Potentially Beneficial Non-Spike Mutations in SARS-CoV-2 Variants

I wanted to post notes on potentially beneficial non-spike mutations in #SARSCoV2 variants XBB.1.16 & XBB.1.9.1, two of fastest growing variants.

These are from estimates of effects of mutations to all SARS-CoV-2 proteins from @richardneher & myself https://t.co/70y9VXAoES

— Bloom Lab (@jbloom_lab) June 5, 2023

Both XBB.1.16 & XBB.1.9.1 have I5T mutation in ORF9b innate-immune antagonist accessory protein. XBB.1.16 also has N55S in this protein.

According to our estimates (https://t.co/Zod11UMfBi), I5T in ORF9b is beneficial while N55S is roughly neutral pic.twitter.com/psZwX9sgII

— Bloom Lab (@jbloom_lab) June 5, 2023

XBB.1.9.1 has the T35I mutation in nsp9 (equivalent to T4175I in ORF1a).

According to our estimates (https://t.co/6yxpgmN0Qm), T35I in nsp9 is beneficial. pic.twitter.com/nAqmu2WVIn

— Bloom Lab (@jbloom_lab) June 5, 2023

XBB.1.16 has L260F mutation in nsp6 (equivalent to L3829F in ORF1a).

According to our estimates (https://t.co/CzufaawNvo), L260F in nsp6 is beneficial

This mutation also likely adaptive in mink (eg, this paper by @seifert_steph & Vincent Munster et al https://t.co/G0wo2wMXzg) pic.twitter.com/GBQQva9mAG

— Bloom Lab (@jbloom_lab) June 5, 2023

According to our fitness estimates, the other non-spike mutations in these variants (D222N in nsp14 and G1001S in nsp3) are likely roughly neutral.

— Bloom Lab (@jbloom_lab) June 5, 2023