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Lipid biophysics and/or soft matter-inspired approach for controlling enveloped virus infectivity

Proven as a natural barrier against viral infection, pulmonary surfactant phospholipids have a biophysical and immunological role within the respiratory system, acting against microorganisms including viruses. Enveloped viruses have, in common, an outer bilayer membrane that forms the underlying structure for viral membrane proteins to function in an optimal way to ensure infectivity. Perturbating the membrane of viruses using exogenous lipids can be envisioned as a generic way to reduce their infectivity. In this context, the potential of exogenous lipids to be used against enveloped virus infectivity would be indicated by the resulting physical stress imposed to the viral membrane, and conical lipids, i.e. lyso-lipids, would be expected to generate stronger biophysical disturbances. We confirm that when treated with lyso-lipids the infectivity three strains of influenza virus (avian H2N3, equine H3N8 or pandemic human influenza H1N1) is reduced by up to 99% in a cell-based model. By contrast, lipids with a similar head group but two aliphatic chains were less effective (reducing infection by only 40–50%). This work opens a new path to merge concepts from different research fields, i.e. ‘soft matter physics' and virology.


Background
Respiratory virus infections pose a significant threat to human health. Influenza viruses continue to cause recurrent epidemic and pandemic infections and the more recently emerged SARS-CoV 2 has threatened to overwhelm healthcare systems globally causing widespread mortality and disease. The human body has many natural or innate defences against viruses including pulmonary surfactant. Surfactant is composed of lipids (approx. 85% of phospholipids, approx. 10% neutral lipids) and proteins (approx. 5%) [1]. The initial physiological role and clinical importance discovered for pulmonary surfactant was its involvement in avoiding the collapse of pulmonary alveolus during endexhalation [2]. More recently, pulmonary surfactant has been shown to participate in the innate host defence against respiratory pathogens [3][4][5]. Within the last decade, single lung surfactant phospholipids have been shown to protect, to some extent, cells from virus infectivity, including respiratory syncytial virus and influenza A [6][7][8][9]. Specific lipids found in the lung surfactant such as DPPG (di-palmitoyl-phosphatidylglycerol), POPG ( palmitoyl-oleoylphosphatidylglycerol) or DPPC (di-palmitoyl-phosphatidylcholine) have been shown to antagonize virus infectivity [5,7]. However, a full understanding of their mechanism of action remains elusive.
The initial stage of replication requires the influenza virus to enter cells based on the interaction between viral surface hemagglutinin protein (HA) and cellular sialic acids. The stereochemistry and collective structure of viral HA, neuraminidase (NA) and matrix protein 2 (M2) are central for sucessful infectivity [10,11].
These proteins are embedded within a bilayer lipid envelope derived from cell membrane on budding.
Although it is often routine to think pharmacologically in terms of drug-target or surfactant component-virus chemical interaction, in the context of lipid surfactant the amphipathic nature of lipids, namely their property of being structurally composed of hydrophobic and hydrophilic parts, needs to be considered carefully.
Indeed, lipids have the unique property to self-assemble physically and it is perhaps not surprising then that in the presence of surfactant lipids, membrane blebs appear on the viral envelope [5]. Following Laplace's Law, without any variation in the osmotic pressure difference between the inside and outside of the virus, the formation of nanometric membrane blebs suggests a direct change in the surface tension of the viral envelope linked to the inclusion of surfactant lipids. As a result, it is possible that lung surfactant lipids interact directly with the bilayer membrane of the viral envelope in turn destabilizing the collective structure of key viral envelope lipoproteins, i.e. HA, NA and M2, with a resulting impact on virus infectivity. Such an effect would not be unexpected, as in mammalian cells the mechanical perturbation of the bilayer membrane linked to the exogenous inclusion of amphipatic materials, e.g. phospholipids, has been shown to affect the function of ion channels [12], drug transporters [13], endocytosis [14] and exocytosis [15].
Therefore, surfactant lipids may provide a biophysics-based generic immunity against a plethora of inhaled pathogens provided they have an outer bilayer membrane. If the physical properties of surfactant lipids are essential to set up this generic immunity, the next question to ask is: can we optimize them, i.e. what lipid surfactant would be the most efficient?
The basic geometry or topology of lipids is essential. Lyso-lipids, i.e. single aliphatic chain lipids, have a tendency to form small unilayer structures due to their conical shape whereas lipids with two aliphatic chains form larger bilayer liposomes due to their cylindrical shape [16]. The changes in the surface pressure generated upon inclusion into a bilayer membrane are expected to be different as lyso-lipids tend to promote sharper curvature.
Given the set of observations [5,17,18], the aim of this work was therefore to connect a physical intuition regarding the physical properties of lipids to virology. The current study is focused on biology/virology rather physics/ modelling as its central purpose was to demonstrate, as a proof of concept, whether specific exogenous lipids reduce the infectivity of the influenza A viruses including H2N3, H1N1 and H3N8. Herein is shown that specific lipids are altering the virus morphology and inhibiting the binding of the virus to the host cell membrane with an impact on the expression of cellular cytokines (IL-8, TNF-α) and the expression of viral M-gene.

Impact of exogenous lipids on H2N3 topology and structure
Hypothesizing that lipids have a physical impact on viruses, this should be visible using transmission electron microscopy (EM). Figure 1a shows a typical H2N3 virus where the surface glycoproteins and spherical shape of the virus are clearly visible. However, upon incubation with different classes of lipids including LPG, DPPG, LPC and DPPC for 30 min at 37°C, the virus morphology changed drastically as a function of concentrations used. EM pictures show that virions are surrounded by lipid structures visible as white foci next to the  virus. Incubation of H2N3 with DPPC showed the least  change in virion appearance, but at the other extreme, LPG  treatment demonstrated rupture of the viral membrane  suggesting an irreversible process (figure 1b). In order to quantify the impact of phospholipids on H2N3, the virus aspect ratio and surface area were measured (figure 1c,d, respectively) to document the observed change from a spherical shape toward a more elongated morphology. Uninfected H3N3 viruses showed a value for the aspect ratio of approximately 1 confirming that H2N3 are natively round (spherical). However, following treatment with amphipathic compounds, the mean aspect ratio increased demonstrating that viruses became ellipsoidal in shape. The change in aspect ratio was more pronounced following treatment with lysolipids (LPG or LPC

Minimal impact of exogenous lipids on mammalian cells
Given the observation that viruses pre-treated with lipids demonstrated an irreversible impact on their morphologies, the direct impact of lipids on cells needed to be assessed as free lipids could also interact directly with cells used in virus infection experiments. Lipid solutions were prepared and incubated directly with Madin Darby canine kidney (MDCK) cells. Direct observation by light microscopy identified minimal differences in cellular morphology (data not shown). Flow cytometry was, therefore, used to assess the impact on cell morphology. The addition of 500 µM LPG to cells for 10 min resulted in a small proportion of cells (approx. 1.4%) showing an increase in side-scatter, suggesting increased cell granularity suggesting a change in the membrane intracellular architecture (figure 2a). As a result, a method was devised to remove free lipids following the treatment of virus to minimize any direct impact on cells. After several optimizations using flow cytometry and measuring cell viability using an MTT essay, the best method found was to centrifuge the solution containing lipids using ultrafiltration. Indeed, the flow cytometry data demonstrated that once the retentate was resuspended with the infection medium only a small fraction (less than 0.1%) of MDCK cells were affected (figure 2b) and that their viability remained unchanged for a period of up to 6 h (figure 2c).

Impact of lipid pre-treatment on the attachment, internalization and infectivity of H2N3 in MDCK cells
As the lipids used had a strong impact on virus morphology it was hypothesized that such an impact could impair their royalsocietypublishing.org/journal/rsif J. R. Soc. Interface 19: 20210943 ability to infect cells. To determine whether H2N3 virus attachment to cells was affected, virus (at a concentration to allow infection at a multiplicity of infection (MOI) of 5) was treated with lipids prior to ultrafiltration and the retentate was resuspended in cold infection medium (4°C). The cold infection solution was then incubated with cells for 10 min on ice. Cells were then washed with cold phosphate-buffered saline (PBS) and were either fixed with ice cold 1% PFA to determine the amount of viruses initially bound to cells, or reincubated with the infection medium at 37°C for different time points prior to fixation with PFA. HA was labelled using immunofluorescence without additional permeabilizing of MDCK cells to allow determination of the amount of viruses remaining on the MDCK surface over time. Figure 3a illustrates that the initial attachment of viruses to cells is impaired upon virus pre-treatment with lipids in comparison with untreated virus. After 30 min, only MDCK cells infected with untreated virus showed a noticeable diffuse fluorescent signal for HA suggesting that virus had entered cells and was detected by immunohistochemistry despite no additional permeabilization having been performed (figure 3b). However when the viruses were pre-treated with lipids a reduction in the fluorescent intensity within cells was clearly visible. In order to assess quantitatively the amount of viruses bound to the cell membrane over time flow cytometry was used. Data in figure 3c derived from flow cytometry analysis of MDCK infected cells demonstrate that the initial attachment of viruses to the MDCK cell membrane is impaired and is a function of the concentration of lipids used to pre-treat the virus. The impact of lipid treatment on virus infection of MDCK cells was also assessed by immunofluorescent staining of cells for viral nucleoprotein. MDCK cells were infected with H2N3 virus at an MOI of 1.0 for 2 h, with or without lipid pre-treatment of virus inoculum, prior to washing cells in PBS and incubation of cells for a further 4 h. Cells were then fixed and the viral nucleoprotein (NP) was labelled using immunohistochemistry to determine the proportion of infected cells (measured as focus forming units (ffu) per ml). Data presented in figure 4a-c demonstrate that H2N3 infectivity was significantly reduced when DPPG, LPG or LPC were used for the virus pre-treatment as opposed to DPPC which showed little impact. LPG used at 500 µM showed the greatest reduction in virus infectivity (to 3.5% compared with untreated virus; table 1).
However, with these data it was not possible to differentiate whether the drop in infectivity was simply linked to a reduction in the number of virions attached to cells initially or resulted from the impairment of the virus to multiply inside cells. To resolve this point, we studied  infectivity over time were similar to the control, in turn suggesting that the ability of H2N3 to multiply inside cells was not affected.
Taken together, the results suggest that a small fraction of pre-treated viruses are still functional and that pre-treating H2N3 with lipids only reduces the initial level of virus infection.  In order to assess whether the cell responses were influenced by the reduced level of virus infection following lipid treatment, H2N3 was pre-treated with either LPG or DPPG and incubated with cells for 2 h prior to resuspending cells in a new infection medium (using untreated virus at an MOI of 5 as performed in figure 3a). After 22 h, cellular RNA was extracted and qRT-PCR used to determine the expression level of key host proinflammatory cytokines (IL-8 and TNF-α). Figure 5a,b demonstrates that the pre-treatment of H2N3 with either LPG or DPPG significantly reduced the expression of these cytokine mRNAs in MDCK cells. Cells treated with 500 µM of DPPG or LPG only, i.e. without viruses, showed no significant change in cytokine expression compared with untreated cells, suggesting that lipid treatment per se is not proinflammatory. Finally, the ability of H2N3 to multiply inside cells was also assessed by measuring the amount of mRNA for the viral M-gene by qRT-PCR. As expected the amount of M-gene mRNA expression was also downregulated when H2N3 viruses were pre-treated with lipids (figure 5c). Altogether, these results confirm that pre-treating H2N3 with lipid reduces the level of virus infection, delays virus replication kinetics and consequently reduces the proinflammatory cell response.

Impact of lipid pre-treatment of H2N3 using A549 cells: attachment, infectivity and cell response
Our previous results demonstrated that H2N3 pre-treated with lipids impacts its ability to bind to and infect MDCK cells. However, such results could be specific to the cell line used. In order to assess this further, experiments were repeated using human adenocarcinomic alveolar basal epithelial (A549) lung cells. As previously determined with MDCK cells, the ultrafiltration method efficiently removed LPG and DPPG, with no impact on A549 cell viability noted using the MTT assay over a period of 6 h (figure 6a). Using the same method as for MDCK cells, H2N3 attachment to A549 cells was visibly impaired when H2N3 (sufficient to give an MOI of 5) was pre-treated with lipids (figure 6b,c). As expected, this resulted in a drop in virus infectivity, assessed as before, using immunohistochemistry for viral NP (at MOI of 1; figure 6d,e) that was more pronounced when LPG was used (infectivity reduced to 0.4% with 500 µM LPG or 5.5% with 50 µM LPG; table 1). IL-8 and TNF-α expression was similarly impacted by pre-treating H2N3 with either DPPG or LPG (figure 6f ). Finally, it was found that DPPG and LPG significantly reduced H2N3 M-gene copy number,

Impact of lipid treatment on filamentous H3N8 virus
Although H2N3 is natively spherical in shape, viruses can differ in their morphology and this is particularly the case for influenza viruses where filamentous viruses appear to be more frequently associated with clinical infections [19,20]. In order to assess the effect of lipid treatment on the infectivity of filamentous virus we used equine H3N8 which exhibits a largely filamentous morphology [21] to perform similar studies as for H2N3, using LPG or DPPG. Using EM, results demonstrated that treatment of H3N8 virus with either LPG or DPPG impacts its morphology ( figure 7a,b), affecting the distribution of envelope glycoprotein. However, the reduction in infection elicited upon DPPG incubation was moderate when compared to greater reductions when H2N3 was used. Only when LPG was used were multilayered viral structures observed suggesting rupture of the viral membrane (compare figure 7a,b for LPG at 500 µM). Given the nature and three-dimensional shape of the filamentous virus it was not possible to quantify those changes through the measurements of H3N8 aspect ratio or its surface area using EM. Regarding H3N8 attachment to cells, it was found that the interaction of the filamentous virus with MDCK cells was lower for untreated virus when compared to H2N3 in similar conditions (compare figure 7c with figure 3a), despite using virus at a similar MOI of 5. This may reflect a greater proportion of defective interfering particles in H2N3 virus preparation which are non-infectious but bind to MDCK cells. However, treatment with either LPG or DPPG still had a clear effect as the fluorescence intensity upon labelling H3N8 HA was much lower than the control (figure 7d ). After a further 30 min incubation, infected cells were clearly visible for the control through the presence of clusters of fluorescence (figure 7d). Those clusters were not visible when H3N8 was pre-treated with either LPG or DPPG.
Measurement of infectious virus, by immunostaining for virus nucleoprotein, following incubation of virus for 30 min with LPG or DPPG (5, 50 or 500 µM) showed that virus pre-treatment with LPG had a more pronounced impact on H3N8 infectivity (MOI 1) when compared with DPPG ( figure 7e,f ). Treatment with 500 µM or 50 µM lipid reduced H3N8 infectivity to 7.4% or 14.7% for LPG and 52.0% or 54.4% for DPPG, respectively (table 2).
Interestingly, it was found that only IL-8 transcription was significantly affected by pre-treatment of H3N8 (MOI 5) with either LPG or DPPG after 24 h infection, producing a modest reduction in the increased IL-8 expression observed following infection with untreated virus (figure 7g), whereas no significant changes were noted for TNF-α.
Those results suggest that the initial morphology of the virus, i.e. spherical or filamentous, has a significant impact on virus sensitivity to lipids. The impact of DPPG on virus infection was less marked when H3N8 was used when compared with H2N3. However, LPG had a greater impact on virus infection than DPPG for both viruses. Those results suggest that LPG is highly efficient whatever the initial morphology of the virus, but that the impact of DPPG is probably a function of the excess of viral membrane surrounding the virus, i.e. that the effect of such lipid is 'diluted' by the amount of lipid membrane forming the envelope of the filamentous virion. To confirm this, another spherical virus, H1N1, was used.

Impact of lipid pre-treatment on H1N1 infectivity
and the transcription of IL-8 and TNF-α using MDCK cells H1N1 (MOI 1) was pre-treated with DPPG and LPG using the same conditions as for H2N3 to measure its infectivity. Both LPG and DPPG altered H1N1 infectivity ( figure 8a,b). The drop in infectivity for H1N1 treated with 500 µM DPPG to 4.6% was more pronounced than for H2N3 (32.1%; table 2). In line with the previous observations, LPG produced greater inhibition of virus infection compared with DPPG, resulting in a decrease to 1.3% or 5.6% infectivity when treated with 500 µM or 50 µM, respectively (table 2). Finally, the transcriptions of IL-8 and TNF-α were significantly and similarly reduced upon lipid pre-treatments of H1N1 (MOI 5) (figure 8c). This is consistent with the changes in IL-8 and TNF-α expression measured for H2N3 but differs from the results obtained using H3N8. Tables 1 and 2 summarize the reduction in virus infectivity that was measured for each combination of lipid, virus and cell line.

Discussion
Influenza virus has a serious, worldwide, effect on human and animal health with a yearly seasonal death toll of many thousands, which increases during deadly pandemic episodes. Inactivated and attenuated vaccines against influenza A and B viruses (IAV and IBV) have been used to control influenza virus in addition to prophylactic and treatment attempts by using antiviral drugs but, still, significant research efforts are needed to control influenza viral infections. More recently the emergence of SARS-CoV 2 has resulted in an unprecedented virus pandemic that has had a devastating effect worldwide; mortality rates remain high and new treatments are urgently required.
The advances made in the field of soft matter physics encompassing lipid membranes and polymers have contributed to a better understanding of complex molecular structures and cell biology as a whole. The aim of this work was, therefore, to provide an interdisciplinary understanding of how lung surfactant phospholipids may function as an innate barrier against host pathogen infection, focusing on IAV. More precisely, based on the physical principle that single chain lipids are more prone to generate curvature upon their insertion into bilayer membrane, lipid surfactant analogues were tested against specific influenza viruses, i.e. H2N3, H3N8 and H1N1. The overarching conclusion is that lysolipids, in our case LPG and LPC, have indeed a more pronounced impact on virus infectivity independently of the cell type used (summarized in tables 1 and 2). It is remarkable that while concepts from soft-matter physics or biophysics have been successfully applied to a wide range of complex living systems allowing a better understanding of those systems, very little has been done in the field of virology.
In normal conditions H2N3 has a spherical shape showing outer glycoprotein spikes evenly distributed around the outer surface of the virus. In the presence of lipids, H2N3 is transformed into a giant/swollen structure and on some occasions, the viral envelope is ruptured. A less quantifiable but similar impact was observed on H3N8, a filamentous virus, suggesting that lipid interaction with the viral membrane is independent of the initial virus morphology. Previous studies have demonstrated that influenza virus binds efficiently with mixed liposomes composed of phospholipids within minutes [22] and that depleting the cholesterol from the viral envelope affects virus morphology, with virions showing nicks or holes in parts of the viral envelope [23]. Our study is therefore aligned with the latter conclusions that lipids interact with viruses and the envelope morphology is impacted upon changing its composition.
Those morphological alterations were associated with a decrease in the ability of viruses to interact with the cell membrane independently of the cell type. However, the ability of the virus to replicate inside cells was not affected, as the kinetics of replication were the same between the control and treated viruses. The influence of lipids on virus infectivity in the current study is in agreement with previous observations showing that the pulmonary surfactant phosphatidylglycerol (PG), which functions as the main innate immunity regulator in the lungs, blocks pulmonary viral infections [24] such as respiratory syncytial virus (RSV). This could provide an explanation for the higher concentration of phosphatidylglycerol in the lung compared to other body organs [7]. The airway epithelium is a primary barrier between the environment and the host, enhancing inflammatory and chemokine production targeting influenza viral infections and improving innate antiviral immunity [25]. Accordingly, and in agreement with a drop in infectivity, alterations in IL-8 and TNF-α cytokine transcription levels were measured together with a change in the number of mRNA copies for the viral M-gene 24 h post infection with influenza viruses.
Within the scope of this study our results demonstrate that pulmonary surfactant lyso-lipids can be used against H2N3, H3N8 and H1N1. The physical impact of lyso-lipids on viruses is expected to be the same across all enveloped viruses provided the presence of a bilayer membrane. While the use of lipids to treat acute respiratory distress has met with mixed results [26], the results presented here suggest that such treatments need to be rethought using optimized lyso-lipids with soft-matter/biophysical 'functionalities' such as to be properly effective against respiratory  The results demonstrate that the infectivity of filamentous viruses is also affected by phospholipids. However, differences were observed and measured between spherical and filamentous viruses that may be related to the amount of membrane involved and the fact that the impact of lipids is diluted when the amount of membrane constituting the virus is larger. (*p < 0.05; **p < 0.01; ***p < 0.001; # p < 0.0001; one-way ANOVA.) In short, this paper is a call, or plea, to urge physicists to consider viruses as an important and central physical system to study.

Transmission electron microscopy
MDCK cells were infected with H2N3 or H3N8 at an MOI of 1.0 with incubation at 37°C with 5% CO 2 for 72 h. The virus-containing supernatant was then harvested, clarified by centrifugation at 1200g for 2 min, and mixed with phospholipid solutions for 30 min at 37°C with 5% CO 2 . The final solutions were then pipetted onto holey carbon support film with 3.05 mm copper grids including 300 hexagonal mesh (EM Resolution, UK) and stained with 2% phospho-tungstic acid (PTA) at pH 7.4 (Sigma, UK). ATecnai G212 Bio Twin Digital TEM system was used to image the samples from different areas of the grids and Image J (Image J 1.47v, National Institute of Health, USA) was used to measure virus aspect ratio and surface area to quantify virus morphology.

Flow cytometry to determine potential impact of lipids on MDCK cells
MDCK cells were cultured in DMEM-10 until 90-95% confluent. The medium was discarded and cells washed twice with cold PBS at 4°C. Cells were then incubated in versene (ethylenediamine-tetraacetic acid, Gibco, UK) at 37°C for 10 min to detach them. DMEM-10 was used to neutralize versene and the cell suspension was centrifuged at 1200g for 6 min. The pellet was resuspended at a concentration of 1 × 10 6 cells ml −1 in IM. Single cell suspensions were then incubated with phospholipids at the desired concentration for 10 min at 37°C. To minimize the potential toxicity of phospholipids on cells, lipids were then removed by ultrafiltration using an Amicon Ultra-15 filter (50 K MWCO, Fisher Scientific, UK). Cells were then fixed in 1% PFA (Fisher, UK) for 20 min at room temperature and washed three times with cold PBS. The samples were then examined with an FC500 flow cytometer (Beckman Coulter, UK), recording 10 000 events, and the data analysed using Weasel software program v. 3.0 (Walter and Eliza Hall Institute, Australia).

Infectivity of influenza A virus pre-treated with phospholipids in MDCK cells or A549 cells
Influenza A viruses H2N3 and H3N8 were pre-treated with phospholipids at a range of concentrations. After ultrafiltration, as described above, the viruses were resuspended in infection medium and incubated with confluent MDCK cells (H2N3 or H3N8) or A549 cells (H2N3) at MOI of 1 for 2 h at 37°C. Cells were then washed three times with PBS at room temperature and incubated for a further 4 h in IM at 37°C before being fixed at 4°C in 1 : 1 acetone-methanol for 10 min at room temperature. Immunocytochemical staining was performed using a primary mouse monoclonal antibody (AA5H, Abcam, UK) for 1 h to detect influenza viral nucleoprotein which was then visualized with an Envision+ horseradish peroxidase phosphate (HRP) kit (DAB; Dako, Ely, UK) following the manufacturer's instructions. Finally, the proportion of cells stained for NP was calculated using counts from five fields captured using light microscopy assisted by Image J software, allowing calculation of focus forming units of virus per microlitre.