Subtyping of Influenza A Isolates in Taiwan—2003 to 2004

Background/PurposeSome isolated influenza strains are untypable. The possibility that a novel and potentially lethal strain, such as H5 virus, might be one of these untypable strains remains a major concern. This study investigated the nature of untypable influenza strains in Taiwan.MethodsSubtyping for unsubtyped isolates was conducted by reverse transcription-polymerase chain reaction (RT-PCR) using different primer sets. Sequence determination and comparison, and characterization of viral growth rate were performed.ResultsAnalysis of viral re-cultures with the different primer sets for RT-PCR revealed that all isolates were of the H3N2 subtype. All isolates resembled A/Fujian/411/02 (H3N2), and were genetically distinct from N2 of A/chicken/Taiwan/1209/03 (H5N2) on phylogenetic analysis. Real-time RT-PCR quantification of viral loads in the 16 clinical isolates revealed that negative results were partially caused by low RNA levels in the culture fluid. Comparison of replication kinetics in Madin-Darby canine kidney cells of recent influenza A H3N2 isolates showed that some Fujian-like isolates from 2003 to 2004 had significantly lower growth rate than Panama-like isolates from 2002.ConclusionThe results of this study suggest that some recent isolates may replicate poorly in tissue culture and fail to be typed by current methodology.