Welcome to DU! The truly grassroots left-of-center political community where regular people, not algorithms, drive the discussions and set the standards. Join the community: Create a free account Support DU (and get rid of ads!): Become a Star Member Latest Breaking News Editorials & Other Articles General Discussion The DU Lounge All Forums Issue Forums Culture Forums Alliance Forums Region Forums Support Forums Help & Search

Science

Showing Original Post only (View all)

NNadir

(34,675 posts)
Thu Jan 12, 2023, 08:32 AM Jan 2023

Some pretty bad news on the XBB.1 Covid Variant. [View all]

My fully vaccinated wife has Covid and was pretty sick, although she seems to be improving. My son is also not feeling well. I have a slight cough.

This situation motivated me to look into the XBB.1.5 variant that seems to be circulating, which I suspect my wife has.

I accessed this paper this morning: Qian Wang, Sho Iketani, Zhiteng Li, Liyuan Liu, Yicheng Guo, Yiming Huang, Anthony D. Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam S. Lauring, Zizhang Sheng, Harris H. Wang, Aubree Gordon, Lihong Liu, David D. Ho, Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants, Cell, 2022, a corrected proof in press.

The paper is fully open sourced, anyone can read it, but I'll produce the opening paragraphs and a pretty depressing graphic from the paper as well.

The intro:

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to rage due to emergence of the Omicron variant and its descendant subvariants.1,2,3,4,5,6,7,8,9,10 Although the BA.5 subvariant is globally dominant at this time (Figure 1A), a diverse array of Omicron sublineages have arisen and are competing in the so-called “variant soup”.11 It has become apparent that four new subvariants are rapidly gaining ground on BA.5, raising the specter of yet another wave of infections in the coming months. BQ.1 and BQ.1.1 were first identified in Nigeria in early July and then expanded dramatically in Europe and North America, now accounting for 67%, 35%, and 47% of cases in France, the United Kingdom, and the United States, respectively (Figure 1A). XBB and XBB.1 were first identified in India in mid-August and quickly became predominant in India, Singapore, and other regions in Asia (Figure 1A). BQ.1 and BQ.1.1 evolved from BA.5, whereas XBB and XBB.1 resulted from a recombination between two BA.2 lineages, BJ.1 and BA.2.75 (Figure 1B). These two sublineages are continuing to evolve and diversify, with an ever-increasing complexity of spike mutations. However, the spike protein of the predominant BQ.1 subvariant harbors the K444T and N460K mutations in addition to those found in BA.5, with BQ.1.1 having an additional R346T mutation (Figures 1C and S1). Strikingly, the spike of the predominant XBB subvariant has 14 mutations in addition to those found in BA.2, including 5 in the N-terminal domain (NTD) and 9 in the receptor-binding domain (RBD), whereas XBB.1 has an additional G252V mutation (Figures 1C and S1). The rapid rise of these subvariants and their extensive array of spike mutations are reminiscent of the appearance of the first Omicron variant last year, thus raising concerns that they may further compromise the efficacy of current COVID-19 vaccines and monoclonal antibody (mAb) therapeutics. We now report findings that indicate that such concerns are, sadly, justified, especially so for the XBB and XBB.1 subvariants.


I added the bold.

The XBB virus has been fully sequenced, and the sites of the mutations are known. "K444T" refers to the substitution at the 444th residue in the spike protein of a threonine for a lysine. "N460K" refers to a substitution at the 460th residue of a lysine for an asparagine.

The following graphic shows the evolutionary history of variants of Covid:



The caption:

Figure 1. The rise of SARS-CoV-2 Omicron BQ.1, BQ.1.1, XBB, and XBB.1 subvariants

(A) Frequencies of Omicron subvariants from the Global Initiative on Sharing All Influenza Data (GISAID). Variants were designated according to their Pango dynamic lineage classification.12 Minor sublineages of each subvariant were grouped together with their parental variant. The values in the upper left corner of each box denote the cumulative number of sequences for all circulating viruses in the denoted time period.

(B) Unrooted phylogenetic tree of Omicron subvariants along with other main SARS-CoV-2 variants. The scale bar indicates the genetic distance.

(C) Key spike mutations found in XBB and XBB.1 in the background of BA.2 and in BQ.1 and BQ.1.1 in the background of BA.4/5. Del, deletion. The positions of these mutations on the spike trimer are shown in Figure S1.


This graphic shows the location of the mutations on the spike protein:



The caption:

Figure S1. Key spike mutations of BQ and XBB subvariants, related to Figure 1

(A and B) Key mutations of BQ.1 and BQ.1.1 in the context of BA.4/5 (A), and key mutations of XBB and XBB.1 in the context of BA.2 (B).

See also Figure 1.


And now for the real depressing graphic, showing the decreased neutralization capacity of antibodies:



The caption:

Figure 3. Resistance of Omicron subvariants to monoclonal antibody neutralization

(A) Footprints of NTD- and RBD-directed antibodies tested are outlined, and mutations within BQ.1, BQ.1.1, XBB, and XBB.1 are highlighted in red.

(B) The fold changes in neutralization IC50 values of BQ.1, BQ.1.1, XBB, XBB.1, and the individual mutants compared with BA.4/5 or BA.2, with resistance colored red and sensitization colored green. The raw IC50 values are shown in Figure S2.

See also Figure S2.


The good news, as I understand it, is that this variant does not seem as severe in terms of illness, and there is some protective effect with vaccination status, although how much is on clear.

The authors make the comforting statement I will put in bold:

Therefore, it is alarming that these newly emerged subvariants could further compromise the efficacy of current COVID-19 vaccines and result in a surge of breakthrough infections as well as re-infections. However, it is important to emphasize that although infections may now be more likely, COVID-19 vaccines have been shown to remain effective at preventing hospitalization and severe disease even against Omicron35,36,37,38 as well as possibly reducing the risk of post-acute sequelae of COVID-19 (PASC or long COVID).39,40,41


But it's also clear from my perspective, we're going to need another vaccine. We do have the machinery to do this now, so that is also good news.

The authors conclusions:

Lastly, we found that the spikes of BQ and XBB subvariants have similar binding affinities to hACE2 as the spikes of their predecessors (Figure 5), suggesting that the recently observed growth advantage for these novel subvariants is likely due to some other factors. Foremost may be their extreme antibody evasion properties, especially considering the extensive herd immunity built up in the population over the last three years from infections and vaccinations. BQ.1, BQ.1.1, XBB, and XBB.1 subvariants exhibit far greater antibody resistance than earlier variants, and they may fuel yet another surge of COVID-19 infections. We have collectively chased after SARS-CoV-2 variants for over two years, and yet, the virus continues to evolve and evade. This continuing challenge highlights the importance of developing vaccine and mAb approaches that protect broadly and anticipate the antigenic trajectory of SARS-CoV-2.


I have heard, peripherally, I will now look into it more deeply, that a "master" vaccine that may work against all or most corona viruses, including those responsible for the common cold, is under development.

My wife is suffering from nausea and diarrhea, before taking Paxlovid, and these are side effects of the drug, so she's reluctant to take it.

I'm going to work from home until it becomes clear what the situation is.

The bottom line: Be careful, keep your Covid supplies handy.


Update: My son just tested positive. The historical test kits seem to respond to this variant. He's sick, but not as sick as my wife.
50 replies = new reply since forum marked as read
Highlight: NoneDon't highlight anything 5 newestHighlight 5 most recent replies
my understanding is that they are working on vaccines and treatments lapfog_1 Jan 2023 #1
Yes, I have heard that peripherally, but have not looked into it any detail. I will though. n/t. NNadir Jan 2023 #2
Yes universal are in pipeline IbogaProject Jan 2023 #26
Yes, have read a bit about it. It would work on the spine that holds the spikes. PortTack Jan 2023 #23
Grrrrr. lark Jan 2023 #3
My wife and I are nearly over this NewHendoLib Jan 2023 #4
How long were you sick? I didn't realize that Paxlovid was a combination drug, with the old... NNadir Jan 2023 #38
Hi there! read on below NewHendoLib Jan 2023 #40
Sorry to hear you and your wife have been mnhtnbb Jan 2023 #47
We've been masking constantly when we're out/about. woodsprite Jan 2023 #5
Florida should never be a destination SuperCoder Jan 2023 #14
That's why I'm just assuming he's coming back with it. woodsprite Jan 2023 #16
Yes, with all of Ron DeFuckwit's lying KS Toronado Jan 2023 #20
I recently cancelled a trip to FL planned mnhtnbb Jan 2023 #48
Day 14?! That's discouraging! deurbano Jan 2023 #18
get a bunch of hepa filters for the house to help nt orleans Jan 2023 #39
I hope that your family members begin to feel better soon. TexasTowelie Jan 2023 #6
That could be where I heard it, from your post. I didn't look in the primary literature though. NNadir Jan 2023 #7
That's odd, I was able to open it without any difficulty. TexasTowelie Jan 2023 #10
It's OK. They mentioned the name of Kayvon Modjarrad in the abstract of the article. NNadir Jan 2023 #13
Thx for the info SheltieLover Jan 2023 #8
Sorry your son is sick, but thank him for at least starting to answer the question re: efficacy of hlthe2b Jan 2023 #9
Thank you for this Abigail_Adams Jan 2023 #11
Thank you for posting this. hay rick Jan 2023 #12
My wife just tested positive yesterday. ificandream Jan 2023 #15
Wishing the best for you and your family, and thanks for the update. nt eppur_se_muova Jan 2023 #17
My wife went from 0 to I'll on 11/27 after we visited.... jaxexpat Jan 2023 #19
Thank you for researching and sharing with us. MLAA Jan 2023 #21
I'm so sorry this is happening to you. Silver Gaia Jan 2023 #22
Answers to your questions: NNadir Jan 2023 #25
I'm so glad your wife is doing better! Silver Gaia Jan 2023 #36
I've been masking. ananda Jan 2023 #24
I hope you are all able to come through this without long-term Covid issues. Bluethroughu Jan 2023 #27
Dogs can get it Farmer-Rick Jan 2023 #34
Thank you. Stay well. I hope everyone recovers quickly. Wicked Blue Jan 2023 #28
Thank you for the very informative post & best wishes HuskyOffset Jan 2023 #29
American made N95 masks are cheap and widely available now IronLionZion Jan 2023 #30
NYC isn't very masked anymore IbogaProject Jan 2023 #32
Same with DC, but I still wear a mask on transit, airports, and crowded indoor spaces IronLionZion Jan 2023 #33
it's not just MAGAts refusing to mask Skittles Jan 2023 #45
I hope your family feels better soon. herding cats Jan 2023 #31
Great post with good information LetMyPeopleVote Jan 2023 #35
best wishes for you and your family getting through this quickly nt orleans Jan 2023 #37
Markedly more contagious but less virulent is what I've been reading Warpy Jan 2023 #41
Thank you for the detailed info! It makes me feel justified in continuing to mask up in public and LaMouffette Jan 2023 #42
We must keep the economy open at all costs and pretend that vaccination alone is sufficient Orrex Jan 2023 #43
All the best to you. Are we supposed to get the booster again? We had ours at the end of September... Hekate Jan 2023 #44
I'm not a physician, however, as I read this, the booster would be ineffective. A new vaccine... NNadir Jan 2023 #50
Thank You for posting This❗My son also contracted a case of Covid Duppers Jan 2023 #46
Thanks for posting this. mnhtnbb Jan 2023 #49
Latest Discussions»Culture Forums»Science»Some pretty bad news on t...»Reply #0