Daily COVID-19 Briefing: Monday

Top news, reports and insights for today:

1. Daily headline summaries for Monday:

• WHO warns the pandemic is worsening across the globe as the number of new cases on Sunday reached an all-time high. Large rises seen in central and South America and South Asia (CNBC)
• Florida is preparing to reopen restaurants, bars, gyms, shops, amusement parks and vacation rentals. At the same time, new cases have been surging after the first wave of reopening, reversing a downward trend. That state has seen new cases exceeding 1,000 a day for 5 straight days (Futurism, see Figure B below)
• New study shows stay-at-home orders in Illinois lowered infections compared to Iowa in the 15 counties on the boarder between those states (Jama, see Figure A below)

FIGURE A: From Lyu and Wehby, JAMA, 5-15-20: https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2766229?utm_source=silverchair&utm_medium=email&utm_campaign=article_alert-jamanetworkopen&utm_content=mthlyforyou&utm_term=060720

FIGURE B: Taken from Futurism: http://91-divoc.com/pages/covid-visualization/

2. U.S. daily cases are flat at 20,000 per day for 12 days, epidemic intensifying in 25 states
   Today, I will focus on recent changes in COVID-19 cases by state (see the 3 figures below). Overall, the U.S. now reports over 1.9 million cases (2 million plus if counting probable cases), or 28% of all global infections. Brazil now has the second most cases at 694,000, 9.7% of the total across the planet. Among countries with 100,000 cases or more, the U.S. now ranks 3rd in cases per 1 million population behind Chile and Spain. As the top graph shows, daily cases have been flat at just over 20,000 since May 26 (based on 7-day moving average). This reflects, I believe, the start of resurgence of transmission intensity in states that have reopened. Over the past 3 days, 5 states have set new record highs for daily cases (Arizona, New Mexico, Utah, Oregon and North Carolina). Utah and North Carolina set records on back-to-back days. Arizona, for example, had reported more than 1,000 daily cases once before. That state had 1,579 cases on June 5. The middle graph shows daily new cases per 100,000 population by state. The positive news is that 21 states had fewer than 5 new cases per day per 100,000. However, cases are spiking at 10 or more a day in Arizona, Utah, Nebraska, Arkansas, and Washington DC. The southern region had the most states with more than 5 a day (11 of 13). The area comprising Iowa, Illinois, Indiana, Minnesota, North Dakota, South Dakota and Wisconsin, all had significant rises in cases, indicating the upper midwest is still a hotspot. The bottom graph shows growth factors by state for change in cases over the last week. Numbers greater than 1 means cases are growing week-over-week. In the northeast, only Vermont is rising although numbers are small. In the south, transmission intensity is rising in 9 of 13 states, the most in Arkansas, now doubling in cases every 10 days. In the midwest, cases are spiking in North Dakota with 80% rise last week. The western region also has all but 3 states with cases climbing, with Alaska, Arizona, Hawaii, New Mexico, Oregon and Utah reporting 50% or more increases in new cases.
   What it means? States continue to reopen even as widespread intensification of infections is seen, particularly in the south and west. Weekly cases are rising in 25 states. I expect the trend of 20,000 daily cases to continue and to rise slowly over the next two weeks.

3. The great influenza of 1918-19: Learning lessons from the “mother of all pandemics”
   We still don’t know whether there will be additional waves of epidemic transmission of coronavirus in the U.S. and other countries in the Fall and Winter of 2020. However, we should be planning now for the possibility that it might. One place to look for insights is the Spanish influenza epidemic of 1918-19, which claimed the lives of more than half a million Americans and more than 50 million world wide. A cautionary tale from that epidemic points to the possibility of major re-ignition of epidemic transmission seen in that pandemic. As the graph below shows, taken from a 2006 paper by two experts, the initial wave starting in March of 1918 (shown here for the UK but the dynamic globally was similar) was quite mild. After a quiet summer, the pandemic exploded in October and November of that year, making it the “mother of all pandemics”. This was followed by a third wave in February-April of 1919, more lethal than round 1 but less so than round 2. It’s still not entirely clear why this happened. Its possible the virus mutated between wave 1 and 2, but this cannot be confirmed due to lack of genes from the wave 1 virus. What is known is that both influenza and coronavirus can manifest this repeating wave phenomenon. We don’t know if this will happen with SARS-CoV-2 but now is the time we need to prepare for the possibility that the pandemic will roar back to life in the fall.

From Taubenberger and Morens, Emerg. Inf. Dis. 2006.

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Daily COVID-19 Briefing: 5/12/20

Top news, reports and insights for today:

1. Daily headline summaries for Tuesday:

• Former FDA commissioner Dr. Scott Gottlieb says we are starting to see cases ramping up in states that have reopened like Texas, Alabama and South Dakota (CNBC)
• Sweden has eschewed wide-spread “lockdown”. Now, that nation must adjust their strategy in response to skyrocketing deaths in nursing homes (Bloomberg)
• Johns Hopkins University in collaboration with New York State now offering online training for contact tracers (Coursera)
• New York City saw 24,172 more deaths than “normal” from March 11 to May 2 based on past trends. About 19,000 were tied to COVID-19, but an additional 5,293 excess deaths remain unexplained and might be coronavirus-related (Bloomberg)
• Southern states are reopening, but patrons are not yet ready to go out for dinner. Data from OpenTable shows that reservations are still down 83-92% in states that have reopened restaurants (Slate, see graph below)

Screen grab from Article by Jordan Weissmann in Slate: https://slate.com/business/2020/05/south-reopening-restaurants-coronavirus-opentable.html

2. The whack-a-mole effect: why you shouldn’t trust the U.S. plateau
   Everyday people are talking as if there is one big epidemic occurring in the U.S. (and every other country for that matter). This is reinforced by our preoccupation with the national numbers we look at each day. I’m as guilty of this as anyone. But, the truth is that like politics, all transmission dynamics are local. I struggle in this blog to convey deep truths about the nature of epidemics, many of which are contrary to our common sense. Here is another one: there is no one American epidemic. That’s just not how infectious outbreaks work. What we have is better thought of as a series of interconnected local outbreaks that rise and fall in traveling wavelets of infectious chain reactions. The coronavirus acts like a sneaky serial killer. It moves into a new area, spreads for a time at an exponential rate, kills a bunch of people, and then packs up and hitches a ride with a trucker to the next town where it starts it’s killing spree all over. Call it the Wuhan strangler! This creates a massively scaled whack-a-mole game, where the virus waxes and wanes in communities, rising in intensity here at the same time it is running out of easy targets there. When we see the national numbers plateau, we falsely believe we are bringing the disease to heal. But because there is not one giant wave, we fail to see that this is an illusion.
   I very much liked an opinion piece by Nathaniel Lash in the New York Times on May 6 that puts this issue into perspective. For weeks, the swell of cases from New York was driving the overall picture. As that hot spot started to burn out, it looked like the national epidemic was slowing. It wasn’t. instead, the serial killer was just shifting locations as the G-men were bearing down on it in the Big Apple. The 4 graphs below, taken from the Lash opinion piece show this clearly. Slide A shows the overall flattening of the national curve in the first week of April. Looks like good news right? Only if you are in New York. Slide B shows the same curve after removing the influence of New York City. It shows a different story; new cases elsewhere continue to rise. Figure C shows the national trend removing New York City, Detroit and New Orleans. There is no plateau. Slide D shows the whack-a-mole effect at the state level in Texas and Oklahoma. Texas looked like it plateaued (at least before early May), but actually, the initial hot spot in Houston was winding down, making it appear that the state was waning when the infectious vanguard had just shifted to other places. The same pattern is seen in Oklahoma. Both states have started reopening, resulting in new case surges both in the initial hot spots and the rest of the state.
   What this means: It’s a mistake to think that the U.S. epidemic is one thing. Transmission dynamics happen on smaller scale geographies. This epidemic, like all others, moves through populations in traveling wavelets that rise and fall and shift locations. Keep the whack-a-mole effect in mind whenever looking at trends in big geographies. We are a long way from herd immunity so don’t make the mistake of thinking we have this sneaky serial killer cornered.

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  Slide A: US overall

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  Slide B: US without NYC

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  Slide C: US without NYC, Detroit & New Orleans

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  Slide D: Texas and Oklahoma

Slides from New York Times opinion by Nathaniel Lash, May 6: https://www.nytimes.com/interactive/2020/05/06/opinion/coronavirus-deaths-statistics.html?searchResultPosition=1

3. U.S. deaths fall to levels not seen since March 31, thirteen states saw deaths climb by a third last week
   On Monday, there were 836 reported deaths, a 1.1% rise, and the lowest total deaths seen since March 31. While this is good news, we are now familiar the drop in reporting seen consistently on Sunday and Monday; we will have to wait to see Tuesday’s numbers. If you read point 2 above, you now know that we must look beneath the overall trend and ask where the epidemic is now surging. The bottom graph, once again, shows change in deaths over the last week across states. New deaths are down in New York (+11%), Michigan (+11%), and Louisiana (+13%). But 13 states reported cumulative growth of 30% or more last week. That’s whack-a-mole. There were several states in each region where deaths were rising. In the West, Arizona, still on the bottom of the list in testing, leads the region with a rise of 54% in total deaths. New Mexico and Utah also saw concerning rises. Six mid-west states reported rising deaths, lead by South Dakota (+60%). Meat processing plants have played a key role in outbreaks in most of these states including South Dakota, Iowa, North Dakota, Missouri, Minnesota and Nebraska. In the South, Alabama and Mississippi saw accelerating growth in deaths. In the northeast, New Hampshire and Pennsylvania remain in the pandemic’s cross-hairs.
   Bottom line: Overall new deaths were down yesterday, a welcome sign, but caution dictates we wait for Tuesday rebound and stay focused on the shifting terrain of traveling wavelets.

Top pick of the day

Their States Are in Crisis. They’re Declaring Victory Anyway.

Article in The Atlantic, Politics by Elaine Godfrey, May 8, 2020

Five republican governors have claimed victory over the virus. In four of those states, cases are rising. The growing disconnect between what some officials are claiming and what the data shows.

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.