(1) Where did it come from? Or, rather, where didn’t it come from? This virus was not intentionally engineered; it’s not a Chinese weapon. That’s propaganda. But scientists cannot rule out at this time that the virus escaped accidentally from a lab, he says. It’s very unlikely, but there is now very circumstantial evidence for it.[2] University of North Carolina scientists and Chinese scientists collaborated on a NIH-funded project studying coronaviruses from 2014-2019. However, their published work shows too few similarities between this second SARS and the many bat coronaviruses they examined. Most likely, this was a bat-to-human zoonotic event, perhaps with a scaly pangolin host in between.[3]

(2) Did I already have COVID-19 last winter? No. Bromage rehearses the detective-story rundown of the outbreak as we know it. The first major crossover event occurred in November in or near Wuhan, but not necessarily at the seafood market.[4] The United States had a few cases but contained them and shut down travel from China by the end of January.[5] Most cases, according to him, likely derived from Europe and ran through the East Coast, not from China and the West Coast. Recent news suggests, however, that the so-called “China travel ban” let in a staggering 430,000 passengers anyway, many of whom were not screened.[6]

(3) What kind of tests are there and how do they work? There are three main kinds of tests: RT-rPCR (reverse transcriptase (RT), real-time (r), polymerase chain reaction (PCR)), a newly developed antigen test, and the serological/antibody test. The RT-rPCR test is the most commonly used one—the one that people complain about because you get a swab on the end of a long stick jammed up your nose until your brain hurts, and then they delicately smoosh that mess into a vial. They mash up your cells, sieve out the RNA and DNA, spinning out all the other cytoplasmic stuff that you learn about in AP Biology, use some reagents to boost it, and violá, you can read whether there’s some coronavirus RNA floating around in your mucus membranes. A positive result for this test is very accurate and means there’s actual SARS-CoV-2 ribonucleic acid in your body, but not necessarily that you’re sick from it yet. A negative result means … well, it could mean they messed up the sample or just did the test wrong or that the virus isn’t floating around in your nose in high enough quantities. There are rising numbers of false negatives with this RT-rPCR.[7] This scenario almost certainly led to China’s decision to switch diagnostic measures to clinical ones like chest X-rays, which, in turn, lead to China’s upward revision of cases and deaths (headlined as a “surge” instead of a change in diagnostic practice) in February.[8]

The second test, an antigen test, is much faster, less invasive, and safer for staff. But as Bromage reports, false and inconclusive results happen more often.

Finally, the serological tests see if you’ve got some coronavirus protein antibodies floating around inside of you, indicating you had a coronavirus at some point. It has an error rate of about 50%, however. Avoid making decisions based on this test, cautions Bromage.

Interestingly, a pre-print appeared on medRxiv this week (with all the caveats about pre-prints) using antibody seroprevalence sampled early this month in Santa Clara, California.[9] The Stanford and USC researchers conclude that there is a far higher infection rate than previously acknowledged. What’s more interesting is that John Ioannidis is an author in the study. Ioannidis is a modern-day legend for instigating the “replication crisis” in the social sciences. Basically, he believes most social scientific statistical work is shoddy and has spent his career trying to debunk both the methods and the conclusions. Nonetheless, a number of other scientists have taken to Twitter peer-reviewing the antibodies study—and casting serious doubt on Ioannidis’ work.[10] They are questioning his numbers and his methodology. This online version of back-street-arm-wrestling-match peer-review is both interesting and a little terrifying, given that the pre-print studies seem to be fed into the broader media at a rate correlating not with their ability to withstand review but merely with the relative celebrity of the authors and their institutions.

Back to Dr. Bromage:

(4) If I am infected, will I later be immune? We don’t know. Versions of the common cold are also caused by a coronavirus, and we don’t remain immune to that for long.

(5) Is it as bad as the flu? It’s probably much worse. Even if the much higher-than-flu mortality rate isn’t as high as it seems, it is spreading like a California forest fire through dry underbrush. His analogy is good:

[A] restaurant can serve 50,000 meals over a year, but the same restaurant can’t fulfill 50,000 orders in a week. Most orders couldn’t be fulfilled….with health care, an unfulfilled order means a death. Remember, from a flu index case, a ten-point transmission chain results in ~15 infections. While with SARS-CoV, a single index case transmission chain results in 59,000 infections [and rising].

My interpretation of Dr. Bromage’s answer to “where are we now?” is: we’re maybe starting to get into a better place. Most of us have sheltered at home, which has begun to flatten the curve. We are far from sorting out the PPE situation, the test situation, and the economic situation even in health care facilities. And just as we’re beginning to get this under control in the metropolises, it seems to be spreading to the smaller cities where people seem less willing to comply with stay at home orders.

Notes

[1] Erin Bromage, “Where We Are Now?,” Erin Bromage, Ph.D.: COVID-19 Musings, April 19, 2020, https://www.erinbromage.com/post/where-we-are-now.

[2] Josh Rogin, “Opinion | State Department Cables Warned of Safety Issues at Wuhan Lab Studying Bat Coronaviruses,” The Washington Post, April 14, 2020, https://www.washingtonpost.com/opinions/2020/04/14/state-department-cables-warned-safety-issues-wuhan-lab-studying-bat-coronaviruses/.

[3] Roujian Lu et al., “Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding,” The Lancet 395, no. 10224 (February 22, 2020): 565–74, https://doi.org/10.1016/S0140-6736(20)30251-8.

[4] Josephine Ma, “China’s First Confirmed Covid-19 Case Traced Back to November 17,” South China Morning Post, March 14, 2020, https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back.

[5] Lily Kuo, “Birth of a Pandemic: Inside the First Weeks of the Coronavirus Outbreak in Wuhan,” The Guardian, April 10, 2020, https://www.theguardian.com/world/2020/apr/10/birth-of-a-pandemic-inside-the-first-weeks-of-the-coronavirus-outbreak-in-wuhan.

[6] Zolan Kanno-Youngs, “Travelers From Coronavirus Hot Spots Say They Faced No Screening,” The New York Times, March 13, 2020, sec. U.S., https://www.nytimes.com/2020/03/13/us/politics/coronavirus-travelers-screening.html; Steve Eder et al., “430,000 People Have Traveled From China to U.S. Since Coronavirus Surfaced,” The New York Times, April 4, 2020, https://www.nytimes.com/2020/04/04/us/coronavirus-china-travel-restrictions.html.

[7] Kristin V. Brown, “False Negatives Raise Doctors’ Doubts About Coronavirus Tests,” Bloomberg.Com, April 11, 2020, https://www.bloomberg.com/news/articles/2020-04-11/false-negative-coronavirus-test-results-raise-doctors-doubts.

[8] Dominique Patton and David Stanway, “China’s Hubei Province Sees Surge in Coronavirus Deaths on Switch to New Methodology,” Reuters, February 13, 2020, https://www.reuters.com/article/us-china-health-hubei-toll-idUSKBN207010.

[9] Eran Bendavid et al., “COVID-19 Antibody Seroprevalence in Santa Clara County, California,” MedRxiv, April 30, 2020, 2020.04.14.20062463, https://doi.org/10.1101/2020.04.14.20062463.

[10] Natalie E. Dean, “A Thread Written by @nataliexdean,” Threader.app, April 18, 2020, https://threader.app/thread/1251309217215942656.