tetano
Editor, Senior Moderator
Front Immunol
. 2026 Aug 20:17:1846973.
doi: 10.3389/fimmu.2026.1846973. eCollection 2026.
Mukesh Kumar Jogi # 1 2 , Sristy Shikha # 1 , Pushpendra Singh # 3 , Devesh Sharma 4 , Shreyansh Shreyansh 5 , Prem Mishra 5 , Aiswariya Priyadarsini 6 , Aahamya Priyadarsini 6 , Deokrishna Kumar Choudhary 7 , Meenu Jain 8 , Ritu Sagar 1 , Anuj Kumar 1 9 , Robin Marwal 4 , Md Kausar Neyaz 4 , Dheeraj Dube Prakashchand 7 , Rakesh Gupta 4 , Shalini Singh 1 9 , Pramod Kumar 1 9
Affiliations Expand
The SARS-CoV-2 XBB variants have been proposed to evolve towards immune evasion against vaccination or natural infection, which may contribute to higher transmissibility. The XBB.1.16 independently emerged due to accumulation of two important substitutions, E180V and T478R in the spike protein. Its pseudoviral infectivity and evasion of humoral immunity were similar to XBB.1 and XBB.1.5. In March 2023, XBB.1.16 had outcompeted other dominant XBB variants in India, which indicate a potential growth advantage. Here, intra-host single nucleotide variations (iSNV) and mutations were screened in SARS-CoV-2 genomes in closely related individuals at two time points: at symptoms onset, and during recovery. The prominence of putative epistatic iSNVs (E180V, G184V, G252V, D253G, and P521S/T) in XBB.1.16 variants were detected during the recovery phase. E180V exhibits mutational constellations with the G252V and P521T in a subset of samples, and this pattern was also detected in contemporary SARS-CoV-2 genomes. Higher order protein structural predictions suggested that the putative epistatic interactions among E180V, G184V, and G252V, D253G may be associated with S protein folding and structural stability. This study involving genomics and computational analyses highlights the potential role of these putative epistatic interactions in immune evasion, which may have contributed to dominance of XBB variants.
Keywords: SARS-CoV2; epistasis; genomics; iSNVs; immune evasion.
. 2026 Aug 20:17:1846973.
doi: 10.3389/fimmu.2026.1846973. eCollection 2026.
The emergence of putative epistatic mutations and iSNVs in SARS-CoV-2 XBB.1.16 variants linked with alteration in immunogenic determinants
Mukesh Kumar Jogi # 1 2 , Sristy Shikha # 1 , Pushpendra Singh # 3 , Devesh Sharma 4 , Shreyansh Shreyansh 5 , Prem Mishra 5 , Aiswariya Priyadarsini 6 , Aahamya Priyadarsini 6 , Deokrishna Kumar Choudhary 7 , Meenu Jain 8 , Ritu Sagar 1 , Anuj Kumar 1 9 , Robin Marwal 4 , Md Kausar Neyaz 4 , Dheeraj Dube Prakashchand 7 , Rakesh Gupta 4 , Shalini Singh 1 9 , Pramod Kumar 1 9
Affiliations Expand
- PMID: 42694107
- PMCID: PMC13538099
- DOI: 10.3389/fimmu.2026.1846973
Abstract
The SARS-CoV-2 XBB variants have been proposed to evolve towards immune evasion against vaccination or natural infection, which may contribute to higher transmissibility. The XBB.1.16 independently emerged due to accumulation of two important substitutions, E180V and T478R in the spike protein. Its pseudoviral infectivity and evasion of humoral immunity were similar to XBB.1 and XBB.1.5. In March 2023, XBB.1.16 had outcompeted other dominant XBB variants in India, which indicate a potential growth advantage. Here, intra-host single nucleotide variations (iSNV) and mutations were screened in SARS-CoV-2 genomes in closely related individuals at two time points: at symptoms onset, and during recovery. The prominence of putative epistatic iSNVs (E180V, G184V, G252V, D253G, and P521S/T) in XBB.1.16 variants were detected during the recovery phase. E180V exhibits mutational constellations with the G252V and P521T in a subset of samples, and this pattern was also detected in contemporary SARS-CoV-2 genomes. Higher order protein structural predictions suggested that the putative epistatic interactions among E180V, G184V, and G252V, D253G may be associated with S protein folding and structural stability. This study involving genomics and computational analyses highlights the potential role of these putative epistatic interactions in immune evasion, which may have contributed to dominance of XBB variants.
Keywords: SARS-CoV2; epistasis; genomics; iSNVs; immune evasion.