SQSTM1 and coinfection: Together the gene expression analyses indicates that some ATG genes (Beclin1/ATG6 and ATG12) could be differentially expressed during co-infection, but that the degradation of LC3B and SQSTM1 proteins caused by Torin1 do not correlate with decreased gene expression of these autophagy markers, but instead is due to an overall increased cellular autophagic flux.