Syndromic Surveillance & Covid-19 Resources

This article is part of the Syndromic Surveillance and Covid-19 collection on Thoughtfaucet.

In the process of developing the Syndromic Surveillance Covid-19 NYC graph I’ve been gathering and reading a variety of resources. Some of these are for specialist audiences and others are for more general audiences. This page is an annotated bibliography of the medical journal articles, Twitter threads, and news reports that inform the project.

Scientific research, projects, articles

Published, pre-print, and other scientific work related to syndromic surveillance, Covid-19, emergency medicine, and related topics.

. “Effectiveness of Surgical and Cotton Masks in Blocking SARS–CoV-2: A Controlled Comparison in 4 Patients.” Annals of Internal Medicine, (). .
4 Covid-19 symptomatic patients in a negative pressure room cough into surgical and paper masks. Coronavirus is present on the outside of the masks and on a petri dish that was placed 20cm in front of them. 2 out of 4 were able to cough through the paper mask to the petri dish. All of them had coronavirus on the outside of the paper mask after coughing. Studies like this are important for understanding steps that populations can take to slow the spread of Covid-19 or other respiratory disease.
expert audience, small study, masks, Covid-19
“Genomic analysis of COVID-19 spread. Situation report 2020-04-17.” Nextstrain, (). .
Interactive map tracing the spread of Coronavirus around the world including the pathways to outbreaks in East Coast, West Coast, West, and Midwest USA.
genomic analysis, coronavirus
“First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020.” Euro Surveill, ():1-7. .
A study and discussion of the first three cases of Covid-19 in France. This article outlines a standard detection and contact tracing method as employed in France at the time of the Coronavirus outbreak.
expert audience, study, process, medical authorities, covid-19, SARS-CoV-2
. “Misinformation During a Pandemic.” Becker Friedman Institute for Economics at UChicago, (). .
A working paper comparing the impact of two different conservative talk shows on viewer behavior relative to Covid-19 during the early stages of the Covid-19 outbreak of March/April 2020.
expert audience, working paper, media
. “Five Things Students and Clinicians Should Know About ‘Biocontainment’.” AMA Journal of Ethics, ():22(1):E22-27. .
Article on the role of trust in public health, set in context with experiences working with Ebola patients and communities, the role of technology in rich and poor countries, and working with communities to achieve health outcomes.
general audience, ethics, community expression, public health, trust
. “Clinical progression of patients with COVID-19 in Shanghai, China.” Journal of Infection, ():80(5):e1-e6. .
A study describing the temporal case progression of Covid-19 from a single medical center in Shanghai China
expert audience, study, covid-19, clinical progression, clinical characteristics, viral clearance
. “Nonpharmaceutical Measures for Pandemic Influenza in Nonhealthcare Settings—Social Distancing Measures.” Emerging Infectious Diseases, 26, no. 5, ():775-776. .
Discussion of the influence of various policy measures on pandemics including isolating ill persons (“we found limited scientific evidence to support the effectiveness of this intervention in the community”), contact tracing (“there is no obvious rationale for the routine use of contact tracing in the general population for control of pandemic influenza” and “There are some specific circumstances in which contact tracing might be more feasible and justified, such as to enable short delay of widespread transmission in small, isolated communities, or within aircraft settings to prevent importation of cases.”), quarantine of exposed persons (“we found that the evidence base was weak for home quarantine”), school dismissals or closures (“found compelling evidence that school closures could reduce influenza transmission”), workplace measures and closures (“We found limited evidence that workplace measures and closures would be effective in reducing influenza transmission.”), and avoiding crowding (“The evidence for avoiding crowding is limited.”). The authors consider the difficulty of implementing each measure as part of their assessments.
policy, isolation, contact tracing, quarantine, school closure, workplace closure, social distancing
“Self-reported fever and measured temperature in emergency department records used for syndromic surveillance.” Journal of the American Medical Informatics Association, 19, no. 5, ():775-776. .
Discussion of the relationship between patient-reported fever and measured temperature along with availability of measured data in emergency department visits.
syndromic surveillance, medical practice, emergency department, implementation
. “Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys.” Harvard SPH Scholarly Articles, (). .
Given the unavailability of genuine Covid-19 tests and the desire to resume the economy, policy-makers may turn to serological testing to get a sense of how many people have already had Covid-19. This study uses models to help inform different ways structuring serological tests for Covid-19.
expert audience, modeling, Covid-19, serological tests
“The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application.” Annals of Internal Medicine, (). .
Study of 181 cases, some in China and some outside China, to estimate the incubation period and window of symptom onset of Covid-19
research, covid-19, symptom onset, incubation period
“Implementing Syndromic Surveillance: A Practical Guide Informed by the Early Experience.” Journal of the American Medical Informatics Association , 11, no. 2, ()141-150. .
Initial interest and funding on syndromic surveillance occurred in the wake of 9/11 terrorism attacks. This article outlines how the tools developed and implemented could be useful for other situations, such as pandemics. The authors helped to launch the first generation of syndromic surveillance in the USA and present guidance for implementing such systems including defining leadership and partners, selecting population and data sources, data collection and storage, data integration, privacy concerns, outbreak detection, measuring quality of data, integrating with public health policy. They also include ideas for next steps for building on the syndromic surveillance capabilities they’ve developed.
syndromic surveillance, data, bioterrorism, coalition building, public health
“Looking for evidence of a high burden of COVID-19 in the United States from influenza-like illness data.” Reichlab UMass-Amherst,, (). .
A study of publicly available data from a variety of health providers on Influenza-like Illness (ILI), all age groups, to see if non-influenza ILI is making a larger portion of ILI visits vs the same time previous years. Data is updated regularly. Key graph shows current Covid-19 era alongside historical and the 2009/10 H1N1 flu for comparison
expert audience, study, data, medical authorities, influenza-like illness, ILI, covid-19, SARS-CoV-2, h1n1
. “Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area.” JAMA , (). .
A study of early outcomes of Covid-19 patients in New York City. Outcomes were available for 2634 patients in the study who either died or were discharged before the conclusion of the study period. 88.1% of those who required mechanical ventilation died.
Covid-19, mortality, co-morbidities
“COVID-19 watch USA: NY, WA, CA, & other states.” Medium, (). .
A computational neuroscientist compares data from WA, NY, and CA to see what there is to watch containment strategies and outcomes.
general audience, data, comparisons
“Estimates of the severity of coronavirus disease 2019: a model-based analysis.” The Lancet Infectious Diseases, ():1-9. .
Study of 24 Covid-19 deaths in China and 118 recoveries outside China to estimate the incubation period and window of symptom onset to death or recovery as well as case fatality ratio.
research, covid-19, symptoms to death, symptoms to recovery, case fatality ratio
“NYC ED syndromic surveillance.” Weinberger Lab Yale School of Public Health, (). .
An interactive tool to view EpiQuery data with graphs for each age bucket and pull-downs to select ILI or Resp(iratory illness) and specific borough. Compare this year against a model adjusting for seasonality, influenza activity, and RSV activity.
data tool, medical authorities, influenza-like illness, ILI, respiratory illness
“Using ExcessILI with US P&I mortality data.” Weinberger Lab Yale School of Public Health, (). .
Plots of weekly death rates, observed/expected deaths, excess pneumonia/ILI mortality for each state plus NYC. Built using data from the CDC.
data tool, research, influenza-like illness, ILI, excess mortality
. “Estimating the early death toll of COVID-19 in the United States.” medRxiv Preprint Server, (). .
Preprint which calculates excess mortality for pneumonia and influenza above seasonal average in the USA. Includes a link to the code and data for the study.
mortality, Covid-19, preprint, expert audience
“Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones.” The University of Texas at Austin COVID-19 Modeling Consortium, (). .
A model-based paper using cell phone surveillance data from SafeGraph to estimate the effectiveness of distancing measures.
data tool, research, influenza-like illness, ILI, excess mortality
“SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases.” MedRxiv Preprint Server, ():1-14. . medRxiv.
Preprint study describing a method of medical surveillance based on analyzing wastewater. This method could be useful in areas and situations in which a population does not have adequate access to healthcare or for other reasons is likely to be missed by healthcare-based syndromic surveillance.
preprint, expert audience, study, process, covid-19, SARS-CoV-2, wastewater-based epidemiology, related-company authors
“Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72?314 Cases From the Chinese Center for Disease Control and Prevention.” JAMA, (). .
Data re: the Wuhan outbreak. A clear display of the lag-time between true cases and confirmed cases. Also it shows the relationship between measures taken to “flatten the curve” and outcomes. Additional statistics on case fatality rates and other characteristics of Covid-19.
expert audience, study, data, medical authorities, Wuhan, covid-19

First person accounts and on-site journalism, NYC Covid-19 March/April 2020 Outbreak

Working in emergency departments and encounters with the medical system during Covid-19.

. “Heard on the Street.” New Yorker, . .
A photograph of a sketchpad featuring drawings, conversations, and scenes of life in New York City during the March/April 2020 Covid-19 outbreak.
general audience, art, conversations, pattern of life, ethnography
“Marines Sprint Down NYC Pier to Deliver Oxygen Tanks to Dying Coronavirus Patients.” Military.com, . .
News report describing the actions of marines operating security checkpoint at the hospital ship USNS Comfort in NYC.
general audience, journalism, covid 19, USNS Comfort, military, ethnography
“‘Code Blue’: A Brooklyn I.C.U. Fights for Each Life in a Coronavirus Surge.” New York Times, . .
A story following a critical care doctor through his work at the Brooklyn Hospital Center during the peak of the Covid-19 intake of late March/early April 2020.
general audience, journalism, covid 19, emergency department, ethnography
. “New Yorkers, Once Again at Ground Zero, in Their Own Words.” Wired, . .
First person accounts of people who live in New York City during the Covid-19 outbreak of March/April 2020. In particular, a section of medical workers. There are some specific observations regarding the nature of Covid-19 relevant to ventilator use and oxygen count which will be of interest to medical researchers.
general audience, journalism, covid 19, emergency department, emergency medicine, NYC, ethnography
“The wait is endless. Supplies are gone. My New York hospital is on the brink.” The Washington Post, . .
A second-year emergency medicine resident discusses the situation in his hospital.
general audience, NYC emergency department, ER burden, ethnography
“Inside a Brooklyn hospital that is overwhelmed with Covid-19 patients and deaths” CNN, . .
A second-year emergency medicine resident discusses the situation in his hospital.
general audience, NYC emergency department, ER burden, ethnography
(@KiraNewmanMDPhD). “After a week of working in the #ICU here in #Seattle caring for patients with #COVID19 (and other illnesses), here are some thoughts.” Twitter, . .
A thread of practical lessons learned and general observations from a Seattle ICU doctor.
general audience, emergency medicine, coronavirus testing, patterns of care
“‘I Am Dreading My Next Shift’: An NYC E.R. Doctor Speaks Out About The Escalating Coronavirus Crisis.” Gothamist, . .
An anonymous interview with an ER Doctor about conditions in NYC emergency departments as of March 13, 2020.
general audience, interview, NYC emergency department, ER burden, ethnography
“‘It’s unlike anything I have ever seen’: A deadly week across America.” Los Angeles Times, . .
Vignettes from around the USA during the March/April Covid-19 outbreak. Includes stories from New Orleans, Detroit, Seattle, New York City, and Albany, Georgia.
general audience, ethnography, covid-19
(@arghavan_salles). ““I haven’t seen a patient leave here to go anywhere except the morgue.” This is what one of the advanced practice providers in the ICU told me. She’s been here 3 weeks..” Twitter, . .
Twitter thread the experience of working in an emergency department during the March/April 2020 Covid-19 outbreak in NYC. Focuses on emotional burden taken on by healthcare workers as well as the medical work they are doing.
general audience, covid-19, emotional burden, healthcare workers, ethnography
. “A String Quartet Is Crushed by the Coronavirus.” New York Times, . .
News report on the impact of Covid-19 on a string quartet and the ancillary businesses they work with.
general audience, NYC, impacts, ethnography
“‘Dead on Arrival’: A N.Y. Fire Chief’s COVID Journal.” ProPublica, . .
An FDNY Chief writes about the nature of his job during Bedford-Stuyvesant during the Covid-19 outbreak of March/April 2020.
general audience, journal, NYC emergency department, fire department, first person, ethnography
(@ASlavitt). “Spent the day talking to hospitals at ground 0. Learned about new problems that will emerge everywhere..” Twitter, . .
Twitter thread on what is needed at hospitals in NYC in the midst of fighting Covid-19 with an eye on logistics and personnel.
general audience, covid-19, medical system operations
. “‘People Are Dying’: 72 Hours Inside a N.Y.C. Hospital Battling Coronavirus.” New York Times, . .
Video report from Elmhurst Hospital’s emergency department.
general audience, news report, covid 19, resourcing, video, emergency department, ethnography
(@Craig_A_Spencer). “So what’s really going on here in NYC? You’re hearing conflicting information on who is tested, who is admitted, who goes home, and what’s going on inside hospitals. Let me shed some light. NYC ER docs are a small and collaborative community, so let me share the scoop:.” Twitter, . .
A NYC ER doctor/Director of Global Emergency Medicine at Columbia talks about protocol who is being hospitalized and tested in NYC.
general audience, emergency medicine, coronavirus testing, patterns of care, ventilators

Context and commentary

Discussions of contextual issues surrounding syndromic surveillance, the operations of a medical system, and Covid-19.

“In Pursuit of PPE.” The New England Journal of Medicine, . .
Correspondence describing the lengths to which health systems must go in order to secure protective equipment for their staffs. This involves bidding against the Federal government and also preventing DHS from re-routing the supplies.
general audience, journalism, covid 19, piracy, PPE, supply chains
(@BhadeliaMD). “Just to break down some #COVID19 issues for those not working in a hospital. First: even if the number of cases in many major US cities are in the 100s (not yet 1000s), hospitals and clinics in those cities are already becoming very busy and stretched. Why is this? [THREAD].” Twitter, . .
A thread on the load put on emergency departments when testing isn’t available during a pandemic.
general audience, medical authorities, emergency services, workflow
. “Emerging Lessons From COVID-19 Response in New York City.” JAMA Health Forum, . .
Observations on NYC’s experience with the March/April 2020 Covid-19 outbreak with a focus on health care systems operations. Specific attention given to clinician morale, healthcare equity, and intelligence gathering/generation.
general audience, covid 19, medical systems, operations, surveillance
. “Global coronavirus death toll could be 60% higher than reported.” Financial Times, . .
Assessment and graphs of excess mortality during the Early 2020 Covid-19 Pandemic.
general audience, covid 19, graphs, excess mortality
(@NAChristakis). “Flu pandemics recur reliably but unpredictably every decade or so, and their extent and intensity varies.” Twitter, . .
A thread on seasonal flu patterns. Focused on the 1957 Flu.
general audience, 1957 Flu, flu patterns
“In Trump’s ‘LIBERATE’ tweets, extremists see a call to arms.” NBC News, . .
News article on the discrepancy between what Donald Trump is encouraging US citizens to do and what people who understand the pandemic, including those in his administration, are recommending US citizen do. Interfering with the non-pharmaceutical interventions such as distancing also interferes with the outcomes we will have.
general audience, journalism, covid 19, re-opening, NPI
“A second wave of covid-19 hits northern Japan.” The Economist, . .
Journalist report on non-pharmaceutical interventions in Hokkaido Japan. In this case the economy opened and then had to shut down again because cases began rising.
general audience, journalism, covid 19, re-opening, NPI
“These ‘disease hunters’ developed a novel technique for tracking pandemics after 9/11, but lost funding right before COVID-19.” CNBC, . .
History of the development of syndromic surveillance while highlighting the relevance of the technique to the challenges posed by the US administration’s response to Covid-19.
general audience, journalism, covid 19, syndromic surveillance, history, bioterrorism
“Fighting COVID-19 in NYC.” Reuters, . .
A collection of graphics and data about how Covid-19 is progressing in NYC includes breakdowns by gender, race, neighborhood.
general audience, NYC, graphs, charts, photos, data
“How much is coronavirus spreading under the radar?.” Nature, . .
Discussion with experts at WHO, USA CDC, and Wellcome re: estimating amount of spread of the coronavirus which causes Covid-19.
general audience, interview, medical authorities, WHO, Wellcome, USA CDC, spread estimate methods, containment, covid-19, coronavirus
“‘Vital and urgent’: Inside New York City’s difficult quest to obtain coronavirus testing kits.” USAToday, . .
A rundown of the challenges and failures of the US government to provide adequate Covid-19 testing supplies and protocols to the NYC. These breakdowns has lead to an increased value for syndromic surveillance within the medical system.
general audience, journalism, covid 19, syndromic surveillance, logistics, US government
. “At NYC hospital treating coronavirus, doctors ‘use their MD license like they haven’t had to before’.” USAToday, . .
News report on the structuring of healthcare at NY Presbyterian with a focus on how doctors are working outside their normal specific practices to make up for shortfalls in necessary emergency service for Covid-19 and coronavirus care.
general audience, NYC, medical doctors, NY Presbyterian Hospital, personnel
(@Farzad_MD). “1/ Reading this history of syndromic surveillance from @chrissyfarr brought back a lot of memories.” Twitter, . .
A thread on the origins of contemporary syndromic surveillance in the US.
general audience, syndromic surveillance, history, policy, CDC
(@Farzad_MD). “ 1/ Is the #COVID19 outbreak in the US going down? Are we ready to lift lockdown? How would an epidemiologist look at the data to help us understand these questions?.” Twitter, . .
A thread discussing the utility syndromic surveillance to policy decisions regarding resuming the US economy.
general audience, syndromic surveillance, policy, resuming the economy
(@EpiEllie). “The scientific method is one way of gaining knowledge about the world. Most of us learn in school about how this works for experimental lab research, but I think very few of us learn how it works if we can’t experiment. So let’s talk about how to get knowledge from observations..” Twitter, . and .
Twitter thread on observational practices in epidemiology and science.
general audience, medical authorities, epidemiology, OODA, knowledge generation
(@vivek_murthy). “Yesterday, I spoke with doctors from one of the nation’s leading academic hospitals located in a state where #COVID19 cases are increasing quickly. This is what they told me: They’ve been seeing *many* patients with symptoms concerning for COVID19 who need testing.” Twitter, . .
Former Surgeon General Murthy describing needs of medical systems based on conversation with people who run leading health care systems.
general audience, medical authorities, health institution needs, medical supplies
. “Trump Accuses New York Of Padding State’s Mortality Rate By Including African American Deaths.” The Onion, ()) 56 issue 17. .
Satire which notes the racial disparities of Covid-19 deaths in the United States and the general tendencies of the government administration.
satire, general audience, Covid-19, race, mortality
“Data insight: Syndromic surveillance should be explored as an early signal for COVID-19.” COVID-19 Weekly Science Review March 28–April 3, 2020, Accessed . .
Newsletter featuring, among other Covid-19 topics, an overview of syndromic surveillance including the same EpiQuery data used for the charts in this project.
general audience, covid 19, syndromic surveillance, history
(@cmyeaton). “I’ve been working with @reichlab and colleagues weekly to assess whether levels of ‘influenza like illness’ that are NOT due to influenza are higher than usual in the US.” Twitter, . .
Brief Twitter thread providing context of the primary chart in the Reich et al study.
general audience, chart, medical authorities, influenza-like illness, ILI, covid-19
(@cmyeaton). “ I am not enthusiastic about using influenza like illness (ILI) data to guide the public health response to Covid. I think @reichlab and I were actually the first team to use ILI data to look for signs of Covid in the US, so I do see the potential. But.. 1/.” Twitter, . .
Twitter thread outlining reasons that Reichlab and Dr Rivers ceased updating their syndromic surveillance study (see journal articles above). Reasons include changing human behavior in relation to seeking healthcare, challenges with the use of percentage-based syndromic data, and concern about the possibility of use syndromic surveillance in lieu of diagnostic testing.
covid-19, syndromic surveillance, caveats
“Historian Frank Snowden: May we be ‘forever changed’ by coronavirus.” Interview by Susan Gonzalez. Yale News, . .
Historian and author Epidemics and Society: From the Black Death to the Present discusses how epidemics reflect the societies in which they take hold, the role of infrastructure in epidemic spread, the human/animal interface of epidemics, and the role of poverty.
general audience, interview, history, epidemics
. “How does coronavirus kill? Clinicians trace a ferocious rampage through the body, from brain to toes.” Science, . .
Lengthy article describing what is known about about how Covid-19 kills patients. Includes caveats about how our learning is still developing as well as information on Covid-19 impact on lungs, kidneys, the brain, and elsewhere.
general audience, Covid-19, lung, kidney, brain, mortality
“‘Cardiac calls’ to 911 in New York City surge, and they may really be more COVID cases.” NBC News, . .
Report on ambulance calls in NYC during the March/April Covid-19 outbreak. Includes some data on calls and fatalities.
general audience, NYC, ambulance, data

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