In a previous post I discussed the sensitivity of sequencing and how, in the limit, sequencing is a more sensitive technique than qPCR. In this post I’m going to discuss a couple of models I put together to try and explore this further. First, let’s briefly review the model from the previous post. In this model we assume there is a single viral/target genome fragment (SARS-CoV-2: 30Kb) in our sample, of a given fragment size. The qPCR column shows the probably that this single fragment will cover the amplification region.
Thank you for the article. Just wanted to comment quickly to help your analysis. If you are on the hunt for sensitivity, you would do ddPCR or smFISH, not qPCR. Both method have single molecule sensitivity given you are able to extract a single molecule of viral nucleic acid from a nasal swab. The efficiency of the extraction itself is highly variable depending on how degraded it is, time since isolation, storage buffer, etc but is independent of the detection method.
qPCR is just quick and easy, that's why it's popular. No need to mess with a keyboard. Sensitivity is not really the point there, usually.
Thanks for your comment! Yes, I think there are more sensitive techniques than qPCR. In this context, I’m trying to evaluate sequencing as an alternative to qPCR for viral diagnostics. qPCR has been considered the “gold standard” here.
Would be interesting to look at ddPCR too however, I think the limitations described in the first model hold here. But it would be interesting to think about this more.
Thank you for the article. Just wanted to comment quickly to help your analysis. If you are on the hunt for sensitivity, you would do ddPCR or smFISH, not qPCR. Both method have single molecule sensitivity given you are able to extract a single molecule of viral nucleic acid from a nasal swab. The efficiency of the extraction itself is highly variable depending on how degraded it is, time since isolation, storage buffer, etc but is independent of the detection method.
qPCR is just quick and easy, that's why it's popular. No need to mess with a keyboard. Sensitivity is not really the point there, usually.
Thanks for your comment! Yes, I think there are more sensitive techniques than qPCR. In this context, I’m trying to evaluate sequencing as an alternative to qPCR for viral diagnostics. qPCR has been considered the “gold standard” here.
Would be interesting to look at ddPCR too however, I think the limitations described in the first model hold here. But it would be interesting to think about this more.