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BackgroundEffective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.Methods and Principal FindingsAnalysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999–2006) showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005–2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution.Conclusion/SignificanceThus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance.

New surveillance approach can analyze >900 polymerase chain reactions per day.

We describe a new approach to the sensitive and specific identification of bacteria, viruses, fungi, and protozoa based on broad-range PCR and high-performance mass spectrometry. The Ibis T5000 is based on technology developed for the Department of Defense known as T.I.G.E.R. (Triangulation Identification for the Genetic Evaluation of Risks) for pathogen surveillance. The technology uses mass spectrometry—derived base composition signatures obtained from PCR amplification of broadly conserved regions of the pathogen genomes to identify most organisms present in a sample. The process of sample analysis has been automated using a combination of commercially available and custom instrumentation. A software system known as T-Track manages the sample flow, signal analysis, and data interpretation and provides simplified result reports to the user. No specialized expertise is required to use the instrumentation. In addition to pathogen surveillance, the Ibis T5000 is being applied to reducing health care—associated infections (HAIs), emerging and pandemic disease surveillance, human forensics analysis, and pharmaceutical product and food safety, and will be used eventually in human infectious disease diagnosis. In this review, we describe the automated Ibis T5000 instrument and provide examples of how it is used in HAI control.

Nascent SH(X 2II;, v" = 0,1) and SD(X 2n;, v" = 0,1) rotational state population distributions, spin-orbit state population ratios, and A-doublet state population ratios have been measured following the UV excimer laser photodissociation of H2 S (A = 193, 222, and 248 nm) and D 2 S (A = 193 and 222 nm), respectively. Nascent SH(X 2 n;, v" = 0) rotational state distributions following 193 nm photodissociation of cold H2 S in a free jet expansion vs 300 K H2 S in a flowing gas cell were essentially the same, indicating that photofragment angular momentum must be originating predominantly in the dissociation event, and not from rotational energy contained in the parent triatom. Laser excitation spectra ofSH(X 2 njl v" = 1) and SD (X 2n;, v" = 1) have been recorded for the first time. Rotational state distributions for SH(X 2njl v") and SD(X 2njl v") are independent of v". A-doublet population ratios of the nascent photofragments are essentially unity for all the cases measured. The nascent rotational state distributions are consistent with an impact parameter model for the dissociating triatomic molecule.