Daily COVID-19 Briefing: Wednesday

Top news, reports and insights for today:

1. Daily headline summaries for Wednesday:

• The U.S. death rate from COVID-19 per 1 million people just passed 340. That’s more than 100 times the rate in China (Time)
• A trend toward a “second U.S. virus wave” emerges in 22 states after reopening (Bloomberg)
• As harvest season nears, outbreaks seen among migratory farm workers in North Carolina, Florida and Washington. The federal government has not made safety rules mandatory, leaving it to farmer’s discretion (Politico)
• Half the states (including California, Florida, North Carolina and New York) are failing to follow CDC guidelines and reporting probable coronavirus cases and deaths, leading to inconsistent and inaccurate surveillance (Washington Post)

2. Back to where they started: Epidemiologic deja vu in 14 states that have matched or exceeded daily cases compared to April/May peaks
   The President continues to say and do things that suggest he believes the epidemic is over and behind us. A journalist sent me an inquiry yesterday asking my opinion on whether a second wave might be in our future now that the first one is over. A new poll suggests that about half the country thinks it’s time to get back to normal life.
   Huh? I remain puzzled and wonder what information people could possibly be looking at. Internationally, we have seen the epidemic move from country to country, rising and falling in the global whack-a-mole pandemic we are in. Months ago it was Italy, France and Spain in the hot seat. Now it’s Brazil, Peru, India, Russia and Chile. The same shifting is occurring in the U.S. as one state grows quiet as another surges. What strikes me when looking at the New York Times tracking data is just how many states seem to be right back where they were during the peak period of April and May. After looking closely, I believe there are 14 states that now meet or exceed the high water mark of daily cases. Take a look at the two image galleries below. The first one shows the 8 states where the recent 7-day moving average for daily new cases is higher (and in some cases much higher) than the peak in April/May. The second gallery is the 6 states where recent average daily cases are about the same as they were at the April/May peak. Some of these states are quite striking. Arizona averaged under 300 cases a day throughout April and May, and is now above 1,000 after an alarming rise starting May 27. Arkansas peaked at under 200 a day April 26 and has now risen to over 300 a day. California, North Carolina and Utah are all essentially on a continuous rise since the start of the outbreak with little notable drop off in new daily cases. Texas and Oregon both appeared to peak twice, with a corresponding dip in new cases in late May, but in both states, cases have surged to all time highs with continued transmission intensity. In the lower gallery, we see that Florida, Kentucky, Nevada, New Mexico and Tennessee, all had noticeable peaks in April/May, and all have seen resurgence of new cases back to about the same peak levels in recent days.
   The bottom line: Overall, new cases remain close to flat in the U.S., as many states are seeing sustained declines. However, the rest of the story is that 14 states are right back to where they were in the peak period of April and May and 8 of those states are setting new records. Texas, Arizona, Florida, Nevada, South Carolina and Mississippi were the most aggressive in reopening 2-3 weeks ago.

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  Arizona

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  Arkansas

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  California

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  North Carolina

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  Oregon

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  South Carolina

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  Texas

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  Utah

States where new cases are higher than April/May peak

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  Florida

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  Kentucky

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  Mississippi

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  Nevada

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  New Mexico

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  Tennessee

States that have matched earlier peaks

3. Not just increased testing: COVID-19 hospitalization rates rising in reopening states, mirroring trend in rising cases
   A story in Bloomberg highlights what the article calls a “second U.S. virus wave” emerging in reopening states. They mention that hospitalizations in Texas jumped 6.3% on Tuesday to 2,056, the highest total since the pandemic emerged. California hospitalizations are at their highest point since May 13 and have risen 9 of the last 10 days. This nudged me to go back to my favorite source of state-level data on hospitalizations from the COVID-19 Hospitalization Tracking Project at the University of Minnesota Carlson School of Management. While their data doesn’t cover all states, the figure and table below captures a few that have surging cases. The graph shows daily COVID-19 hospitalizations per 100,000 adults for 6 states. Since May 17, the largest increase has been in Arizona, where rates rose by 56%. North Carolina saw the second highest rate rise and 57%. Rates are up nearly a third in Kentucky, Texas and Utah. California is back to where it was in late April.
   Why does this matter: Tracking hospitalizations may be a more accurate window into the epidemic than other measures that depend on testing. These data show, I believe, that hospitalizations are rising in line with expectations of post-reopening increases in transmission intensity. The situation in Arizona is especially extreme.

State	May 17	June 9	Change	% Change
Arizona	14.9	23.3	+8.4	+56%
California	10.3	11.4	+1.1	+11%
Kentucky	11.4	15.7	+4.3	+38%
North Carolina	6.3	9.9	+3.6	+57%
Texas	7.4	9.4	+2	+27%
Utah	4.8	5.9	+1.1	+23%

From the COVID-19 Hospitalization Tracking Project, University of Minnesota, Carlson School of Management, captured 6/10/20

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Daily COVID-19 Briefing: Sunday

Top news, reports and insights for today:

1. Daily headline summaries for Sunday:

• New study from the South Korean CDC finds no evidence that “re-infection” cases resulted in a new secondary case. Crucially, they also did viral cell culturing in 108 such cases finding that all were negative. Taken together, this is the strongest evidence yet that getting infected a second time is not happening and that those who re-test positive are not passing the disease to others. The vast majority of these cases are test errors or a period of prolonged recycling of viral waste that cause a positive test result, not a true second infection in the same person (KCDC)
• Social distancing measures aimed at COVID-19 have stopped influenza in its tracks 6 weeks early (Nature)
• New study from China (not yet peer reviewed) examined 319 outbreaks in detail finding most occurred at home and on transportation. Importantly, they find evidence of only 1 outbreak that occurred outdoors. Study may provide important evidence of substantially lower risk of transmission outside (medRxiv)
• CBS News and others have reported that CDC guidance has been updated to say that COVID-19 is “…not caught easily” from touching surfaces and that “…40% of transmission occurs before people feel sick”. I can’t find either of those statements on the CDC website (CBS News)

2. Map check, 4 weeks later: the epidemic has shifted to places nobody notices or wants to talk about
   I am a map fanatic. I enjoy staring at them. It actually is a pretty useful fetish if you are a disease detective because the spatial patterning of disease is often among our most vital clues. I last showed you a U.S. map of incidence (confirmed COVID-19 cases per 100,000 residents) back on April 30, just under 4 weeks ago. I grabbed a picture from a similar map today from my colleagues at coronashutdown. Comparing the 2 maps tells us where we have been in recent weeks. Here are my take-home messages from this comparison:
   1. The epidemic has shifted from the east coast to the midwest, south and southwest.
   2. Epidemic radiation from last month’s hotspots can be seen from southwest Georgia all the way to Eastern Texas and Northern Florida, Southern New Jersey into Delaware and eastern Maryland, southern Utah and western New Mexico, the Texas panhandle, and Ford county in southern Kansas.
   3. New hotspot counties include (marked on map) Franklin Parish in Louisiana (1433), Liberty County Florida (2442), Duplin County North Carolina (927), Buckingham Co. Virginia (2560).
   4. Continuous corridors of higher infection can be seen along major transportation routes. Compare for example the area from New Orleans all the way to Chicago. Or note the increasing connection of high incidence counties going west from Chicago into parts Illinois, Wisconsin, Iowa, Minnesota and South Dakota.
   5. Ford County Kansas was a hotspot on April 30 at 2,088 per 100,000. That county has now more than doubled to 4,634, which is twice the rate of infection in the county containing part of New York City. The rates have gone to more than 1,000 in 5 surrounding counties.
   6. The bottom line: while many congratulate themselves on winning the battle against COVID-19, these maps tell us that what has really happened is that the epidemic has shifted to places nobody notices or wants to talk about.

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  April 30, 2020

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  May 24, 2020

3. Severe illness similar to Kawasaki disease impacting children
   Recent articles in Science, the Lancet, and Nature have drawn attention to a rare and severe post-infection syndrome associated with coronavirus that is occurring in children. While children are at lower risk of severe illness during the pandemic, it now appears that a small number are becoming very sick with a condition that looks similar to Kawasaki disease – a rare condition affecting about 1 in 10,000 children in Western countries, characterized by a hyperactive immune response to viral infection leading to rash, fever, and dangerous inflammation in blood vessels (also called vasculitis). The disease named after a Japanese physician who was the first to describe it is associated with dangerous heart complications, most notably aneurisms. Hot spots for this newly recognized Kawasaki-like illness have been noted in Bergamo Italy and New York city. A study in the Lancet found a 30-fold increase in the incidence of Kawasaki-like illness in one region of Italy. New York state is investigating about 157 cases. Outbreaks have also been noted in the UK (where it was first noticed) and Los Angeles. Kawasaki disease is not new. It is generally assumed to be a post-viral syndrome involving an immune system “overshoot”. Currently, experts are not certain whether the outbreak of cases is Kawasaki disease or something similar. In Europe they are using the term paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS), or multisystem inflammatory syndrome (MIS-C) at the CDC. So far, children treated for MIS-C have had good survival, but when it occurs, it requires urgent and comprehensive medical intervention. The condition has been seen mostly in children under age 18 but is increasingly appearing in somewhat older ages. There is no certain diagnostic test for Kawasaki or MIS-C and more will be learned in the coming weeks.
   What this means? While it’s scary to think that we have to add very sick kids to the list of things to worry about, the disease detective in me believes at this point that the emergence of super-rare autoimmune reactions to a novel virus is an inevitable development in a disease impacting almost 5.5 million people. At this time, I do not believe this is cause for concern. Having said that, it is urgent that experts determine whether children and young adults with a previous history of Kawasaki disease should be considered at elevated risk for MIS-C.

Daily COVID-19 Briefing: 5/13/20

Top news, reports and insights for today:

1. Daily headline summaries for Wednesday:

• Lebanon, Iran, South Korea, Germany and Wuhan China move to reimpose lockdown restrictions due to resurgence of the virus after easing restrictions (The Washington Post)
• Preliminary results from best-in-class seroprevalence study of 90,000 persons in Spain shows approximately 5% have been infected. This suggests a CFR about 1.5% (New York Times)
• Antibody tests don’t yet answer the immunity question. Widely used tests may deliver false negative results 15-40% of the time. Rushing to get an antibody test may not be warranted now (CNN)
• Abstinence didn’t work for HIV or addiction. Growing quarantine fatigue shows that it doesn’t work for COVID-19 either. We should focus on risk reduction strategies that are sustainable (The Atlantic)
• The technical challenges and political minefields inherent in counting deaths in an epidemic are constants going back at least to the plague in 17th century England. Then as now, counting the dead is a frought but vital tool for those managing disease outbreaks (WIRED Opinion)

2. U.S. cases and deaths rose on Tuesday, but less than past 4 weeks
   On Tuesday as expected, cases and deaths rose due to the weekend lag in reporting. New cases rose 1.6% adding 21,475 yesterday; an additional 1,581 Americans were reported dead from COVID-19, a rise of 2.1%. While the Tuesday death toll was almost double the Monday report, this week’s Tuesday spike was less than the past 6 weeks. The 7-day trend in new cases continues to decline while deaths remain too unstable to characterize. Last week, new cases grew by 30% or more in four mid-western states: Kansas (+30%), Minnesota (+59%), Nebraska (+35%) and South Dakota (+35%). Last week, deaths rose substantially in 11 states including Arizona (+46%), New Mexico (+35%), Utah (+30%), Iowa (+40%), Minnesota (+35%), Missouri (+39%), North Dakota (+51%), South Dakota (+61%), Alabama (+40%), Mississippi (+34%), and New Hampshire (+54%). Less than 10% growth in deaths were seen in Hawaii, Montana, Maine, and Vermont. New York, Louisiana and Michigan, the states with the worst initial waves all reported small increases in both deaths and new cases.

3. Meat-processing plants are infection incubators
   Attention has focused in recent weeks on outbreaks of coronavirus tied to meat-processing plants. A story in Business Insider on May 11 documents over 4,500 COVID-19 cases and 18 deaths related to plants owned by Tyson foods across 15 states. The company has taken recent steps to protect workers including requiring face masks, additional cleaning and taking temperatures. Like most meat processing companies, Tyson does not offer paid sick leave but requires employees to take short term disability, which disincentives sick workers from staying home. According to the Midwest Center for Investigative Reporting, there were at least 12,500 COVID-19 cases and 53 deaths in the meatpacking industry across 29 plants in 20 states as of yesterday. Slaughterhouses have become hot spots in many states. For example, in Texas, the highest infection rates are not in Houston or Dallas, but in rural Moore County, far north in the panhandle. With just 20,000 residents, it now has 2,454 infections per 100,000, a rate that is 10-fold greater than Dallas and one of the highest in the country. It also has one of the largest beef processing plants in the nation, which cleans up to 5,000 cattle carcasses a day and has been the epicenter of a case cluster under investigation by the state. In Cass County, Indiana at least 900 Tyson workers tested positive, boosting the number of known cases from 50 to more than 1,400 over three weeks. 
   Some context: On April 28, President Trump signed an execute order requiring meat-processing plants to stay open to avoid shortages. That hasn’t stopped them from closing anyway. Those that remain open place workers in a difficult position. More than half of workers in the meat-processing industry are immigrants; 44% are Latino and 25% are African-Americans. Thus, the meat-processing industry is one explanation for the disproportionate impact of the COVID-19 outbreak on people of color. According to Politico, Alex Azar, the secretary of health and human services has been among the government officials who claim workers are getting infected at home and not at work, despite mounting evidence that infection rates are higher in communities with meat-processing facilities. Data has been hard to get; companies, states and some unions have refused to release the numbers. A May 8 CDC report in MMWR reported less than half the cases and deaths found on the MCIR site.
   Why this matters: The reasons why meat-processing plants are so risky is not yet clear. Large numbers of workers spending prolonged periods in close quarters in enclosed areas with fast moving air currents may be one key. Such workplace outbreaks are some of the best evidence we have yet that the SARS-CoV-2 virus may be spreading from airborne droplets. An influential study in China found that viable virus could be found in the ventilation system of hospitals treating COVID-19 patients. Taken together, meat-processing plants have been incubators for the epidemic, helping to ignite chains of transmission in rural America and driving the racial and ethnic disparities in suffering and deaths.