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

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.