Diagnosis of 2009 pandemic influenza A (pH1N1) and seasonal influenza using rapid influenza antigen tests, San Antonio, Texas, April-June 2009.

Clinicians frequently use influenza rapid antigen tests for diagnostic testing. We tested nasal wash samples from 1 April to 7 June 2009 from 1538 patients using the QuickVue Influenza A+B (Quidel) rapid influenza antigen test and compared the results with real-time reverse transcription polymerase chain reaction (rRT-PCR) assay (gold standard). The prevalence of 2009 pandemic influenza A (pH1N1) was 1.98%, seasonal influenza type A .87%, and seasonal influenza type B 2.07%. The sensitivity and specificity of the rapid test for pH1N1 was 20% (95% CI, 8-39) and 99% (95% CI, 98-99), for seasonal influenza type A 15% (95% CI, 2-45) and 99% (95% CI, 98-99), and for influenza type B was 31% (95% CI, 9-61) and 99% (95% CI, 98-99.7). Rapid influenza antigen tests were of limited use at a time when the prevalence of pH1N1 and seasonal influenza in the United States was low. Clinicians should instead rely on clinical impression and laboratory diagnosis by rRT-PCR.

Department of Defense Global Laboratory-Based Influenza Surveillance: 1998-2005.

The Department of Defense (DoD) Global Laboratory-Based Influenza Surveillance Program was initiated in 1997 to formally consolidate and expand existing influenza surveillance programs within the DoD and in areas where DoD was working. Substantial changes in 2008 provided an opportunity to review the operation of the surveillance program as it existed during seven complete influenza seasons (1998-2005); the review was conducted in 2008. A unique aspect of the DoD program was the global reach for specimen collection and the ability to rapidly ship, process, and evaluate specimens from 27 countries. The resulting epidemiologic data combined with the culture results from >46,000 patients provided information that was shared with similar national and international programs, such as those of the CDC. Likewise, selected influenza isolates were molecularly characterized and shared with the CDC to be compared with other surveillance programs. Timeliness of the samples contributed to the information available for annual influenza vaccine selection.

Reproductive tract complications associated with Chlamydia trachomatis infection in US Air Force males within 4 years of testing.

BACKGROUND: Chlamydia trachomatis (CT) is a common sexually transmitted infection for which young, sexually active persons are at highest risk. Health consequences such as orchitis/epididymitis, prostatitis, infertility, and urethral stricture have been described among CT-infected males, although not all of these are indisputably linked to CT. Current literature lacks population-based studies needed to examine these associations on a larger scale, to evaluate the true risk of developing complications after a CT infection. The US Air Force contains a large population of young, sexually active males, making it suitable for conducting such a study. METHODS: We conducted a retrospective cohort study between 2001 and 2005 comparing the incidence of orchitis/epididymitis, prostatitis, infertility, and urethral stricture among male Air Force members with and without prior CT infections. Cumulative incidence rates were calculated and Cox proportional hazard models were generated to evaluate the risk of developing complications and to adjust for potential confounders. RESULTS: Among 17,764 men enrolled in the study, 913 (5.14%) experienced a reproductive tract outcome. Among CT-positive men, cumulative incidences of orchitis/epididymitis, prostatitis, infertility, and urethral stricture were 4.28%, 1.41%, 1.27%, and 0.13%, respectively. Orchitis/epididymitis [Hazard ratio (HR) = 1.38 (1.13-1.70)] and "any" outcome [HR = 1.37 (1.16-1.61)] were positively associated with CT; infertility was marginally associated [HR = 1.36 (0.93-2.00)]. CONCLUSIONS: Overall, the burden of reproductive health outcomes among Air Force males is small. Significant associations were observed between CT and both orchitis/epididymitis and any outcome; a larger cohort or longer follow-up may have detected a significant association between CT and infertility.

Real-time RT-PCR assays for type and subtype detection of influenza A and B viruses.

Influenza viruses type A (H3N2 and H1N1 subtypes) and B are the most prevalently circulating human influenza viruses. However, an increase in several confirmed cases of high pathogenic H5N1 in humans has raised concerns of a potential pandemic underscoring the need for rapid, point of contact detection. In this report, we describe development and evaluation of 'type,' i.e., influenza virus A and B, and 'subtype,' i.e., H1, H3, and H5, specific, single-step/reaction vessel format, real-time RT-PCR assays using total RNA from archived reference strains, shell-vial cultured and uncultured primary (throat swab/nasal wash) clinical samples. The type A and B specific assays detected all 16 influenza type A viruses and both currently circulating influenza B lineages (Yamagata and Victoria), respectively. 'Type' and 'subtype' specific assays utilize one common set of thermocycling conditions, are specific and highly sensitive (detection threshold of approximately 100 target template molecules). All clinical specimens and samples were evaluated using both the unconventional portable Ruggedized Advanced Pathogen Identification Device (RAPID) and standard laboratory bench LightCycler instruments. These potentially field-deployable assays could offer significant utility for rapid, point of care screening needs arising from a pandemic influenza outbreak.

Identifying influenza viruses with resequencing microarrays.

Identification of genetic variations of influenza viruses is essential for epidemic and pandemic outbreak surveillance and determination of vaccine strain selection. In this study, we combined a random amplification strategy with high-density resequencing microarray technology to demonstrate simultaneous detection and sequence-based typing of 25 geographically distributed human influenza virus strains collected in 2004 and 2005. In addition to identification, this method provided primary sequence information, which suggested that distinct lineages of influenza viruses co-circulated during the 2004-2005 season, and simultaneously identified and typed all component strains of the trivalent FluMist intranasal vaccine. The results demonstrate a novel, timely, and unbiased method for the molecular epidemiologic surveillance of influenza viruses.

Influenza A (H3N2) outbreak, Nepal.

In July 2004, an outbreak of influenza A (H3N2) was detected at 3 Bhutanese refugee camps in southeastern Nepal. Hemagglutination inhibition showed that approximately 40% of the viruses from this outbreak were antigenically distinct from the A/Wyoming/3/03 vaccine strain. Four amino acid differences were observed in most of the 26 isolates compared with the A/Wyoming/3/2003 vaccine strain. All 4 substitutions are located within or adjacent to known antibody-binding sites. Several isolates showed a lysine-to-asparagine substitution at position 145 (K145N) in the hemagglutinin molecule, which may be noteworthy since position 145 is located within a glycosylation site and adjacent to an antibody-binding site. H3N2 viruses continue to drift from the vaccine strain and may remain as the dominant strains during the 2005-2006 influenza season. Thus, the 2005-2006 Northern Hemisphere vaccine strain was changed to A/California/7/2004, a virus with all 4 amino acid substitutions observed in these Nepalese isolates.

A rapid, single-step multiplex reverse transcription-PCR assay for the detection of human H1N1, H3N2, and B influenza viruses.

BACKGROUND: Influenza is a viral respiratory pathogen responsible for frequent seasonal epidemics. There are currently three major human influenza viruses in global circulation, H1N1, H3N2 and B. OBJECTIVES: A one-step multiplex reverse transcription (RT)-polymerase chain reaction (PCR) assay targeting the HA1 segment of the human hemagglutinin gene was developed as a rapid surveillance method. STUDY DESIGN: A researcher-blind study was performed using 112 randomly selected, culture-positive clinical samples collected through the Department of Defense (Global Emerging Infectious Surveillance (DOD-GEIS) influenza network during the 2000-2001 influenza season. Three subtype specific primer sets capable of producing PCR products with base-pair lengths of 585, 402 and 290 corresponding to influenza H1, H3, and B subtypes, respectively, were utilized together in a one step, one tube, reaction. RESULTS: Multiplex primers were able to simultaneously type, and subtype 100% (112/112) of positive cultures. CONCLUSIONS: The results confirm that this assay is a highly sensitive and timely surveillance tool for rapid detection and simultaneous subtyping of clinical influenza specimens isolated worldwide.

Genetic and antigenic analysis of the first A/New Caledonia/20/99-like H1N1 influenza isolates reported in the Americas.

From February through May of 1999, 13 cases of Influenza A virus (FLUAV), type H1N1 were reported at a Department of Defense influenza surveillance sentinel site in Lima, Peru. Genetic and antigenic analysis by hemagglutination inhibition and direct nucleotide sequencing of the HA1 region of the hemagglutinin gene were performed on two isolates, A/Peru/1641/99 and A/Peru/1798/99. Both isolates were distinct from the Bayern/7/95-like viruses circulating in the Americas and closely related to a Beijing/262/95-like variant, A/New Caledonia/20/99. With the exception of travel-related cases, the detection of these isolates represents the first appearance of New Caledonia/20/99-like viruses in the Americas. Since the characterization of these Peru isolates, a number of New Caledonia/20/99-like viruses have been reported worldwide. For the 2000/01 and 2001/02 influenza seasons, the World Health Organization (WHO) has recommended the inclusion of A/New Caledonia/20/99 as the H1N1 vaccine component for both the southern and northern hemispheres.