Antibodies to the virus faded quickly in asymptomatic people, scientists reported. That does not mean immunity disappears.

You May Have Antibodies After Coronavirus Infection. But Not for Long.

Moderna Therapeutics has just entered phase two of its clinical trials. Here's how mRNA vaccines work and what the latest developments mean.

A COVID-19 vaccine has passed its first human trial. But is it the frontrunner?

Immune warriors known as T cells help us fight some viruses, but their importance for battling SARS-CoV-2, the virus that causes COVID-19, has been unclear. Now, two studies reveal infected people harbor T cells that target the virus—and may help them recover. Both studies also found some people never infected with SARS-CoV-2 have these cellular defenses, most likely because they were previously infected with other coronaviruses. “This is encouraging data,” says virologist Angela Rasmussen of Columbia University. Although the studies don’t clarify whether people who clear a SARS-CoV-2 infection can ward off the virus in the future, both identified strong T cell responses to it, which “bodes well for the development of long-term protective immunity,” Rasmussen says. The findings could also help researchers create better vaccines.

T cells found in COVID-19 patients ‘bode well’ for long-term immunity

Human coronaviruses (HCoVs) are zoonotic pathogens with large and complex genomes. Some HCoV accessory proteins were acquired from host genes, and some were lost or split during HCoV evolution. Most likely SARS-CoV ORF8 became dispensable during the shift to the human/civet host.HCoV spike proteins adapted to use diverse cellular receptors. This occurred by divergence followed, in some cases, by convergent evolution to bind the same receptor.Recombination and positive selection shaped the diversity of CoV genomes, especially the S gene. Positive selection in the S gene of MERS-CoV and related CoVs mainly acted on the heptad repeats.In MERS-CoV and other lineage C beta-CoVs, positive selection targeted the nonstructural components, particularly ORF1a. Most adaptive events occurred in nsp3, which acts as a viral protease and contributes to suppression of interferon responses.Human coronaviruses (HCoVs), including SARS-CoV and MERS-CoV, are zoonotic pathogens that originated in wild animals. HCoVs have large genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ in number and sequence even among closely related CoVs. Thus, in addition to recombination and mutation, HCoV genomes evolve through gene gains and losses. In this review we summarize recent findings on the molecular evolution of HCoV genomes, with special attention to recombination and adaptive events that generated new viral species and contributed to host shifts and to HCoV emergence.

https://doi.org/10.1016/j.tim.2016.09.001

Molecular Evolution of Human Coronavirus Genomes

After months of study, scientists have better clarity on the coronavirus's lethal potential—which makes recent case surges all the more alarming.

How scientists know COVID-19 is way deadlier than the flu

Case surges, overrun hospitals, and a second lockdown this summer could deal a heavy blow to the United States. Here's what we need to turn the tide.

Here's how to stop the virus from winning

The latest updates on the COVID-19 pandemic.

Coronavirus Coverage

31. Another way to think about it is that the bad things that COVID does occur after transmission and only to a small fraction of people, so natural selection can't really "see" those things or operate effectively on them.

30. That means that evolutionary changes in virulence will not necessarily not change transmission much, unless they change other things by coincidence as well. And *that* means that selection on COVID-19 virulence is likely very weak.

29. The really bad things that COVID-19 does to people happen (1) only in a small subset of people and (2) after most or all of the transmission has already taken place.

28. Second, when death occurs, it typically occurs long after the usual window of disease transmission, a couple of weeks or more after the onset of symptoms. Why do these thing matter?

27. There are really a couple of key observations to make about the virulence of SARS-CoV-2 in this respect. First, note that disease severity varies widely among patients. Most infected people do not suffer severe disease. Approximately 5% are hospitalized. 0.5-1.0% die.

26. Taking stock, the theory is telling us that (1) the first successful mutations may not move us toward reduced virulence and (2) even if they do, it'll take years to get there. Now let's look at how natural selection operates on virulence in a pathogen like SARS-CoV-2.

25. A new mutation is *very rare* because there are millions of active cases worldwide, and it is just one of them. If it transmits say 10% more effectively (a very big advantage by evolutionary standards) it would take hundreds of generations—multiple years—to become common.

24. (Technical aside: if R0 isn't much bigger than 1, the new mutation probably goes extinct. We can approximate transmission as a Poisson branching process, and calculate exactly what that probability is. But let's ignore that, by supposing the mutation arises and persists.)

23. It matters because of the nature of competition and the nature of exponential growth. Suppose that tomorrow a new mutation arises that decreases virulence but increases transmissibility—just the kind that Ridley is hoping for in his argument. What happens to it?

22. As we think about timescales, the next thing to keep in mind is that we are currently in expansion phase of a pandemic to which comparably few people on earth are already immune. Why does this matter?

21. Given the limited genetic variation we are seeing in SARS-CoV-2 and some other factors I'm about to discuss, "early on" will be on the order of years or even decades. So any predictions of the sort Ridley is making pertain to the 2030s or later better than to 2021.

20. So early on, basically any old thing could happen to virulence, depending on what mutations arise first. In this short piece below, I briefly describe a lovely modeling paper by Jim Bull and Dieter Ebert, that explains how this works.

19. If the virus is originally more virulent than optimal, the first successful mutations could make it more virulent still, so long as they help it spread. Only once the virus gets "really good" at spreading in humans could we expect it to approach any sort of virulence optimum.

18. That's SARSCoV2 as of last November. What happens next? Well, that depends on what mutations happen to arise and what those mutations do. In general, those that increase how well the virus transmits will also increase in frequency. (But we'll revisit this; it's also subtle.)

17. When a virus emerges into the human population from another species, we don't expect it to be perfectly adapted for transmission. It may be inefficient at replicating, or may colonize the wrong parts of the body. It may be too virulent, or not virulence enough.

16. If we could expect it to happen over the course of a year or so, that could help should a vaccine fail to materialize. If it would take 100 years that's little consolation to me—and while Viscount Ridley may not agree, I think we're going have other, bigger problems by then.

15. I can't cover all that here but I do want to raise a few key points. Let's start with time scale and mutation supply. *Even if* evolutionary theory unambiguously predicted a major decrease in COVID virulence, we still ought to be asking how long it would take.

14. These include the vertical vs. horizontal transmission, competition between co-infecting strains, effects of an immune system, heterogeneity in host condition or genetics, and the role of vector spread. I sometimes spend 2 weeks on this in my course. It's not nearly enough.

13. So if we just look this far, we might expect to see the evolution of intermediate levels of virulence. But of course this only scratches the surface. There are a whole host other considerations and there have been literally hundreds of papers written about these.

12. If a strain is to transmit, it needs to reproduce within the host and facilitate its own spread. This is hard to do without harming the host somewhat. But if it is too virulent, it may kill the host too quickly and miss out on opportunities for transmission.

11. The most basic idea behind the theory of virulence evolution is that viruses face tradeoffs between virulence (the harm they cause to the host) and transmissibility (how well they spread to other hosts.

10. Ridley is telling us an evolutionary story based in the theory of virulence evolution. So what does that theory actually say about what we should expect SARS-CoV-2 to do over the next few years? Let's take a look.

9. Virulence evolution is not a simple, predictable, one-way trajectory.

8. Indeed, myxoma virus did evolve reduced lethality, from nearly 100% to less below 50%. At the same time, the rabbits also evolved increased immune resistance. But here is the scary part: that trend turned around. Myxoma became more lethal again.

7. Other endemic virus remain highly virulent. Influenza remains far worse than a common cold. Measles, even more so. Smallpox, worse yet. When spinning these evolutionary tales, people often invoke myxoma virus, introduced into Australia in the 1950s to control wild rabbits.

6. We simply do not have the evidence to draw that conclusion with any kind of certainty. I can't think of a human viral pathogen that has evolved this level of reduced virulence in recent enough history that we were able to monitor it. In any case, it's clear that not all do.

5. Even if OC43 was the Asiatic flu—a pretty huge leap—I wouldn't want to gamble that SARS-CoV-2 would follow its trajectory. The final sentence is striking. No speculation, no "maybe"—just the assertion that unchecked COVID-19 will become indistinguishable from every other cold.

4. Ridley goes on to speculate that perhaps if the Asiatic flu was OC43, it then rapidly evolved lower virulence. Maybe, he suggests, SARS-CoV-2 would do the same thing—if we just ended the lockdowns and let it spread through the population.

3. The basis is a single paragraph in a 2005 paper about the OC43 genome, quoted below. The main evidence seems to be chronology and symptoms. But phylogenetic dating is notoriously imprecise, and some serological evidence suggests that the 1889-90 pandemic was a flu.

2. First, let's get the blog post out of the way. Ridley is speculating that the Asiatic flu of 1889-90 was not an influenza pandemic at all, but rather the emergence of the now-mild OC43 coronavirus into humans. According to his story, it subsequently evolved lower virulence.

1. In short, no. This is going to take a detailed thread to unpack.

The coronavirus crisis poses major challenges for citizens, politicians and civil servants alike. Shortcomings of recent decades, as with the lack of digitalization in education, are quickly becoming apparent. Not yet visible are many new concepts people all over Europe are implementing right now to help us to cope with this situation.   The current situation creates a lot of confusion in a broad spectrum of policy areas. But confusion can also be the mother of innovation. What is happening now in terms of self-organization in one context has the potential to be implemented elsewhere. Despite all justified concerns, and the primacy of protecting the health of all, the implementation of innovative and useful best practice is therefore an important task for politics and society. A whole host of new practices are currently emerging in many places – most of them simply out of creative necessity. Many will disappear again, but some have the potential to change the system. Estonia, for example, has quickly organized a public hackathon to generate ideas within a very short time – such as an app that guarantees people in quarantine quick and reliable access to help. We from the Innovation in Politics Institute in cooperation with Act.Now are therefore launching this project to collect, document and provide innovative practices in dealing with the crisis across Europe and at all political levels. Here, we make the best practices available to politics and society. 

Coping with the Secondary Effects of the CORONAVIRUS crisis

All IZA Pub­li­ca­tions

Research Search Results for 'Covid'

Having worked with the population of Bristol for almost 30 years, we have lots of information about biology, lifestyle and other factors that might contribute to different COVID-19 outcomes. We're also collecting data to help us better understand the effect mitigation is having on our physical and mental wellbeing.

Avon Longitudinal Study of Parents and Children menu

A dramatic slowdown in testing turnaround times is undermining the U.S. response to the coronavirus, rendering tools like contact tracing almost useless in some instances.Quest Diagnostics, one of the main companies doing coronavirus testing, said Monday that “soaring demand” due to the surge in cases across the South and Southwest had pushed back their average turnaround time for getting results of a coronavirus test to at least seven days for all but the highest priority patients.LabCorp, another major testing company, said last week that its turnaround times were only slightly better, at four to six days, because of “significant increases in testing demand and constraints in the availability of supplies and equipment.”ADVERTISEMENTgoogletag.cmd.push(function() {googletag.display("dfp-ad-incontent_desk_1");});The longer delays from previous waits of around two days as recently as late June in getting test results make it much harder to slow the spread of the virus. The fundamental strategy to help contain the virus is to test people quickly so that those who test positive can isolate. Contact tracers can then reach out to people who have been in contact with those infected to avoid spreading the virus on to others.A seven-day wait for test results, however, magnifies the risks that an infected person has already spread COVID-19, making it too late to effectively implement contact tracing.

Long waits for test results spark new COVID-19 fears

NEW: #COVID19 cases continue to spread at alarming rates. CA is now closing indoor operations STATEWIDE for: -Restaurants -Wineries -Movie theaters, family entertainment -Zoos, museums -Cardrooms Bars must close ALL operations.

Three months ago, the epidemiologist weighed in on what we must do to defeat this new threat. We went back to ask: How are we doing, and what comes next?

Larry Brilliant on How Well We Are Fighting Covid-19

The first report of COVID-19 by the Chinese government was at the end of last year, but it is likely that by late November, there were transmissions spreading in Wuhan City and surround areas of Hubei Province. Spread of COVID-19 in Japan had two major waves so far. The first wave was originated by people with travel history to Wuhan and other places in China. From January to early February, the number of cases from China found in Japan was 11. Of course, there were considered to be more imported cases from China in reality, but it was likely somewhere around several tens to about a hundred. These people traveled to Japan for sightseeing or other purposes, and later, through places where people congregate, such as sports gyms and small concert houses, transmissions spread across the country including Hokkaido, Tokyo, Aichi, and Osaka. This first wave had come under control by mid March with number of cases relatively low, but the second wave came as the first wave was calming down. Second wave was originated by infected people from a wide range of countries, such as Europe, US, Southeast Asia, and Egypt. We confirmed about 300 cases who had entered Japan from such countries, so the actual number of cases who entered Japan is estimated to be around 1,000 ~ 2,000. Although local transmissions of the second wave in Japan began in early February, infected people from abroad were coming to Japan and able to move around the country almost without any restriction, until the government put restrictions on travel at the end of March. This resulted in a large outbreak. The delay in action during that time is regrettable. However, by early May, I believe that we managed to suppress the transmission of the second wave. At least, the second wave is already peaked. There will still be transmissions going forward, but we believe that we can maintain the number of new cases relatively low.

Infectious Disease Response — to see the forest, not just the trees: What differentiated Japan from the Western countries?

Measures at each of these scales will come with a different degree of short- and long-term disruption and effectiveness. But countries will need to find a successful, sustainable combination over the coming year (at least) if they want to avoid large outbreaks. 2/2

Controlling COVID-19 means reducing interactions between infectious and susceptible people. This can include measures at individual scale (test/trace/isolate), community scale ('local lockdowns'), or national scale (closed borders/traveller quarantines). 1/

Growing evidence shows most infected people aren’t spreading the virus. But whether you become a superspreader probably depends more on circumstance than biology.

Most People With Coronavirus Won’t Spread It. Why Do a Few Infect Many?

Pittsburgh, a sister city to Wuhan, China, saw only modest cases for months. In the last two weeks, cases are suddenly soaring.

Pittsburgh Seemed Like a Virus Success Story. Now Cases Are Surging.

It isn’t safe to reopen watering holes, nightclubs, and concert venues. Congress should pay to keep them closed.

Bail Out the Bars

What actions could we take to mitigate this? @SciBeh and here, please:

will lack of clarity about the guidelines directly impact adherence, and influence peer pressure?Yes100%No0%4 votes · Final results

How should the new advice best be communicated? Should we be aiming forconcrete detail0%general principles33.3%info on levels of risk66.7%3 votes · Final results

Should advice be simplified so that it can be better communicated, even if the result is "inferior" from an economic and/or public health point of view?Yes100%No0%Dumb question0%3 votes · Final results

This means it is getting substantially more complex. + Can this advice be successfully communicated the general public?Yes66.7%No33.3%3 votes · Final results

last week's issue radar had little response. So will try out polls. The issue: As countries come out of hard lockdown their advice is becoming more nuanced (potentially applying differently across age groups, health conditions, professions, and parts of the country).... 1/6

I had an initial stab at this data yday and compared apples to pears. Was saved some blushes by a contingent of dedicated Twitter data warriors inc @fascinatorfun @0liver_03 @jneill and many, many others who've also dug through the data and shared ideas. Thank you.

Here's a statement from @DHSCgovuk. Impression I get is they're sincerely doing their best to clean up a horrendously messy dataset thrown together in fraught circumstances early on in #COVID19. Tho is releasing this crucial data surreptitiously the right way to go about it...?

And lo and behold this new data series reveals that while @DHSCgovuk was reporting that around 2m people had been tested as of around 21 May, the real total was around 1.8m. It was overstating the reach of its testing effort quite considerably.

Then, yesterday, after @skynews's investigation, @DHSCgovuk quietly posted this data series, which finally ends the mystery. Bit rum. Still: put it alongside data for the rest of the UK and we can finally get a firmer grasp of how many have been tested

A mystery with real consequences, since data on people tested (as opposed to tests carried out) is v v important. Many people end up taking more than one test - so there's double counting there. Comparing cases to people is a crucial metric for judging the spread of the disease.

But on May 23 it abruptly stopped publishing the data. From then until this week we haven't been given any update on how many people in total have been tested in England (Scotland, NI & Wales continued publishing). It's been one of the longest-running mysteries of #COVID19

You may recall that up until late May @DHSCgovuk published daily figures for how many people had been tested alongside its deaths numbers. This is one of the key datapoints in confronting the disease and building a track & trace system. Here's the fig for May 21: over 2m

This revelation stems from data released by @DHSCgovuk yesterday in the wake of our investigation into the handling of #COVID19 data. Full thing here:

Breaking: UK government was routinely overstating the total number of people who’d been tested for #COVID19 by as many as 200,000 at the height of the coronavirus pandemic, according to new Sky News analysis.

Insiders reveal that data collection was haphazard, as officials went against accepted practice and "buffed the system".

Coronavirus: The inside story of how UK's 'chaotic' testing regime 'broke all the rules'

Historic data for the number of people tested for coronavirus (COVID-19) from 30 January to 27 May 2020, before the launch of NHS test and trace.

Number of people tested for coronavirus (England): 30 January to 27 May 2020

i mean, we had nurses wearing yankees rain ponchos, we were sending Covid patients back to nursing homes, and the Surgeon General was telling everyone not to wear masks -- and you're here in July saying, ah, but Florida isn't as bad as NY was? Better fucking not be!

in short, most states had the good fortune to get spared while New Yorkers endured a once-in-a-lifetime tragedy. you got to go second! personally, i'd set the bar for success a little higher than "but look we don't have tent hospitals in the parks!"

also: I am aware that places like AZ and TX are currently at about 20 percent the estimated true infection rate of NY when it became the global epicenter of the disease. This is not, actually, a point in favor of their strategy.

At least New York's hometown newspaper, the one that has more subscribers than the WSJ, WaPo, and the 250 Gannett papers combined, nailed this, right?

As one well-compensated columnist put it, "America shouldn't have to play by New York's rules." Well, it didn't. Congrats?

That's what gave Texas and Florida the space to say, "Couldn't happen here!" Even though there was plenty of evidence, even in the early days, that it could and would — that NYC's outbreak was NOT, say, tied to certain subway lines....

I hope the pundits who said that New Yorkers got Covid because of density, the subway, or apartment buildings (NY's own self-serving governor among them!) take a moment to reflect on how much damage that opinion did

Politicians and pundits are acting like the city was destined for a tragedy. They’re wrong.

Nothing About New York’s Outbreak Was Inevitable

A quick hack of a function to add emojis to forest plots

forest_emojis

Breaking: Los Angeles and San Diego school districts will be remote-only in the fall. California’s 2 largest public school districts said instruction will be remote-only in the fall, citing concerns that surging coronavirus infections pose too dire a risk for students & teachers.

He believes bearing this virus is possible. He hasn’t seen anything thrown at us by this virus, as nasty as it is, that we can’t defeat. He got evidence today. Thank you to our heroes in New York & in memory of all who we lost. /end

Our country’s leading pandemic epidemiologist and I spoke for a while today. He gave a Ted talk in 2006 on this pandemic. He has advised presidents of both parties. I have been talking to him fairly continuously for the last 4 months. 26/

I spoke to Bernie Sanders about this today. He was worked with Mark Warner & Doug Jones (the full expanse of the Democratic caucus) on a Bill to protect Americans’ paychecks. Your move Mitch McConnell. Now that this is in red states apparently he’s taking another look. 25/

The Senate must also honor what they’ve seen. Bar & restaurant owners should be protected. Unemployment ins. Prevent evictions. Help Americans get through this. Hire the contact tracers, get us the testing. Understand without a president, you need to work with the governors. 24/

I have talked to governors & mayors across the country. Follow Abbott. Don’t learn the lesson a third time. We CAN do it. “Yes we can” someone I know said. 23/

And for other states, the movement to begin closing bars today, to consider starting school online, to close churches, to roll things back is the beginning of the political courage they need to show. 22/

The way they can make it up is with a rapid steep decline. 5ey should follow Greg Abbott in TX. He also got it late & didn’t learn the lesson of NY. But once he saw it, he acted w seriousness. All these states can achieve the same sharp drop as NY if they get serious.21/

Sadly, some are deciding they must learn for themselves. AZ has now passed NY in peak cases/mm with 528, eclipsing NY’s 508. FL is now at 436. Both governors openly flaunted their lack of preparation & lack of seriousness. They disrespected the sacrifice of their countrymen.20/

Them way to honor them? Let them be our teachers. Sit there in Phoenix & Houston & Charlotte & Miami and don’t doubt them when they tell you not to mess around with this very scary virus. 19/

New York now takes the virus as seriously as the rest of the world & they know how to contain this. Their vigilance is just beginning. And sustaining it will be hard. But the backside of that curve brings tears to my eyes. The nurses. The doctors. The paramedics. 18/

It’s no longer just foreign countries who have shown this can be done. New Yorkers, who many rallied for, flew to NY, and jumped in to help, showed us THIS IS POSSIBLE. WE CAN DO THIS. 17/

People died for 120 straight days in NY. It is 64 days after peak. 508 cases/million at peak. Overall 20,600 cases/million. 32,075 people gone, 22,795 in NYC alone. Yesterday, in every ICU, nursing home, ER & hospital bed, it was quiet. Not a single reported death. 16/

We have seen the death by infection & by suicide of so many many New York health care workers, one of whom saw 40 ICU visitors in a row die. For all of them, yesterday was for them....

The only thing as steep as NY’s rising curve was NY’s falling curve. It was spectacular & historic. And that is a credit to New Yorkers. To discipline. To community. To respect for the medical workers. 14/

But this isn’t a defense of Cuomo. The fact is NY became the world’s epicenter of COVID-19 for reasons we are still understanding: a new strain, dense conditions, late reaction, nursing home controls. But what happened next was remarkable. 13/

It turns out that the nursing home deaths were caused by the same reason as in every other state. Staff bringing it in, untested, from the community. 1 in 4 staff got infected. And they lacked sufficient PPE. Same thing is now happening in the Sun Belt. 12/

Trump Admin, out of state operators, state inspectors. Yes to all. And sadly while this meme was great as a way to shift the state to blue states, today 40% of Texas cases are coming from nursing homes. Turns out it’s difficult to keep spread out. 11/

The Trump Administration began in 2017 announcing they would not enforce the sweeping nursing home rules the Obama Admin put in place. Too many regulations. And it got worse from there. Many people have their hands on this mess.10/

The nursing home meme was generally spread by people whose principal skill is retweeting unread click bait. I ran the agency the Agency that oversaw nursing home safety & have been talking about this on TV, in writing & with governors. You can watch. 9/

This isn’t about Cuomo as much as it is about New Yorkers. But I have to make one more comment. There’s a right wing meme about how Cuomo killed people in nursing homes. 8/

For all his flaws, when Trump was hiding under his desk, pointing fingers, searching for credit, ignoring scientists, Cuomo was fully present. 7/

I have had my issues with Cuomo & don’t like the way he runs NY’s Medicaid program. But I respected what he was doing. I have never mentioned this but I saw the data Cuomo was first presented with that he later shared. And I saw the model Trump was presented with. 6/

Something else. He didn’t lie. He didn’t sell. He didn’t pat himself on the back. Or avoid responsibility. We had that already. He told the hard truths. He showed data. He asked for help. He demonstrated some empathy & some effort. And the country needed that. 5/

At the time, he was doing what Angela Merkel, Jacinda Ardern, Katrin Jakobsdottir & others around the world were: -This situation is going to be difficult -I know it will be hard for you -Here’s what we need to do and why -We will pull through this 4/

So some thought it was unfair that Cuomo drew such high praise for his handling of the crisis. He earned it for one reason. He talked to people. 3/

New York did not get off to a good start. In fact, it was the example of what not to do. California acted 6 days earlier than NY did when they had cases hit. The mayor clearly didn’t take it seriously & Cuomo was slower to act. Mostly @CoreyinNYC was ringing loud alarms. 2/

COVID UPDATE July 13: There are successful examples of taking on COVID-19. And there is one story like no others. New York. 1/