Review 1: "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants"

RR:C19 Evidence Scale rating by reviewer:

• Strong. The main study claims are very well-justified by the data and analytic methods used. There is little room for doubt that the study produced has very similar results and conclusions as compared with the hypothetical ideal study. The study’s main claims should be considered conclusive and actionable without reservation.

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Review:

The manuscript by Farley et al., “A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants,” is clearly presented, well-structured, well-written, and is easy to follow. The main study claims are well-justified by its methods and data. Furthermore, the findings contribute to broader virus research understandings, not necessarily limited to SARS-COV-19.

After 24 hours after SARS-CoV-2 infection, approximately 80% of the host lipids were statistically different. Glycerolipids and phospholipids accounted for the largest changes; triglycerides increased, and cardiolipin decreased in infected versus mock-infected human cells. After exogenously expressing each of the proteins of the SARS-CoV2 separately, the authors performed lipidomic profiling of the transfected cells. They identified specific lipids that were enriched most commonly upon transfection of the viral proteins. The study then correlates the two lipidomic data sets and discovers an increase in triacylglycerides, ceramides, and polyunsaturated phospholipids; and a decrease in lysolipids diacylglycerides, cardiolipin, and saturated phospholipids. Interestingly, each of these lipidomic changes was recapitulated by at least one viral protein. The authors ruled out that the virus uses lipid droplets as a site for replication. Finally, the authors investigated viral replication in the presence of several small-molecule inhibitors of lipid synthesis (at different concentrations) and found that many steps of lipid biosynthesis are essential for virion production. Notably, for the intracellular stages, the virus is dependent on both de novo synthesis of triglycerides and fatty acids released through lipolysis. The authors also show sensitivity to the inhibitors in the fours strains testes – alpha through delta