#17,812
Last August a new, and heavily mutated, BA.2.86 SARS-CoV-2 variant appeared in the UK and parts of Europe which raised concerns that it might out-perform previous Omicron variants (see UKHSA To Move COVID/Flu Jabs Forward Due To Concerns Over BA.2.86).
While its path to global dominance has been slower than expected, it - and its direct offshoot JN.1 - continue to gain ground, and last week JN.1 debuted in 2nd place in the CDC's Nowcast.
- JN.1 was first detected in the United States in September 2023. By the end of October, it made up less than 0.1% of SARS-CoV-2 viruses.
- CDC projects that the variant JN.1 comprises an estimated 15–29% of in the United States as of December 8, 2023.
- CDC projects that JN.1 will continue to increase as a proportion of SARS-CoV-2 genomic sequences. It is currently the fastest-growing variant in the United States.
- Updated COVID-19 vaccines are expected to increase protection against JN.1, as they do for other variants.
- At this time, there is no evidence that JN.1 presents an increased risk to public health relative to other currently circulating variants.There is no indication of increased severity from JN.1 at this time.
One of the ways we can make up for those reporting gaps are laboratory studies on emerging variants, such as provided by the Kei Seto Lab at the University of Tokyo.
Last September we looked at their initial analysis of the parental BA.2.86 variant (see Preprint: Transmissibility, Infectivity, and Immune Resistance of the SARS-CoV-2 BA.2.86 Variant), which suggested that ` . . . BA.2.86 is one of the most highly immune evasive variants ever.'
Over the weekend the Sato Lab released their preprint on the JN.1 offshoot, which differs from BA.2.86 by only a single change (L455S) in the spike protein, and 3 others in the non-S proteins. The L455S mutation has previously been linked to increased immune evasion.
While the analysis that follows is somewhat technical, the bottom line is that JN.1 appears to be even more immune evasive than its parental BA.2.86, which suggests that it - and its descendants - may have a growth advantage over the the older XBB Omicron lineage in the months ahead.
First some excerpts from the preprint, after which I'll have a postscript:
Virological characteristics of the SARS-CoV-2 JN.1 variant
Yu Kaku, Kaho Okumura, Miguel Padilla-Blanco, Yusuke Kosugi, Keiya Uriu, Alfredo Amolong Hinay Jr., Luo Chen, Arnon Plianchaisuk, Kouji Kobiyama, Ken J Ishii, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jiri Zahradnik, Jumpei Ito, Kei Sato
doi: https://doi.org/10.1101/2023.12.08.570782
Abstract
The SARS-CoV-2 BA.2.86 lineage, first identified in August 2023, is phylogenetically distinct from the currently circulating SARS-CoV-2 Omicron XBB lineages, including EG.5.1 and HK.3. Comparing to XBB and BA.2, BA.2.86 carries more than 30 mutations in the spike (S) protein, indicating a high potential for immune evasion. BA.2.86 has evolved and its descendant, JN.1 (BA.2.86.1.1), emerged in late 2023. JN.1 harbors S:L455S and three mutations in non-S proteins. S:L455S is a hallmark mutation of JN.1: we have recently shown that HK.3 and other "FLip" variants carry S:L455F, which contributes to increased transmissibility and immune escape ability compared to the parental EG.5.1 variant. Here, we investigated the virological properties of JN.1.
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The SARS-CoV-2 BA.2.86 lineage, first identified in August 2023, is phylogenetically distinct from the currently circulating SARS-CoV-2 Omicron XBB lineages, including EG.5.1 and HK.3. Comparing to XBB and BA.2, BA.2.86 carries more than 30 mutations in the spike (S) protein, indicating a high potential for immune evasion.1-4BA.2.86 has evolved and its descendant, JN.1 (BA.2.86.1.1), emerged in late 2023. JN.1 harbors S:L455S and three mutations in non-S proteins (Figure 1A). S:L455S is a hallmark mutation of JN.1: we have recently shown that HK.3 and other "FLip" variants carry S:L455F, which contributes to increased transmissibility and immune escape ability compared to the parental EG.5.1 variant.5Here, we investigated the virological properties of JN.1. We estimated the relative effective reproductive number (Re) of JN.1 using genomic surveillance data from France, the United Kingdom and Spain, where >25 sequences of JN.1 have been reported, using a Bayesian multinomial logistic model (Figures 1B, 1C, Table S3).6The Re of JN.1 in these three countries was higher than that of BA.2.86.1 and HK.3, one of the XBB lineages with the highest growth advantage at the end of November 2023 (Figure 1B).5These results suggest that JN.1 may soon become the dominant lineage worldwide.
Indeed, by the end of November 2023, JN.1 has already overtaken HK.3 in France and Spain (Figure 1C). The in vitro ACE2 binding assay7 showed that the dissociation constant (KD) value of the JN.1 receptor-binding domain (RBD) is significantly higher than that of the BA.2.86 RBD (Figure 1D), suggesting that S:L455S decreases the binding affinity to the human ACE2 receptor.In contrast, the pseudovirus assay showed that the infectivity of JN.1 is significantly higher than that of BA.2.86 (Figure 1E). This discrepancy (Figures 1D, 1E) would be due to the difference between monomeric RBD and trimerized whole S protein (see also Supplementary Discussion).We then performed a neutralization assay using rodent sera infected with BA.2.86 or immunized with BA.2.86 S protein. In both cases, the 50% neutralization titer (NT50) against JN.1 was comparable to that against BA.2.86 (Figures 1F, 1G), suggesting that S:L455S does not affect the antigenicity of BA.2.86.On the other hand, the NT50 of breakthrough infection (BTI) sera with XBB.1.5 and EG.5.1 against JN.1 was significantly lower than that of HK.3 (2.6- to 3.1-fold) and BA.2.86 (3.8-fold) (Figures 1H, 1I). Furthermore, JN.1 shows robust resistance to monovalent XBB.1.5 vaccine sera compared to BA.2.86 (Figure 1J).Taken together, these results suggest that JN.1 is one of the most immune-evading variants to date. Our results suggest that S:L455S contributes to increased immune evasion, which partly explains the increased Re of JN.1
None of this speaks to the severity or presentation of JN.1 compared to XBB Omicron, only its virological `fitness'.
So far we've seen no evidence of increased morbidity or mortality from this new lineage.
On Saturday the Sato Lab twitter/X account posted a series of explanatory tweets, including the following post which raises concerns over the amount of protection offered by the updated COVID vaccine.
This, admittedly, appears to differ somewhat from other recent studies (see Preprint: XBB.1.5 Monovalent mRNA Vaccine Booster Elicits Robust Neutralizing Antibodies Against Emerging SARS-CoV-2 Variants) and the most recent assessment from the CDC.
Laboratory results don't always translate into real-world results, and so we'll simply have to wait for better data.
But even assuming reduced protection against breakthrough infection - the vaccine may still provide valuable benefits - including less severe acute infections and a lower chance of developing Long COVID.
While it is always possible that something even more transmissible, or immune evasive, will emerge to usurp it, right now the JN.1 SARS-CoV-2 variant appears destined to ring in the new year in a big way.
