Wednesday COVID-19 Briefing

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Top news, reports and insights for today:

1. Curated headline summaries for Wednesday:

• Researchers combined information from 32 studies of COVID-19 risk in children, finding that children and adolescents had 44% lower odds of secondary infection with SARS-CoV-2 compared with adults (JAMA Pediatrics)
• Moderna CEO says its coronavirus vaccine won’t be ready until spring of next year (CBS News)
• The White House coronavirus task force again this week strongly recommending mask usage in some states like Iowa and Georgia that still do not have statewide mask mandates (CNN Politics)
• Hospitals feel the squeeze as cases spike in upper Midwest states Wisconsin, North Dakota (ABC News)
• Facebook removes 38 versions of Trump campaign ads claiming (without evidence) that admitting refugees increases COVID-19 risk (NBC News)
• Largest study yet of COVID-19 transmission in India published in Science highlights the role of super-spreaders, a small subset responsible for a high percentage of infections. Study also finds that children transmit the disease as easily as adults (Los Angeles Times)
• Remember how COVID-19 exploded on a cruise ship? The Trump administration has again over-ruled the CDC recommendation to extend the “no-sail” order on cruise ships to next year (ARS Technica)

2. U.S. passes 7 million lab-confirmed COVID-19 cases. Last million cases added in 26 days
    Let’s start with the big picture today. Over the weekend, based on the Wikipedia data, the U.S. passed 7 million cases (See Figure A). On average, the U.S. has added a half million cases every 12 days. We went from 6.5 to 7 million in exactly 12 days. On average, each million cases has been accruing every 26 days. The jump from 6 to 7 million was just that (26 days). That’s a million cases a month. The more important idea here is that the COVID-19 outbreak is now steady-as-she-goes in terms of the pace of growth. On a big picture basis, the epidemic is locked in to an oddly consistent, even robust degree. Seasonality has been less than expected, surges and falls have been less steep than might have been predicted, and overall, the epidemic curve looks more like an endemic than a pandemic.
   What does this mean: Buckle up for the long hall because SARS-CoV-2 is not going away.

Figure A

3. U.S. daily cases holding largely steady. Transmission intensity highest in the Midwest, growing fastest in the West
     Figure B shows daily cases; the 7-day average remains just over 40,000 a day. We are now adding cases about twice as fast as the nadir of the epidemic in the first week of June. Today, I wanted to point out how different ways of looking at the same data are needed to address different questions. What questions? First, where are infections being generated most intensively right now? Second, where is the rate of new infections growing the fastest? Sometimes the answers will be the same. But, if a particular state has high sustained transmission intensity for a long time, the rate of growth of new cases will be very low. Conversely, a state with very low transmission intensity might be growing the fastest through regression to the mean in a natural cycle of change.
    Take a look at Figure C showing new daily cases per 100,000 residents by state over the last week. Let’s remind ourselves that the benchmarks we care about are a) less than 5 indicating “low” transmission intensity, and b) greater than 20, or 4-fold higher, indicating “high” transmission intensity. As has been consistently true for weeks, the Northeast is in the best shape with 5 states in the low category and only Delaware is over ten. The South is, thankfully, also relatively quiet with only Arkansas reporting high spread. The region that is clearly most hot is the Midwest with eight of thirteen states in the red zone. Three stand out in particular: North Dakota (54) is 10x higher than the “low” benchmark, while South Dakota (45) and Wisconsin (39) are surging at a white hot pace. Michigan (9.6) and Ohio (7.8) are the only “warm” states below 10. Iowa (29), Kansas (32), Missouri (22), Nebraska (24) and Oklahoma (26) are all hot. In the West, while Arizona remains coolish, Idaho (25), Montana (27) and Utah (32) are all hot.
    So what about the second question? Have a look at Figure D showing 7-day growth factors in cases. The picture is different. Intensity is low in the Northeast, but growth in new cases is strong with five states seeing a week-over-week increase of 10% or more: Delaware, Massachussetts, New Jersey, New York and Pennsylvania. New cases are falling in nine of thirteen states in the South. The region where the most growth is occurring is the West. Cases are rising fastest in New Mexico (+58%), Wyoming (+53%), Nevada (+46%), Washington (+41%), Alaska (+39%), and Montana (+39%) in that order. Whereas transmission intensity is highest in the Midwest, case growth is over 20% in only Michigan (+21%), South Dakota (+28%), and Wisconsin (+23%). Let’s take special notice of the states that pop out of both figures. Montana, South Dakota and Wisconsin, all regionally propinquitous, all have both high intensity and rapid growth.
    Bottom line: Something big and scary is going on in the upper midwest plains states!

Figure B

Figure C

Figure D

4. Quirky Qorner: Republic of Kazakhstan social influencer Borat tweets praise for U.S. coronavirus handling: “Because of Trump, 350 million Americans still alive”
    If rumors are correct, the long awaited followup to Borat is on its way to Amazon Prime Video sometime soon. According to this piece in Vanity Fair, twitter was shaken by a video appearing just before the first debate, handle @KazakhstanGovt, congratulating “Premier Trump” for his handling of the crisis. Very Nizzzze!

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Daily COVID-19 Briefing: Friday

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Top news, reports and insights for today:

1. Daily deadline summaries for Friday:

• Coronavirus now in a second wave? Nope. The U.S. is still stuck in the first one (NPR)
• CDC deputy director told reporters today that states may need to reimplement strict social distancing measures if coronavirus cases rise “dramatically” (CNBC)
• A new study suggests that population-wide face masks and coverings could push coronavirus transmission down to manageable levels. This matches new WHO recommendations that everyone wear a mask in public (Reuters)
• WHO says cases in Africa have doubled in the last 18 days to more than 200,000 (New York Times, see graph below)

From the New York Times website, captured 6/12

2. U.S. cases remain stable and flat at 20,000 a day: this wave isn’t over
   On Thursday, 21,773 new COVID-19 cases were reported in the U.S., a cumulative rise of about 1%, bringing the total number of U.S. cases to at or above the 2 million mark, depending on the data source. Last week, 139,959 new cases were reported, less than 1,000 fewer than the week previously. The 7-day moving average has been right around 20,000 daily cases a day since Memorial day and it remains there on Thursday. The bottom graph shows what’s going on by state. The first thing to notice is just how much Arizona remains an outlier, with almost 17 new daily coronavirus cases per 100,000 residents. Total cases grew by 37% last week, a figure that we have not seen in a month in any other state. Other states with 10 or more daily new cases per 100,000 include Utah, Alabama, Arkansas, and South Carolina. In the Northeast, only Washington DC and Rhode Island had more than the benchmark 5 cases per 100,000, the other states continue to have low transmission. On contrast, in the South, transmission is low only in Kentucky and West Virginia. California, Nevada, New Mexico, Iowa, Illinois, Minnesota, Nebraska and South Dakota still have vigorous and active community transmission.
   The bottom line: Despite talk of the epidemic being under control, the data continue to tell us that the first wave is not over. The U.S. looks to be on a continued pace of 20,000 daily new cases, which may soon rise with the increase in social mixing.

3. Coronavirus and influenza: What might happen when 2 epidemics collide this fall?
   Two articles caught my attention this week, related to the perils and possibilities arising from the joint occurrence of interlaced epidemics of influenza and coronavirus this fall and winter. One, by ethicist and policy expert Lawrence Gostin published in JAMA, tackles what needs to be done to prepare for these “dual epidemics”. The other, an editorial in Science, emphasizes how little we know about what happens when flu and coronavirus happen together. The bottom line here is that we must take steps as a nation now to prepare for the possibility that the two concurrent public health challenges will produce the kind of over-whelming devastation seen in 1918-1919.
   Based on these articles, here are the top 10 key issues:
   1. Because the flu season is just starting in the Southern hemisphere, we will get some clues by watching what happens there.
   2. It’s very unlikely that we will have a COVID-19 vaccine available before the coming flu season gets under way. The two diseases are likely to peak at the same time.
   3. It is not known if co-infection of flu and SARS-CoV-2 amplifies viral shedding or increases disease severity. Both are possible.
   4. Because symptoms for both overlap, a critical challenge is to improve our ability to distinguish flu and COVID-19 in testing to avoid draining scarce testing materials.
   5. To avoid putting hospitals under extreme stress, it is critical that we do all we can to vaccinate as many people as possible against influenza.
   6. Uncertainty about demand for flu vaccine leaves manufacturers uncertain about how much to make. The U.S. government must step in now to absorb that risk.
   7. The urgent need for an evidence-based communication strategy to ensure the highest possible compliance with flu vaccination, especially among vulnerable groups.
   8. Declining vaccination rates for other diseases (especially among children) during the COVID-19 pandemic raises concerns about the success of flu vaccination next season.
   9. Adult influenza vaccination has never been mandatory in the U.S., but given the risks this fall, mandatory vaccination should be a “last resort” that remains on the table.
   10. While most experts now do not expect a COVID-19 vaccine before 2021, when it does arrive, a lingering concern is vaccine hesitancy. Surveys suggest that only 30% of adults say they would get a new vaccine as soon as it is made available.

Daily COVID-19 Briefing: 5/14/20

Top news, reports and insights for today:

1. Daily COVID-19 headline summaries for Thursday:

• Patrons pack Wisconsin bars immediately after the state’s Supreme Court struck down the Governor’s stay-at-home order; video goes “viral” (CBS News)
• Virologists in Frankfurt Germany have identified a potential new way to treat COVID-19 patients by blocking viral replication. This could be done with a number of existing drugs. Clinical trials are now being launched (Futurism)
• Virginia has begun to cook it’s COVID-19 books by combining viral and antibody testing, yielding a more rosy public picture and numbers that exaggerate the state’s testing capacity. The lack of national leadership and data sharing standards means more states are likely to cook their COVID-19 books (The Atlantic)
• Scientists report new evidence supporting the efficacy of masks, finding that normal speech causes airborne virus transmission in confined environments for up to 14 minutes (Proceedings of the National Acadamy of Sciences)

2. Which states have peaked? Which are still surging in cases?And what’s up with this weird zig-zagging?
   It’s been two weeks since I showed you the latest plots from #COVIDMonitor, a fantastic site run by Ralph Straumann. His plots show newly tested cases in the previous week vs. cumulative cases since the start of the outbreak using data from the New York Times. The plots are displayed on the log scale for both last week and cumulative, so the horizontal axis is not time. I like these so-called log-log plots because they show a clear downward hook when a given place has reached peak cases. This hook is the best way to detect the inflection point between accelerated (non-linear) growth and simple additive growth in cases. The graphic below is a screenshot from his site today.
   The first point to make is that thankfully, there are some states that clearly look to have peaked. That includes out West Alaska, Idaho, Montana, and Hawaii. In all those states, we see the obvious hook. Similarly, we see the peak signal in Vermont, New York, and Connecticut in the Northeast. In the South and Midwest, things look good for Michigan and Louisiana. That’s just 9 states where cases have peaked. The other 41 fall into 3 categories. First, there are twice as many states (16) where cases continue to rise non-linearly, meaning new cases are increasingly increasing. Most are in the middle of the country: Arizona, New Mexico, Kansas, Colorado, Nebraska, Iowa, Minnesota, Illinois, Indiana, Mississippi, Kentucky, Maryland, Virginia, Washington DC, North Carolina and Massachussetts fall in this box. What surprises me most (although perhaps surprise is not the right term) is the 12 states that display a zig-zag pattern, where the peak seemed to arrive over the last few weeks, then cases ramp up again. Instead of a clear downward hook, we see a jagged pattern of downturn followed by upturn. Take a close look at Washington, Oregon, Wyoming, South Dakota, Wisconsin, Tennessee, Missouri, Arkansas, Alabama, Ohio, West Virginia, and South Carolina. I believe this is an important observation. The states that are zig-zagging outnumber those that have peaked. A final group of states have turned flat in recent weeks, but the hook has not yet materialized. I would count California, North Dakota, Nevada, Utah, Indiana, Oklahoma, Texas, Pennsylvania, Georgia, Florida and South Carolina in this camp. Although there may be a faint glimmer of an upward zig-zag at the very tail in Texas and Oklahoma.
   The Bottom Line: It is crucial that we look for a key-like zig-zag pattern in these plots because that is where we are likely to see a rebound of new infections in states that reopen, as small transmission chain brush-fires ignite that have the potential to agglomerate and restart the whole exponential growth phase, sending states right back to where we were in March and April.

From #COVIDMonitor, United States, captured 5/14/20 at https://rastrau.shinyapps.io/covid-us/

3. ORIGINAL ANALYSIS: The U.S. has a long way to go in testing: A look at test positivity rate (TPR), a vital sign of the health of a testing regime
   The testing talk hasn’t died down, nor is it likely to in the near term. Earlier this week, “Uncle Toni” Fauci warned congress in a surreal video testimony that the U.S. is taking a big risk by opening states too soon before we increase our capacity for testing and contact tracing. For many, this isn’t actionable enough. We need some concrete things we can track to see how well our testing is actually doing. In past briefings, I have talked about differences across states in testing rates (See May 7 briefing). Here’s something new I cooked up and I think it’s pretty interesting. Another key metric is the test positivity rate, or the percentage of tests that are performed that are positive. It’s a vital sign on the health of a testing regime. Early in an outbreak, testing resources are scarce and most tests are done only for people who are already sick. But almost 3 months into the epidemic, we expect to see the TPR come down. Way down. If it does, it tells us that we are testing a broader swath of the population beyond those who are already sick and have a high likelihood of being infected. The goal is to cast an increasingly large net, testing people with a lower probability of being positive. In an ideal scenario, when we could test everyone in the population, the TPR would equal the population prevalence. As long as it’s much larger, it means we are still testing selectively.
   As a nation, the U.S. is not doing well. The top graph below compares TPR by countries using data from FactCheck.org. While the number has been coming down, we are still seeing over 13% of our tests come back positive. The nations that have become models of effective testing and epidemic control, like Iceland, Denmark, New Zealand, South Korea, Germany and Taiwan, are all at or below 5%. That’s casting a broad net. Five percent is a good goal because the prevalence estimates from Europe have been around that range. The bottom graph shows how states are doing using data from the very handy COVID Tracking Project. Keep in mind this is one overall number for the entire period of the pandemic, so the states that had the biggest outbreaks first will have large TPRs. The take home messages here are three:
   1. Fifteen states have test positivity rates over 15%. Six of those, all in the northeast, are still above 20%. This tells us that the states at the front edge of the epidemic still have a lot of catching up to do.
   2. Good news: 11 states are below 5%, indicating wide and deep testing systems. Not surprisingly, these are mostly states that have not had huge outbreaks. Congratulations are especially due to West Virginia, Vermont and North Dakota, all get high marks across a range of testing measures.
   3. Several hot spot states have reopened despite rising rates of new cases. This is especially troubling in those states that also have persistently high TPRs, such as Maryland, Pennsylvania, Illinois, Virginia, Iowa, Georgia and Nebraska.

Test positivity rate by country, screen capture from FactCheck.org on May 13, 2020: https://www.factcheck.org/2020/05/testing-by-the-numbers/

THIS SLIDE WAS UPDATED FRIDAY DUE TO AN ERROR IN THE COLOR OF THE BARS. THANKS FOR POINTING THAT OUT TO ME IY!