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      Fast evolution of SARS-CoV-2 BA.2·86 to JN.1 under heavy immune pressure

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          ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5

          SARS-CoV-2 subvariants BQ.1.1 and XBB.1 have been circulating globally with superior growth advantages over most omicron mutants (appendix p 5). However, XBB.1.5, a subvariant of the recombinant mutant XBB, has shown a substantial growth advantage compared with BQ.1.1 and XBB.1. Because of its enhanced transmissibility, XBB.1.5 has rapidly become the dominant SARS-CoV-2 strain in the USA and is highly likely to cause the next global wave of COVID-19 (appendix p 5). 1 XBB and XBB.1 has already been shown to be extremely evasive against the neutralisation of plasma and serum from vaccinated or convalescent individuals and monoclonal antibodies (mAbs), with a greater evasive ability than the BQ.1.1 variant.2, 3, 4, 5 Compared with XBB.1, XBB.1.5 carries a Ser486Pro mutation on the spike protein, a rare two nucleotide substitution compared with the ancestral strain (appendix p 5). The mechanism behind the rapid transmission of XBB.1.5, especially the effect of Ser486Pro, requires immediate investigation. We used vesicular stomatitis virus-based pseudovirus neutralisation assays to evaluate the neutralisation titres against XBB.1.5 of convalescent plasma from individuals who had received three doses of CoronaVac (Sinovac) before BA.1 (n=50), BA.5 (n=36), or BF.7 (n=30)breakthrough infection. A cohort of patients with convalescence from BA.5 breakthrough infection who had received at least two doses of BNT162b2 (Pfizer-BioNtech) or mRNA-1273 (Moderna) is also included in the analysis (n=10). Human ACE2 (hACE2)-binding affinity of XBB.1.5 receptor-binding domain was compared with that of XBB.1, BQ.1.1, and BA.2.75 using surface plasmon resonance. Plasma samples associated with CoronaVac were collected on average 27 days (SD 8) after hospital discharge (appendix pp 7–8). Plasma samples associated with the mRNA vaccine were collected within 2–3 weeks after hospital admission (appendix pp 7–8). The absence of BQ.1.1 breakthrough infection in individuals who were convalescent is a limitation of the ability of this study to estimate the scale of immune evasion of XBB.1.5 for this group. Plasma samples from individuals who had received three doses of CoronaVac and had a BA.1, BA.5, or BF.7 breakthrough infection showed a substantial decrease in plasma 50% neutralisation titre (NT50) against XBB.1 and XBB.1.5 compared with that against B.1 (ASP614Gly) variant (figure A ). Plasma from patients who received CoronaVac and had a BA.5 breakthrough infection showed a 44-times lower NT50 against XBB.1 compared with the NT50 after B.1. The decrease was 40-times lower for XBB.1.5. For patients who received CoronaVac and had a BF.7 breakthrough infection, the plasma NT50 against XBB.1 was 31-times lower and XBB.1.5 was 27-times lower compared with the NT50 for B.1. A similar trend was also observed in plasma from patients who received two doses of an mRNA vaccine and had a BA.5 breakthrough infection and patients who received CoronaVac and had a BA.1 breakthrough infection. These findings suggest that Pro486 is also a strong neutralising antibody evading mutation, and that the humoral immune escape ability of XBB.1.5 is similar to that of XBB.1. Figure Comparison of antibody evasiveness and hACE2 binding affinity of XBB.1 and XBB.1.5 (A) NT50 against SARS-CoV-2 B.1 (Asp614Gly), XBB.1, and XBB.1.5 pseudovirus using plasma from patients with BA.1 (n=50), BA.5 (n=36), or BF.7 (n=30) breakthrough infection convalescents who had received three doses of CoronaVac, and those with a BA.5 breakthrough infection convalescents who had received three or four vaccinations, including at least two doses of mRNA vaccines (BNT162b2 or mRNA-1273; n=10). p values were calculated using two-tailed Wilcoxon signed rank tests. (B) Pseudovirus IC50 of therapeutic neutralising antibodies. (C) Surface plasmon resonance sensorgrams measuring the hACE2-binding affinity of SARS-CoV-2 BQ.1.1, XBB and XBB.1, and XBB.1.5 receptor-binding domain. Surface plasmon resonance data were fitted to a 1:1 binding model using Biacore 8K Evaluation Software (version 3.0.12; Cytiva, Uppsala, Sweden). All neutralisation assays were done in at least two independent experiments. hACE2=human ACE2. IC50=50% inhibition concentration. ka=fitted association rate constant. kd=fitted dissociation rate constant. KD=dissociation equilibrium constant. *10 000 was the upper limit of detect; these analyses gave values more than 10 000. Compared with XBB.1, XBB.1.5 had similar evasion against therapeutic mAbs (figure B); Evusheld and bebtelovimab did not neutralise XBB.1.5 pseudovirus. Sotrovimab is still active but weak against XBB.1.5. Another BA.5-effective mAb, SA58, is escaped by both XBB.1 and XBB.1.5. However, SA55 remains highly effective against XBB.1.5.2, 6 Previous deep mutational scanning studies have shown that Pro486 might enhance the affinity to hACE2 compared with Ser486. 7 The binding affinity of the XBB.1.5 receptor-binding domain to hACE2 (dissociation constant [KD] 3·4 nM) was similar to that of BA.2.75 (KD 1·8 nM) and much stronger than that of XBB.1 (KD 19 nM) and BQ.1.1 (KD 8.1 nM; figure C; appendix p 6). These results suggest that the probable reason for the significant growth advantage of XBB.1.5 over XBB.1 is that it gained substantially higher ACE2 binding affinity through the Ser486Pro mutation, while retaining an extremely high immune evasion capability. With stronger immune escape ability but weaker ACE2 binding affinity than BQ.1.1, XBB and XBB.1 have only prevailed in a few countries, such as Singapore and India, since September, 2022. Whereas BQ.1.1 has quickly become the dominant global strain. Because of its enhanced hACE2-binding affinity and similar ability to evade the immune system, the prevalence of XBB.1.5 shows that receptor-binding affinity will substantially affect the transmissibility of the strain. The underlying mechanism needs to be investigated. Also, whether the increased receptor-binding affinity would cause a difference in pathogenicity compared with XBB is unclear and requires immediate research. 8 Moreover, the strong affinity to hACE2 might allow XBB.1.5 to acquire additional immune-escape mutations, similar to the evolution trend of BA.2.75, when met with substantial immune pressure. 9 Therefore, the circulation of XBB.1.5 needs to be closely monitored, and the development of effective neutralising antibodies and vaccines against XBB.1.5 is urgently needed. YC is a cofounder of Singlomics Biopharmaceuticals and inventor of provisional patents associated with SARS-CoV-2 neutralising antibodies, including SA55 and SA58. All other authors declare no competing interests. CY and WS contributed equally.
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            Potent cross-reactive antibodies following Omicron breakthrough in vaccinees

            Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1 and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site, however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focussed in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains and many show broad reactivity with variants of concern.
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              Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75

              Recently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a growth advantage over circulating BA.2.38, BA.2.76 and BA.5 in India. However, the underlying mechanisms for enhanced infectivity, especially compared to BA.5, remain unclear. Here we show BA.2.75 exhibits substantially higher affinity for host receptor ACE2 than BA.5 and other variants. Structural analyses of BA.2.75 Spike shows its decreased thermostability and increased frequency of the receptor binding domain (RBD) in the “up” conformation under acidic conditions, suggesting enhanced low-pH-endosomal cell entry. Relative to BA.4/BA.5, BA.2.75 exhibits reduced evasion of humoral immunity from BA.1/BA.2 breakthrough-infection convalescent plasma, but greater evasion of Delta breakthrough-infection convalescent plasma. BA.5 breakthrough infection plasma also exhibits weaker neutralization against BA.2.75 than BA.5, mainly due to BA.2.75’s distinct neutralizing antibody escape pattern. Antibody therapeutics Evusheld and Bebtelovimab remain effective against BA.2.75. These results suggest BA.2.75 may prevail after BA.4/BA.5, and its increased receptor-binding capability could support further immune-evasive mutations.
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                Author and article information

                Journal
                The Lancet Infectious Diseases
                The Lancet Infectious Diseases
                Elsevier BV
                14733099
                December 2023
                December 2023
                Article
                10.1016/S1473-3099(23)00744-2
                38109919
                73be71b8-5b10-4ccd-8e97-756442a5c8b4
                © 2023

                https://www.elsevier.com/tdm/userlicense/1.0/

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