TMEM106B mediates ACE2-independent replication of the SARS-CoV-2 SE484D variant in airway-derived cell models
12 affiliations
- 1Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- 2Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- 3Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- 4Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- 5Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- 6Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- 7Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- 8Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- 9Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO USA.
- 10Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA.
- 11Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, USA
- 12Institute for Informatics, Data Science & Biostatistics, Washington University School of Medicine, St. Louis, MO, USA.
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause significant respiratory disease, particularly in vulnerable populations. Although ACE2 is the primary receptor for viral entry, previous studies have identified a naturally occurring, ACE2-independent entry pathway that depends on cell surface heparan sulfates and the E484D substitution within the receptor-binding domain of Spike (S). In this study, we expand the panel of airway-derived cell lines that support ACE2-independent, S-E484D-dependent entry and identify the host lysosomal transmembrane protein TMEM106B as the alternative receptor for infection. Specifically, we show that knockout of TMEM106B completely abolishes infection by SARS-CoV-2 SE484D in NCI-H522 and NCI-H661 cells. Ectopic expression of the luminal C-terminal domain (CTD) of TMEM106B-either alone or redirected to the plasma membrane - is sufficient to enable viral entry largely independent of cell surface heparan sulfates in non-permissive cells. We show that S-E484D is required for TMEM106B utilization, whereas other Variants of Concern substitutions at S-E484 are unable to mediate entry. Fc-TMEM106B-CTD fusion protein binds to a chimeric VSV-SARS-CoV-2 SE484D with a higher affinity than WT virus and blocks infection by SARS-CoV-2 SE484D, supporting a direct interaction between S-E484D and TMEM106B-CTD. Serial passaging experiments with VSV-SARS-CoV-2 SE484D identify a V951A mutation within the heptad repeat 1 region that enhances viral spread and fusogenicity in the ACE2-independent cell models. Together, these findings demonstrate that TMEM106B is a key mediator of a naturally occurring ACE2-independent pathway in multiple airway-derived cell lines and suggest that variation in the S protein can expand receptor usage by SARS-CoV-2.
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BibTeX
@misc{xia2026tmem106b,
title = {{TMEM106B mediates ACE2-independent replication of the SARS-CoV-2 SE484D variant in airway-derived cell models}},
author = {Ming Xia and Qibo Wang and Maritza Puray-Chavez and Kyle LaPak and Zhuoming Liu and Sathvik Palakurty and Paul Rothlauf and Sean Hui and Natalie Stegman and Marjorie Cornejo Pontelli and Jacob Marsh and Anayat Bhat and Celeste M. Karch and Daved H. Fremont and Ramon Lorenzo-Redondo and Michael S. Diamond and Sean P.J. Whelan and Michael B. Major and Dennis Goldfarb and Sebla B. Kutluay},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.03.14.711762},
url = {https://doi.org/10.64898/2026.03.14.711762},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - TMEM106B mediates ACE2-independent replication of the SARS-CoV-2 SE484D variant in airway-derived cell models
AU - Ming Xia
AU - Qibo Wang
AU - Maritza Puray-Chavez
AU - Kyle LaPak
AU - Zhuoming Liu
AU - Sathvik Palakurty
AU - Paul Rothlauf
AU - Sean Hui
AU - Natalie Stegman
AU - Marjorie Cornejo Pontelli
AU - Jacob Marsh
AU - Anayat Bhat
AU - Celeste M. Karch
AU - Daved H. Fremont
AU - Ramon Lorenzo-Redondo
AU - Michael S. Diamond
AU - Sean P.J. Whelan
AU - Michael B. Major
AU - Dennis Goldfarb
AU - Sebla B. Kutluay
PY - 2026
DA - 2026/10/30
PB - bioRxiv
DO - 10.64898/2026.03.14.711762
UR - https://doi.org/10.64898/2026.03.14.711762
AB - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause significant respiratory disease, particularly in vulnerable populations. Although ACE2 is the primary receptor for viral entry, previous studies have identified a naturally occurring, ACE2-independent entry pathway that depends on cell surface heparan sulfates and the E484D substitution within the receptor-binding domain of Spike (S). In this study, we expand the panel of airway-derived cell lines that support ACE2-independent, S-E484D-dependent entry and identify the host lysosomal transmembrane protein TMEM106B as the alternative receptor for infection. Specifically, we show that knockout of TMEM106B completely abolishes infection by SARS-CoV-2 SE484D in NCI-H522 and NCI-H661 cells. Ectopic expression of the luminal C-terminal domain (CTD) of TMEM106B-either alone or redirected to the plasma membrane - is sufficient to enable viral entry largely independent of cell surface heparan sulfates in non-permissive cells. We show that S-E484D is required for TMEM106B utilization, whereas other Variants of Concern substitutions at S-E484 are unable to mediate entry. Fc-TMEM106B-CTD fusion protein binds to a chimeric VSV-SARS-CoV-2 SE484D with a higher affinity than WT virus and blocks infection by SARS-CoV-2 SE484D, supporting a direct interaction between S-E484D and TMEM106B-CTD. Serial passaging experiments with VSV-SARS-CoV-2 SE484D identify a V951A mutation within the heptad repeat 1 region that enhances viral spread and fusogenicity in the ACE2-independent cell models. Together, these findings demonstrate that TMEM106B is a key mediator of a naturally occurring ACE2-independent pathway in multiple airway-derived cell lines and suggest that variation in the S protein can expand receptor usage by SARS-CoV-2.
SN - 2692-8205
ER -