#18,192
While the testing and reporting of COVID cases have dropped markedly over the past couple of years - making comparisons to previous years difficult - the CDC's tracking web page (above) shows COVID cases are rising once again across the nation.
The SARS-CoV-2 virus continues to evolve and diversify (see diagram below), introducing new, often more `biologically fit', variants every few months. Four months ago JN.1 appeared to be firmly in control, but by May its dominance was under assault by a tag-team of KP2 and KP.3.
Limited testing and surveillance around the globe makes it very difficult to accurately gauge the trajectory of these new variants, but the Sato Lab is back today with another analysis, one which finds that the KP.3.1.1 variant appears to have an even bigger advantage over its competition.
Yesterday The Sato Lab (Kei Sato) @SystemsVirology posted a brief summary( a few excerpts below) of their findings on Twitter/X.
Virological characteristics of the SARS-CoV-2 KP.3.1.1 variant
Yu Kaku, Keiya Uriu, Kaho Okumura, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato
doi: https://doi.org/10.1101/2024.07.16.603835
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Abstract
The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), arising from BA.2.86.1 with spike protein (S) substitution S:L455S, outcompeted the previously predominant XBB lineages by the beginning of 2024. Subsequently, JN.1 subvariants including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired additional S substitutions e.g., S:R346T, S:F456L, and S:Q493E, have emerged concurrently.Thereafter, JN.1 subvariants, such as LB.1 (JN.1.9.2.1), KP.2.3 (JN.1.11.1.2.3), and KP.3.1.1 (JN.1.11.1.3.1.1), which convergently acquired a deletion of Serine at the 31st position in S (S:S31del) in addition to the above substitutions, have emerged and spread as of June 2024. We recently reported the virological features of JN.1 subvariants including KP.2, KP.3, LB.1, and KP.2.3.2,3Here, we investigated the virological properties of KP.3.1.1. First, we estimated the relative effective reproduction number (Re) of KP.3.1.1 using a Bayesian multinomial logistic model4 based on genome surveillance data from Spain, the USA, France, Canada, and the UK, where this variant has spread as of June 2024. In Spain, the Re of KP.3.1.1 is over 1.2 fold higher than that of JN.1 and even higher than those of KP.2, KP.3, LB.1, and KP.2.3. Additionally, the other countries under investigation herein show higher Re for KP.3.1.1.However, it must be noted there is the possibility of overestimation in these countries due to more limited KP.3.1.1 sequence numbers. These results suggest that KP.3.1.1 will spread worldwide along with other JN.1 sublineages.We then assessed the virological properties of KP.3.1.1 using pseudoviruses. The pseudovirus of KP.3.1.1 had significantly higher infectivity than that of KP.3.
Neutralization of KP.3.1.1 was tested using i) convalescent sera after breakthrough infection (BTI) with XBB.1.5 or EG.5, ii) convalescent sera after the infection with HK.3 or JN.1, and iii) sera after monovalent XBB.1.5 vaccination. The 50% neutralization titer (NT50) against KP.3.1.1 was significantly lower than KP.3 (1.4-1.6 fold) in all four groups of convalescent sera tested. KP.3.1.1 also showed a 1.3 fold lower NT50 against XBB.1.5 vaccine sera than KP.3. Moreover, KP.3.1.1 showed stronger resistance with a 1.3 fold lower NT50 with statistical significances to the convalescent sera infected with EG.5 and HK.3 than KP.2.3.Altogether, KP.3.1.1 exhibited a higher Re, higher pseudovirus infectivity, and higher neutralization evasion than KP.3. These results align with our recent report that the JN.1 subvariants with S:S31del (e.g., KP.2.3 and LB.1) exhibited enhanced Re and immune evasion compared to the other JN.1 subvariants without S:S31del (e.g., JN.1, KP.2, and KP.3), highlighting the evolutionary significance of S:S31del in the JN.1 lineages.
Despite reassurances (4 years ago) that we were only months away from achieving `herd immunity', and predictions the SARS-CoV-2 virus would eventually stabilize, and become a minor `seasonal' threat, COVID shows few signs of taking early retirement.
While KP.3.1.1 appears to be the newest contender for the viral throne, there are no guarantees another - more biologically `fit' variant - isn't already spreading somewhere in the world.
At the same time, we are increasingly concerned over the spillover of novel H5 viruses into humans. A confluence of events that should have us rethinking our short-sighted and ill-timed decision to dismantle surveillance and reporting systems around the globe.
