Altered host protease determinants for SARS-CoV-2 Omicron

Abstract

Successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requires proteolytic cleavage of the viral spike protein. While the role of the host transmembrane protease serine 2 in SARS-CoV-2 infection is widely recognized, the involvement of other proteases capable of facilitating SARS-CoV-2 entry remains incompletely explored. Here, we show that multiple members from the membrane-type matrix metalloproteinase (MT-MMP) and a disintegrin and metalloproteinase families can mediate SARS-CoV-2 entry. Inhibition of MT-MMPs significantly reduces SARS-CoV-2 replication in vitro and in vivo. Mechanistically, we show that MT-MMPs can cleave SARS-CoV-2 spike and angiotensin-converting enzyme 2 and facilitate spike-mediated fusion. We further demonstrate that Omicron BA.1 has an increased efficiency on MT-MMP usage, while an altered efficiency on transmembrane serine protease usage for virus entry compared with that of ancestral SARS-CoV-2. These results reveal additional protease determinants for SARS-CoV-2 infection and enhance our understanding on the biology of coronavirus entry.

Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue

“…The TMPRSS2-independence of Omicron infection has been reported by multiple groups, and as a result, it has been inferred that Omicron uses an endosomal, cathepsin-dependent route to enter human cells 31,32,36 . However, a recently described metalloproteinase-mediated entry pathway for SARS-CoV-2 that may enable virus fusion at the plasma membrane 11,45 prompted us to test the effect of incyclinide, a broad-spectrum inhibitor of MMP and ADAM metalloproteinases. WA1, Delta, and BA.1 infections were reduced by incyclinide treatment in primary ALI, but BA.1 was particularly sensitive (inhibited by 27-fold compared to 4-fold inhibition of WA1 and 5-fold inhibition of Delta) (Figure 3A) .…”

“…In general, it is thought that factors aiding virus attachment enable subsequent ACE2 binding. Engagement of ACE2 alters Spike conformation and facilitates its processing by cellular proteases, such as serine transmembrane proteases like TMPRSS2, matrix metalloproteinases (MMPs), or a disintegrin and metalloproteinases (ADAMs) 2,[10][11][12][13][14] . Protease cleavage enables Spike to trigger fusion between viral and cellular membranes to complete cellular entry 15 .…”

“…It has also been reported that Omicron utilizes a distinct cellular entry pathway compared to ancestral or early forms of SARS-CoV-2 [28][29][30][31][32] . Specifically, the proteolytic activation of Omicron Spike is less dependent on TMPRSS2 but may be more dependent on cathepsin activity in endolysosomes or MMP activity at the plasma membrane 11 . However, the precise characterization of the entry pathways used by Omicron in physiologically relevant primary cells is lacking, and whether they are sensitive to cell-intrinsic antiviral barriers has not been determined.…”

Omicsynin B4 potently blocks coronavirus infection by inhibiting host proteases cathepsin L and TMPRSS2

“…Meanwhile, other host proteases may also be involved in cleavage activation of SARS-CoV-2 spike. Recent studies have identified several metalloproteinases as well as thrombin as redundant routes to enhance SARS-CoV-2 infection by promoting viral entry ( Chan et al, 2023 ; Jocher et al, 2022 ; Kastenhuber et al, 2022 ; Yamamoto et al, 2022 ). Therefore, effectively targeting additional host proteases that facilitate the infection simultaneously should be considered to achieve a synergistic potentiation of antiviral activity.…”

Type‐II IFN inhibits SARS‐CoV‐2 replication in human lung epithelial cells and ex vivo human lung tissues through indoleamine 2,3‐dioxygenase‐mediated pathways

“…SARS‐CoV‐1 GZ50 (GenBank accession number: AY304495) was an archived clinical isolate at the Department of Microbiology, The University of Hong Kong. All experiments involving live SARS‐CoV‐2 or SARS‐CoV‐1 followed the approved standard operating procedures of the Biosafety Level 3 facility at Department of Hong Kong, The University of Hong Kong 5,25 …”