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 probably using 🐀s wrong, at least for Omicron, if we follow the advice to swab our noses. Should you add a throat swab to your at-home covid test? tl;dr: yes.

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.

Reducing transmission

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

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 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.

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

I find it very clarifying, although I do not take it literally. Onbiously heck 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 activities; you 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 most events of interest.

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


A fraught and contentious area.

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

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.


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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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