title: (In)validating experimentally derived knowledge about influenza A defective interfering particles.
abstract: A defective interfering particle (DIP) in the context of influenza A virus is a virion with a significantly shortened RNA segment substituting one of eight full-length parent RNA segments, such that it is preferentially amplified. Hence, a cell co-infected with DIPs will produce mainly DIPs, suppressing infectious virus yields and affecting infection kinetics. Unfortunately, the quantification of DIPs contained in a sample is difficult because they are indistinguishable from standard virus (STV). Using a mathematical model, we investigated the standard experimental method for counting DIPs based on the reduction in STV yield (Bellett & Cooper, 1959, Journal of General Microbiology 21, 498-509 (doi:10.1099/00221287-21-3-498)). We found the method is valid for counting DIPs provided that: (i) an STV-infected cell's co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions), (ii) a cell co-infected by STV and DIP produces less than 1 STV per 1000 DIPs and (iii) a high MOI of STV stock (more than 4 PFU per cell) is added to perform the assay. Prior work makes no mention of these criteria such that the method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs.
authors.affiliation: Department of Physics, Ryerson University, Toronto, Canada.
authors.forename: Laura E
authors.identifier: 0000-0001-6069-2633
authors.initials: LE
authors.lastname: Liao
authors.affiliation: Department of Biology, Kyushu University, Fukuoka, Japan.|CREST and PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Iwami
authors.affiliation: Department of Physics, Ryerson University, Toronto, Canada cbeau@ryerson.ca.|Interdisciplinary Theoretical Science (iTHES) Research Group at RIKEN, Wako, Japan.
authors.forename: Catherine A A
authors.identifier: 0000-0003-0599-0069
authors.initials: CA
authors.lastname: Beauchemin
mesh_terms: D003673:Defective Viruses / Q000502:physiology*; D006801:Humans; D009980:Influenza A virus / Q000502:physiology*; D008954:Models, Biological; D014771:Virion / Q000502:physiology*
keywords: co-infection; defective interfering particles; influenza A virus; interference assay; mathematical model; reduction of infectious virus yield