Through the surge of December 2021 omicron infections in NYC, my role as CEO and Founder of Infectious Economics was to guide safety teams embedded at in-person businesses to reduce the likelihood of transmissions at the workplace. It was a scary and hard time. The outbreaks looked very different from what we had experienced with prior variants of concern. We sequenced clusters of positive cases and conducted extensive genomic epidemiology investigations to better understand what was happening, update testing policies, and prevent future workplace outbreaks.
Shortly after sharing our discoveries in this paper on MedRxiv Jan 5, 2022, the story was picked up by 275 media outlets and shared more than 3000 times on Twitter. More than 100,000 people read our paper within a month. The de-identified dataset and R code made open access and allowed other researchers to reproduce the results and rapidly build on the findings.
Omicron cases were infectious for several days before positive by rapid antigen tests
Here is a summary of what we learned about the time-dependent sensitivity of COVID-19 tests.
ABSTRACT: The performance of Covid-19 diagnostic tests must continue to be reassessed with new variants of concern.
The objective of this study was to describe the discordance in saliva SARS-CoV-2 PCR and nasal rapid antigen test results during the early infectious period. We identified a high-risk occupational case cohort of 30 individuals with daily testing during an Omicron outbreak in December 2021.
Based on viral load and transmissions confirmed through epidemiological investigation, most Omicron cases were infectious for several days before being detectable by rapid antigen tests.
Blythe Adamson, Robby Sikka, Anne Wyllie, Prem Premsrirut. Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series. medRxiv 2022.01.04.22268770; doi: https://doi.org/10.1101/2022.01.04.22268770
Shown are Cycle Threshold (Ct) counts and rapid antigen test results from paired samples of infected patients.
See the full article for Panel B showing the Kaplan Meier analysis of time from positive PCR to positive rapid antigen test.
Press coverage found our study timely and actionable
- STAT. Study raises doubts about rapid Covid tests’ reliability in early days after infection. By Matthew Herper. 5 Jan 22. article
- The New York Times. Emerging Data Raise Questions About Antigen Tests and Nasal Swabs. By Emily Anthes and Christina Jewett. 5 Jan 22. article
- Reuters. Rapid nose swab tests for COVID may not detect Omicron quickly enough – expert says. By Nancy Lapid. 7 Jan 22. article
- TIME. Nose or Throat? The Best Way to Swab for At-Home COVID-19 Tests. By Alice Park. 13 Jan 22. article
- Scientific American. When Should You Get a COVID-19 Test? By Sara Reardon. 26 Jan 22. article
- National Geographic. Is Omicron really less severe than Delta? Here’s what the science says. By Emily Sohn. 11 Jan 22. article
- Vogue. What Is Throat Swabbing (And Should You Be Doing It to Detect Omicron)? By Emma Specter. 12 Jan 22. article
- The Atlantic. America’s COVID Rules Are a Dumpster Fire. By Katherine Wu. 6 Jan 22. article
- BuzzFeed. This Is What You Should Know Before Taking A Rapid COVID Test. 6 Jan 22. By Theresa Tamkins and Dan Vergamo. article
- Vox. Rapid tests, omicron, and you. By Rebecca Heilweil. 10 Jan 22. article
- Axios. Rapid nasal COVID tests feared to be returning false negatives. By Caitlin Owens. 6 Jan 22. article
- CNBC. What to do if you can’t get a PCR test — and 2 other doctor-approved Covid test hacks you should know. By Hallie Levine. 23 Jan 22. article
- NPR. All Things Considered: As omicron spreads, here’s the best and most accurate way to use rapid antigen tests. 7 Jan 22. radio clip
- NPR. Why rapid COVID tests aren’t more accurate and how scientists hope to improve them. By Maria Godoy 23 Jan 22. article
- The Washington Post. They relied on rapid coronavirus tests to gather safely. Some wish they hadn’t. By Katie Shepherd. 17 Jan 22. article
- WebMD. Swab Nose, Throat, or Both for COVID-19 Rapid Tests? By Damian McNamara. 11 Jan 22. article
- Bloomberg. Balance of Power: Can Rapid Tests Detect Omicron? (Radio). 10 Jan 22. radio episode
The World Health Organization cited our study in three separate editions of their bulletin:
- World Health Organization. (2022). COVID-19 weekly epidemiological update, edition 76, 25 January 2022. World Health Organization. https://apps.who.int/iris/handle/10665/351190
- World Health Organization. (2022). COVID-19 weekly epidemiological update, edition 78, 8 February 2022. World Health Organization. https://apps.who.int/iris/handle/10665/351853
- World Health Organization. (2022). COVID-19 weekly epidemiological update, edition 84, 22 March 2022. World Health Organization. https://apps.who.int/iris/handle/10665/352608
Real-time data science can start the old fashioned way… with chalk, pen and paper
Modern scientists don’t leave home without liquid chalk markers in case of emergency. I didn’t bring my computer to the sandy beach where I rested and recovered during the last few days of December 2021. The longer I thought, the clearer it became what needed to be communicated to the public asap for societal good.
Remote visibility into the dataset was available through my phone, so I pulled out pen and paper to graph the time to positive test result for a small group of people who were receiving PCR and antigen tests every day at work. With the hand-sketched version of the graph complete (see below), I used the sliding glass door of my hotel room like a chalkboard to hand write the lines of R code needed to analyze the data and generate the same plot on the computer later.
Notice the similarity in appearance between the original hand-drawn version below and the final figure featured in this STAT article and shown above!
Transparency allowed other scientists to reproduce and extend study findings
One key benefit from being transparent with your analysis code and data is that other scientists can further interrogate and extend the research findings to advance the scientific understanding as fast as possible.
Here is an example of a success story about the benefits of transparency and open access. A PhD student at the Centre for Mathematical Modelling of Infectious Diseases at the London School of Hygiene & Tropical Medicine found a link to our paper on Twitter and was inspired to use the dataset to explore a new question about testing with nasal vs saliva samples.
Special thanks to partners and collaborators
Special thanks to Lisa Kussell, Charlene Speyerer, and Cat Miller for scaling the effort and impact of Infectious Economics to support economic revitalization across the United States. Much of the routine occupational safety saliva PCR testing conducted by workplaces participating in this study was conducted at Mirimus Labs in Brooklyn, NY.
