Top pick of the day

Why the Coronavirus Is So Confusing

A guide to making sense of a problem that is now too big for any one person to fully comprehend

 Story by Ed Yong posted online at The Atlantic, April 29, 2020, 7:00 AM

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More great coverage by the Atlantic.  Tackles sources of confusion in the current pandemic: SARS-CoV-2, a novel coronavirus came from bats; no sign of alarming mutation; will the real CFR please stand up; where are we on hydroxychloroquine; suddenly, everyone thinks they are an epidemiologist. 

Today’s bite-sized, handpicked selection of important news, information or science for all who want to know where this epidemic is going and what we should do.

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Daily COVID-19 Briefing: 4/15/20

Top news, reports and insights for today:

1. COVID-19 deaths surge on Tuesday to a new record high
   After 2 consecutive days of falling deaths, Tuesday saw a return to double-digit increases as 2,378 new deaths were reported, a 10% rise. Fourteen states tied or exceeded their highest one-day death toll including New Jersey (362), Maryland (40), Massachussetts (113), Washington DC (15), Texas (31), North Carolina, Mississippi (13), Louisiana (129), Florida (72), Alabama (11), Ohio (56), Missouri (19), Idaho (6), and California (71).
   What this means? This unwelcome news may be a signal that reporting of deaths was delayed over the holiday weekend. Another possibility is that states (New York among them) are starting to report “probable” COVID-19 deaths. It is also possible that daily ping-ponging of deaths will to continue in the short run. Hope that we were near peak was probably pre-mature.

2. Coming clean on immunity to SARS-CoV-2
   Yesterday, a well respected epidemiologist, Marc Lipsitch, wrote an opinion piece in the New York Times on the tricky question of immunity to the SARS-CoV-2 virus. People tend to think that once someone has been infected with a disease, they are immune to the disease forever. Like so many things in epidemiology, that is a cartoon of how things really work. Some diseases, like measles, do work that way. History buffs may be interested in how a Danish physician and early disease detective named Peter Panum figured this out in the 19th century by careful observation of an outbreak that occurred in the Faroe Islands in 1846. So far, what we don’t know about immunity to coronavirus is much greater than what we do know. Based on a few studies done of earlier coronavirus strains (SARS and MERS), it appears that immunity lasts for at least 2-3 years after initial infection. That’s tentative though because since both SARS and MERS are so lethal, we can’t do studies in which we intentionally expose patients to the virus, we can only observe those who get it naturally. Those studies have shown that over time, the effectiveness of antibodies declines, meaning that it seems unlikely that once infected, a person will have lifetime immunity. Dr. Lipsitch stresses we still don’t have enough hard evidence to know, but that we can make an “educated guess”. Based on his conceptual framework and statistical models, he suggests the following:
   1) Most people will make antibodies that can neutralize the virus and protect against future infection, but the extent of protection will vary between people;
   2) Antibodies will offer some protection over the medium term (“at least a year”)
   3) the effectiveness of that immunity will decline over time.
   The author cautions that there is still a lot we don’t know. For example, it’s still very unclear if some people can get re-infected with this virus after they recover. There is some data from South Korea and elsewhere showing that people who test negative after recovering later test positive again. We don’t yet know whether these are actual re-infections or that the negative test was a false result.
   Why is this important? The lack of good data and careful studies is a source of frustration for everyone. When we get a particularly useful new study, we take notice and toss in on the pile of gradually accumulating evidence. We don’t fully trust any one study, but instead look at the big picture pattern, cross-referencing and comparing each individual piece of the puzzle. That’s what good disease detectives do. This study is an important one because it gives us pretty good reason to think that asymptomatic transmission is a big part of the COVID-19 story. PS: In the article, Dr. Lipsitch also suggests that because of inadequate testing, we may be under-estimating the number of people infected by as much as a factor of 10 in some places.
   
3. New study demonstrates what we suspected: asymptomatic transmission is real
   An important study was just published as a brief communication in Nature Medicine. The study was based on a careful look at 94 lab-confirmed COVID-19 infections in Guangzhou China. The study is important because they looked at viral load (the amount of virus present in a sample) from over 400 throat swabs in order to see when and for how long patients were contagious. Through painstaking contact tracing, they were able to give us a clearer picture of how this virus spreads. In the study, they documented 77 transmission events (defined as a new secondary infection resulting from contact with an index case). The main conclusions of this study were:
   A) viral load peaked around the time that symptoms appeared or slightly earlier;
   B) COVID-19 patients became infectious 2.3 days before the appearance of symptoms;
   C) 44% of secondary infections occurred during the index cases’s pre-symptomatic period; and
   D) peak infectiousness occurred about 1 day before symptoms started. The study does not tell us anything about whether patients who never have symptoms can pass the illness to others.
   Why this matters? We have suspected that the SARS-CoV-2 virus must be spreading before symptoms are noticed, but before now we lacked confirmation. This kind of study is hard to do and very welcome because it gives us some of the most solid evidence yet that pre-symptomatic transmission is occurring: people can pass the disease before they know they are sick. This study reinforces the recent guidance that people should be wearing cloth face coverings in public.

Daily COVID-19 Briefing: 3/21/20

1. New York tops 10,000 cases. Major national disaster is declared
   Multiple news organizations report on the dire situation in New York state where confirmed COVID-19 cases now top 10,000 with 6,211 cases in New York City alone. The federal government declared New York a major disaster on Friday, making the state eligible for Federal Emergency Management Agency (FEMA) aid. Gov. Cuomo said the state anticipates that between 40 and 80 percent of New Yorkers will be infected with SARS-CoV-2, the virus that causes COVID-19.
   What does this mean? The goal for New York (and all other U.S. states) must be to flatten-the-curve so that the burden of disease can be spread out over time to avoid overwhelming hospitals, something that is already happening in this, the hardest hit state.
2. Viral mutation, everyone’s talking about it
   Public discourse and social media are filled with conjectures about how the SARS-CoV-2 virus might have, or might in the future mutate into something more dangerous. I am not a virologist, but I listen to what they say. Mutation is one of those scary words that has gone, well, viral! The reality is that all viruses mutate randomly all the time. That is because the replication process for an RNA virus is very prone to error. As a result, the SARS-CoV-2 virus, like all viruses is constantly mutating. There is no surprise in that. In fact, within one infected person, there will be countless different “versions” of the virus in circulation, like documents spewing from an old broken Xerox machine. All viruses mutate; those mutations rarely make any meaningful difference in how the virus works or how it spreads. The vast majority of mutations are just genetic noise; they don’t take hold and change the behavior of the pathogen because they don’t produce a meaningful survival advantage. Big changes do occur in viruses, but not generally on the time-scale of a specific outbreak. We do know that one such big change occurred when this coronavirus ‘spilled over’ from it’s natural host to people (possibly though an as yet unknown intermediate host).
   What does this mean? In science fiction, viruses (like superheroes) mutate suddenly and acquire extraordinary capabilities. In real life, meaningful mutations that matter are rare, unlikely and impossible to predict. That doesn’t mean that a qualitative change in the disease due to a mutation is impossible. But, we now have more tools than ever in human history to monitor this pathogen in real time, to watch for mutations that change the infectivity, transmissibility or lethality of the disease. That usually doesn’t happen. Nature is more complex. Yes, the virus is always mutating. That’s all part of what experts described in a comment in Nature Microbiology as the “…humdrum aspect of life for an RNA virus”. Most mutations don’t matter.
3. U.S. cases doubling every day, deaths doubling every 3 days
   If you follow my blog you are used to seeing a graph showing growth in cases. We are all trying to get our heads around the reality of exponential change. Below is a look at what is going on with deaths in the U.S. using data collated daily by Wikipedia. The bad news is that deaths are starting to escalate in a similar exponential way. The good news, if you want to call it that, is that deaths are doubling more slowly than cases.
   What does it mean? The fact that deaths are rising exponentially is not surprising. It is important though because deaths are a more reliable gauge of the actual epidemic (as opposed to being a measure of how much testing we are doing). We expect deaths to continue to rise. It’s too early to say when these numbers will peak.

4. Emerging evidence suggests that up to half of infections are covert cases
   According to a March 20 article in Nature News, The first evidence is now coming together to show that up to half of all infections of COVID-19 are covert cases, meaning they are infections in people with mild symptoms or no symptoms at all. This is important because it is widely believed that some covert cases have the potential to spread the disease to others. Because people with mild or no symptoms are much less likely to seek medical treatment and are not being tested, they may be driving the epidemic.
   What does this mean? We know that this novel coronavirus is more contagious than the flu. A big reason why is that people are out and about and spreading the disease without being tested or knowing that they are sick. That’s why the R0, or basic rate of reproduction continues to be around 2 or higher (meaning that every sick person transmits the illness to 2 other people). This is why it is so critical to continue to enact social distancing measures. It makes good sense that states are asking people to stay home.