Pandemic avian influenza

Subtyping clinical specimens of influenza A virus by use of a simple method to amplify RNA targets

This work presents the clinical application of a robust and unique approach for RNA amplification, called a simple method for amplifying RNA targets (SMART), for the detection and identification of subtypes of H1N1 pandemic, H1N1 seasonal, and H3N2 seasonal influenza virus. While all the existing amplification techniques rely on the diffusion of two molecules to complex RNA structures, the SMART achieves fast and efficient amplification via single-molecule diffusion. The SMART utilizes amplifiable single-stranded DNA (ssDNA) probes, which serve as reporter molecules for capturing specific viral RNA (vRNA) sequences and are subsequently separated on a microfluidic chip under zero-flow conditions. The probe amplification and detection are performed using an isothermal (41°C) amplification scheme via a modified version of nucleic acid sequence-based amplification (NASBA). In our study, 116 consecutive, deidentified, clinical nasopharyngeal swab samples were analyzed independently in a blinded fashion using the SMART, reverse transcription-PCR (RT-PCR), antigen (Ag) testing, and viral culture. The SMART was shown to have a limit of detection (LOD) of approximately 10(5) vRNA copies/ml, corresponding with a time-to-positivity (TTP) value of 70 min for real-time detection. The SMART correctly detected influenza virus in 98.3% of the samples with a subtyping accuracy of 95.7%. This work demonstrates that the SMART represents a highly accurate diagnostic platform for the detection and subtyping of influenza virus in clinical specimens and offers significant advantages over the current commercially available diagnostic tools.

A simple method for amplifying RNA targets (SMART)

We present a novel and simple method for amplifying RNA targets (named by its acronym, SMART), and for detection, using engineered amplification probes that overcome existing limitations of current RNA-based technologies. This system amplifies and detects optimal engineered ssDNA probes that hybridize to target RNA. The amplifiable probe-target RNA complex is captured on magnetic beads using a sequence-specific capture probe and is separated from unbound probe using a novel microfluidic technique. Hybridization sequences are not constrained as they are in conventional target-amplification reactions such as nucleic acid sequence amplification (NASBA). Our engineered ssDNA probe was amplified both off-chip and in a microchip reservoir at the end of the separation microchannel using isothermal NASBA. Optimal solution conditions for ssDNA amplification were investigated. Although KCl and MgCl(2) are typically found in NASBA reactions, replacing 70 mmol/L of the 82 mmol/L total chloride ions with acetate resulted in optimal reaction conditions, particularly for low but clinically relevant probe concentrations (≤100 fmol/L). With the optimal probe design and solution conditions, we also successfully removed the initial heating step of NASBA, thus achieving a true isothermal reaction. The SMART assay using a synthetic model influenza DNA target sequence served as a fundamental demonstration of the efficacy of the capture and microfluidic separation system, thus bridging our system to a clinically relevant detection problem.

Disease Mongering and the Fear of Pandemic Influenza

The catastrophic H1N1 pandemic of 1918, which killed tens of millions, is now legendary, and influenza policy has centered on preventing another such disaster. There is reason for concern about influenza A. It can rapidly alter its genetic makeup to increase virulence and can jump from other species to humans. Nonetheless, ignorance about influenza in 1918, the lack of effective vaccines or antibacterial and antiviral drugs, and the social disruption caused by World War I also contributed heavily to the lethality, and it is unlikely that influenza of similar destructiveness will recur. The stupefying publicity over the threat of influenza has been generated partly by those, such as the pharmaceutical industry and influenza researchers, who benefit from the increased expenditures the publicity provokes. It is, in effect, disease mongering, the promotion of disease or dread of disease for one's own gain. Huge expenditures on influenza preparedness have produced little demonstrable benefit and some harm, independent of the wasted resources. Disease mongering, including spreading fear of influenza, is widespread and unhealthy and should be vigorously opposed.

Spatial-temporal patterns of dengue in areas at risk of dengue hemorrhagic fever in Kaohsiung, Taiwan, 2002

OBJECTIVE

This study aimed to examine whether spatial-temporal patterns of dengue can be used to identify areas at risk of dengue hemorrhagic fever (DHF).

METHODS

Three indices - probability of case-occurrence, mean duration per wave, and transmission intensity - were used to differentiate eight local spatial-temporal patterns of dengue during the 2002 epidemic in Kaohsiung, Taiwan. DHF densities (DHF cases/km(2) per 100 dengue cases) in each spatial-temporal typed area were compared.

RESULTS

Areas with three high indices correlated with the highest DHF density: (1) high transmission intensity only; (2) long duration of wave only, and (3) high transmission intensity plus long duration of wave. However, cumulative incidences of dengue cases were not correlated with DHF densities.

CONCLUSION

Three spatial-temporal indices of dengue could provide useful information to identify areas at high risk of DHF.

Risk parameters of fulminant acute respiratory distress syndrome and avian influenza (H5N1) infection in Vietnamese children

A clinical picture of patients with acute respiratory distress syndrome (ARDS) induced by highly pathogenic avian influenza A (H5N1) has been reported. We reviewed 37 sets of clinical data for pediatric patients with ARDS at the National Hospital of Pediatrics (Hanoi, Vietnam); 12 patients with H5N1-positive and 25 with H5N1-negative ARDS were enrolled. The H5N1-negative patients had a clinical picture and mortality rate similar to that for the pediatric ARDS patients. However, the H5N1-positive patients had ARDS with normal ventilation capacity at the time of hospital admission, then rapidly proceeded to severe respiratory failure. The survival probability and days until final outcome in groups of H5N1-positive (n=12) vs. H5N1-negative (n=25) patients were 17% versus 52% and 12.3+/-5.7 days (median, 11 days) versus 21.5+/-13.8 days (median, 22 days), respectively. Our observations clarified the clinical picture of H5N1-induced fulminant ARDS and also confirmed that relatively older age (approximately 6 years of age), high fever at onset, and leukopenia and/or thrombocytopenia at the time of hospital admission are risk parameters for H5N1-induced fulminant ARDS.

Direct sequence detection of structured h5 influenza viral RNA

We describe the development of sequence-specific molecular beacons (dual-labeled DNA probes) for identification of the H5 influenza subtype, cleavage motif, and receptor specificity when hybridized directly with in vitro transcribed viral RNA (vRNA). The cloned hemagglutinin segment from a highly pathogenic H5N1 strain, A/Hanoi/30408/2005(H5N1), isolated from humans was used as template for in vitro transcription of sense-strand vRNA. The hybridization behavior of vRNA and a conserved subtype probe was characterized experimentally by varying conditions of time, temperature, and Mg2+ to optimize detection. Comparison of the hybridization rates of probe to DNA and RNA targets indicates that conformational switching of influenza RNA structure is a rate-limiting step and that the secondary structure of vRNA dominates the binding kinetics. The sensitivity and specificity of probe recognition of other H5 strains was calculated from sequence matches to the National Center for Biotechnology Information influenza database. The hybridization specificity of the subtype probes was experimentally verified with point mutations within the probe loop at five locations corresponding to the other human H5 strains. The abundance frequencies of the hemagglutinin cleavage motif and sialic acid recognition sequences were experimentally tested for H5 in all host viral species. Although the detection assay must be coupled with isothermal amplification on the chip, the new probes form the basis of a portable point-of-care diagnostic device for influenza subtyping.

Bioterrorism

Bioterrorism is defined as the deliberate and malicious deployment of microbial agents or their toxins as weapons in a non-combat setting, represents perhaps the most overt example of human behavior impacting epidemic infectious diseases. There is historical precedent for the use of biological agents against both military and civilian populations. The use of biological (and chemical) agents as weapons of war has been well documented. The German biological warfare program during World War I included covert infections of Allied livestock with anthrax and glanders. The Japanese army began conducting experiments on the effects of bacterial agents of biowarfare on Chinese prisoners in occupied Manchuria in 1932 at their infamous Unit 731. The United States began its own offensive biological weapons program in 1942 and, during its 28-year official existence, weaponized and stockpiled lethal biological agents, such as anthrax, as well as incapacitating agents, such as the etiologic agent of Q fever. There are some recent examples of bioterrorism, though not necessarily resulting in attacks causing morbidity or mortality, may serve as harbingers of future events. Saddam Hussein's regime in Iraq developed and deployed anthrax and botulinum-laden warheads in the years leading up to the Gulf War. The reasons that these weapons were never used in an actual attack probably had more to do with the implicit threat of overwhelming US retaliation and Iraqi technological deficiencies rather than the regime's reluctance to violate any moral principles. Biological agents have also been used to forward political ideologies: in 1984 a religious cult, intent on influencing voter turnout during a local election, contaminated restaurant salad bars in The Dalles, Oregon.

Highly pathogenic H5N1 avian influenza: entry pathways into North America via bird migration

Given the possibility of highly pathogenic H5N1 avian influenza arriving in North America and monitoring programs that have been established to detect and track it, we review intercontinental movements of birds. We divided 157 bird species showing regular intercontinental movements into four groups based on patterns of movement—one of these groups (breed Holarctic, winter Eurasia) fits well with the design of the monitoring programs (i.e., western Alaska), but the other groups have quite different movement patterns, which would suggest the importance of H5N1 monitoring along the Pacific, Atlantic, and Gulf coasts of North America.

A Spatial-Temporal Approach to Differentiate Epidemic Risk Patterns

The purpose of disease mapping is to find spatial clustering and identify risk areas and potential epidemic initiators. Rather than relying on plotting either the case number or incidence rate, this chapter proposes three temporal risk indices: the probability of case occurrence (how often did uneven cases occur), the duration of an epidemic (how long did cases persist), and the intensity of a transmission (were the case of chronological significance). By integrating the three indicators using the local indicator of spatial autocorrelation (LISA) statistic, this chapter intends to develop a novel approach for evaluating spatial-temporal relationships with different risk patterns in the 2002 dengue epidemic, the worst outbreak in the past sixty years. With this approach, not only are hypotheses generated through the mapping processes in furthering investigation, but also procedures provided to identify spatial health risk levels with temporal characteristics.