Rates of COVID transmission and vaccination impact on vaccine-resistant strains

https://www.nature.com/articles/s41598-021-95025-3

by rualca • 5 years ago

4 5 5 years ago

nature.com

rualca• 5 years ago

Submitter here.

I had to edit down the title of the article to comply with HN's 80-character limit.

Here's the original title:

* Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains

nabla92• 5 years ago

TL;DR Reducing restrictions too soon after most people have been vaccinated greatly increases the probability of resistant strains.

nanis2• 5 years ago

Using simulations to provide justification for forced vaccinations AND prolonged lockdowns AND continued mass-scale testing of people with no symptoms.

The authors make some honest statements about the shortcomings of their method, but the "Ethics" section is surprisingly silent on whether such recommendations should be made purely on simulation runs, especially without code.

We implemented a modification of a SIR model

Where is the code?

The simplest model for the spread of an infection is the SIR model1,2, which tracks the fraction of a population in each of three groups: susceptible, infectious and recovered (Fig. 1a). The sizes of these groups are functions of time t — we will write them as S, I and R, with dependence on t implied. During a virgin epidemic, we often assume that spread is so rapid that we can ignore any change in the population due to births and deaths — this is a so-called ‘closed epidemic’ with a fixed population size S + I + R = N. The SIR model has no probabilistic component, except for the assumption that the population can mix at random and is large enough that predictions based on average rates can be used.
... The model is initialized with the entire population being in the susceptible group except for a single infectious individual: I(0) = 1, S(0) = N – 1, R(0) = 0. At each time unit (for example, day), any infected individual can come into contact with k other individuals in the population. On average, per unit time they will come into contact with kS/N susceptible individuals and infect kπS/N of them, if π is the probability of infection on contact. Conventionally, k and π are combined into a transmission rate, β = πk, which is the average rate at which an infected individual can infect a susceptible. [1]

Discuss the path-dependence of simulated evolutions on choice of initial values.

[1] https://www.nature.com/articles/s41592-020-0822-z

nabla92• 5 years ago

Where is the code?

Look under the section Code availability.

nanis2• 5 years ago

I had missed that. Thank you.

https://github.com/Simon-Re/mut-vacc

Update: If any simulation is going to have real life bearing, it should be able to produce a similar seasonal component of waves we have seen so far.

Rates of COVID transmission and vaccination impact on vaccine-resistant strains

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