geosciencebigpicture

A seasonal second wave of SARS-2 infections has spread around the Northern Hemisphere since the last post. Generally deaths are far fewer, both because many of the most vulnerable have been exposed and because a younger and healthier group is getting it now.
We digitized the available graphs of deaths for the 1918-19 pandemic. these were available for several US cities and for England.

The three Eastern Seaboard Cities of Boston, D.C., and Baltimore are pretty similar with DC having more of a preamble in July and Baltimore getting off easier on the second wave. San Francisco was more like the Eastern Seaboard but shifted. It had an easier first wave and a rougher second. Augusta had two more equal waves, with the second worse than the first. England got off easy in both waves and its first wave was opposite phase. There were substantial regional variations in phase and severity.

There are considerable phase and severity variations in the current pandemic around the US as well. What is really striking is how we have dragged the current pandemic out so much longer than prior ones.

Data for 1918 uses SF as a proxy, and requires a 50x separate scale. December data  for Covid is incomplete and will increase a bit. If we did actually flatten the Covid death curve with our interventions, the unflattened curve would have been impressively steep. I suspect we just delayed the waves.

A joke last winter was that if Covid lasted until summer, we could have corona with Lyme (disease). It did.

Last year’s seasonal flu vaccine was judged 45% effective. This is typical effectiveness for a seasonal flu vaccine after half a century of practice. Now let’s say 50% of the people will take the vaccine in line with recent studies. This is multiplicative so the population effectiveness is 22.5%. SARS 2 has an Ro of at least 3, so a vaccine would need to be effective for 70% of the population. 22.5% will help but will not end the pandemic. However, natural immunity from recovery has been building. Unlike vaccine immunity based only on who was given or will take the vaccine, natural immunity is based on the virus finding the most susceptible first. Natural group immunity may require only ~20% of the population to end the pandemic. The extent of natural immunity is currently unknown. The pandemic will end when either the natural or vaccine threshold of group immunity is achieved, or some combination thereof. What is clear is that a significant contribution from natural immunity will be necessary for a vaccine to work.

The time scale of viral evolution is hours. The infectious vectors called virions can each produce thousands of copies of themselves from a single infected cell. Within hours, natural selection will determine which virions will successfully infect another cell/organ/individual; and which will die.

In ecology, the opposing reproductive strategies of wide dispersal and rapid colonization vs. taking a stand and extracting maximal resources are mathematically modeled as r and k selection, respectively. R selection favors being a weed. K selection favors being a giant sequoia.

The hypothesis of seasonal Darwinism attempts to explain the mysterious seasonality of some viruses as near real time r selection, favoring dispersal and transmissivity, during the summer when human populations are better fed, more dispersed, more outside, and more vitamin D enriched; and k selection, favoring virulence, in the winter when these factors are reversed.

SARS 2 is a single stranded positive RNA virus. It must first create a negative copy for replication, making replication and translation at the same time more difficult. The virus must balance these two processes, and the balance struck determines how many copies of itself it makes–its virulence. Selection based on this balancing strategy, with virulence favored when it is easy to find new hosts, and transmission–producing fewer copies for a longer period of time–when finding new hosts becomes more difficult. 

One might argue that SARS 2 is not seasonal since a resurgence has taken place over much of the northern hemisphere summer, but this resurgence has clearly been less virulent, with a far lower case fatality ratio. The coming winter will tell.

Credit: These ideas are strongly influenced by Patrick Stewart on his blog, oldwivesandvirologists. He believes strongly in a temperature switch in the viral RNA secondary structure. Whether or not this proves to be the case, natural selection based on conditions of the host population–seasonal Darwinism–can explain much of viral seasonality.

Perusing the state new case curves on https://rt.live/ some patterns become apparent.

Some states with early exposure are on a clear downward trend.

Some southern states with later exposure are on an upward trend, California being an exception by early exposure.

Some  early starting midwestern states seem over the hump, DC being eastern with similar shape.

Some later starting states also seem over the hump.

Some northerly late starting states are climbing.

Some states are cruising.

Some show a second wave, and Wyoming which never lifted off.

1. There is no consistent relationship between lifting house arrest and new cases.
2.  There is no indication that seasonality is slowing the spread.
3.  Below Rt=1 (faintly visible in background) Rt can rise and new cases can still fall. The inverse is also true.
4.  Washington State has managed a modest decline with Rt>1.
5.  Utah has had steady Rt>1 for the entire period. A month elapesd before there was appreciable increase in cases, and it experienced a striking rise without any increase in Rt.

The more you know, the more you know you don’t know Jack.