For what it's worth: At an estimated 30% FLiRT (JN.1* (Nextclade) + S:R346T, S:F456L) end of wk 10, the impoverished Singapore Covid monitoring shows reduced ARI levels and reduced SARS2 ARI specimen positivity, when comparing wks 9 and 10.
If the FLiRT subvariants have the capacity to drive Rt over 1, this trend would be expected to turn in the coming weeks.
And a trend reversal in week 12, with slightly rising ARI numbers and SARS2 positivity, at an extrapolated 60% JN.1* (Nextclade) + S:R346T, S:F456L.
It's a shame that Singapore is left with these limited data. Why wouldn't they at least have wastewater.
Possibly, rising SARS2 infections are masked by lowering influenza infections, as flu positivity among ILI samples is steadily decreasing.
This is the state of guessing based on the impoverished surveillance.
Clear signs of a Covid wave (albeit still below last year's May wave) in week 17, with SARS2 positivity among ARI samples at 18%.
No new sequences since weeks in covSPECTRUM.
Update wk 18 (29.4.-5.5):
Still rising ARI numbers, SARS2 positivity has plateaued at 16%, while flu positivity went down to 10%. It looks like a minor Covid wave.
Updated seqs on covSPECTRUM:
FLiRT variants are highly dominant as per April 24 (50% beginning of April, wk 14).
Of note, there are almost no KP.3 sequences (15 as compared to 408 FLiRT).
covSPECTRUM queries:
Multilineage JN.1 Spike with S:R346T and S:F456L (FLiRT):
KP.3:
(can't share the link properly, add the star manually)
Development so far, tabulated.
Note that the covSPECTRUM growth extrapolation, with much fewer seqs, was predicting dominance for wk 14, as the current estimate now shows too.
Attached: 2 images Extrapolation with new sequences (last available in covSPECTRUM 26.03.) would see JN.1 Spike + S:R346T, S:F456L (FLiRT) dominant in wk 14.
Interesting, the MOH itself is seeing a wave now. They even have case numbers. Did I overlook publication of these numbers?
Covid wave in Singapore, update wk. 20: Highest SARS2 positivity among ARI since wk.9, 21%. I wonder if they are at peak yet.
No new seqs in covSPECTRUM since April 25. FLiRT highly dominant with the last data, KP.3 <10%.
Covid wave in Singapore, update wk. 22 (wk. 21 missing): The wave might have peaked in wk. 21, ARI numbers and SARS2 positivity markedly lower.
In terms of ARI, May 2023 wave magnitude. In case numbers and hospitalisations, who knows.
Covid wave in Singapore, update wk. 23 (wk. 21 still missing): Further reduction of ARI cases, stable SARS2 positivity.
In terms of ARI, April/May 2023 wave magnitude. Case numbers and hospitalisations: Who knows, maybe these secrets will be revealed in another press release.
Peaked Singapore Covid wave: The MOH now supplied the missing peak week 21 ARI data and promulgated case estimates and hospitalisation data.
SARS2 positivity reached 25% in the peak week 21.
I could not find cases and hospitalisations for the weeks 20 and 21.
Peaked Singapore Covid wave: Update wk. 24, SARS2 positivity thankfully continued to go down. This was a FLiRT and (S:S31del + FLiRT) wave, and large. No KP.3* contribution.
KP.2.3 reached dominance around when the wave peaked in wk 21.
Sources:
https://moh.gov.sg/resources-statistics/infectious-disease-statistics/2024/weekly-infectious-diseases-bulletin
https://github.com/MurrellGroup/lineages?tab=readme-ov-file
Development so far:
Variant fraction estimates from the covSPECTRUM tool, using Collection 42 query, last data point 29.05.
FLiRT: Multilineage JN.1 Spike with S:R346T and S:F456L
DeFLiRT: Multilineage JN.1 Spike with S:S31del, S:R346T, S:F456L
Dominik Steiger
