Top pick of the day: Saturday

Are coronavirus cases in the US actually going down? Here’s what we know.

Article by Dylan Scott published on line at VOX, May 27, 2020 at 4:35pm EDT.

Wrestles with the big picture question of where we are right now in the U.S. epidemic. Three takeaway messages: 1) Nationally, new COVID-19 cases are on a gradual decline; 2) While new cases are declining in 17 states, they are increasing in 13; The pandemic started in wealthier environs but has shifted to working-class settings.

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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.

Screen grab taken from Vox.com on May 30: https://www.vox.com/2020/5/27/21272276/us-coronavirus-cases-update-states-reopening

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Daily COVID-19 Briefing: Saturday

Top news, reports and insights for today:

1. Daily headline summaries for Saturday:

• Despite widespread belief that the epidemic has moved past New York, over 47,000 people in New York, New Jersey and Connecticut tested positive over the last two weeks, over 13,000 in New York City alone. Essential workers (including medical personnel on the front lines) are still falling ill (New York Times)
• Historian John Barry who wrote the definitive account of the “Spanish” influenza of 1918-19, said that President Trump has ignored the most important lesson of that tragedy: National leaders must tell the truth (CBS News)
• New Harvard working paper reviews data on impact of weather, pollution and sunshine finding that warmer temperatures and moderate outdoor UV exposure may offer a modest reduction in the rate of viral transmission. They warn that weather alone will not be enough to fully contain the epidemic (Harvard University). 
• As U.S. funnels billions toward companies rushing to create a COVID-19 vaccine before the election, Gail Van Norman, a professor of medical ethics at University of Washington said this week that “A new investigational drug that’s going into human trials has a 90% chance of failing” (Vanity Fair)

2. New case update: Which state has the most newly reported daily COVID-19 cases? Maryland
    On Friday, 23,862 new COVID-19 cases were reported, a rise of 1.4% in total cumulative cases, now standing at 1.73 million. Last week, there were 143,328 reported new cases, a 9% increase, but the growth factor for the week was 0.92, indicating that overall, growth in cases is nearly flat. The bottom graph is something new. This figure compares daily new case reports per 100,000 people over the last week by state. This is a useful number to watch because it gives a rate of new cases which evens the playing field among states with very different population sizes. Also, numerous experts have said that new cases should be below 5 per day per 100,000 people before we can say that widespread transmission has stopped. As with other graphs I have made, this one shows states grouped by region in different colors. The vertical axis is daily new cases per 100,000 averaged over the last seven days. Looking at the data this way, the west is doing best, with no state reporting more than 6 daily cases per 100K, and 8 states with fewer than 5. Southern states are mixed with Florida, Kentucky, South Carolina, Texas and West Virginia with sub-5 new cases per day. Alabama, Mississippi and Virginia are all above 9. Four midwestern states saw 11 or more new cases per day per 100K last week: Iowa, Illinois, Minnesota and Nebraska. Only 1 northeastern state meets this benchmark (Vermont), the remaining states have seen 5 or more per 100,000 new cases. The fastest rate of growth in new cases came from my state, Maryland, which had 15.5 new cases per day per 100K. This comes after 2 consecutive days of more than 1,200 new cases on Thursday and Friday. By this metric, Maryland is a clear hotspot with more than 3 times the rate of new daily cases that are safe for reopening.
    The bottom line: Different metrics tell different stories about where the epidemic is going. Despite reassuring signs that things are slowing in the northeast, daily new case rates indicate there is a long way to go before the epidemic is under control in this region. Maryland, DC and Delaware continue to be in the cross-hairs of this disease.

3. Big news: the first evidence that previous exposure to other coronaviruses may offer some partial immunity
   The top story today is one I am particularly excited about. I don’t want to overstate the case, but this may turn out to be an important turning point in solving the case of this disease. First, a little context. Two days ago, David Wallace-Wells, who is perhaps my favorite health journalist, posted a terrific article in New York Magazine, posing a good and simple question: Has the epidemic peaked? In that article, he reminds us that 3 weeks ago, the New York times broke a story about an internal CDC model, predicting 200,000 cases and 3,000 deaths a day by June 1. That’s tomorrow. We are now at about 20,000 cases and 950 deaths a day. The biggest question right now is why those models were so wrong? Even though it’s a positive development, that cases and deaths are not soaring as our models predicted, but it means we have some part of the bigger story wrong. Where is the equivalent of “dark matter” in cosmology that will make the math add up? Over the next week I will be covering several of the hypotheses that have gained traction to explain this, but first I am excited to tell you about one of them.
    A big idea: It’s possible that the rate of infections is slowing because some percentage of the population is partially immune to the new SARS-CoV-2 virus as a result of previous exposure to other coronaviruses. This idea has been sitting in the background waiting for some foundational scientific research start teasing this apart. The first compelling evidence came out in a paper published in the journal Cell on May 14 by Alba Grifoni and colleagues from the Center for Infectious Disease and Vaccine Research at the La Jolla Institute for Immunology in California. They looked at immune system response to SARS-CoV-2 in patients who were known to have had the disease and found more good evidence that the key cells in charge of spotting and attacking the virus were widely circulating in recovering patients, meaning that they were now immune to re-infection. Most interestingly, they also found that several of the primary immune system sentry cells capable of recognizing SARS-CoV-2 were present in about half of the people who were as yet unexposed to the new virus. This may be due to cross-immunity. That means previous exposure to one of the four coronaviruses that cause the common cold may have created a partial immune memory that allows some individuals to recognize and mount a response to the new virus. The study was small, using just 20 previous COVID-19 patients and 20 “unexposed” patients. Much more work needs to be done to determine whether the presence of immune cells that might recognize SARS-CoV-2 translates to actual partial or full immunity to the disease because of a prior common cold. One very cool feature of this study is that they used blood from samples taken years before COVID-19 started to make sure that the unexposed group really had not been infected.
    Bottom line: This is the first well-done peer-reviewed study that demonstrates it’s possible that COVID-19 cases and deaths are less than expected because some fraction of the population may be partially immune. That would be a game changer, because it would mean the threshold for herd immunity may be much closer. This doesn’t prove that half the population is partially immune, but its one piece of a very big and growing puzzle.

Daily COVID-19 Briefing: Thursday

Top news, reports and insights for today:

1. Daily headline summaries for Thursday:

• Scientists at Yale have found that viral RNA found in sewage sludge predicts COVID-19 cases and hospital burden. This paper, while not yet peer-reviewed, suggests the potential power of poop in biosurveillance (medrxiv)
• Asked why New York City was hit so hard by the first waves of COVID-19, experts point to 4 key factors: 1) large influx of travelers from Europe, 2) early reluctance to close subways and buses, 3) hesitation to issue stay-at-home orders by the Governor, 4) sending recovering patients back to nursing homes (Bloomberg)
• U.K. scientists honing in on the identification of blood markers for mysterious Kawasaki-like multisystem inflammatory syndrome in children (MISC-R) (NBC News)

2. A focus on growth factors by state: Hot spots in Kansas and the south
    As the epidemic has slowed in recent weeks, it makes sense to shift the time scale of how we track it. Daily ups and downs of cases and deaths at the national level have been choppy and unclear. We know that looking at numbers for the whole country can be misleading given that the outbreak has slowed in New York, Detroit and New Orleans, only to disseminate to smaller towns and rural areas. Let’s zoom out a bit and focus instead on longer term trends at the state and regional levels. The graphs below show 7-day week-over-week growth factors, which I have said previously can be a better metric to gauge the current situation compared to looking at the daily numbers. Growth factors are ratios, so looking at them gives a different perspective. In epidemiology, we get lots of practice with ratios. If we want to know the strength of a relationship between a risk factor and a disease, we can look at the absolute amount of disease attributed to the risk factor (also called Attributable risk) or the ratio of disease in those with and without the risk factor (also called Relative risk). There are definite plus-minus trade-offs in choosing which numbers to focus on, but in this case, we can improve the signal-to-noise ratio by looking at the ratio of cases/deaths last week to the cases/deaths the week before.
    The top graph shows the growth factors for new cases. States with values greater than 1 are more active, with positive growth in new cases week over week. What this shows is that all states with stable numbers in the northeast saw negative case growth except Maine. The midwest was a mixed bag with cases rising in 6 states and falling in 6. Cases grew 20% or more in Iowa, South Dakota and Wisconsin. Michigan is slowing fastest with just over half the cases last week as the week before. While little attention has been paid to the West, new cases rose in three states (California by 16%, Idaho by 24%, and Nevada by 23%). In my view, the biggest take-home message here is that cases grew last week substantially in the south, where 10 of 12 states saw cases rise. West Virginia more than doubled new cases adding 322 compared to the 141 the week before. Cases grew sizably also in Alabama (48%), Arkansas (66%) South Carolina (26%), Tennessee (28%) and Virginia (21%).
    The bottom graph covers growth in deaths. In the northeast, deaths rose in Maine (14%) and Rhode Island (54%). All western states saw deaths decrease last week. The fastest rise in new deaths occurred in Kansas where deaths nearly doubled week-over-week. In the south, new deaths increased in half the states, led by Alabama (24%), Arkansas (30%), Georgia (21%), South Carolina (31%) and Tennessee (22%).

3. The state of testing: which states are ready to reopen?
    Today’s Top Pick of the Day article from Vox is based on interviews and discussions with a number of infectious disease experts who were asked to list the top criteria that should be used to decide when it is safe for states to relax outbreak control measures and reopen. I thought I would take my own deeper look into two of those criteria related to testing. The two benchmarks suggested are:
    1) New daily tests of at least 150 per 100,000 population to insure adequate testing capacity for spotting new infections and tracing their contacts.
    2) A test positivity rate of less than 5% indicating that the testing is no longer selective and that a wide net is being cast.
    You can read the paper to see what they conclude about these numbers. I created two new graphs using numbers from the COVID Tracking Project (the same source they used) but looking slightly differently. The top graph below ranks 50 states and DC from highest to lowest on new daily tests per 100,000 residents, averaged over the last month. As was true before, the testing regimes in the northeast are considerably more mature than in most southern and midwestern states. Rhode Island is still in the lead, testing an average of 176 per 100,000 per day and is the only state clearly above the threshold of 150 per day. New York, Massachussetts, Louisiana and Utah are the other states that are over 100 per day. North Dakota is the only midwestern state testing more than 75 a day, which may explain why cases are growing in that state. Twenty six states are now testing less than a third of the 150 benchmark. Arizona continues to have the lowest testing rate of all states by any metric. States below average are very likely under-estimating their current case prevalences, some quite dramatically.
    The bottom graph shows the test positivity rate (or TPR) for the last month. Since lower TPR is “better” in this case, the ranking of states is reversed. A total of 21 states have a TPR in the last month that is below 5%, while 16 states still have a TPR that is high (greater than 10%). Maryland, Washington DC, Delaware and Virginia constitute a block of Atlantic seaboard states that have ramped up their testing capacity (top graph) but still are seeing a large fraction of tests come back positive.
    The bottom line: No states qualify to reopen just using these two benchmarks as proposed in the VOX analysis. Testing remains widely discrepant across states. This shows what happens when there is a complete absence of national leadership and standards for testing. We remain largely and unsettlingly in the dark about this epidemic in the vast majority of U.S. states.