COVID-19 in practice

SARS-CoV-2 to its friends

Epidemiology of

See also epidemiology, contact tracing.

Testing dynamics

Current public health advice boils down to a heuristic that the Rapid Antigen Tests (🐀) are a good proxy for actual contagiousness.

How we hope the rapid antigen tests function, according to ABC News, who claim to have gotten it from a prestigious journal but don’t actually give a reference so you have to take it on faith I guess?

Possible test negativity model for covid variants in 2021, by Jarvis and Kelley

The actual story is complicated and nuanced. Small sample trial, updated for Omicron: Adamson et al. (2022), observes Covid transmission with saliva PCR cycle threshold (Ct) values between 23-28 for the N gene in an \(n=30\) trial. tl;dr: For their tests at least the start of the infection window was not detected by 🐀s (all false negatives.) At the end of the infection, 🐀s produces both false positives and false negatives wrt/ infectiousness. Data here.

Bonus complication: we are possibly using 🐀s wrong, at least for Omicron, if we follow the advice to swab only our noses. Should you add a throat swab to your at-home covid test?. update: This is ambivalently helpful and may even get a false positive (Killingley et al. 2022). Here is a new graph of test efficacy from that study, which was small but well controlled (it was the first challenge trial).

Test specificity in Killingley et al. (2022). Approximately speaking, the black (sensitivity) tells us how likely we are to get a true positive, and the white (specificity) tells us how likely we are to get a true negative, in this cohort of 32 test subjects. The specificity is 100% here because the baseline is PCR.

Personal risk calculators

For now, as a good tool for thinking things through (very approximately!) I recommend a microlife-style COVID risk calculator to consider the risk of various activities.

I find it clarifying, although I do not take it literally. Obviously, check the dates and specificity of the data for your region, and bear in mind that it is just an estimator, and written by non-epidemiologists. For example there is something funky about how they account for duration of activities; my risk for catching covid should asymptotically approach a constant as time goes on, but it seems to increase linearly? That approximation is probably fine for many events of interest, but use care in planning long events.

Evaluating societal cost

Actuarial lives and quality-adjusted-life-years were not popular for costing public interventions in the pandemic (Hall and Viney 2021). Subhash Pokhrel explains at length Why standard ways of valuing health were set aside during the pandemic. He argues, basically, that we use a risk-averse decision rule to value public interventions as a kind of precautionary principle. Implicitly, this leads us to ask, why did we not do better experiments to reduce uncertainties so we could make that trade-off better? It seemed that uncertainty was extremely expensive and therefore that we had a massive budget to reduce it. This is the platform of organisations like 1Day Sooner who advocate accelerated medical trials by participants who volunteered to be infected. I volunteered for this.

Human challenge trials deliberately expose participants to infection, to study diseases and test vaccines or treatments.

This is cheap talk though. There was not really anywhere to take my volunteer energy in Australia, and thereby prove that I would put my money where my mouth is on this.

Now that we have acquired more precise estimates of COVID dynamics, Paul Dolan and Christian Krekel advocate a return to QALY-like measures in How should we measure the impact of Covid-19 policies on our wellbeing?; There are some nifty links in the citation list.

I am curious about the risk of new variants of COVID and the implications of the new regime. I do not know enough epidemiology or virology to understand the risks we face there, but I suspect it is going to be a classic Black swan tail-risk (Cirillo and Taleb 2020). that is, we want to account for the possibility of large extreme downsides to whatever policies we adopted.

Optimising for Expected QALY is not enough if it comes with a significant risk of extreme QALY loss. That said, the economic consensus is strongly against substantial public health interventions at this stage.

Also, the question of how to trade-off wellbeing, happiness and disease risk is tricky and deep. To read: Dolan and Kahneman (2008) on what hedonism even is.

Virulence and risks upon infection

Death and life years

As measured by lost lifetime, some COVID deaths are crueller than others. When a 90 year old victim with multiple health complaints goes one month earlier to their grave because of COVID, that is sad, but it is not so awful as when a child is cut down decades early. Mercifully, COVID vastly prefers the former case to the latter — it is more likely to scrape some time off the end of a long life than to cut down a short one. So, if some of us die of COVID, how much of my life will it have cost me, on average? Wouterse, Ram, and van Baal (2022) we would have lost 3-4 quality-adjusted life years (QALY) on average. This was before Omicron and may need updating, if the age profile has changed substantially.

Relative rate compared to normal life risk

We might wonder how much catching COVID adds to your risk rate. Back before Omicron David Spiegelhalter asked How much ‘normal’ risk does Covid represent? and answered (Spiegelhalter 2020)

roughly speaking, we might say that getting COVID-19 is like packing a year’s worth of risk into a week or two.

In fact it is complicated, with slightly more risk for over 55s and much less for 20 school children.

Long covid

Seems to be real, dammit (Blomberg et al. 2021). Well then, how bad is it? How much risk of it should I tolerate? Elizabeth Van Nostrand argues Long Covid Is Not Necessarily Your Biggest Problem, i.e. that it is a real problem but does not loom particularly large amongst in all the other real problems. Scott Alexander that it looms reasonably large. There has been a methodological update which revises the probability of long covid symptoms down: UK Office for National Statistics: Technical article: Updated estimates of the prevalence of post-acute symptoms among people with coronavirus (COVID-19) in the UK. It is not compactly summarized in that report, but you can scroll down a Zvi Mowshowitz article to find highlights.

As far as long-ish COVID, i.e. all the other non-death inconveniences, a report based on Maltese data (Cuschieri et al. 2021) estimates that 95% of the impact of COVID in Disability-adjusted life years from 2020 is being dead; the remaining 5% is other stuff. The report is also pretty interesting as far as working out how much of the impact of sickness is tiredness after the initial phase etc. They argue that the community impacts of long term COVID are probably somewhat higher than the acute impacts of COVID, although not by much. Worth a read.

TODO: C&C with Long influenza

Omicron variant

Why are we slow to pump out relative morbidity estimates for the notionally civilisation-defining moment of Omicron dominance?

Best I could find was Lewnard et al. (2022) which doesn’t break out the relative morbidity versus vaccine, except to note omicron sufferers were more likely to be vaccinated than delta sufferers. Across all patients

Omicron variant infections were associated with 52%, 53%, 74%, and 91% reductions in risk of any subsequent hospitalization, symptomatic hospitalization, ICU admission, and mortality, relative to Delta variant infections. Median duration of hospital stay for patients admitted with symptomatic Omicron variant infections was approximately 70% (∼3.4 days) shorter than that observed among patients with symptomatic Delta variant infections.

Realistically, this means we can estimate the mortality risk from Omicron as around 4-5 days of normal risk.

Histories of patients with Omicron (SGTF) versus other which is in practice probably Delta, reproduced from the Lewnard article.


I need to collect some articles on these theme, when I have a moment to spare.

Which interventions are best? Jeremy Howard summarises lower cost interventions: improved masks, better ventilation, rapid antigen testing.

A cursory inspection of the literature seems to suggest that surface transmission is not worth worrying about (but why not wash your hands?)

Transmission comes down mostly to airflow, afaict. Where are those airborne virions going?

Masking well is hard, but makes a difference if you do it well.

Distancing is not entirely pointless but effectiveness depends on airflow.

What is easy to do well and makes a difference is ventilation. Do things outside if possible. Do things with the windows open if possible. If the windows don’t open, check that the aircon has a HEPA filter. If the aircon does not have a filter, just get an air purifier. They are not that expensive. I have a Breville the Easy Air Purifier, although I have not assayed its effectiveness against COVID-19 specifically. At AUD229, its ticket price is less than the cost of skipping work for a week due to COVID.

Since I have presented these assertions without evidence, please don’t take them on trust. Supporting citations or refutations welcome.

Modeliing airborne transmission

Is the Wells-Riley model any good? (Noakes and Sleigh 2009; Sze To and Chao 2010).


A contentious area.

David McCandless, Tom Evans, Paul Barton, COVID-19 treatments by evidence level and media attention.. Click through to view full, interactive, version.

There is a reasonably current overview of various options in 11-16-2021_JHMI Clinical Recommendations for Pharmacologic Treatment of COVID-19. Notably includes several off-the-shelf treatments. I’m not even listing the monoclonal antibodies.

Vitamin D

Wow, why is the Vitamin D literature so spammy?

tl;dr; AFAICT the case that Vitamin D is helpful is weak, and the case that it is not hurtful is strong so, take vitamin D if you want.

Current restrictions where I live

The ultimate in COVID-safety

Too confusing, gave up trying to understand. Using own judgment.


Adam, David. 2020. Special Report: The Simulations Driving the World’s Response to COVID-19.” Nature 580 (7803): 316–18.
Adamson, Blythe, Robby Sikka, Anne L. Wyllie, and Prem Premsrirut. 2022. Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series.” Cold Spring Harbor Laboratory Press.
Agrawal, Virat, Jonathan Cantor, Neeraj Sood, and Christopher Whaley. 2021. The Impact of the COVID-19 Pandemic and Policy Responses on Excess Mortality.” w28930. Cambridge, MA: National Bureau of Economic Research.
Arpino, Fausto, Giorgio Grossi, Gino Cortellessa, Alex Mikszewski, Lidia Morawska, Giorgio Buonanno, and Luca Stabile. 2022. Risk of SARS-CoV-2 in a Car Cabin Assessed Through 3d CFD Simulations.” Indoor Air 32 (3): e13012.
Banerjee, Amitava, Laura Pasea, Steve Harris, Arturo Gonzalez-Izquierdo, Ana Torralbo, Laura Shallcross, Mahdad Noursadeghi, et al. 2020. Estimating Excess 1-Year Mortality Associated with the COVID-19 Pandemic According to Underlying Conditions and Age: A Population-Based Cohort Study.” The Lancet 395 (10238): 1715–25.
Bazant, Martin Z., and John W. M. Bush. 2021. A Guideline to Limit Indoor Airborne Transmission of COVID-19.” Proceedings of the National Academy of Sciences. National Academy of Sciences.
Bazant, Martin Z., Ousmane Kodio, Alexander E. Cohen, Kasim Khan, Zongyu Gu, and John W. M. Bush. n.d. Monitoring Carbon Dioxide to Quantify the Risk of Indoor Airborne Transmission of COVID-19.” Flow 1.
Berwanger, Otavio. 2022. Fluvoxamine for outpatients with COVID-19: where do we stand? The Lancet Global Health 10 (1): e2–3.
Blomberg, Bjørn, Kristin Greve-Isdahl Mohn, Karl Albert Brokstad, Fan Zhou, Dagrun Waag Linchausen, Bent-Are Hansen, Sarah Lartey, et al. 2021. Long COVID in a Prospective Cohort of Home-Isolated Patients.” Nature Medicine, June, 1–7.
Brenner, Hermann. 2021. Vitamin D Supplementation to Prevent COVID-19 Infections and Deaths—Accumulating Evidence from Epidemiological and Intervention Studies Calls for Immediate Action.” Nutrients 13 (2): 411.
Briggs, Andrew H., Daniel A. Goldstein, Erin Kirwin, Rachel Meacock, Ankur Pandya, David J. Vanness, and Torbjørn Wisløff. 2021. Estimating (quality-adjusted) life-year losses associated with deaths: With application to COVID-19.” Health Economics 30 (3): 699–707.
Burridge, Henry C., Shiwei Fan, Roderic L. Jones, Catherine J. Noakes, and P. F. Linden. 2021. Predictive and Retrospective Modelling of Airborne Infection Risk Using Monitored Carbon Dioxide.” Indoor and Built Environment, September, 1420326X211043564.
Cevik, Muge, Krutika Kuppalli, Jason Kindrachuk, and Malik Peiris. 2020. Virology, Transmission, and Pathogenesis of SARS-CoV-2.” BMJ 371 (October): m3862.
Chang, Sheryl L., Nathan Harding, Cameron Zachreson, Oliver M. Cliff, and Mikhail Prokopenko. 2020. Modelling Transmission and Control of the COVID-19 Pandemic in Australia.” Nature Communications 11 (1): 5710.
Cirillo, Pasquale, and Nassim Nicholas Taleb. 2020. Tail Risk of Contagious Diseases.” Nature Physics 16 (6): 606–13.
Cuschieri, Sarah, Neville Calleja, Brecht Devleesschauwer, and Grant M. A. Wyper. 2021. Estimating the Direct Covid-19 Disability-Adjusted Life Years Impact on the Malta Population for the First Full Year.” BMC Public Health 21 (1): 1827.
Dolan, Paul, and Daniel Kahneman. 2008. Interpretations Of Utility And Their Implications For The Valuation Of Health*.” The Economic Journal 118 (525): 215–34.
Entrenas Castillo, Marta, Luis Manuel Entrenas Costa, José Manuel Vaquero Barrios, Juan Francisco Alcalá Díaz, José López Miranda, Roger Bouillon, and José Manuel Quesada Gomez. 2020. ‘Effect of Calcifediol Treatment and Best Available Therapy Versus Best Available Therapy on Intensive Care Unit Admission and Mortality Among Patients Hospitalized for COVID-19: A Pilot Randomized Clinical Study’.” The Journal of Steroid Biochemistry and Molecular Biology 203 (October): 105751.
Hall, Jane, and Rosalie Viney. 2021. Quality Adjusted Life Years in the Time of COVID-19.” Australian Health Review 45 (1): 12.
Herbrich, Ralf, Rajeev Rastogi, and Roland Vollgraf. 2020. CRISP: A Probabilistic Model for Individual-Level COVID-19 Infection Risk Estimation Based on Contact Data,” June.
Howard, Jeremy, Austin Huang, Zhiyuan Li, Zeynep Tufekci, Vladimir Zdimal, Helene-Mari van der Westhuizen, Arne von Delft, et al. 2021. An Evidence Review of Face Masks Against COVID-19.” Proceedings of the National Academy of Sciences 118 (4).
Jarvis, Katherine F., and Joshua B. Kelley. 2021. Temporal Dynamics of Viral Load and False Negative Rate Influence the Levels of Testing Necessary to Combat COVID-19 Spread.” Scientific Reports 11 (1): 9221.
Karlinsky, Ariel, and Dmitry Kobak. 2021. Tracking Excess Mortality Across Countries During the COVID-19 Pandemic with the World Mortality Dataset.” Edited by Miles P Davenport, Marc Lipsitch, Marc Lipsitch, Lone Simonsen, and Ayesha Mahmud. eLife 10 (June): e69336.
Killingley, Ben, Alex Mann, Mariya Kalinova, Alison Boyers, Niluka Goonawardane, Jie Zhou, Kate Lindsell, et al. 2022. Safety, Tolerability and Viral Kinetics During SARS-CoV-2 Human Challenge.”
Kimmitt, P.T., and K.F. Redway. 2016. Evaluation of the Potential for Virus Dispersal During Hand Drying: A Comparison of Three Methods.” Journal of Applied Microbiology 120 (2): 478–86.
Lescure, Francois-Xavier, Lila Bouadma, Duc Nguyen, Marion Parisey, Paul-Henri Wicky, Sylvie Behillil, Alexandre Gaymard, et al. 2020. Clinical and virological data of the first cases of COVID-19 in Europe: a case series.” The Lancet Infectious Diseases 20 (6): 697–706.
Lewis, Dyani. 2021. COVID-19 Rarely Spreads Through Surfaces. So Why Are We Still Deep Cleaning? Nature 590 (7844): 26–28.
Lewnard, Joseph A., Vennis X. Hong, Manish M. Patel, Rebecca Kahn, Marc Lipsitch, and Sara Y. Tartof. 2022. Clinical Outcomes Among Patients Infected with Omicron (B.1.1.529) SARS-CoV-2 Variant in Southern California.” medRxiv.
Miles, David, Mike Stedman, and Adrian Heald. 2020. Living with Covid-19: Balancing Costs Against Benefits in the Face of the Virus.” National Institute Economic Review 253 (August): R60–76.
Murai, Igor H., Alan L. Fernandes, Lucas P. Sales, Ana J. Pinto, Karla F. Goessler, Camila S. C. Duran, Carla B. R. Silva, et al. 2020. Effect of Vitamin D3 Supplementation Vs Placebo on Hospital Length of Stay in Patients with Severe COVID-19: A Multicenter, Double-Blind, Randomized Controlled Trial.” medRxiv, November, 2020.11.16.20232397.
———, et al. 2021. Effect of a Single High Dose of Vitamin D 3 on Hospital Length of Stay in Patients With Moderate to Severe COVID-19: A Randomized Clinical Trial.” JAMA 325 (11): 1053.
Neve, Jan-Emmanuel De, Andrew E. Clark, Christian Krekel, Richard Layard, and Gus O’Donnell. 2020. Taking a Wellbeing Years Approach to Policy Choice.” BMJ 371 (October): m3853.
Noakes, Catherine J., and P. Andrew Sleigh. 2009. Mathematical Models for Assessing the Role of Airflow on the Risk of Airborne Infection in Hospital Wards.” Journal of the Royal Society Interface 6 (Suppl 6): S791–800.
Piroth, Lionel, Jonathan Cottenet, Anne-Sophie Mariet, Philippe Bonniaud, Mathieu Blot, Pascale Tubert-Bitter, and Catherine Quantin. 2021. Comparison of the characteristics, morbidity, and mortality of COVID-19 and seasonal influenza: a nationwide, population-based retrospective cohort study.” The Lancet Respiratory Medicine 9 (3): 251–59.
Quilty, Billy J., Samuel Clifford, Joel Hellewell, Timothy W. Russell, Adam J. Kucharski, Stefan Flasche, W. John Edmunds, et al. 2021. Quarantine and testing strategies in contact tracing for SARS-CoV-2: a modelling study.” The Lancet Public Health 6 (3): e175–83.
Randall, K., E. T. Ewing, L. C. Marr, J. L. Jimenez, and L. Bourouiba. 2021. How Did We Get Here: What Are Droplets and Aerosols and How Far Do They Go? A Historical Perspective on the Transmission of Respiratory Infectious Diseases.” Interface Focus 11 (6): 20210049.
Reddy, Sanjay G. 2020. Population Health, Economics and Ethics in the Age of COVID-19.” BMJ Global Health 5 (7): e003259.
Reis, Gilmar, Eduardo Augusto dos Santos Moreira-Silva, Daniela Carla Medeiros Silva, Lehana Thabane, Aline Cruz Milagres, Thiago Santiago Ferreira, Castilho Vitor Quirino dos Santos, et al. 2022. Effect of early treatment with fluvoxamine on risk of emergency care and hospitalisation among patients with COVID-19: the TOGETHER randomised, platform clinical trial.” The Lancet Global Health 10 (1): e42–51.
Robinson, Lisa A., Ryan Sullivan, and Jason F. Shogren. 2021. Do the Benefits of COVID-19 Policies Exceed the Costs? Exploring Uncertainties in the Age–VSL Relationship.” Risk Analysis 41 (5): 761–70.
Spiegelhalter, David. 2020. Use of ‘Normal’ Risk to Improve Understanding of Dangers of Covid-19.” BMJ 370 (September): m3259.
Stapelberg, Nicolas J. C., Nicolas R. Smoll, Marcus Randall, Dinesh Palipana, Bryan Bui, Kristine Macartney, Gulam Khandaker, and Andre Wattiaux. 2021. A Discrete-Event, Simulated Social Agent-Based Network Transmission (DESSABNeT) Model for Communicable Diseases: Method and Validation Using SARS-CoV-2 Data in Three Large Australian Cities.” PLOS ONE 16 (5): e0251737.
Sze To, G. N., and C. Y. H. Chao. 2010. Review and Comparison Between the Wells–Riley and Dose‐response Approaches to Risk Assessment of Infectious Respiratory Diseases.” Indoor Air 20 (1): 2–16.
University Hospital, Angers. 2021. COvid-19 and Vitamin D Supplementation: A Multicenter Randomized Controlled Trial of High Dose Versus Standard Dose Vitamin D3 in High-Risk COVID-19 Patients (CoVitTrial).” Clinical trial registration NCT04344041.
Wang, Chia C., Kimberly A. Prather, Josué Sznitman, Jose L. Jimenez, Seema S. Lakdawala, Zeynep Tufekci, and Linsey C. Marr. 2021. Airborne Transmission of Respiratory Viruses.” Science 373 (6558): eabd9149.
Wang, Wensi, Feng Wang, Dayi Lai, and Qingyan Chen. 2022. Evaluation of SARS-COV-2 Transmission and Infection in Airliner Cabins.” Indoor Air 32 (1): e12979.
Weitz, Joshua S., Stephen J. Beckett, Ashley R. Coenen, David Demory, Marian Dominguez-Mirazo, Jonathan Dushoff, Chung-Yin Leung, et al. 2020. Modeling shield immunity to reduce COVID-19 epidemic spread.” Nature Medicine 26 (6): 849–54.
Wong, Jessica Y., Heath Kelly, Dennis K. M. Ip, Joseph T. Wu, Gabriel M. Leung, and Benjamin J. Cowling. 2013. Case Fatality Risk of Influenza A(H1N1pdm09): A Systematic Review.” Epidemiology (Cambridge, Mass.) 24 (6): 10.1097/EDE.0b013e3182a67448.
Wouterse, Bram, Frederique Ram, and Pieter van Baal. 2022. Quality-Adjusted Life-Years Lost Due to COVID-19 Mortality: Methods and Application for The Netherlands.” Value in Health, February.
Xie, Gang. 2020. A Novel Monte Carlo Simulation Procedure for Modelling COVID-19 Spread over Time.” Scientific Reports 10 (1): 13120.
Zhao, Hongwei, Naveed N. Merchant, Alyssa McNulty, Tiffany A. Radcliff, Murray J. Cote, Rebecca S. B. Fischer, Huiyan Sang, and Marcia G. Ory. 2021. COVID-19: Short Term Prediction Model Using Daily Incidence Data.” PLOS ONE 16 (4): e0250110.

No comments yet. Why not leave one?

GitHub-flavored Markdown & a sane subset of HTML is supported.