24Quantum dots (QDs) possess optical properties of superbright fluorescence, excellent photostability, narrow 25 emission spectra, and optional colors. Labeled with QDs, single molecules/viruses can be rapidly and 26 continuously imaged for a long time, providing more detailed information than labeled with other 27 fluorophores. While they are widely used to label proteins in single-molecule tracking studies, QDs have 28 rarely been used to study virus infection, mainly due to lack of accepted labeling strategies. Here, we report 29 a general method to mildly and readily label enveloped viruses with QDs. Lipid-biotin conjugates were used 30 to recognize and mark viral lipid membranes, and streptavidin (SA)-QD conjugates were used to light them 31 up. Such a method allowed enveloped viruses to be labeled in 2 hours with specificity and efficiency up to 32 99% and 98%. The intact morphology and the native infectivity of viruses could be furthest preserved. With 33 the aid of this QD labeling method, we lit wild-type (WT) and mutant Japanese encephalitis virus (JEV) up, 34 tracked their infection in living Vero cells, and found that H144A and Q258A substitutions in the envelope 35 (E) protein didn't affect the virus intracellular trafficking. The lipid-specific QD labeling method described 36 in this study provides a handy and practical tool to readily "see" the viruses and follow their infection, 37 facilitating the widespread use of single-virus tracking and the uncovering of complex infection 38 mechanisms.
39Author summary 40 Virus infection in host cells is a complex process comprising a large number of dynamic molecular events.
41Single-virus tracking is a versatile technique to study these events. To perform this technique, viruses must 42 be fluorescently labeled to be visible to fluorescence microscopes. Quantum dot is a kind of fluorescent tags 43 that has many unique optical properties. It has been widely used to label proteins in single-molecule tracking 44 studies, but rarely used to study virus infection, mainly due to lack of accepted labeling method. In this 45 study, we developed a lipid-specific method to readily, mildly, specifically, and efficiently label enveloped 46 viruses with quantum dots by recognizing viral envelope lipids with lipid-biotin conjugates and recognizing 47 these lipid-biotin conjugates with streptavidin-quantum dot conjugates. Such a method is superior to the 48 commonly used DiD/DiO labeling and the other QD labeling methods. It is not only applicable to normal 3 49 viruses, but also competent to label the key protein-mutated viruses and the inactivated high virulent viruses, 50 providing a powerful tool for single-virus tracking. 51 Introduction 52 Single-particle tracking is a powerful tool to study the dynamic molecular events in living cells. An essential 53 prerequisite to perform this technique is fluorescently labeling the targets. In the past decade, various 54 fluorescent tags such as organic dyes [1], fluorescent proteins [2], metal complex of dppz [3], and QDs ...