It's like trying to decide if it's too rainy to go out by figuring out how many people are watering their yards right now, when you could just look out and see if it's raining.
Looking at the vaccine numbers for this week is a worse proxy. How does it help?
Sure, you could use the projected vaccinations for next March to decide how likely it is that you'll be able to go and watch a broadway show in March, but, like the weather forecast, you'll need to know what the actual positivity is in March to make the final decisions.
Israel is over 40% on first dose and should have interesting reault sun the next month or two.
As someone mentioned upthread, Israel will be an early indicator here.
If you look at the entire population, it's only about 28% got 1st dose and 12% got second dose, many within the last week.
But with a population of about 9.3 million (size and population comparable to New Jersey) and they just ramped up to about 1million vaccinations a week, we could be at "full" vaccination March 26th - 85% of eligible population, 2nd dose, and 1 week for it to take affect.
Source: Israel's ministry of health https://datadashboard.health.gov.il/COVID-19/general and wikipedia's population information https://en.wikipedia.org/wiki/Demographics_of_Israel#Age_str...
Name a vaccine that doesn’t reduce onward transmission even as it cures disease. It’s overwhelmingly likely that the vaccine will slow transmission and foolish to throw our priors in the garbage bin.
What we don’t know yet is how much onward transmission will be reduced.
There is a difference between HIV vs SARS-Cov2: If you get AIDS, your body does not have the capacity to recover from it on its own. So, 1) the chances of detecting dead material from a long gone infection are nil; and 2) the cost of a false negative is much higher than the cost of a false positive.
Since most people seem not to be seriously affected by a SARS-Cov2 infection, neither is true for SARS-Cov2. So, not agreeing on a fixed, reasonable, standard number of cycles which everyone uses has the consequence of inflating false positives for no gain. Note WHO's updated information[1].
> WHO guidance Diagnostic testing for SARS-CoV-2 states that careful interpretation of weak positive results is needed (1). The cycle threshold (Ct) needed to detect virus is inversely proportional to the patient’s viral load.
If you are not sick and your viral load is barely detectable, what's the point?
See also Figure 1 in WHO's lab guidance[2].
[1]: https://www.who.int/news/item/20-01-2021-who-information-not...
[2]: https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-...
Everyone should use the same number in all tests. From what I understand, about 20 is a reasonable number which might still result in positives up to a month post-infection. I consider having a standard more important that the specific number chosen. It seems when people go to > 30 it is in a quest to ensure a positive test result.
Also I’d only heard of people speak in terms of “positive” for pcr. You can be positive but not infectious, if there are a lot of cycles and you’re tested as the disease winds down.
Whooping cough - that treats the symptoms but does not stop the patient from spreading the disease
Edit: Added context
* Those positive for antibodies but pcr negative —> had been exposed, cleared virus without infection
* those pcr positive but asymptomatic
* those pcr positive and symptomatic
About 30% were in the seropositive group which didn’t have pcr positivity. So it seems like transmission was reduced at least 30%. It’s also possible the other two groups would have had lower transmission rates than if they had had no vaccine.
If you have a more precise source I’d be interested to see it, but if this is the worst case it’s pretty good!
> We used PCR, EIA, and culture to confirm B. pertussis infection in two highly vaccinated groups of children in two day-care centers. Three (10%) of 30 2- to 3-year-old children were seropositive for recent infection; one had nasopharyngeal colonization and a clinical illness that met the modified WHO case definition. In the day-care center for the 5- to 6- year-old group, 9 (55%) of 16 children were IgM positive, 4 (25%) of whom had nasopharyngeal colonization. Of these four children, three had nonspecific cough, and only one met the modified WHO definition for pertussis. None of the children in our study, including those who met the WHO definition, had been examined by a physician before our investigation.
>Children who were seropositive and re- mained both asymptomatic and PCR negative probably had sufficient immunity from vaccines or natural boosters to protect them against persistent colonization and clinical disease. Their seropositivity could not be due to vaccine because the children were tested more than a year after having been vaccinated.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2627963/pdf/109...
The real worry here is unfortunately human behaviour and not science. The science is clear, and it's been said/written/screamed/spraypainted that the #1 reason we have all of these restrictions is actually human behaviour as opposed to the virus itself.
Nope, if the virus didnt exist, there would be no restrictions; therefore, it is the primary reason.
Has there ever been a control group or any historical precedence to scientifically support the questionable hypothesis that a highly contagious virus can be can be globally controlled simply by controlling human behavior? (i.e. locking down entire nations while "essential workers" -- poor people -- are still forced to go to work)
Sticking only with positivity rates is misleading even if one ignores all the costs of lockdowns. As the WHO pointed out on 13 January 2021[1]:
> WHO reminds IVD users that disease prevalence alters the predictive value of test results; as disease prevalence decreases, the risk of false positive increases (2). This means that the probability that a person who has a positive result (SARS-CoV-2 detected) is truly infected with SARS-CoV-2 decreases as prevalence decreases, irrespective of the claimed specificity.
You may find this comment[2] by me and the link to the calculator to understand the impact of varying prevalence keeping false positive and false negative rates constant.
Note also,
> Most PCR assays are indicated as an aid for diagnosis, therefore, health care providers must consider any result in combination with timing of sampling, specimen type, assay specifics, clinical observations, patient history, confirmed status of any contacts, and epidemiological information.
In plain English, that says that with no illness and no contact with people suffering from Covid19 etc, a positive test does not necessarily mean that the person testing positive is infected.
This is all basic Stats but it has been conspicuously ignored for almost year now.
> The cycle threshold (Ct) needed to detect virus is inversely proportional to the patient’s viral load.
So, before the test, pick a Ct, and stick with it instead of keeping on going until you get a positive result. At higher counts, the test might be detecting left over material from a long gone infection.
> Where test results do not correspond with the clinical presentation, a new specimen should be taken and retested using the same or different NAT technology.
So, if you are sick and get a negative, test again to make sure you can rule out SARS-Cov2. But, equivalently, if you are not sick and test positive, also make sure that this is not a false positive.
The latter is what has been globally ignored with one positive test on healthy people is regarded as proof of infection and illness. It is what is being ignored when people are not allowed to travel or work due to a positive test result. Basically, a positive test result, even without symptoms, and even with a subsequent negative, puts a scarlet letter on you which cannot be erased.
The flowchart in Figure 1 in this document[3] might also be useful. Note the first box is labeled "Patient meets the clinical criteria for COVID-19". That's where these diagnostic tests are applicable as proof of infection.
The fact that the test is useful for confirmation of infection conditional on presenting symptoms doesn't mean it is useful for screening an entire population or deciding on how much GDP to destroy because of the simple facts that in that scenario a large portion of positive test results will be false positives and these tests have high false negative rates.
[1]: https://www.who.int/news/item/20-01-2021-who-information-not...
[2]: https://news.ycombinator.com/item?id=25894449
[3]: https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-...