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> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every inst

> Though the NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant, we have not been able to establish that in every instance the variant is Omicron as the PCR machine in use at the SBAH laboratory does not screen for the S-gene. A reasonable assumption is being made that the cases described here represent infection with the new variant. Translation(?): It's omicron all right, but we didn't test for it because we don't have the equipment. Still, it's reasonable to assume we're dealing with omicron. This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions.

bhouston 5y ago
I think that their reasoning is solid though. Omicron is the majority of SA cases now. It is early days and it is great to get any information like this out into the world, even if it is imperfect.
- encryptluks2 5y ago
  Unless it favors unvaccinated people, then it should definitely be censored. Sarcasm but not.
mmastrac 5y ago
It's in your quote: "NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant". They have confirmed almost all of them. That's a far cry from "we didn't test for it because we don't have the equipment".
matthewdgreen 5y ago
>This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions. This is an emerging situation where all data may be useful. At present, the authors have access to some imperfect data due to circumstances beyond their control, and are clearly reporting the data -- complete with appropriate caveats about the limitations of their measurement equipment. This is exactly what competent practitioners should be doing, and to impugn their competence is completely inappropriate.
shkkmo 5y ago
The NICD has (presumably) been doing sample sequencing of local positive covid cases. This is how the NICD knows that almost all new covid cases in Tshwana are omicron. The SBAH lab is using PCR tests to confirm cases. Some PCR tests detect the "s gene", which omicron lacks. Thus a positive PCR test that lacks the s-gene is quite probably a case of omicron. The SBAH lab's PCR tests doesn't check for the "s gene" so can't be a direct indicator that the particular strain of covid is omicron. However, because the NICD sequencing has shown that almost all covid cases in the area are omicron, it is pretty safe to assume that almost all the cases at SBAH are omicron (as long as you trust NICD's data.) The responsible thing as a scientist is make such assumptions explicit, even when those assumptions are pretty safe. This statement should increase your confidence in the credibility of the scientist issuing it, not call it into question. Edit: If you don't think the assumption is safe, do you think it is less safe than relying on the lack of an "s gene" to indicate omicron without doing the sequencing? Both are assumptions whose reasonableness depend entirely on assumptions about the current local genetic pool of variations.
deleted 5y ago
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cycomanic 5y ago
No offense, but what are your qualifications to question the competence of the author?

bhouston 5y ago

I think that their reasoning is solid though. Omicron is the majority of SA cases now. It is early days and it is great to get any information like this out into the world, even if it is imperfect.

encryptluks2 5y ago
Unless it favors unvaccinated people, then it should definitely be censored. Sarcasm but not.

mmastrac 5y ago

It's in your quote: "NICD has confirmed that almost all cases of SARS-C0V-2 in Tshwane are due to the new variant". They have confirmed almost all of them. That's a far cry from "we didn't test for it because we don't have the equipment".

matthewdgreen 5y ago

>This statement alone throws into question, at a minimum, the competence of the author and likely all of the report's data and conclusions. This is an emerging situation where all data may be useful. At present, the authors have access to some imperfect data due to circumstances beyond their control, and are clearly reporting the data -- complete with appropriate caveats about the limitations of their measurement equipment. This is exactly what competent practitioners should be doing, and to impugn their competence is completely inappropriate.

shkkmo 5y ago

The NICD has (presumably) been doing sample sequencing of local positive covid cases. This is how the NICD knows that almost all new covid cases in Tshwana are omicron. The SBAH lab is using PCR tests to confirm cases. Some PCR tests detect the "s gene", which omicron lacks. Thus a positive PCR test that lacks the s-gene is quite probably a case of omicron. The SBAH lab's PCR tests doesn't check for the "s gene" so can't be a direct indicator that the particular strain of covid is omicron. However, because the NICD sequencing has shown that almost all covid cases in the area are omicron, it is pretty safe to assume that almost all the cases at SBAH are omicron (as long as you trust NICD's data.) The responsible thing as a scientist is make such assumptions explicit, even when those assumptions are pretty safe. This statement should increase your confidence in the credibility of the scientist issuing it, not call it into question. Edit: If you don't think the assumption is safe, do you think it is less safe than relying on the lack of an "s gene" to indicate omicron without doing the sequencing? Both are assumptions whose reasonableness depend entirely on assumptions about the current local genetic pool of variations.

deleted 5y ago

[deleted]

cycomanic 5y ago

No offense, but what are your qualifications to question the competence of the author?