Cao博士の連ツイ。
備忘録として。
Sharing our latest work on SARS-CoV-2 immune imprinting.
Main finding:
Repeated Omicron infection/boosting alleviates WT vaccine-induced immune imprinting by generating many potent XBB-neutralizing Omicron-specific antibodies that target new RBD epitopes.https://t.co/cqWNisbp3u— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
First, let's revisit the major concept of SARS-CoV-2 immune imprinting:
When we experience a variant-vaccine boosting or breakthrough infection, our immune system will mainly recall WT vaccination-induced memory B cells and rarely produces variant-specific antibodies. 2/n— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
The problem caused by this concept is that when the boosting/infecting variant has a long antigenic distance to WT, the majority of memory B cells recalled will be those that target conserved and non-neutralizing epitopes, which will greatly hinder the antibody response. 3/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
As a result, when the antigenic distance between the stimulating variant and WT increases (BA.1->BA.5->XBB), the overall serum neutralization response will substantially decrease, as shown in our data from WT-primed mice models and human cohorts. 4/n pic.twitter.com/oO3AZdmTvh
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Increasing the interval between the WT priming and Omicron boosters or using mRNA boosters (higher immunogenicity) didn't help much to alleviate immune imprinting either unless you use a 10μg mRNA booster; however, that relatively high dosage is impractical in the real world. 5/n pic.twitter.com/eeR17vs8Ew
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
The above data showed the impact of immune imprinting on single Omicron-boosters using variants with long antigenic distances to WT. Nevertheless, we found repeated Omicron boosting significantly ameliorates the situation, especially with prolonged intervals between boosters. 6/n pic.twitter.com/4akVTfurtp
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
However, we found that two Omicron-boosters after WT priming (4 doses) still generated lower titers compared to corresponding Omicron priming (2 doses) against the boosting variant, suggesting immune imprinting isn't entirely overcome and still limits antibody response. 7/n pic.twitter.com/dm8IsuTmFr
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
One additional interesting observation is that XBB vaccines demonstrated lower immunogenicity compared to BA.5 and BQ.1.1 in mice. We have confirmed this observation with multiple vaccine manufacturers. 8/n pic.twitter.com/rEMZ3DB1Of
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Is our observation in mice applicable to humans? To verify this, we followed individuals with BA.1 breakthrough infections (BTIs) over a year and found that indeed repeated Omicron infections can generate much higher titers across Omicron variants, including XBB.1.5. 9/n pic.twitter.com/95qsQMsfkX
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
This is also validated in BA.2 BTI cohorts, indicating repeated Omicron infections could alleviate immune imprinting. However, similar to mice, people who got repeated Omicron infections without WT vaccination still generated the highest neutralizing titers across Omicron. 10/n pic.twitter.com/gcj1sIKXEr
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Compared to one-time Omicron breakthrough infections, repeated Omicron infections generated significantly higher neutralization responses toward circulating SARS-CoV-2 variants, including XBB.1.5, XBB.1.16, and XBB.1.5+F456L, in both plasma and nasal mucosa. 11/n pic.twitter.com/Gx45sWxqpD
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Using FACS, we saw an enriched proportion of RBD-binding Omicron-specific memory B cells in cohorts that experienced long-period maturation after BA.1/BA.2 BTI or repeated Omicron infections, which is very different compared to single Omicron BTIs. 12/n pic.twitter.com/DrvudRrteC
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
We also isolated those RBD-binding B cells and expressed their encoding antibodies. Indeed, an increase in the proportion and maturation of Omicron-specific antibodies can be observed in repeated Omicron infection cohorts, which explains the alleviation of immune imprinting. 13/n pic.twitter.com/a79VkSEKLK
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
To analyze whether new RBD epitopes are introduced by these Omicron-specific mAbs, we determined their escaping mutation profiles through deep mutation scanning (DMS) based on BA.5-backbone (can't bind WT RBD) alongside previously isolated BA.5-binding mAbs (1350 in total). 14/n pic.twitter.com/6WjfzUZImH
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
By unsupervised clustering based on the DMS data, we identified some novel RBD epitopes that mainly comprised Omicron-specific mAbs, which we defined as Group A2, D3, D4, and F3. Their epitopes are centered around Omicron mutations N501Y, Y505H, N440K & Q498R. 15/n pic.twitter.com/HZbX4VN1my
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Omicron-specific mAbs in A2, D3, D4 and F3 are enriched with highly potent neutralizing mAbs against BQ.1.1 and XBB.1.5. Notably, most mAbs in F3 here do not cross-react with WT, different from the rare sarbecovirus-neutralizing mAbs in F3 described previously, such as SA55. 16/n pic.twitter.com/mpZ3030hKV
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Importantly, consistent with B cell FACS data, single Omicron BTI induces >50% mAbs targeting non or weakly-neutralizing epitopes, while repeated Omicron infection induces only ~20% mAbs targeting such epitopes, indicating striking alleviation of immune imprinting. 17/n pic.twitter.com/8uPKOU8TFc
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Similar to our previous evolution predicting approach, based on the new DMS data, we integratively evaluated the preference of each mutation, considering their impacts on NAb escape, ACE2 binding, and codon constraints and calculated a preference score for RBD mutations. 18/n pic.twitter.com/OyXKnh7ERW
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Here's what the result looks like when inferring the evolution trend for XBB.1.5 RBD only considering mAbs from Omicron BA.5/BF.7 single BTI only. Significant hotspots are R403, N405, N417, Y453, L455, F456, and H505. 403K, 456L, and 453F have already appeared on XBB.1.5. 19/n pic.twitter.com/SyHdr9dC8J
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
With NAbs from repeated Omicron infections included, scores of N439, K440, K444, and P445 become higher, corresponding to Group D3 and D4, which are consistent with the enriched epitope distributions of mAbs from each cohort. 445S has started appearing on XBB lineages. 20/n pic.twitter.com/Hy9a8viwEt
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Notably, N405D and N417K reversions should hardly appear due to the potential recovery of previously escaped NAbs. However, K440N and H505Y reversions might appear since the mutations aren't really that immune evasive, so the reversions won't cause noticeable NAb recovery. 21/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
K478X is also not identified here due to the low level of 478-sensitive mAbs in our cohort. It's possible that Delta-imprinted convalescents with reinfections generate abundant K478X-sensitive mAbs, as Delta carries T478K. That's why K478X is mostly observed in India. 22/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
It's critical to test how these RBD hotspots could combine to achieve max immune evasion without losing affinity to ACE2. After careful consideration, besides the emerging K478R/F456L, we selected 7 additional mutations and sequentially added them to XBB.1.5 pseudovirus. 23/n pic.twitter.com/4Mr3XpH1LB
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
The 7 mutations are selected from a larger set of mutation candidates considering their impacts on hACE2-binding affinity as determined by surface plasmon resonance (SPR) and @jbloom_lab's DMS data. Y453F and R403K were chosen to maintain high ACE2 binding. 24/n pic.twitter.com/gIsZ0nu2Mo
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
…as well as their NAb escaping capability, based on the neutralization test of 131 potent XBB.1.5-effective NAbs from 8 epitope groups. F456L, H505Y, K444T, K440N, A484P & N405K are strong mAb-evading mutations that combine together could escape the majority of the panel. 25/n pic.twitter.com/6XprIqdzsS
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
As expected, XBB.1.5-S7 significantly escapes plasma from all tested cohorts, with 505Y&440N contributing mostly. Notably, reinfections with prior BA.1 or BA.2 BTI results in distinct patterns of evasion. 26/n pic.twitter.com/UjUHKSnpzr
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Indeed, mAbs from BA.1 BTI+BA.5 reinfection elicit more D3 mAbs that are weak to 444T/440N, while BA.2 BTI+BA.5 reinfection elicit more F3 and A2 mAbs that are weak to H505Y. This indicates Omicron BTI history also introduces new Omicron-based imprinting. 27/n pic.twitter.com/90gDaQ8kNZ
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Notably, K440N and H505Y reversions will not cause substantial recovery of neutralization of WT-reactive NAbs, as verified by testing plasma from BA.5/BF.7 single BTI. 28/n pic.twitter.com/bTNqVnq3Kt
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
In sum, we demonstrated that matured Omicron-specific mAbs are critical to the alleviation of WT vaccination-induced immune imprinting, and repeated Omicron stimulation would generate a high proportion of them. 29/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
These Omicron-specific NAbs target new RBD epitopes compared to WT-induced mAbs and exhibit potent activity across Omicron lineages, including XBB.1.5. They will soon become the major viral immune pressure contributor, and new mutations may emerge as we have predicted. 30/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
Our findings also suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who haven't been exposed to Omicron yet should receive two updated vaccine boosters. 31/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
The updated BA.5-based DMS data, analyzed mainly by @jianfcpku, will be shared via @jbloom_lab's online calculator very soon for people to play with. 32/n
— Yunlong Richard Cao (@yunlong_cao) May 3, 2023
◆Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting【bioRxiv 2023年5月3日】
Abstract
The continuous emergence of highly immune evasive SARS-CoV-2 variants, like XBB.1.5 and XBB.1.16, highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by wildtype (WT)-based vaccination would compromise the antibody response to Omicron-based boosters. Vaccination strategies that can counter immune imprinting are critically needed. In this study, we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. By isolating 781 RBD-targeting mAbs from repeated Omicron infection cohorts, we revealed that double Omicron exposure alleviates immune imprinting by generating a large proportion of highly matured and potent Omicron-specific antibodies. Importantly, epitope characterization using deep mutational scanning (DMS) showed that these Omicron-specific antibodies target distinct RBD epitopes compared to WT-induced antibodies, and the bias towards non-neutralizing epitopes observed in single Omicron exposures due to imprinting was largely restored after repeated Omicron stimulation, together leading to a substantial neutralizing epitope shift. Based on the DMS profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated the combinations of these mutations could further boost XBB.1.5’s immune-evasion capability while maintaining high ACE2 binding affinity. Our findings suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who haven’t been exposed to Omicron yet should receive two updated vaccine boosters.