Sequencing Swabs

Lots of great questions!

the SIREN 2.0 study, running this winter, will generate some more data to answer this question.

Thanks for pointing this out; I hadn't seen it and it's super relevant. I don't see what sample type they're using in the press release, but any kind of ongoing metagenomics to look at respiratory viruses is great!

how do you relate relative abundance to detection probability? I would have thought the total number of reads of the pathogen of interest also matters.

It depends on your detection method, but modeling it as needing some number of cumulative reads hitting the pathogen is a good first approximation.

If you think it would take N reads of the pathogen to flag it then if you know RA(1%) and the exponential growth rate you can make a back of the envelope estimate of how much sequencing you'd need on an ongoing basis to flag it before X% of people had ever been sick. For example, if you need 100 reads to flag, it doubles weekly, and RAi(1%) is 1e-7 then to flag at a cumulative incidence of 1% (and current weekly incidence of 0.5%) you'd need 100/1e-7 = 1e9 reads a week.

(I chose 1% cumulative incidence and weekly doubling to make the mental math easier. At 1% CI half the people got sick this week and half in previous weeks, and the cumulative infection rate across all past sequencing should sum to 1%, so we can use RAi(1%) directly. Though I might have messed this up since I'm doing it in my head lying in bed.)

if you tested the entire population you would have some reads on every pathogen even if the relative abundance of some pathogens is very low.

If you collected a large enough sample volume and sequenced deeply though, yes.

Relatedly, does the cost of the sequencing scale roughly linearly with the relative abundance required? That is, if your 40,000x figure is correct, would that imply swabbing is ~40,000x cheaper than wastewater?

It doesn't, for three reasons:

• Sequencing in bulk is a lot cheaper per read. You might pay $13k for 10B read pairs, or $1k for 100M. But that's just ~10x.

• Some components (lab time, kits) vary in proportion to the number of samples and don't go up much as your samples are bigger.

• It's only your sequencing costs that vary with relative abundance, and while with wastewater I expect the cost of sequencing to dominate that's not the case for any other sample type I can think of (maybe air?) If you're sampling from individuals the cost of getting the samples is likely quite high (we were recently quoted $80/person from a contractor, and while I think we can do better if you want 1k people per pooled sample it's almost certainly more expensive than the sequencing charge).

Why does the number of swabs affect the relative abundance? If you double the number of swabs, I would expect that both the total reads and the number of SARS-COV-2 reads double, hence holding the relative abundance constant.

Some people have vastly higher viral loads than others, and the relative abundance you see for a pool depends on whether you get some of these people. Your intuition would be correct for pools large enough that this variation was no longer relevant.

I don't see it being contained in hard-to-target populations.

Sorry, I was unclear! The easiest way to collect a pooled sample is the walk around some building and sample everyone. This gets you a big sample pretty cheaply, but it's not a great one if you want to understand the containing city because it's likely that many people in the building will get sick on a similar timeframe. The sample members are too correlated in their exposure.

In your UK example, I'm guessing you could sample some office buildings of 1k people and find 0 cases and others and find 200 cases.

To avoid this you need broader sample collection, but that's logistically more difficult and so more expensive.

Airport arrivals would be great, though that's a difficult setting to work in.

I'm sceptical this is bridging a 40,000x gap (maybe 40,000x isn't the relevant benchmark here - see comments previously).

I'm also skeptical! I think sampling from individuals is extremely promising. It seems like you ought to be able to get down to more like $2/person in which case a pool of 1k costs you $2k in collection. Then add in $1k for sequencing and you're still well above wastewater. But my initial attempts to partner with people already doing sampling haven't turned up good leads.

Thanks! I'm most interested in viral load in the sense of the relative abundance you get with untargeted shotgun sequencing (since you need sequencing (or something similarly general) to detect novel threats and/or avoid having a trivially-bypassable detection system) but there's not much literature on this.