Uncontrolled spread, p.54
Uncontrolled Spread, page 54
77.James Gorman and Carl Zimmer, “Another Group of Scientists Calls for Further Inquiry Into Origins of the Coronavirus,” New York Times, May 13, 2021.
78.Hudson Institute, “Virtual Event—The Origins of COVID-19: Policy Implications and Lessons for the Future,” March 12, 2021.
79.Jesse D. Bloom et al., “Investigate the Origins of COVID-19,” Science 372, no. 6543 (2021): 694.
80.David A. Relman, “Lab leaks happen, and not just in China. We need to take them seriously,” Washington Post, June 2, 2021.
81.Scott Gottlieb, “The CIA Can Help Spot the Next Pandemic,” Wall Street Journal, February 28, 2021.
82.Saeed Shah, “CIA Organised Fake Vaccination Drive to Get Osama Bin Laden’s Family DNA,” Guardian, July 11, 2011.
83.Editorial Board, “Polio Eradication: The CIA and Their Unintended Victims,” Lancet 383, no. 9932 (2014): 1862.
84.Ibid.
85.Ibid.
86.W. John Kress, Jonna A. K. Mazet, and Paul D. N. Hebert, “Opinion: Intercepting Pandemics Through Genomics,” Proceedings of the National Academy of Sciences 117, no. 25 (2020): 13852–5.
87.One of the most significant obstacles to leveraging sequencing data alone to deduce the clinical features of a virus is limits on the ability to correlate clinical information to the different virus samples. If you want to do more sophisticated analysis, by the time a viral sample makes its way to researchers for sequencing, all the clinical information has been stripped away. Much of this is to address patient privacy considerations, but those considerations can perhaps be safeguarded while still allowing anonymized clinical information to ride along with patient samples. What happens now is that researchers and providers decide that the easiest way to sidestep privacy concerns is to just strip away the information on how patients fared, even though that information is valuable in correlating sequencing with clinical outcomes. One reform is to change patient privacy laws for samples used to inform public health surveillance.
88.Stephen K. Gire et al., “Genomic Surveillance Elucidates Ebola Virus Origin and Transmission During the 2014 Outbreak,” Science 345, no. 6202 (2014): 1369–72; and Joshua Quick et al., “Real-Time, Portable Genome Sequencing for Ebola Surveillance,” Nature 530 (2016): 228–32.
89.National Academies of Science, Engineering, and Medicine, Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies (Washington, DC: National Academies Press, 2021).
90.White House Homeland Security Council, “National Strategy for Pandemic Influenza: Implementation Plan.”
91.Matthew Herper, “At Illumina, the ‘Era of the Genome’ Has Arrived. But What Role Will the Company Play?,” STAT, May 17, 2021; and National Human Genome Research Institute, “The Cost of Sequencing a Human Genome,” December 7, 2020, https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost.
92.US Centers for Disease Control and Prevention, “Advanced Molecular Detection,” January 8, 2021, https://www.cdc.gov/amd.
93.Dylan George and Tara O’Toole, “Tackling the Next Epidemic: Data Technology to the Rescue,” In-Q-Tel, Inc., 2017, https://www.bnext.org/wp-content/uploads/2017/07/data-tech-to-the-rescue_0710207-FINAL.pdf.
94.David Cameron, “Scientific Coalition Developing Surveillance System for Detecting Emerging Pandemics in Real-Time,” Broad Institute, May 11, 2020.
95.US Centers for Disease Control and Prevention, “National Wastewater Surveillance System (NWSS),” March 19, 2021.
96.World Health Organization, “WHO-Convened Global Study of Origins of SARS-CoV-2: China Part,” March 30, 2021, https://www.who.int/publications/i/item/who-convened-global-study-of-origins-of-sars-cov-2-china-part; and Mackenzie, The Pandemic That Never Should Have Happened, and How to Stop the Next One.
97.Giuseppina La Rosa et al., “SARS-CoV-2 Has Been Circulating in Northern Italy Since December 2019: Evidence from Environmental Monitoring,” Science of the Total Environment 750 (2021): 141711; and Antonella Amendola et al., “Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019,” Emerging Infectious Diseases 27, no. 2 (2021): 648–50.
98.A. Deslandes et al., “SARS-CoV-2 Was Already Spreading in France in Late December 2019,” International Journal of Antimicrobial Agents 55, no. 6 (2020).
99.Gislaine Fongaro et al., “SARS-CoV2 in Human Sewage in Santa Catalina, Brazil, November 2019,” medRxiv, June 29, 2020, https://www.medrxiv.org/content/10.1101/2020.06.26.20140731v1; and Lorenzzo Lyrio Stringari et al., “Covert Cases of Severe Acute Respiratory Syndrome Coronavirus 2: An Obscure but Present Danger in Regions Endemic for Dengue and Chikungunya Viruses,” PLOS One 16 (2020).
100.Melody Schreiber, “If the U.S. Already Had a Covid Variant, We Wouldn’t Know,” New Republic, December 22, 2020.
101.Mackenzie, The Pandemic That Never Should Have Happened, and How to Stop the Next One.
102.Trevor Bedford (@trvrb), “We also now have direct serological evidence of antigenic drift in 229E from @eguia_rachel, @jbloom_lab et al, suggesting that reinfection by seasonal coronaviruses that occurs every ~3 years is in part due to evolution of the virus. 6/18,” Twitter, December 19, 2020, 4:33 p.m.
103.Kirsty Needham, “Special Report: COVID Opens New Doors for China’s Gene Giant,” Reuters, August 5, 2020.
104.Donald G. McNeil Jr. and Thomas Kaplan, “U.S. Will Revive Global Virus-Hunting Effort Ended Last Year,” New York Times, September 2, 2020.
105.Elisabeth Rosenthal, “On the Front: A Pandemic Is Worrisome but ‘Unlikely,’” New York Times, March 28, 2020.
106.McNeil and Kaplan, “U.S. Will Revive Global Virus-Hunting Effort Ended Last Year.”
107.Mackenzie, The Pandemic That Never Should Have Happened, and How to Stop the Next One.
108.Donald G. McNeil Jr., “Scientists Were Hunting for the Next Ebola. Now the U.S. Has Cut Off Their Funding.,” New York Times, October 25, 2019; and James Rainey and Emily Baumgaertner, “Trump, Congress Scramble to Revive Virus-hunting Agency that Was Marked for Cuts,” Los Angeles Times, April 11, 2020.
109.Some of USAID’s work in the 2014 timeframe was done in collaboration with the Wuhan Institute of Virology. See USAID, “Predict 2 Factsheet,” November 2014, https://www.usaid.gov/sites/default/files/documents/1864/Predict2-factsheet.pdf.
110.Scott Gottlieb, “Don’t Let Covid and the Flu Team Up to Pound America,” Wall Street Journal, August 9, 2020.
111.Jemma L. Geoghegan et al., “Virological Factors that Increase the Transmissibility of Emerging Human Viruses,” Proceedings of the National Academy of Sciences 113, no. 15 (2016): 4170–5; Mackenzie, The Pandemic That Never Should Have Happened, and How to Stop the Next One; R. Carrasco-Hernandez et al., “Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review,” ILAR Journal 58, no. 3 (2017): 343-58; Nancy H. L. Leung, “Transmissibility and Transmission of Respiratory Viruses,” Nature Reviews Microbiology, (2021); and Amesh Adalja et al., “The Characteristics of Pandemic Pathogens,” Johns Hopkins Center for Health Security, May 10, 2018, https://www.centerforhealthsecurity.org/our-work/pubs_archive/pubs-pdfs/2018/180510-pandemic-pathogens-report.pdf.
Conclusion
1.Wright, “The Plague Year.”
2.Zeke Miller, “Trump Valet has Coronavirus; President Again Tests Negative,” Associated Press, May 7, 2020.
3.Gottlieb and Levin, “The Trump Coronavirus Spread.”
4.Katherine J. Wu, “The White House Bet on Abbott’s Rapid Tests. It Didn’t Work Out.,” New York Times, October 6, 2020.
The machine they used, the Abbott ID Now, for all of its virtues, also could forfeit some accuracy to achieve its speed and convenience. It was authorized by the FDA for use on people who were already showing symptoms of COVID-19. There was a reason that the product’s label was restricted to these parameters. When patients are symptomatic, they are more likely to have higher levels of virus in secretions, and therefore be detected using the instruments.
5.Jessica L. Prince-Guerra et al., “Evaluation of Abbott BinaxNOW Rapid Antigen Test for SARS-CoV-2 Infection at Two Community-Based Testing Sites—Pima County, Arizona, November 3–17, 2020,” Morbidity and Mortality Weekly Report 70, no. 3 (2021): 100–5.
6.Larry Buchanan et al., “Inside the White House Event Now Under Covid-19 Scrutiny,” New York Times, October 5, 2020.
7.Michael C. Bender and Rebecca Ballhaus, “Inside the Week That Shook the Trump Campaign,” Wall Street Journal, October 21, 2020.
8.William Cummings, “‘The Data Speak for Themselves’: Dr. Anthony Fauci Says White House Held a ‘Superspreader Event’ for Coronavirus,” USA Today, October 9, 2020; and “Margaret Brennan: Did anyone ever say this is a national security risk and we need to nail down who brought this in and who infected the commander in chief? Dr. Birx: I never heard those conversations. Margaret Brennan: There was no serious contact tracing that happened after the fact? Dr. Birx: I don’t know if there was contact tracing or not.” See CBS News, “Transcript: Dr. Deborah Birx on “Face the Nation,” January 24, 2021,” January 24, 2021.
9.Jordan Fabian (@Jordanfabian), “@JenniferJJacobs was the unofficial contact tracer of last year’s WH coronavirus outbreaks, a feat made even more impressive by the fact the previous admin was not forthcoming about officials who tested positive for Covid-19. A herculean effort that rightly received recognition,” Twitter, April 19, 2021, 12:16 p.m.
10.James Glanz, “Tests Show Genetic Signature of Virus That May Have Infected President Trump,” New York Times, December 31, 2020.
11.At the time of the White House coronavirus cluster in October, more than 40,000 SARS-CoV-2 virus genomes had been sequenced and publicly shared from the United States alone. See Trevor Bedford et al., “Viral Genome Sequencing Places White House COVID-19 Outbreak into Phylogenetic Context,” medRxiv, November 13, 2020, https://www.medrxiv.org/content/10.1101/2020.10.31.20223925v2.
12.Glanz, “Tests Show Genetic Signature of Virus That May Have Infected President Trump.”
13.Gertner, “Unlocking the Covid Code.”
14.National Academies of Science, Engineering, and Medicine, Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies (Washington, DC: National Academies Press, 2021).
15.As the authors note, viral genome sequencing represents a largely novel and very effective tool for tracing the origin of outbreaks and the direction of viral spread as part of epidemiological investigations. However, as Bedford and his authors state, deploying these tools as an adjunct to traditional approaches to epidemiology generally requires that a large fraction of infections have already been sequenced and that these sequences are made publicly available. This is necessary to provide critical comparisons for the sequence or group of sequences in question. See Bedford et al., “Viral Genome Sequencing Places White House COVID-19 Outbreak into Phylogenetic Context.”
16.“Pfizer and BioNTech Initiate a Study as Part of Broad Development Plan to Evaluate COVID-19 Booster and New Vaccine Variants,” Pfizer press release, February 25, 2021; and “Moderna Announces It Has Shipped Variant -Specific Vaccine Candidate, mRNA-1273.351, to NIH for Clinical Study,” Moderna press release, February 24, 2021.
17.“Can a Vaccine for Covid-19 Be Developed in Record Time?,” New York Times Magazine, June 9, 2020; and Richard Conniff, “A Forgotten Pioneer of Vaccines,” New York Times, May 6, 2013.
18.US Centers for Disease Control and Prevention, “National Center for Health Statistics: Nursing Home Care,” March 1, 2021, https://www.cdc.gov/nchs/fastats/nursing-home-care.htm.
19.Owen Dyer, “Two Strains of the SARS Virus Sequenced,” British Medical Journal 326, no. 7397 (2003): 999; and Marco A. Marra et al., “The Genome Sequence of the SARS-Associated Coronavirus,” Science 300, no. 5624 (2003): 1399–404.
In April 2003, two different strains of the SARS virus were sequenced. The Tor2 strain was isolated in Toronto, Canada, the city hit hardest in the West by the epidemic while the Urbani strain was sequenced by the US CDC. The latter strain was the more common Asian strain, named after Carlo Urbani, an infectious disease specialist at the WHO’s office in the Vietnamese capital, Hanoi. He helped identify the disease as a coronavirus but later died from it.
20.Maggie Fox, “Countries Re-Think Swine Flu Vaccine Orders,” Reuters, January 12, 2010.
“First, as Canada’s only domestic influenza vaccine manufacturer, GSK provided priority access to a secure supply of the H1N1 vaccine for all Canadians.” See Paul N. Lucas, “GlaxoSmithKline Inc. Appearance before the Standing Committee on Social Affairs, Science and Technology,” October 6, 2010.
“In Australia, the government pressured vaccine maker CSL Limited to turn over 36 million doses of H1N1 vaccine contracted for by the U.S. and produced in an Australian-based manufacturing plant. Meanwhile, in Canada, where British drug maker GlaxoSmithKline maintains its US-focused flu vaccine facility, the company had to assure the local government that Canadians would be served from that manufacturing plant before Americans could receive any of their vaccine orders.” See Scott Gottlieb, “No More Pandemic Hysterics,” Forbes, February 22, 2010.
21.Benjamin Mueller and Matina Stevis-Gridneff, “Desperate Italy Blocks Exports of Vaccines Bound for Australia,” New York Times, March 10, 2021.
22.World Trade Organization, “COVID-19: Measures Affecting Trade in Goods,” accessed March 10, 2021, https://www.wto.org/english/tratop_e/covid19_e/trade_related_goods_measure_e.htm.
23.Matina Stevis-Gridneff, “E.U. Will Curb Covid Vaccine Exports for 6 Weeks,” New York Times, March 28, 2021.
24.Jeremy Konyndyk, “It’s Time for a ‘No Regrets’ Approach to Coronavirus,” Washington Post, February 4, 2020.
25.G. Dennis Shanks and John Brundage, “Did Coronaviruses Cause ‘Influenza Epidemics’ Prior to 1918?” Journal of Travel Medicine 28, no.2 (2021); and Anthony King, “An Uncommon Cold,” New Scientist 246, no. 3280 (2020): 32–5.
26.Bloomberg, “China Culls 18,000 Chickens After H5N1 Bird Flu Cases in Hunan,” February 2, 2020.
Index
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Abbott, 141, 150, 382, 423n
Abbott ID Now, 382, 466n
AbCellera Biologics Inc., 311
Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV), 289
ACE2 receptor (angiotensin-converting enzyme 2), 5, 331–32, 355, 358, 371–72
Adjuvants, 324, 432n
Advanced Molecular Detection, 373–74
Aerosol transmission, 7, 159, 212–13, 214, 220–21, 230, 247, 250
African Americans, 209–10, 236, 390–91
Ai Fen, 30, 31, 41
Airflow and filtration, 7, 85, 212–13, 222, 232
Air Force One, 385
Airline flight attendants, and mask wearing, 249–50
Airport screenings, 18, 22, 91–93, 352–53
Air travel bans, 18, 20–21, 90–92, 131, 352–53
Albany, Georgia, superspreader event, 221
Alpha coronaviruses. See Bat coronaviruses
American Clinical Laboratory Association, 135–36
American Enterprise Institute (AEI), 148, 243, 297
COVID-19 Test Capacity Tracker (@COVID2019tests), 148
“National Coronavirus Response: A Road Map to Reopening,” 250–52
American Health Care Association, 145
American Red Cross, 299
American Society for Microbiology, 349
Amgen, 268–71, 454n
Anthrax, 159, 172, 180–81, 270, 284, 310, 329–30
Antibiotics, 26, 27, 295
Antibodies, 141, 177, 185, 223–24, 321–22, 331–32, 376
Antibody drugs, 285–86, 296–97, 305–19, 389
development of, 310–11
Eli Lilly, 308–9, 311–14, 388, 453n
manufacture of, 311–15
Regeneron, 283, 305–7, 309–12, 388, 453–54n
Antibody tests, 216–17, 273, 423n
Antigenic drift, 376, 378, 465n
“Antigenic load,” 321–22
“Antigenic modification,” 184–85
Antigen tests, 138–40, 141–46, 218
Antimasking, 252–53
Antiviral drugs, 27, 75, 176, 178, 193, 295–96
Apollo’s Arrow (Christakis), 344
Arizona, stay-at-home orders, 215–16
Association of Public Health Laboratories, 110, 116, 126–27, 157, 158
American Public Health Lab Association, 115–16
AstraZeneca vaccine, 317, 392
Asymmetric risk, 54, 379
Asymptomatic testing, 142–44, 146
Asymptomatic transmission, 7, 49, 58, 80, 83–85, 89, 97, 131, 211, 220–21, 412n
syndromic surveillance, 80–81, 83–85
Atlantic, The, 131, 232
Australia, 15, 92, 214
H1N1 vaccine, 392, 467n
Aviano Air Force Base, 154
Azar, Alex
community spread, 78, 89–90
Crimson Contagion, 201
hydroxychloroquine, 291
initial reporting, 17–18, 37, 38, 50–51
mask shortage, 158–59
pandemic preparedness, 200
reporting systems, 240–41
sentinel surveillance, 73–74
testing, 98, 124, 125–26, 134–35, 149, 153, 278
Baidu, 44
Baker, Charlie, 165–66
Bar closures, 231
BARDA (Biomedical Advanced Research and Development Authority), 134, 142, 154, 278, 310–11, 378
