The Next (Predicable) Test SNAFU

Testing is key and it is expanding in the US and our community — finally! However, I believe that we need to integrate a “suspect” or clinical case definition as part of Influenza-like Illness (ILI) and COVID-19 surveillance. We want to track and trace all possible cases. ( Until we are responding to clinical COVID-19 and testing all contacts we will be hobbled in epidemic control and, importantly, we invalidate the experiences of people in the community. The clinical diagnosis of a suspect COVID-19 case allows public health interventions to be initiated and to be systematic.

Testing is key however, regrettably, the test used for diagnosis of the virus (RT-PCR that picks up viral nucleic acid) is not as good as we wish. Based on data from China, Italy, and the US it appears that 30% of persons with COVID-19 are “false negatives”.  Every laboratory test has problems with “sensitivity” and this particular test is a bit worse than some other tests in that regard. Thus, it is estimated that the test picks up 70% of people with COVID-19 and misses at least 30%. These misses may be because collecting the specimens is difficult and sometimes the swab will miss the virus.  In addition, if the test is done early in the disease or late in the course of illness there may be fewer viruses in the naso-pharynx (way back in the nose and throat). (See photo at top) These realities mean that a person may have COVID-19 but test negative. In fact you can have a person test negative then on re-test have a positive result. This uncertainty is frustrating but it is not uncommon. It does not mean that someone is re-infected. These tests are picking up bits of viral RNA and often those traces of virus are detectable for a while and sometimes may simply mean specimen contamination.  It does not absolutely mean that a person is contagious still however, more work is needed.

In the Journal of the American Medical Association published May 6, 2020 there is a valuable contribution about testing that provides a useful timeline of diagnostic markers for detection of COVID-19 (Figure above)

In a quote from the article “In a study of 205 patients with confirmed COVID-19 infection, RT-PCR positivity was highest in bronchoalveolar lavage specimens (93%), followed by sputum (72%), nasal swab (63%), and pharyngeal swab (32%).5 False-negative results mainly occurred due to inappropriate timing of sample collection in relation to illness onset and deficiency in sampling technique, especially of nasopharyngeal swabs. Specificity of most of the RT-PCR tests is 100% because the primer design is specific to the genome sequence of SARS-CoV-2. Occasional false positive results may occur due to technical errors and reagent contamination.”

Testing is key. It is another storm on our horizon as we try to discern who actually needs to be isolated and quarantined and when those periods can end. There are many decisions that need support from reliable and valid testing. What will happen as we are trying to stringently control the flares of COVID-19 in the community is that the test performance will bedevil us. This is an area where technological innovation will be welcome!

Guest lectures with Maine Public Health Association

We (Sharon McDonnell MD MPH and Gib Parrish MD) are collaborating with Maine Public Health Association and the New England Public Health Training Center to provide presentations as part of the 2020 Webinar Series.

Join Maine Public Health Association for a 10-part webinar series, funded generously through the New England Public Health Training Center. The webinar series starts with an Introduction to Public Health, including an overview of Maine’s public heath system, and roles and responsibilities in public health; then launches into more detail about disease outbreaks and surveillance. All events will have time for questions and answers, and are free and open to the public, except where indicated. The webinars are intended for a general audience, but even the most seasoned public health professional will glean new information! You may register for any or all of the webinars during the registration process.

The link to the series is:

Our part of the series starts this week and continues to the end of summer. Welcome to all! You can register free online. Extra thanks to the Maine Medical Center/Maine Health and the Preventive Medicine Residency Program whose Fellows are helping with the course preparation.

The “Suppressed” CDC Guidance for “Opening up America”

Many friends are trying to figure out if/how to reopen their businesses and activities in the context of SARS-CoV-2 pandemic. The information (and bravado) that we need to think through these decisions as safely as possible — balancing the competing interests– has been made more difficult because of a decision by the US government (White House) to not include the complete recommendations by the CDC. These recommendations documents were developed by the US CDC to provide step-by-step advice designed for local authorities on how and when to reopen public places during the SARS-CoV-2 pandemic. If you have questions about childcare, summer camps, workplace guidance for “vulnerable” workers, guidance for restaurants and bars, and mass transit you might find the specifics in these documents helpful. These are important, difficult decisions and we need information. Note: The recommendations were obtained from a federal official who was not authorized to release them publicly. The official explanation is that the CDC guidance is too prescriptive.

I have provided background – perhaps too much for you and if so skip it– about the context because I had questions. For example, the recommendations refer to phases of the epidemic that I believe come from the document from the White House called “Guidelines for opening up America again”.

There are criteria – the “Proposed State or Regional “Gating” criteria– that should be satisfied before proceeding to phased opening. It cannot be said enough that none of the states “reopening” have met these criteria. We need to agree on what we will watch to determine how the steps are going because if it matters, measure it. It cannot be said enough that none of the states “reopening” have met these criteria.

Symptoms: Downward trajectory of influenza-like illnesses (ILI) reported within a 14-day period AND Downward trajectory of COVID-like syndromic cases reported within a 14-day period

Cases: Downward trajectory of documented cases within a 14-day period AND Downward trajectory of positive tests as a percent of total tests within a 14-day period (flat or increasing volume of tests)

Hospitals: Treat all patients without crisis care AND Robust testing program in place for at-risk healthcare workers, including emerging antibody testing.

Moreover, it is said that prior to these phased openings there are “core state preparedness responsibilities” that should be in place.

1. Testing and Contact Tracing

-Ability to quickly set up safe and efficient screening and testing sites for symptomatic individuals and trace contacts of COVID+ results

-Ability to test Syndromic/ILI-indicated persons for COVID and trace contacts of COVID+ results

-Ensure sentinel surveillance sites are screening for asymptomatic cases and contacts for COVID+ results are traced (sites operate at locations that serve older individuals, lower-income Americans, racial minorities, and Native Americans)

2. Health Care System Capacity

-Ability to quickly and independently supply sufficient Personal Protective Equipment and critical medical equipment to handle dramatic surge in need

-Ability to surge ICU capacity

3. Plans in Place

-Protect the health and safety of workers in critical industries

-Protect the health and safety of those living and working in high-risk facilities (e.g., senior care facilities)

-Protect employees and users of mass transit

-Advise citizens regarding protocols for social distancing and face coverings

-Monitor conditions and immediately take steps to limit and mitigate any rebounds or outbreaks by restarting a phase or returning to an earlier phase, depending on severity

This may be more background that you need to simply dive into the materials from CDC. The first link 17 page document describing the type of place and the actions by phase of the pandemic. This is followed by a link that takes you to graphic decision support flowcharts.

“Guidance for Implementing the Opening Up America Again Framework,”

As I have been working with people trying to decide how to determine if they can have horse-camp, restaurants/bars, music lessons…. just to name a few I have been asking them the following issues

a. What are the recommendations and laws where you live?. This epidemic is national but also very local.

b. Can you follow the primary recommendations about hand washing, physical distancing, wearing masks while nearer than 6 feet, and helping people not touch their face?

c. Finally, if you have a case of COVID-19 (either asymptomatic or symptomatic) after you open how many people will be shuttled into quarantine? Can you afford to lose the staff and deal with the fallout? What changes can you make to your operations that reduce exposure so that if there is a case you can maintain operations? This might include keeping people in smaller groups, using barriers, and working in shifts. This is where innovation really makes a difference. Knowing about how case investigation and contact tracing works might help you figure out ways to work more safely and make sure you do not lose staff.

Note, the information that I have provided here is the best I have been able to piece together about the phases and placement of CDC guidance. I want to be sure these recommendations are available to people. If you know more details about the background of these materials, how they connect, and what happened to make them generally unavailable I would appreciate it if you can leave comments or links. Taxpayers paid for some smart people to put their heads together to think deeply about these issues and we should have access to them.

What the Heck? Ask an Epidemiologist(s)

As a chance to see friends, neighbors, and anyone interested in epidemiology and pandemics, Sharon McDonnell MD MPH and Gib Parrish MD will have a weekly zoom session to talk about the SARS-CoV-2 pandemic. We enjoy our calls with our epidemiology students, the Yarmouth Community Coronavirus Neighborhood communicators and the Call Center volunteers so, to answer questions, and we want to hold a more regular event. Everyone welcome for all or part of the sessions! Bring your confusion and your ideas.

These sessions may have some brief presentations – “Cool things this week in epidemiology” – but we hope to leave most of the time for questions and discussion. Please feel free to put questions that you would like us to think about in the comments below and we will give them priority.

WHEN: Thursdays 4pm to 5:30 pm
WHERE: Zoom. Link: Meeting ID: 207 536 632

Background :
Sharon McDonnell BSN, MD, MPH., Yarmouth, Maine

Sharon received her BSN at the University of Florida, MD from the University of California, San Diego, and MPH from Johns Hopkins University.  After training in Family Medicine she went to Pakistan/Afghanistan to work with NGOs and then WHO in Geneva. She joined the US CDC as an EIS Officer and is board certified in Preventive Medicine and Public Health.   She has worked in the state health departments in Florida and Vermont. After CDC She was on Faculty at Dartmouth Medical School and has continued to do work in International Disease Surveillance and Response and epidemiology training.  She worked in Liberia for 2 years for the Ebola response with IRC and CSTE/CDC.  Currently she teaches epidemiology with the University of New Hampshire and consults with the Leadership Preventive Medicine Residency Program at the Maine Medical Center.  She helps co-found the Yarmouth Community Coronavirus Task Force in Yarmouth Maine.

Gib Parrish, M.D., Yarmouth, Maine

Gib trained in laboratory medicine, pathology, and epidemiology and spent 20 years at the U.S. Centers for Disease Control and Prevention (CDC). At the CDC, he worked on environmental health problems, improving mortality data, assisting state health departments with public health assessment activities, and improving national and state health information systems. After retiring from CDC,  he has worked as a consultant  on various population-health information-related projects, most recently on the Reportable Condition Knowledge Management system, which is identifying and evaluating potential cases of reportable conditions using data from electronic health records.

Nothing changes yet everything is different

From April 20, 2020 “Road Map to Pandemic Resilience” and Updated May 5, 2020

What I hear this week is this, “Help me envision the “future” – like even next month or next fall. I can do this – the hunkering down, the waiting– for awhile but, when I picture doing it with without end, I get overwhelmed“

We have an outbreak challenge and a communication challenge. A novel pandemic afflicts us and we are groping our way forward. As the curve in NYC declined the media and many people have taken this in as “it is time to get back to the way things were”. I am concerned that we do not have much of a plan for what that looks like. Not only do we not know what to do but now our fear is coupled with a sense that it is everyone for themselves.

Helplessness is a terrible thing. We can do this and we need to push a bit from the grassroots to not let ourselves be helpless. There are things, local things, that we can do. We will share lessons learned in our local community Task Force and we are asking others who have found action helfpul to share their experiences and advice.

This pandemic is different depending on our geography and as Mike Osterholm says, “What’s happening is a series of “mini-epidemics,” ……..the national numbers offer a deceptive picture: All the mini-epidemics are laid on top of one another, coming at different moments and infecting different populations. These mini-epidemics take off regionally and put hundreds of lives at risk while the statewide numbers appear to be flat or dropping.” So, we need to look at the “right” data to decide where we are and we need to have a plan. Otherwise, we will feel overwhelmed and lost. Otherwise, we will blunder.

Today (April 20, 2020) the report by the Edmond J. Safra Center for Ethics at Harvard titled “Massive Scale Testing, and Supported Isolation (TTSI) as the Path to Pandemic Resilience for a Free Society” was released.  It is available at this link.

For a nice introduction there is a 13-minute video summary of the report with graphics that helps you get a feel for what is proposed. In spite of the report’s very grand title, the video has graphics that helps you get a feel for what is proposed. The tone of the video and the report is warm and upbeat but the challenges it presents are very real.

The video and report give dates that are aspirational and possibly attainable but at this point it is a black box. We need to know how “real” these timelines are for the US and for us in Maine.  What is key is that we have a plan and then all of us can chip in to make that plan real. We also need to know when our plan is not working and we need to change direction.

Updating from the report and video is an interview from the NPR show “On Point” (5/4/2020) with Danielle Allen, lead author of the recent Harvard paper on COVID-19 resiliency. (Two people are interviewed in this podcast. Danielle is the second interview.)

The podcast is available online at NPR. You can find it here:

As my friend Margaret Downing says, “She does an excellent job describing what COVID19 resiliency is and why it’s important. It answers the question of how we can get back to some version of normal life. What struck me most was her full-throated call for a grass roots movement of citizens demanding their state’s government create and publish NOW a detailed plan, with numbers, for testing, contact tracing and isolation support that will lead the state to resiliency. Now these are the three components we know are required to corral the virus- but it was her call for citizen action that got my attention.”

Many communities are making grassroots movements to step-up for what is needed. I hope your community is as well.

One Health and SARS-CoV-2: A presentation

One Health is an emerging and critical science in public health that relies on the collaborative efforts of multiple disciplines working locally, nationally, and globally, to attain optimal health for people, animals and our environment.

SARS-CoV-2 the virus responsible for COVID-19 illness is believed to have zoonotic origins and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus. Research is underway to establish an intermediate animal reservoir, such as a pangolin, to its introduction to humans. The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019.

Friday May 1, 2020 at 3pm, Dr. Vanessa Grunkemeyer DVM, MPH and Sharon McDonnell MD MPH will discuss One Health, spillover events between humans and animals, and what factors represent the most important risks to global health. Notably, media attention on infections of domestic and zoo animals have thrown a spotlight on the connection between all living organisms and the implications of these findings in cats, tigers and dogs will be discussed.

This presentation is open to the public. To register for this free online for the zoom session to go this link:

Epidemiology and the NFL

NFL Draft video

This was one of the most unusual interviews in my life and also very fun. Thanks so much to the NFL and the staff of their communications team for inviting me and asking about the Yarmouth Community Coronavirus Task Force. I really am star-struck and enamored with some of the players I met in the “Green Room”.

There are two regrets that I have.

  1. When Rich Eisen asked me “what can we do to help?” I was caught off guard. I wish I had given short statement to say how the CDC foundation is a worthy cause and well positioned to support public health. Here is a link to their site:
  2. I want to learn how to make any cause I have seem as fun and compelling as Guy Fieri.

Thanks to Winston Wu for recording this!

Yarmouth Community Coronavirus Task Force

The Yarmouth Coronavirus Community Task Force is a grassroots organization. We work in collaboration with Yarmouth and Cumberland County service organizations to assist with the disruptions and uncertainties caused by the Coronavirus epidemic. We stand together to help the increasing number of people who may experience food shortages, social isolation, medical and transportation needs in the wake of this Coronavirus epidemic. We are part of a larger community strategy that has been initiated by our Town Council, our Town Manager, EMS, Police, Fire, and all public servants. It is our goal that we participate in efforts to keep core services open, provide residents with safe ways to meet their needs and work together to mitigate the epidemic and maintain our personal/community health. This is a moderated site that aims to help people in our area access good information, resist nonsense and panic, and get needed resources. This Task Force is evolving and networking to evaluate the current needs of our neighbors and friends and to plan for the coming weeks and beyond. More information to come shortly.

Shown here is our report of activities for the past 2 weeks. It is mind-boggling to see what has been accomplished just since March 10, 2020 when we had our first meeting in the Community Room in the Town Hall in Yarmouth Maine.

Thanks to everyone that has supported us in multiple ways to help with this effort

A presentation: Interactive session on monitoring the SARS-CoV-2 epidemic

Join us for this Public interactive session via Zoom. We will describe and demonstrate key epidemiology terms used for epidemic response and monitoring. No public health training needed and everyone is welcome. Use this link to register to make it easy to get in at the time of the talk. The presentation will be recorded and available afterwards.

We will use one of the data visualization systems available online to show how these factors of infectious disease models interact with each other.

Here is the link for the recording:

The PowerPoint is available on request here in comments or from UNH.

Track, test, trace, & isolate

April 14 2020

Most asked question is what next in this pandemic?

The discussion in the media about the pandemic has changed as NYC reaches the top of their epidemic curve. Such big numbers! There is apparently a sense of relief and suddenly the talk is impatient about “opening” and releasing restrictions for physical distancing.  However, before we get too self-congratulatory, let us pause, the US is made of many separate epidemics and the peak in New York was on schedule but for the rest of the country the timing is different.

Regrettably the advice from the White House is at odds with everything coming from medical and public health experts.  The experts are expressing concern that decisions will be made without careful consideration of the trade-offs and risks. Fortunately, one can go to local sources to find excellent and measured descriptions of what it takes to plan the next steps. My personal favorite is Governor Andrew Cuomo of NY and Janet Mills of Maine with the Maine CDC director Nirev Shah.

To speak of the future it is important to remember that this virus in new. We can speculate about the post-infection immunity based on what we have seen and use examples from previous epidemics or other coronavirus strains but, these are just speculation.  

But, what I do know is this…it is a chorus that every expert is saying…. Track, test, trace, isolate. There are no shortcuts. Rinse and repeat.  If we do these activities systematically then we will be able to reopen our social and economic lives in a step-wise careful process that will be nerve-wracking as outbreaks inevitably re-kindle however, it will give us the information we need to proceed.  The big change will come with a vaccine (12-18 months at best) or when there is a proven treatment.

To make these steps happen and to begin to relax physical distancing we need laboratory tests and an army of people capable of interviewing every case (case investigation) and to establish their exposures and contacts.  Then contact tracers will reach out to all these contacts and ask (require) that they go into quarantine for 14 days.  To get a sense of this ask yourself how many people did you have contact with in the past 14 days – within 6 feet for longer than 15 minutes?  Since the Stay at Home order the number of contacts per case are much smaller and this makes the work involved with contact tracing more manageable.   A close contact is defined by the state health department in collaboration with the US CDC.  (Provided in another post)  

While in quarantine or isolation people would be called daily by contact tracers to establish if they are experiencing symptoms, if they have need for food or medicine, and if they need to be tested or referred. All of this information about cases (suspect or confirmed), contacts, and quarantine must be linked.  If someone cannot be reached then a call is made to the CDC (contact tracing or epidemiology team) to follow up and make sure they are alright and that they are protecting their neighbors by respecting quarantine. These follow-up calls are the simplest place to use volunteers if cases or contacts agree.

When I traveled home from Liberia to the US I got a call every day from the Maine CDC asking me about symptoms, fever, and how I was doing.  This call signaled to me that what I was doing was important.

Today the US CDC and FEMA released a draft plan for “reopening” parts of the country:

The plan lays out three phases: Preparing the nation to reopen with a national communication campaign and community readiness assessment until May 1. Then, the effort through May 15 would involve ramping up manufacturing of testing kits and personal protective equipment and increasing emergency funding. Then staged reopenings would begin, depending on local conditions. The plan does not give dates for reopenings but specified “not before May 1.”

……” The plan also carries this warning: “Models indicate 30-day shelter in place followed by 180 day lifting of all mitigation results in large rebound curve — some level of mitigation will be needed until vaccines or broad community immunity is achieved for recovering communities.”

“The document says reopening communities in this phased approach “will entail a significant risk of resurgence of the virus.” Any reopening must meet four conditions:

  • Incidence of infection is “genuinely low.”
  • A “well functioning” monitoring system capable of “promptly detecting any increase in incidence” of infection.
  • A public health system that is “reacting robustly” to all cases of covid-19 and has surge capacity to react to an increase in cases.
  • A health system that has enough inpatient beds and staffing to rapidly scale up and deal with a surge in cases.

The plan describes the conditions under which it is reasonable to lift some community mitigation measures, the phased steps to reduce those measures and indicators to monitor the impact of transmission on public health and health system capacities.”


To pull this off going forward means we need to reverse decades of lack of funding in public health infrastructure and create an army of Americans (and Mainers in our case) to help with case investigation, contract tracing and to support those in quarantine/isolation.  In the situation where tests are as limited as they are now, then we will need to use a “suspect” case definition for some cases and some contacts.  (See previous blog link here).  The inherent uncertainty is dissatisfying but it allows transparent decision-making and errs on the side of caution.

Managing case investigation during the Ebola outbreak in Liberia meant creating an army of smart street-wise people with a broad array of backgrounds. We looked for people that were persistent, good interviewers, and could manage on their feet.

In many articles that are coming out we are given dazzling visions about the promise of phone apps for contact tracing and follow-up. They use South Korea and other parts of Asia as examples. My experience with phone app tracking has been unimpressive.  It is harder than the developers promise to start up and it needs to fit the context– especially where there are multiple platforms, where the public fears loss of privacy, and there is not a public health system infrastructure to actually manage it.  There is far more training and support needed and the equipment is fussy.  I believe that the use of technology and phones will be a great tool but they are inadequate without a system and people.

How do we mange the pandemic and transition to the next phase?  The next phase — after this part where we are hunkered down hoping the storm doesn’t kill us – happens when we feel that we have a handle on community transmission and can track the epidemic.  Track, test, trace, isolate.  It is “over” when there are no cases of community transmission within at least 1 or 2 incubation periods.

The economy is a disaster but lets us not lose our resolve and sacrifice people unnecessarily. What our response tells us is that people matter. 

Here are three very good sources for thinking about our next steps:

The new CDC and FEMA draft plan:


2. How Liberia knocked out Ebola and our reliance on Governors in the US.

“….a collection of governors, former government officials, disease specialists and nonprofits are pursuing a strategy that relies on the three pillars of disease control: Ramp up testing to identify people who are infected. Find everyone they interact with by deploying contact tracing on a scale America has never attempted before. And focus restrictions more narrowly on the infected and their contacts so the rest of society doesn’t have to stay in permanent lockdown.”

In America, testing — while still woefully behind — is ramping up. And households across the country have learned over the past month how to quarantine. But when it comes to the second pillar of the plan — the labor-intensive work of contact tracing — local health departments lack the necessary staff, money and training.  There are ways to build this and that is the job we need to be doing right now in April 2020. 

3.  Advice from experts in Seattle about what comes next. There is a bit more excitement in this article about electronic tracking than I might express but for a problem this big we need many strategies.

A great resource:

Ian Lipkin MD, Professor of epidemiology at the Mailman school of Public Health at Columbia University who gave a fantastic talk at the University of New England this evening.  It was sponsored by the Center for Global Humanities and it was recorded.   He is a true expert in these pandemics and a very clear speaker. It is worth the 60 minutes for the talk and if you are really feeling it there is another 30 minutes of Q&A.  Show it to all your friends that have also become pandemic geeks.

Finally, good news!  The viral RNA found in stool samples appears to not be infectious.  It is just viral bits making their way out of the body (Nature April 2020).  As the body destroys and deals with the virus there are bits of RNA that are around to tweak and tease virologists and to confuse the tests looking for them.  The studies into SARS-2 in various bodily fluids are fascinating and MIGHT lead to a better understanding of ways to test and how the virus behaves. Meanwhile, not to fret, it seems transmission via feces is not likely.

Wash your hands, don’t touch your face, be kind and stay home