Rapid molecular epidemiologic studies of human parainfluenza viruses basedon direct sequencing of amplified DNA from a multiplex RT-PCR assay

Sequencing studies of limited regions of the human parainfluenza viruses (H PIVs) genomes have helped describe patterns of virus circulation and charac terize institutional outbreaks of HPIVs-associated respiratory illness. In this study, we sequenced reverse transcription polymerase chain reaction (R T-PCR)-amplified HPIVs RNA obtained from a multiplex RT-PCR assay described previously for simultaneous detection of HPIV-1, 2 and 3. Differences in t he nucleotide sequences of limited regions of the HN gene allowed us to dis tinguish temporally and geographically diverse HPIV isolates (43 HPIV-1, 7 HPIV-2, 12 HPIV-3 isolates from this and previously published studies). In addition, an outbreak of HPIV-3-associated illness among infants on a pedia tric ward was investigated by comparing sequences of three ward isolates wi th three matched community controls. Sequences of all ward isolates were id entical and differed from those of the community controls, suggesting a sin gle introduction and nosocomial transmission of the virus. Combining multip lex reverse transcription polymerase chain reaction (RT-PCR) assays with di rect sequencing of the PCR products can provide an integrated system for ra pid diagnosis and characterization of HPIVs. (C) 2000 Elsevier Science B.V. All rights reserved.