Update information including data from week 6, 2021
Weekly proportion of SGTF and SGTL positive samples among all TaqPath positive samples detected, between week 49 (2020) and week 6 (2021), by a large laboratory distributed throughout the Portuguese territory (n = 52004 TaqPath positive samples).
After the rampant increase in frequency observed from week 52 (2020) to week 3 (2021), we now clearly see a decelerating trend.
Notes
- SGTF (S gene target failure) = positive test with non-detectable S gene and <=30 Cycle threshold (Ct) for N and ORF1ab targets;
- SGTL (S gene target late detection) = positive test having Ct values for S gene >5 units higher than the maximum Ct value obtained for the other two targets (N and ORF1ab) of the assay (exclusively includes positive samples with <=30 Ct for N and ORF1ab targets).
- The mean Ct difference between S gene and N/ORF genes for SGTL samples was consistently around 5-8 Ct values (median=6.60, IQR=5.79-7.59).
- Until week 3, the proportion of SGTF/SGTL cases that are B.1.1.7 was estimated as 0.918 (0.845 to 0.964, CI 95%) based on a sub-sample of sequencing cases (90 B.1.1.7 cases in 98 known SGTF/SGTL sequenced samples). So far, we have generated 242 B.1.1.7 genome sequences (SARS-CoV-2 Portugal).