Jeffrey Shaman returns to TWiV to explain how epidemiologists measure SARS-CoV-2 movement among humans, including calculation of the reproductive index, secondary transmission, and what factors affect transmission.
Hosts: Vincent Racaniello, Kathy Spindler, and Brianne Barker
Guest: Jeffrey Shaman
Click arrow to play
Download TWiV 792 (65 MB .mp3, 109 min)
Subscribe (free): iTunes, Google Podcasts, RSS, email
Become a patron of TWiV!
Links for this episode
- A guide to R (Nature) 1:07:42
- Epidemiology of three SARS-CoV-2 VOC (medRxiv)
- Impact of delta variant in India (medRxiv)
- Letters read on TWiV 792 1:09:18
- Timestamps by Jolene. Thanks!
Weekly Picks 1:30:37
Brianne – The Social Lives of Giraffes
Kathy – Saturn’s Iapetus, moon in 3-D
Vincent – Arkansas Governor Wants To Reverse A Law That Forbids Schools To Require Masks
Intro music is by Ronald Jenkees
Send your virology questions and comments to email@example.com
Review of mask RCT results. Also observational trials.
Many thanks and congratulations to all involved. This is so helpful to those of us who have to try to inform others. Some that I encounter, will want to see this episode for themselves.
I agree that models are a problem here. .
This dissociation sounds like it’s essentially argument by elimination. Eliminate the environmental and NPI factors and what’s left are the virus’ intrinsic factors. But the problem is that when you add together these nonvirus factors you also have to add their margins of error.
I expect it would look something like this:
1 – factor1(+/- error1) – factor2(+/- error 2) – factor3(+/- error3) = virus factor.
So when you include the errors, will you get a negative virus factor in the worst case?
What is the margin of error in the epidemiological model of the proportion of greater spread caused by factor1 (say, abandonment of masking), what is the margin for factor2 (say, increased use of public transit), and so on?
After you do the elimination, you have to state the error that now applies to the “virus factor”, or the proportion of greater spread caused by characteristics of the virus . That error might be huge, maybe enough to negate the virus factor.
Now, this doesn’t mean that the increased spread is not influenced by viral characteristics of Delta, but rather that this may not be a good way to prove it, or even theorize it. We need a really good inventory of sources of error and a really honest evaluation of the limitations of epidemiology’s ability to model the influences of NPIs and environmental factors on viral transmission. In the absence of adequately reliable models, this process of elimination will not offer a reliable way to estimate the contribution of viral characteristics to transmission.
On masking or getting a vaccinated.
My sister has told me that she is not getting a vaccinate shot because way back in the last century some one tried using tissue from a aborted baby to look for a cure for a disease. Guess the fear of dying or spending time in a hospital bed has not occur to her that it can be prevented by sucking in your pride and get that life saving shot.
But she is religious so what do you expect.
A friend went local county fair and she said that no one worn a masked. Since she is vaccinated she took off her mask to fit in.
If she dies I’m on her Will.
Thanks TWiV team for another great podcast.
I understand the difference between virology and epidemiology, is that virology is a study of the tree and epidemiology is a study of the forest. Both have their place in science. I understand and respect Vincent’s views and Vincent greatly, I hold him up there with Richard Feynman as a great public educator of our time! I can also relate to his grumpy attitude at times.
I do however think Australia is a good test case. More than 100 infected people were dumped into Sydney with classic SARS-CoV2 at the start of 2020 when the Ruby Princess cruise ship dumped over 100 infected passengers into Sydney and lockdowns still worked in Australia. Even after that it was controlled and we had almost zero cases from the start of 2020 until the 16th of June 2021 when a limousine driver was infected transporting a US air crew from a FedEx flight to a hotel quarantine infected him with the Delta variant. That one case has since seen the Delta variant cause for just today another 466 locally acquired cases to create one of the worst outbreaks in Australia, 94 deaths since June and 5887 active cases since June up from zero at the start of June. Delta doesn’t behave like the 2019 SARS-CoV2 IMHO. I understand Vincent has his view on “fitness” over “transmission”. We have seen younger people demonstrably dying and in ICU than ever before and despite extreme measures to lockdown, we can’t control the virus like we did in 2020. Lockdowns in Australia are hard lockdowns:
Quote from today: “Fines for breaching public health orders, including lying to contact tracers, will be raised from $1000 to $5000.
A $3000 on the spot fine will be issued to people who breach the two person exercise rule.
A permit will be required for anyone leaving Greater Sydney to enter regional NSW.
Exemptions will be granted for those leaving to visit holiday homes for urgent repairs, but only one person will be permitted to go.
People in singles bubbles in the 12 “areas of concern” within Sydney’s west and southwest must register their bubble, and those involved must live within five kilometres of each other.”
Cheers Cameron Rogers MSc.
That should have read from the “the start of 2021 until the 16th of June 2021”, We all make mistakes.
I recently listened to the TWIV 792 and after reading the Nature article , curiously googled “R naught measles”. Worth a try! A chart from one of the reviews of studies over the years is startling. If you think 8-12 is a large range of possible transmission numbers, look at the many case studies estimating measles’ infectious ness over the years, with R from about 5 to over 50. Local context and constraints determine so so much in any outbreak. I wish there had been more clarity on this in early stages of the US situation. I live in NYC and was gulping info as frantically as anyone in early days, but I just never understood why anyone on that ranch in Eastern Montana would need to have the slightest concern or change in behavior in response to our crazy city problems, unless they were picking people up from an airport. Understanding of local (even hyper-local) prevalence and trends has been key to recommending credible policy and behavior changes. I’m so grateful to live in a place where the city and state health department info is easily accessed and generally coordinated with the news about what folks should do. It has taken me a fair amount of time to take a breath and discount my alarm at some of what I read (the Provincetown news, most recently, which became more interesting and less alarming time,)