Ebola:  Last contacts have finished follow up, and have not caught the virus.  Very close to the last Ebola update (until the next outbreak).

Coronavirus:  We’ve still been brisk on the testing, so comments will be brief.

–There are several distinct strains of coronavirus, if you have seen those headlines.  That does not mean the virus is mutating to be more dangerous.  There are just distinct “families” with a similar genetic fingerprint.  In fact, this is a very slowly mutating virus—mostly because it doesn’t need to change much right now to be very infectious. 

The ideal state for SARS-CoV-2, if it wants to replicate itself as much as possible (the goal of any virus), is to become less symptomatic and less likely to hospitalize people (while being as or more infectious) so that the hosts (us) start aggregating again and it can find new ones.  If it mutates to kill easier, it will have to become MORE infectious at the same time, because it will start burning through hosts faster than it can jump.  

Again, you can model this in Plague, Inc., the game on your smart phone.  The most consistently effective strategy, for you as a virus/fungus/bacteria in the game, is to be highly infectious (as infectious as you can get) but as asymptomatic and mild as you can be, so humanity does not notice you until it is way too late and you have infected everyone. 

So take cytomegalovirus, CMV.  Do you remember that time you caught CMV?  Almost certainly not.  Unless you are immunosuppressed or a newborn, CMV is not much of a threat.  If you noticed that time you got CMV at all, it was a week or so where you felt more tired than usual (it’s EBV-negative mono).  If I tested everyone this email series has been going to, somewhere between 60-80% have caught CMV at some point in your life.  By time you are 80, the chances that you have caught CMV are more than 90%.

That is a virus that knows how to get it done.  From the perspective of a virus, you don’t -want- to kill a host.  That’s an accident if you do, and a bad one, because the dead host can no longer carry you to meet other hosts.  And you need hosts to replicate.  CMV, running as silent as it does, is an -almost- perfect virus.  Honestly, if it wasn’t for the rare CMV complication of a transplant or chemo patient, newborn, or in utero baby, we probably wouldn’t know anything about it.  It would never hit the research radar. 

Anyways, like many epidemics, the case fatality rate is likely to fall over time and  the most likely mutation direction will be towards LESS severe disease, because it REALLY needs us to stop this quarantine nonsense so it can please get back to infecting us all.  The strains that survive of SARS-CoV-2 will have been selected for being still being present and infectious (probably for longer), but more hosts are more asymptomatic, to get the restrictions lifted that are cramping its style right now. 

So don’t get too worked up by any scare “THE VIRUS IS MUTATING!” headlines.  That doesn’t mean we are all going to die.

–But hey, speaking of moves by SARS-CoV-2 to become more asymptomatic, though still able to be spread…  We have noticed several patients with virus right at the limit of detection of our assay (so not much, but still definitely there).  A lot of them seem to be in patients we have been told did not have particularly noticeable symptoms.  We are not the only ones to notice this:

So if you do catch the ol’ corona, stick to the recommended isolation procedures, EVEN IF THE SYMPTOMS ARE GONE.  You may still be infectious to others.

–The Northern California correspondent on this e-mail list sent an article this afternoon that raised some interesting points.  First, there is growing suspicion among researchers in Italy and the US that SARS-CoV-2 started far earlier than the first reported cases and was likely spreading in early autumn of 2019.  Second, California had an especially intense flu season with more hospitalizations and deaths in late fall/early winter of 2019, which was attributed to a less common “flu B” strain, since the flu A tests kept coming up negative.  California also receives an enormous number of Chinese tourists every day (at least until the planes stopped running).  So there is a question as to whether SARS-CoV-2 may have been in California much sooner than expected, and perhaps an unrecognized (at the time) contributor to the flu season there.  If so, it might help explain (along with some of the earliest lock downs in the country) why California has been getting off comparatively easy, while New York is getting crushed.  Many Californians may have already -had- SARS-CoV-2.  Remember, most cases are flu-like only, and MANY cases show no or very few symptoms. 

Basically, we desperately need a good serologic assay.  The antibodies your body makes to SARS-CoV-2 are the best way to know how many people have been exposed already (and thus have antibodies circulating in their blood), and the best way to get the true denominator of the disease.  It’s also the best “back to work” test running.  The PCR I’m doing is only good for rapidly finding -active- disease (or at least that the virus is there right now). 

–In other news, more mixed reports about hydroxychloroquine in small, underpowered studies.  So still a maybe?  We’ll see.

–Lastly, the re-stocking rate in grocery stores still seems surprisingly light.  After the first round of hoarding, there really isn’t all that much more hoarding to be had.  You don’t see people walking out with all the hamburger in the place anymore (those people still have a freezer full of hamburger right now, after all).  This looks more like a supply chain issue, and there are rumors about issues at warehouses having enough staff available to work, as well as lockdowns affecting the amount of people harvesting food.  Food coming internationally will be hampered by the global supply chain problems overall.  But even stuff available locally is becoming tough to come by.  I order meat direct from a local farm just east of town (why you might want to do the same where you live is a topic for another day).  They have been running out of everything too, although that may in part be more people here discovering my farm guys since they can’t find what they want in the local grocery stores often enough anymore—and that farm delivers to your door, so easier social distancing as a bonus.  I mean, maybe more people have found them and they are out of stock of more stuff due to increased demand?  Could be.  But that even locally grown stuff out here, in one of the most productive agricultural regions in the world, is getting tough to come by is a little… concerning.  Especially as lock downs start to get extended.  Historically, spring is actually the starving time.  You are already running low on all the tubers and other winter stable crops you ate over the winter, and you are out of animals you can afford to sacrifice for meat and still have new animals to rear the next year.  Meanwhile, none of the new crops are fully grown yet—they will be growing during the spring.   Don’t believe me?  Here’s a “what’s in season” calendar (partial–from http://www.thespruceeats.com).  Just count the number of entries for the following months:

July: apricots, blackberries, blueberries, cantaloupe, corn, cucumbers, green beans, kiwi, kohlrabi, lettuce, mangoes, okra, peaches, peppers, plums, raspberries, strawberries, summer squash, Swiss chard, tomatoes, watermelon, zucchini.

August: acorn squash, apples, apricots, blueberries, butternut squash, cantaloupe, corn, cucumbers, eggplant, figs, green beans, kiwi, kohlrabi, lettuce, mangoes, okra, peaches, peppers, plums, raspberries, strawberries, summer squash, Swiss chard, tomatoes, watermelon, zucchini.

September: acorn squash, apples, beets, butternut squash, cantaloupe, cauliflower, eggplant, figs, grapes, green beans, lettuce, mangoes, mushrooms, okra, peppers, persimmons, pomegranates, pumpkins, spinach, sweet potatoes, Swiss chard, tomatoes.

October: acorn squash, apples, beets, broccoli, Brussels sprouts, butternut squash, cabbage, cauliflower, cranberries, grapes, leeks, lettuce, mushrooms, parsnips, persimmons, pomegranates, pumpkins, rutabagas, spinach, sweet potatoes, Swiss chard, turnips, winter squash.

November: beets, broccoli, Brussels sprouts, cabbage, cauliflower, cranberries, leeks, mushrooms, oranges, parsnips, pears, persimmons, pomegranates, pumpkins, rutabagas, spinach, sweet potatoes, tangerines, turnips, winter squash.

And now, here’s March and April:

March: artichokes, broccoli, Brussels sprouts, cauliflower, leeks, lettuce, mushrooms, parsnips, pineapples, radishes, rutabagas, turnips.

April: artichokes, asparagus, broccoli, cauliflower, leeks, lettuce, mushrooms, pineapples, radishes, rhubarb, spring peas.

(and note that parsnips, radishes, rutabagas and turnips are not “in season” because they are growing—they are merely still around as over winter storage crops)

The point?  I don’t expect a complete collapse in food production and distribution.  After all, deus impeditio esuritori nullus—and governments know that.  But no one expects the Spanish Inquisition either.  That month supply of food I suggested you consider, long before hoarding was even a thing among the general public?  If you got it, avoid the urge to dip into that.  Keep focused on minimizing grocery trips, but stick to what is there now.  Your 1 month supply is really your hedge against the worst possible outcome, especially considering the season of the year all of this fun is happening in.  I want to stress that I very seriously doubt it will come to that.  Just hedge your downside risk anyways.

–And continue to expect a very unusual year.

–Your chances of catching Ebola are all but nil.  Your chances of catching coronavirus are very good in most parts of the world.  Stick to social distancing recommendations.

Love in the Time of Coronavirus:

Where the virus is found, and how it got there, in pictures:

What does this map (above) have in common with this one below it?

The virus favors population centers (the map of the electoral college works just as well as the megaregions) broadly speaking.  How many cases you have is almost a function of population density and how much you have been testing at this point.  SARS-CoV-2 favoring dense population regions (mathematically as well as biologically) also holds at smaller levels of geography.  For instance, you can match cases/county to population/county in Indiana with a nearly perfect correlation.  And of course, getting stuck on a high population density cruise ship is a really good way to catch the ol’ corona.

I remember being struck by the cases per county map the ISDH publishes about two weeks ago (~March 20, which is shown above).  If you scroll back up to the map of the US economic/political/cultural megaregions above, all of the white nodes in the Great Lakes region have one thing in common—they are all about 1 day’s drive or less from each other via semi-truck.  How did the virus get to Indiana?  Look at the March 20 map above, and it’s clear.  The virus hopped on the interstates.  You can trace most of the interstates crossing Indiana through the counties with known cases on March 20.  And once it got off the interstates in a population center, it took off (see the more recent map of Indiana above).  I will wager I can draw a map like this for most everywhere in the world.  The only difference will be the dominant form of economic transportation into and out of that region.

“It’s 106 miles to Chicago.  We’ve got a full tank of gas, half a pack of cigarettes, it’s dark, and we’re a respiratory virus.  Hit it.”

–SARS-CoV-2 (probably)

Thanks for the birthday wishes this week.  40 and loving it?

<Paladin>