Talk:Basic reproduction number

Omicron

@Ftrebien: The Omicron variant needs to be in that table. If you don't like the references, please provide better ones. Without that entry, it's harder to find the Wikipedia article on "Omicron variant" and makes this article look dramatically deficient, especially since "Omicron is now the dominant COVID strain in the U.S., making up 73% of new infections", according to NPR. Mediocre references are universally better than nothing, unless they are likely blatantly dishonest, I think.

I don't have time now to research this further, but I'm reverting your deletion. This will make it easier for someone else to find the information needed to improve it. DavidMCEddy (talk) 14:41, 21 December 2021 (UTC)

@DavidMCEddy: I have added the appropriate templates to alert readers about the significant unreliability of this information. --Fernando Trebien (talk) 17:07, 21 December 2021 (UTC)

@Ftrebien: Thx. DavidMCEddy (talk) 18:39, 21 December 2021 (UTC)

@Mvolz: Why are you removing Omicron? It already has its own Wikipedia article based on its rapid spread, making it currently the dominant variant in hospitals worldwide if I understand correctly what I've read. I'm reverting your deletion. DavidMCEddy (talk) 15:09, 22 December 2021 (UTC)

Because there is no reliable source for the R naught value. No one has published a paper with it in it. Once there is, it can go back in. Mvolz (talk) 15:10, 22 December 2021 (UTC)

I think that Omicron is the Covid Equivalent of Measles. One source said that the "R number of Omicron is 15". To me, that fact is shocking. "Omicron is the second most contagious virus in the world" Ant1234567 (talk) 15:17, 22 December 2021 (UTC)

@Ant1234567: It may be. But if you look around a bit, you'll see people proposing wildly different numbers. From WP:MEDRS, we, wikipedians, should not be the judge. Take a look at the reference for the R0 of the ancestral strain, you'll see that their data sources also indicated a variety of numbers, especially in the beginning of the pandemic. This could be due to various biases and sometimes also local environmental factors. So what should we do in Wikipedia? I know people who, pointing out to WP:MEDRS, argue that only secondary sources can be used. For the ancestral strain, it took many months for reviews and meta-analyses to be published. A better approach is to accept primary sources initially, but the source we had in the article was not even primary, it was an expert opinion, which according to WP:MEDRS is very unreliable. Another expert, working in a different place with different data, may have a very different opinion. Another problem is that that opinion was published in some little known news portal, which is not good enough even for more trivial pieces of information. We should try to balance the need to inform quickly with the need to inform correctly. --Fernando Trebien (talk) 15:59, 22 December 2021 (UTC)

I just found out that Omicron has been removed from this article. This is unfair for people like us? Why would someone remove this in such an important article? I researched and found that Omicron has a R0 of 15. That variant needs to be placed between Measles and Chickenpox. Here a source to confirm - Omicron is the ‘second most contagious’ virus in the world. Add it ASAP. If not, I would add it back. Thanks. Ant1234567 (talk) 19:21, 22 December 2021 (UTC)

It's important, and that's why it's important to get it right. Unfortunately the source you've provided is not a reliable source for that information. See discussion here:Talk:Basic_reproduction_number#Omicron and also WP:MEDRS for what counts as a reliable source. Mvolz (talk) 10:12, 23 December 2021 (UTC)

I agree that we need reliable sources and that it is important to include Omicron's R. The good news is that since last month, there are now three good reliable sources from PubMed that we can quote. So I will grab the R estimates from those articles and add them to the main article. Keep in mind that _all_ R estimates for _all_ human diseases are imprecise. R is very hard to measure. It changes over time and in different populations. And there are different methods (formulas) for estimating it, so even with the same data, R can differ between scientists. So every R in the table is an uncertain range, not just the one for Omicron. Jaredroach (talk)

Those papers report *relative* reproductive rates. You can't multiply them; these are NOT WP:Routine calculations. There are no papers reporting absolute basic reproduction numbers because it's hard, actually. Mvolz (talk) 19:52, 29 January 2022 (UTC)

@Mvolz: Isn't there something that can be reported?

Can we add a separate column or some other symbol to indicate that we are including "relative" not "basic" reproduction numbers, and include those, with an explanation of "relative to what"?

People are making decisions. They will make decisions on no information, if we are not allowed to post the best information that's available. I think we should post here the best information that's available with appropriate explanations of the deficiencies.

Thanks, DavidMCEddy (talk) 20:21, 29 January 2022 (UTC)

Sorry, I wasn't clear enough in my comment. These are relative reproduction rates; they are not even relative BASIC reproduction rates. This is an article about BASIC reproductive rates. The key difference is a basic reproductive rate is in a hypothetically immunologically naive population. This is actually really, really important for Omicron because it is immune evading variant. What that means is that a large part of increase in transmissibility reported in those papers is due to immune evasion, NOT having a higher R0.

One of the papers that was added does a sensitivity analysis that *does* address relative BASIC reproductive rates. They specifically says most of the increase in transmissibility of Omicron is due to immune evasion (which does not affect R0) and that their analysis did not even have enough power to say whether the ratio of R0delta/R0Omicron was less than 1 (Figure 1B). Nishiura, Hiroshi; Ito, Kimihito; Anzai, Asami; Kobayashi, Tetsuro; Piantham, Chayada; Rodríguez-Morales, Alfonso J. "Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa". Journal of Clinical Medicine. 11 (1): 30. doi:10.3390/jcm11010030. Namely, the transmission advantage of Omicron over Delta is likely gained by the mechanism of Omicron to escape from existing immunity in the population... Of course, our exercise does not refute the actual elevation of the transmissibility of Omicron compared with the Delta variant. However, at least the order elevation of four times entirely due to increased transmissibility is unlikely.{{cite journal}}: CS1 maint: unflagged free DOI (link)

Reporting that Omicron has a higher R0 is actively misinforming people. What we DO know is that Omicron has higher transmissability, and a big part of that is immune evasion. What we DON'T know yet is whether or not it has a higher R0 (basic reproductive rate/higher intrinsic transmissibility). The science on that is still unsettled. Mvolz (talk) 20:52, 29 January 2022 (UTC)

We have a minimally reliable source for Omicron now, but by no means definitive. I think it makes sense to leave it there and update it when better sources become available. --Fernando Trebien (talk) 13:39, 23 May 2022 (UTC)

The long view on the "Sample values for various infectious diseases" table

For this page - the general page on Basic reproduction number - we need to start thinking about what this page looks like years and decades from now. We have perhaps, justified or not, been overly focused on SARS-CoV-2 edits over the past three years. In the long run, it does not make sense to have multiple rows for the same pathogen, even if there are multiple strains of that pathogen (Flu, SARS-CoV-2, etc.). As discussed above, it is incredibly hard to know what the R₀ is for any given strain (even to the point of there being many different R₀s – each population and circumstance dependent). Even if there were not a problem with uncertainties in both the definition and the measurements of R₀s, the table will end up being cluttered. It will also be biased towards certain pathogens that have more strains documented by editors. And it becomes a venue for endless debate among us editors over which strains should be included (and what the values to enter in the table should be). Of course, there can be lots of information on the differences in reproduction numbers between strains and circumstances for each pathogen. These discussions, perhaps with mini-tables, should go on each pathogen-specific page, not on this main page. We can still put ranges on reproduction numbers for each pathogen. We can link these ranges to pathogen-specific pages. I'll try to work on these simplifications as I get an opportunity in the coming months, but feel free to jump the gun. Discussion/comments welcome. Jaredroach (talk) 20:25, 18 August 2022 (UTC)

SEIR model

Unfortunately the description of the SEIR model is flawed. It is apparently based on reference 21, but the content of this reference does not correspond to the content of the relevant section. The whole thing should be completely rewritten; maybe I'll do it when I have more time. Jt omega (talk) 09:01, 16 November 2022 (UTC)

Please. You've probably already noticed this, but this section refers to a section on the same topic in Compartmental models in epidemiology. I've found it useful with similar cases to compare the two. DavidMCEddy (talk) 10:05, 16 November 2022 (UTC)

In Compartmental models the SEIR model is correctly stated, while here it is not. Also otherwise the discussion here is nonsense. Jt omega (talk) 13:41, 16 November 2022 (UTC)

Ideally we move all the stuff on compartmental models from here to Compartmental models in epidemiology. We should link from here to there. We should not duplicate stuff here. We can summarize it in a sentence here. I'll start moving stuff when I get the time if nobody beats me to it. Jaredroach (talk) 17:36, 17 November 2022 (UTC)

I have now made most of these moves. There may still be a little bit of excess detail remaining in this article, but it is looking much less cluttered now. Jaredroach (talk) 18:21, 20 February 2024 (UTC)

"Reff"

Is the effective reproduction number often referred to by the term "Reff" (R_eff)? If so, why not add this information to the article? 173.88.246.138 (talk) 03:51, 25 May 2023 (UTC)