An update on SARS-COV-2 mortality

We are now in to the third year of dealing with this virus and pandemic, so we’ve got some long term trend data to digest despite the fact our real time surveillance and monitoring is terrible. It is amazing that in this technically advanced country it takes over a month to collect and collate reliable mortality statistics. But that said, here’s a go at a summary of where we stand. Note that the CDC mortality statistics are compiled on a weekly basis, which makes sense as day to day variations and record keeping anomalies like holidays and weekends get smoothed out. Here I’m looking at “excess mortality” – people who died in any given week who probably would not have if it had not been for COVID. Also note that the typical course of the disease is that death occurs 2-3 weeks or so after infection, so the “death” curve lags the “infection” curve by around three weeks.

First, we have to pick a “start date.” For that we can’t use the calendar year because in the US the pandemic really didn’t get going and become widespread until the end of March or early April. So let’s use the 13th week of the year, March 28 2020 as our reference. That means year one is from March 28 2020 to March 26 2021, and year two is March 27 2021 to March 25 2022, and we are now about 17 weeks into year three. Here is a plot of excess deaths due to the pandemic by week. The blue line is the first year, the orange line the second year, and the yellow line is this year so far. I’ll explain the green line further down.

Click to see full size.

The blue line, 2020, clearly shows the initial wave (with the sharp rise as the disease spread and vulnerable populations fell) as the infection spread across the country. The “summer peak”, which is unusual for a respiratory virus, is also clear, and happened between mid June and early September. Then the big one, the massive winter wave of 2020 between weeks 30 and 52 (early November to early March). Enter 2021 (the orange line). Here we have three factors: first, the various masking and social distancing measures were in full force, and second vaccination was kicking off. By week 1 of year two (first week of April 2021) 25% of Americans were “fully vaccinated” (the initial two dose sequence), and there was no spring wave or early summer peak as seen in 2020. Unfortunately by Summer 2021 restrictions were being lifted, and there was still a significant population that was either not exposed and unvaccinated. So the delayed summer peak hit with almost as many deaths as the initial wave in the spring of 2020. By disease week 40 62% of the population had been vaccinated, so perhaps 80% of the population had some kind of immunity from either having COVID or being vaccinated. So why was there a sharp uptick in the orange line? The third factor: variants like Omicron. While technically not as deadly, the variants spread more easily than COVID Classic. But, as the graph shows, the peak was not as high, and not as many people fell sick and died. So how bad was the first year? We lost 555,242 people who would not have otherwise died. SARS-COV-2 had a whole population mortality rate of 0.168%. The 2017 Flu season had a whole population mortality rate of 0.0187%. So it was far worse than a normal influenza epidemic, almost ten times as bad. However, it wasn’t as bad as the Spanish Flu of 1918, which had a rate of around 0.3%. The two year rate for Spanish Flu was 0.65%, SARS-COV-2 was 0.30%. However, a caution, in that the full story of COVID has yet to be told. Spanish Flu went away, and immunity was long lasting. it doesn’t look like this new virus is going to go so quietly.

Where do we stand? At first things looked pretty good this year. The mortality trend was going down. But the new variant (BA5) is more easily transmitted and appears to be more deadly. Starting at the end of March, the death rate in 2022 became higher than in 2021 – and the trends aren’t good. The yellow line is reported, but as noted above there is a problem. It takes at least a month for all of the mortality data to come in. Even so what we have the line is above 2021, and if we estimate statistically what the line might look like when all the data is in, we get the green line. I sure hope that’s wrong, but in any event it does look like we might be in for another wave.

One last note of interest, the consensus computer models (not the extreme ones that got all the attention in public) at the end of February 2020 estimated the mortality in the US for the first year of the pandemic at 0.1326%. That’s not too bad given what was observed (0.168%).

Caveats: this isn’t a formal scientific study, just a brief overview. I think it’s pretty close, it’s just plotting processed numbers so not terribly complex, but obviously not peer reviewed. The primary reference data for this analysis is the CDC’s Excess Deaths Associated with COVID-19 data set (link to CSV). Vaccination data also from CDC is located here (link). Both are raw data sets, be sure to read and understand the technical notes before you do any number crunching – like hurricane track data, spaghetti must be cooked before consumed 😛 .

Roost Rings

The Charleston SC Doppler radar (really located south of Hampton, SC) picked up something that, if you’ve never seen them before, might send you scurrying to the news to see if something blew up, or the nearest UFO meeting to see what you missed:

Radar from KCLX (“Charleston” radar), Saturday Morning, 23 July 2022

Here is one frame zoomed in on the source, which seems to be east of Columbia, near Irmo, SC …

And here is what is there on Google Earth:

Click any graphic to embiggen.

So what is going on? The lake is a strong clue. It is a “Roost Ring”, radar returns from massive numbers of birds leaving their roosts to head out to forage for the day. Here is an article from the National Weather Service with more details (link). In this case we are seeing Purple Martins leaving Lake Murray, which holds the largest sanctuary in North America, Bomb Island, home to something like one million of these birds.

The above radar images are reflectivity (strength) on the left, and direction of motion relative to the radar station on the right. Green means it is moving towards the radar station, red away. On the zoomed in view, that “arrow” pointing towards the station is an artifact of the earth’s curvature, the height the birds are flying, and the scan angle of the radar. Another neat thing to see is that thunderstorm cluster that flared up over Myrtle Beach, visible in the top animation which covers from 5:30 to 7:30 am. At 6:15 it was nothing, by 7am it was a strong, 50dBZ return. That goes to show that this time if year it doesn’t take long for an innocent looking cloud to turn into a dangerous thunderstorm, so boaters and aviators beware! Just because the radar is clear now doesn’t mean it will be that way in 20 or 30 minutes.

FYI, there’s no threatening activity to speak of in the tropics anywhere in the world. JTWC is watching a weak circulation south of Japan, and NHC is watching activity in the Eastern Pacific, but staying offshore of Mexico and fading out before nearing Hawai’i, so no big risks there. No major earthquakes recently, and the situation in Ukraine continues to be Russia methodically working their way towards their objectives, not that you’d know that from Western media. The COVID pandemic is entering a new phase, with lots of interesting research and much better understanding of both the virus and how the vaccines interact. Unfortunately the data collection system and advice for the public, over two years after the virus appeared, is still substandard, with many states (like Georgia) not having updated their public data pages since April, and the news media jumping from issue to issue with no consistent coverage. The environment is so hostile for rational discourse that it’s hard to get the energy to write up something on either of those topics, but maybe I’ll give it a go next week.

#Europe and the UK on Fire

Temperatures in the UK and Europe are on track to set all time records today. Headlines on BBC are “Warnings of Heat Apocalypse (link)”, which for once are actually not far off …

Click to embiggen. Expected high temperature in degrees F for the ignorant colonists.

France has been suffering for several days, with not just high temperatures but extensive fires in the Southwest of the country. Portugal and Spain also have extensive fires, here is one as observed by the EU’s Sentinel satellite system:

European Union, Copernicus Sentinel-2 imagery of Castilla y Léon , in western Spain.

London is under its first ever “Red Extreme Heat Warning (link)” and is on track for records today. The overall high temperature record is the UK us 38.7F, or 101.7. That record will almost certainly be broken somewhere in southern England today. But records are broken all the time, given the fact our record of observations is relatively limited. So just how unusual is this? Let’s take a closer look.

The observatory at Greenwich has been collecting data since 1841. That’s a pretty good record, but it’s only 180 years. Using data from 1991 to 2020, the average high in July is 74.8F, the record is 95.5F, the all time record, set in August 2003, is 99.5F. The previous record was set in 1990 at 95F. So if the temperature does hit 106F as forecast then both the July and all time records will be shattered. So this is a pretty unusual event. Is it related to climate change? Well, that’s a more complicated question. The temperatures are likely higher due to anthropogenic (human caused) factors. Pointing the finger at any given day or event and screaming “J’ACCUSE!” is really tricky (and scientifically unsound). What we can say is that events like this are more likely, and we will see more of them going forward. That’s not a good thing.

Coastal GA/SC Rain 9-11 July

There has been an interesting (and needed) rain event over Coastal GA (Savannah) and the South Carolina Low Country the last few days. Here is the Multi Radar Multi Sensor (MRMS) 72 hour accumulation from 8am 9 July to 8am 12 July 2022:

Click to embiggen and see location labels

The gauge at the Enki office in Midtown Savannah is showing 5.99″, which is close to the MRMS estimate. Notice the very sharp gradient and the southwest-northeast line area of heavy rain running along the coast. This is caused by storm cells following roughly the same ground track during the big rain events the last few days. Saturday and Sunday night’s rain each of dropped over 2″, and 1.8″ another last night. So far in July our gauge is showing 8.08″. But compare that to the Savannah International Airport, located 8.5 miles inland, which has only had 2.15″ over the same period. For this weekend’s rain, rain totals varied from under an inch in parts of Pooler to over 6.5″ in parts of downtown, around 5.5″ midtown, 4.5 at Hunter Army Air Field, and over 5″ at Skidaway and parts of the Islands.

Rain is one of the hardest weather variables to forecast. This example shows why – sites located only a few miles apart (indeed, only a few city blocks apart) can show radically different rain totals depending on the exact track of thunderstorm cells. Winter rains (stratiform rain) tend to be more uniform. But summer rain, which is typically convective (produced by thunderstorms), can be far more localized.

Thing in the Gulf, First Webb Images

There is an area in the northern Gulf of Mexico being watched by the National Hurricane Center. If you like watching paint dry, you can too, otherwise, by far the most likely outcome is heavy rain along the Gulf Coast. Elsewhere, the only actual storm is Hurricane Darby, about halfway between Baja and Hawai’i. So you can relax and enjoy the first Webb Space Telescope images. As good as the Hubble images were, Webb is an order of magnitude better. Here is a comparison of galaxies seen in the first public image released yesterday:

Webb (left), HST (right)

To make this even more incredible, the HST images are from a 10 day (240 hour) exposure. The Webb images are from only a 12 hour exposure! More images are coming this morning … this is an amazing view of the early universe, and Webb should provide fertile ground for advances in many areas of astronomy and astrophysics.

#Bonnie still going …

Bonnie is still a tropical storm, an incredible 6,800 miles from where it started off the coast of Africa. Before finally dissipating it may well have traveled 7,650 miles from it’s origin. That’s more than 1/3 the way around the earth. It’s very close to the all time record (Hurricane Faith, which traveled over 7800 miles).

Only twenty storms are recognized as “crossing over” from Atlantic to Pacific. Bonnie is one of only three storms to cross from the Atlantic to the Pacific and become a major hurricane. While we have to note the records and near records, we shouldn’t forget the death and destruction it caused in Nicaragua as a tropical storm, killing at least three.

Bonnie probably won’t make it to Hawai’i or the Central Pacific hurricane warning area (which starts at 140 degrees east longitude), but it might get close. The forecast is for the storm to fade out just before reaching that point. But any way you look at it, that’s quite a ride.

#Colin Collapses, #Bonnie Builds, Typhoon Chaba hits China

The briefly lived (if it every really existed) Tropical Storm Colin has completely dissipated. Looking at the NWS Local Storm Reports this morning, it didn’t seem to have any onshore impact; all of the reports were associated with an approaching front, not Colin …

Colin swath and Weather Service local storm reports.

Bonnie, the Atlantic storm that hit Nicaragua, is now an East Pacific storm and still causing a risk of flash floods and mudslides as it moves further from shore. It is forecast to become a hurricane tomorrow as in parallels the coast of Mexico, carrying the risk of rain northward with it before turning out to sea south of Baja.

Bonnie swath

Finally, Typhoon Chaba hit southern China yesterday. Twenty seven are missing from a ship offshore that split in two, only three rescued so far and not much hope for the rest. Southern China has seen a lot of rain over the last few months and most rivers were already full; this storm won’t help and widespread flooding is expected. Estimated economic impacts on the 31 Million people in the tropical storm damage swath are probably approaching $2 Billion USD.

The only other activity in the tropics is Tropical Storm Aere, which is decaying as it heads towards Japan. Shouldn’t be anything other than a rain and gusty wind event.

Tropical Storm Colin??? #SouthCarolina under warnings (but don’t worry)

In a bit of a shock, as of 5am this morning (Saturday) the US National Hurricane Center has started advisories on the weak low pressure system hugging the South Carolina coast and called it Tropical Storm Colin. Here are their Key Messages regarding Tropical Storm Colin (en Español: Mensajes Claves). The short version is that impacts on land are expected to be minimal other than rain – any significant sustained winds are expected to stay offshore. Here is the impact forecast swath …

click to embiggen.

On satellite as the sun comes up the view isn’t spectacular:

InfraRed (Cloud Top Temperatures) left, Visible on the right

And on radar, the center is near the comma shaped thing just inland from Georgetown, SC …

Composite low level reflectivity

This is one of those cases where this may technically be a tropical storm, but the impacts are hardly going to any different from a strong frontal passage or cluster of afternoon thunderstorms. Interestingly, the somewhat more organized state of the low is drawing in drier are over coastal Georgia and the Low Country. We may still get thunderstorms this afternoon, but the threat of flooding is greatly diminished (outside the usual stuff with thunderstorms).

For the curious here is an excerpt from the initial discussion from NHC …

Deep convection formed near the low center as it was moving inland and has persisted and become better organized over the past 6 to 12 hours. In addition, surface observations and ASCAT data from 02-03 UTC indicated that an area of sustained 35-kt winds had developed offshore and near the coast of South Carolina. As a result, and rather unexpectedly, Tropical Storm Colin has formed near the South Carolina coast, centered just inland a bit to the northeast of Charleston.

Yellow X of Doom off the Georgia Coast!

NHC has tagged a low pressure system just off the Georgia coast with a 10% chance of becoming a tropical depression. TLDR: threat condition “Meh” unless you driving some place that floods all the time like the aptly named Waters Avenue in Savannah. For coastal GA/SC, this slow moving system has the potential to dump a lot of rain. But you wouldn’t really think it a tropical cyclone risk unless some weather dude or dudette told you it was …

Swirl of Doom near Georgia; Tropical Storm Bonnie at bottom.

In actual tropical news, Tropical Storm Bonnie is making landfall in Nicaragua this evening, with the threat of flooding and mudslides. Key Messages regarding Tropical Storm Bonnie (Link to NHC).