5 ms·

Name a disease where the measure of infection is a PCR test with a 40+ cycle threshold.

nickthemagicman 6y ago
Whats the normal cycle threshold for identifying pathogens? This is interesting.
yread 6y ago
In this paper they've used 45 for HIV. What's your point? https://www.hindawi.com/journals/art/2016/7954810/ https://www.hindawi.com/journals/art/2016/7954810/
- nanis 6y ago
  > In this paper they've used 45 for HIV. What's your point? 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-notice-for-ivd-users-2020-05 https://www.who.int/news/item/20-01-2021-who-information-not... [2]: https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-2019-nCoV-laboratory-2020.6-eng.pdf?sequence=1&isAllowed=y https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-...
  - yread 6y ago
    So you think they should use some lower Ct number for which it would be possible to show that eg 99.5% of people who are over it (i.e. have lower viral load) don't infect anyone? Interesting. I've read that most of the false negative for a PCR test actually come from sample collection (makes sense, PCR is super reliable) so it could be that you would miss people with high viral load where the sample was just not taken in a perfect way. Especially early in the infection it could be quite localized.
    - nanis 6y ago
      > So you think they should use some lower Ct number 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.
graeme 6y ago
I fail to see what this has to do with vaccines and infectivity. 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.

Whats the normal cycle threshold for identifying pathogens? This is interesting.

In this paper they've used 45 for HIV. What's your point? https://www.hindawi.com/journals/art/2016/7954810/ https://www.hindawi.com/journals/art/2016/7954810/

nanis 6y ago
> In this paper they've used 45 for HIV. What's your point? 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-notice-for-ivd-users-2020-05 https://www.who.int/news/item/20-01-2021-who-information-not... [2]: https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-2019-nCoV-laboratory-2020.6-eng.pdf?sequence=1&isAllowed=y https://apps.who.int/iris/bitstream/handle/10665/334254/WHO-...
- yread 6y ago
  So you think they should use some lower Ct number for which it would be possible to show that eg 99.5% of people who are over it (i.e. have lower viral load) don't infect anyone? Interesting. I've read that most of the false negative for a PCR test actually come from sample collection (makes sense, PCR is super reliable) so it could be that you would miss people with high viral load where the sample was just not taken in a perfect way. Especially early in the infection it could be quite localized.
  - nanis 6y ago
    > So you think they should use some lower Ct number 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.

graeme 6y ago

I fail to see what this has to do with vaccines and infectivity. 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.