CDC Nowcast
#18,037
While COVID has taken a back seat to other infectious disease concerns the past few weeks, and rates of infection appear to be currently low in the United States, it continues to evolve into new, and potentially worrisome variants.
Despite this ongoing evolution, over the past 2 years the world has intentionally dismantled the bulk of their global surveillance, testing, and reporting system in order to `move on' from the pandemic emergency (see No News Is . . . Now Commonplace).
The most recent WHO Update (Apr 12th) indicates:
Globally, the number of new cases decreased by 11% during the past 28-day period of 4-31 March 2024 compared to the previous 28-day period (5 February to 3 March 2024), with over two hundred and seven-five thousand new cases reported. The number of new deaths decreased by 41% as compared to the previous 28-day period, with over 4200 new fatalities reported
But these numbers are admittedly incomplete, with only about 20% of the world's nations still reporting hospitalizations and deaths, and the quality of that data is unknown.
The latest CDC Nowcast map of the United States (see below) is blank. Not enough samples were collected over the previous 2 weeks to generate a graphic, and while the Nowcast pegs the new KP.2 variant as the new leader in the United States, their estimate is unusually vague (range 12.9% - 42.1%).
This `don't test, don't tell' policy extends far beyond COVID, with novel flu infections in some countries often going weeks or months before being reported (assuming they are reported at all).
A year ago, in Lancet Preprint: National Surveillance for Novel Diseases - A Systematic Analysis of 195 Countries, we looked at an independent analysis which suggested that many nations have substantially overstated their compliance with the 2005 IHR regulations, and that surveillance and reporting are far less robust than advertised.
It is against this backdrop that we look at a recent preprint from the Sato Lab on the rapidly emerging KP.2 variant, which appears to have - compared to the JN.1 variant - increased transmissibility and immune resistance.
This variant has been dubbed a FLiRT variant, due to two substitutions (S:F456L and S:R346T), which appear to give it an epidemiological advantage over earlier variants.
First, the link and Abstract from the preprint, after which I'll have more.
Yu Kaku, Keiya Uriu, Yusuke Kosugi, Kaho Okumura, Daichi Yamasoba, Yoshifumi Uwamino, Jin Kuramochi, Kenji Sadamasu, Kazuhisa Yoshimura, Hiroyuki Asakura, Mami Nagashima, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato
doi: https://doi.org/10.1101/2024.04.24.590786
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Abstract
The JN.1 variant (BA.2.86.1.1), arising from BA.2.86(.1) with the S:L455S substitution, exhibited increased fitness and outcompeted the previous dominant XBB lineage by the biggening of 2024. JN.1 subsequently diversified, leading to the emergence of descendants with spike (S) protein substitutions such as S:R346T and S:F456L.
Particularly, the KP.2 (JN.1.11.1.2) variant, a descendant of JN.1 bearing both S:R346T and S:F456L, is rapidly spreading in multiple regions as of April 2024.
Here, we investigated the virological properties of KP.2. KP.2 has three substitutions in the S protein including the two above and additional one substitution in non-S protein compared with JN.1. We estimated the relative effective reproduction number (Re) of KP.2 based on the genome surveillance data from the USA, United Kingdom, and Canada where >30 sequences of KP.2 has been reported, using a Bayesian multinomial logistic model.
The Re of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide. Indeed, as of the beginning of April 2024, the estimated variant frequency of KP.2 has already reached 20% in United Kingdom.
The pseudovirus assay showed that the infectivity of KP.2 is significantly (10.5-fold) lower than that of JN.1. We then performed a neutralization assay using monovalent XBB.1.5 vaccine sera and breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections. In all cases, the 50% neutralization titer (NT50) against KP.2 was significantly lower than that against JN.1.
Particularly, KP.2 shows the most significant resistance to the sera of monovalent XBB.1.5 vaccinee without infection (3.1-fold) as well as those who with infection (1.8-fold). Altogether, these results suggest that the increased immune resistance ability of KP.2 partially contributes to the higher Re more than previous variants including JN.1.
If we had better global surveillance and reporting, we might know more . . . but we don't.
Ignorance may be bliss, but that happy state of affairs only lasts until we get blindsided by the next global health crisis. A least, when that inevitably happens, our leaders will be able to honestly say:
`Nobody saw it coming.'
