recorded about 150 more deaths than China, which has a population of more than 1 billion. (Independent)
23. March to ??? In Scotland.
24. On March 17, France imposed a nationwide lockdown, prohibiting gatherings of any size and postponing the second round its municipal elections. The lockdown was one of Europe’s most stringent. While residents were told to stay home, officials allowed people to go out for fresh air but warned that meeting a friend on the street or in a park would be punishable with a fine. By this time, France had more than 6,500 infections with more than 140 deaths, according to the W.H.O. (NYT) China on March 19 reported no new local infections for the previous day, a milestone in the ongoing fight against the pandemic. The news signaled that an end to China’s epidemic could be in sight. However, experts said the country would need to see at least 14 consecutive days without new infections for the outbreak to be considered over. And the announcement did not mean that China recorded no new coronavirus cases. Officials said that 34 new cases had been confirmed among people who had arrived in China from elsewhere. March 23 Prime Minister Boris Johnson locks Britain down. The lockdown closed all nonessential shops, barred meetings of more than two people, and required all people to stay in their homes except for trips for food or medicine. Those who disobey risked being fined by the police. March 24 The Tokyo Olympics delayed until 2021. Officials announced that the Summer Olympics in Tokyo would be postponed for one year. Only three previous Games had been canceled, all because of war: The 1916 Summer Olympics were canceled because of World War I, and the Summer and Winter Games were canceled in 1940 and 1944 because of World War II. March 26 The United States officially became the country hardest hit by the pandemic, with at least 81,321 confirmed infections and more than 1,000 deaths. This was more reported cases than in China, Italy or any other country.
25. Glasgow, Scotland James and Frances Welsh take the air during lockdown in the Easterhouse area Photograph: Robert Perry/EPA On March 23, prime minister Boris Johnson put the UK under lockdown saying that police will now have the power to fine people who gather in groups of more than two or who are outside for non-essential reasons. People with the main coronavirus symptoms – a fever or dry cough – are required to stay at home for seven days while households in which at least one person is displaying symptoms should quarantine themselves for 14 days. Four days later the prime minister and health secretary Matt Hancock both tested positive for the virus – they are currently (April 1st) self-isolating while working on the UK's response. (Wired)
26. Donald Trump repeated misleading and false claims at a coronavirus briefing. During the briefing, the president invited several executives — including My Pillow CEO and Trump rally fixture Mike Lidell — to tout their coronavirus efforts. Even as US hospitals complained of shortages and struggles, Trump boasted that the US would soon have a surplus, and be able to provide millions in aid to Italy, France and Spain. He came under fire today over reports that the US provided nearly 18 tons of ventilators and other equipment to China, weeks after the first cases were reported in Washington state.
27. March 31
28. April 1st
29. Passengers look from the windows of Holland America’s cruise ship Rotterdam as it docks at Port Everglades.
30. During the daily coronavirus task force briefing, Donald Trump blamed states for the shortages of medical equipment. He repeatedly noted that he saw aid from the federal government as a “last resort” for states. Of course, many governors have said they’re desperate. Jared Kushner, the president’s son-in-law made an appearance at the briefing. Kushner, a real estate developer with no medical expertise, said he is coordinating between federal agencies, hospitals and the White House. !!!
31. April 3rd.
32. The US has been accused of “modern piracy” after reportedly diverting a shipment of masks intended for the German police, and outbidding other countries in the increasingly fraught global market for coronavirus protective equipment. About 200,000 N95 masks made by the manufacturer 3M were diverted to the US as they were being transferred between planes in Thailand, according to the Berlin authorities who had ordered the masks for the police force.
33. March 08
34. Postponed! Hope we see it this year!