1. https://www.bloomberg.com/news/articles/2021-07-23/what-make...

How do hospitals identify individual patients infected by Alpha, Delta or other variant?

Do they perform genetic sequencing of a virus sample from each patient, to determine what mutations are present? If they are doing statistical sampling, what percentage of patients are being sampled for variant identification?

It would helpful to have variant-specific numbers of cases and deaths added to national data, so that accurate graphs can be drawn for each variant. More granular data would support data analytics of local, variant-specific, policy interventions, to evaluate cause-effect on local health metrics.

Of course, there is a sampling bias there for variants that result in hospitalizations.

Variant-specific proportions can be found here: https://covid.cdc.gov/covid-data-tracker/?ACSTrackingID=USCD...

https://covid.cdc.gov/covid-data-tracker/#monitoring-varaint...

For nations like the US, we are measuring the variant by looking at sewage. It doesn't tell us anything about who ends up hospitalized, but it does give us a good indication of what the is the common variant in a community (and inferences are drawn from there).

The UK has been doing probably the most covid genome sequencing of any nation.

How about the cost of sequencing one drop of the vaccine vial they received, as a quality control sample of the distribution supply chain?

Sure. It'll run under $50 in bulk. Less, but not that much less, if you're only interested in sequencing the spike.

> How about the cost of sequencing one drop of the vaccine vial they received, as a quality control sample of the distribution supply chain?

This isn't a useful quality check. A negative result implicates your field assay rather than manufacturing.

> This isn't a useful quality check. A negative result implicates your field assay rather than manufacturing.

What if there were multiple samples of the same lot number, collected in different geographical regions at different times?

What's the confidence interval?

The problem with the SARS-COV2 virus is that infected individuals are infected before they're symptomatic, let alone dead. Thus there is no evolutionary pressure that would make this virus less lethal, as is the case for viruses that kill their hosts early in the course of infection.

Early 2020 reports of asymptomatic transmission from South Korea were later retracted. There was a contact tracing study of 10 million people in Wuhan which found no asymptomatic transmission.

Here is a paper looking at viral shedding over time in COVID patients: https://www.nature.com/articles/s41591-020-0869-5

I also anecdotally know a few different people who caught COVID from someone who felt fine at the time they interacted, so I'm quite confident it is possible, although I'm not sure I'd make a strong statement about the prevalence.

As far as presymptomatic transmission, this is a good case study from Germany: https://wwwnc.cdc.gov/eid/article/27/4/20-4576_article. A 59 case cluster in which little/no asymptomatic transmission was observed, but 75% of transmission was presymptomatic.

Another interesting paper, also out of Germany covering 400k individuals, 25k infections: https://science.sciencemag.org/content/373/6551/eabi5273. I can't write a summary better than the one in the paper: The role that individuals with asymptomatic or mildly symptomatic severe acute respiratory syndrome coronavirus 2 have in transmission of the virus is not well understood. Jones et al. investigated viral load in patients, comparing those showing few, if any, symptoms with hospitalized cases. Approximately 400,000 individuals, mostly from Berlin, were tested from February 2020 to March 2021 and about 6% tested positive. Of the 25,381 positive subjects, about 8% showed very high viral loads. People became infectious within 2 days of infection, and in hospitalized individuals, about 4 days elapsed from the start of virus shedding to the time of peak viral load, which occurred 1 to 3 days before the onset of symptoms. Overall, viral load was highly variable, but was about 10-fold higher in persons infected with the B.1.1.7 variant. Children had slightly lower viral loads than adults, although this difference may not be clinically significant.

The second paper is a bit dense, but there is a great discussion at https://www.youtube.com/watch?v=p4AR7qPxz_Q, with discussion of this paper beginning maybe 47:00. 1:14:08 beings a discussion about how a large number of cases might be caused by a small number of individuals. Interestingly, these individuals are not necessarily the same as those who go on to be seriously ill, hospitalized, or die.

In practice, the difference between presymptomatic and asymptomatic makes little difference. The key is that we have ample evidence that an infected person can infect others while they do not have symptoms.

Vaccination reduces the infection rate. Among vaccinated individuals who suffer breakthrough infection the time at peak viral load is significantly reduced.

CDC recommends testing of vaccinated people, since they can be infected and the vaccine suppresses symptoms, so they won't know to self-isolate, https://www.webmd.com/lung/news/20210729/cdc-reverses-guidan... (July 29, 2021)

> Even if they’re not showing symptoms, fully vaccinated people should “get tested 3-5 days after exposure to someone with suspected or confirmed COVID-19 and wear a mask in public indoor settings for 14 days after exposure or until they receive a negative test result,” ... “Our updated guidance recommends vaccinated people get tested upon exposure regardless of symptoms,” CDC Director Rochelle Walensky, MD, told The New York Times