2D zonal integration with unordered data.

Numerical integration of two-dimensional gradient data is an important step for many slope-measuring optical instruments. However, existing methods are limited by low accuracy or data location restrictions. The zonal integration algorithm in this paper is a generalized process that works with unordered data via Taylor series approximations of finite difference calculations. This method does not require iteration, and all significant steps rely on matrix calculations for a least-squares solution. Simultaneous integration and interpolation is achieved with high accuracy and arbitrary data locations.

The C Terminus of the Herpes Simplex Virus UL25 Protein Is Required for Release of Viral Genomes from Capsids Bound to Nuclear Pores.

The herpes simplex virus (HSV) capsid is released into the cytoplasm after fusion of viral and host membranes, whereupon dynein-dependent trafficking along microtubules targets it to the nuclear envelope. Binding of the capsid to the nuclear pore complex (NPC) is mediated by the capsid protein pUL25 and the capsid-tethered tegument protein pUL36. Temperature-sensitive mutants in both pUL25 and pUL36 dock at the NPC but fail to release DNA. The uncoating reaction has been difficult to study due to the rapid release of the genome once the capsid interacts with the nuclear pore. In this study, we describe the isolation and characterization of a truncation mutant of pUL25. Live-cell imaging and immunofluorescence studies demonstrated that the mutant was not impaired in penetration of the host cell or in trafficking of the capsid to the nuclear membrane. However, expression of viral proteins was absent or significantly delayed in cells infected with the pUL25 mutant virus. Transmission electron microscopy revealed capsids accumulated at nuclear pores that retained the viral genome for at least 4 h postinfection. In addition, cryoelectron microscopy (cryo-EM) reconstructions of virion capsids did not detect any obvious differences in the location or structural organization for the pUL25 or pUL36 proteins on the pUL25 mutant capsids. Further, in contrast to wild-type virus, the antiviral response mediated by the viral DNA-sensing cyclic guanine adenine synthase (cGAS) was severely compromised for the pUL25 mutant. These results demonstrate that the pUL25 capsid protein has a critical role in releasing viral DNA from NPC-bound capsids.IMPORTANCE Herpes simplex virus 1 (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. Early steps in infection include release of the capsid into the cytoplasm, docking of the capsid at a nuclear pore, and release of the viral genome into the nucleus. A key knowledge gap is how the capsid engages the NPC and what triggers release of the viral genome into the nucleus. Here we show that the C-terminal region of the HSV-1 pUL25 protein is required for releasing the viral genome from capsids docked at nuclear pores. The significance of our research is in identifying pUL25 as a key viral factor for genome uncoating. pUL25 is found at each of the capsid vertices as part of the capsid vertex-specific component and implicates the importance of this complex for NPC binding and genome release.

Subaperture stitching tolerancing for annular ring geometry.

Subaperture stitching is an economical way to extend small-region, high-resolution interferometric metrology to cover large-aperture optics. Starting from system geometry and measurement noise knowledge, this work derives an analytical expression for how noise in an annular ring of subapertures leads to large-scale errors in the computed stitched surface. These errors scale as sin(πp/M)(-2) where p is the number of sine periods around the annular full-aperture and M is the number of subaperture measurements. Understanding how low-spatial-frequency surface errors arise from subaperture noise is necessary for tolerancing systems which use subaperture stitching.

Binary pattern deflectometry.

Deflectometry is widely used to accurately calculate the slopes of any specular reflective surface, ranging from car bodies to nanometer-level mirrors. This paper presents a new deflectometry technique using binary patterns of increasing frequency to retrieve the surface slopes. Binary Pattern Deflectometry allows almost instant, simple, and accurate slope retrieval, which is required for applications using mobile devices. The paper details the theory of this deflectometry method and the challenges of its implementation. Furthermore, the binary pattern method can also be combined with a classic phase-shifting method to eliminate the need of a complex unwrapping algorithm and retrieve the absolute phase, especially in cases like segmented optics, where spatial algorithms have difficulties. Finally, whether it is used as a stand-alone or combined with phase-shifting, the binary patterns can, within seconds, calculate the slopes of any specular reflective surface.

Recombinant Hendra viruses expressing a reporter gene retain pathogenicity in ferrets.

BACKGROUND: Hendra virus (HeV) is an Australian bat-borne zoonotic paramyxovirus that repeatedly spills-over to horses causing fatal disease. Human cases have all been associated with close contact with infected horses. METHODS: A full-length antigenome clone of HeV was assembled, a reporter gene (GFP or luciferase) inserted between the P and M genes and transfected to 293T cells to generate infectious reporter gene-encoding recombinant viruses. These viruses were then assessed in vitro for expression of the reporter genes. The GFP expressing recombinant HeV was used to challenge ferrets to assess the virulence and tissue distribution by monitoring GFP expression in infected cells. RESULTS: Three recombinant HeV constructs were successfully cloned and rescued; a wild-type virus, a GFP-expressing virus and a firefly luciferase-expressing virus. In vitro characterisation demonstrated expression of the reporter genes, with levels proportional to the initial inoculum levels. Challenge of ferrets with the GFP virus demonstrated maintenance of the fatal phenotype with disease progressing to death consistent with that observed previously with the parental wild-type isolate of HeV. GFP expression could be observed in infected tissues collected from animals at euthanasia. CONCLUSIONS: Here, we report on the first successful rescue of recombinant HeV, including wild-type virus and viruses expressing two different reporter genes encoded as an additional gene cassette inserted between the P and M genes. We further demonstrate that the GFP virus retained the ability to cause fatal disease in a well-characterized ferret model of henipavirus infection despite the genome being an extra 1290 nucleotides in length.

Establishment of a longitudinal pre-clinical model of lyssavirus infection.

Traditional mouse models of lyssavirus pathogenesis rely on euthanizing large groups of animals at various time points post-infection, processing infected tissues, and performing histological and molecular analyses to determine anatomical sites of infection. While powerful by some measures, this approach is limited by the inability to monitor disease progression in the same mice over time. In this study, we established a novel non-invasive mouse model of lyssavirus pathogenesis, which consists of longitudinal imaging of a luciferase-expressing Australian bat lyssavirus (ABLV) reporter virus. In vivo bioluminescence imaging (BLI) in mice revealed viral spread from a peripheral site of inoculation into the central nervous system (CNS), with kinetically and spatially distinct foci of replication in the footpad, spinal cord, and hindbrain. Detection of virus within the CNS was associated with onset of clinical disease. Quantification of virus-derived luminescent signal in the brain was found to be a reliable measure of viral replication, when compared to traditional molecular methods. Furthermore, we demonstrate that in vivo imaging of ABLV infection is not restricted to the use of albino strains of mice, but rather strong BLI signal output can be achieved by shaving the hair from the heads and spines of pigmented strains, such as C57BL/6. Overall, our data show that in vivo BLI can be used to rapidly and non-invasively identify sites of lyssavirus replication and to semi-quantitatively determine viral load without the need to sacrifice mice at multiple time points.

Domestic pigs and Japanese encephalitis virus infection, Australia.

To determine whether relocating domestic pigs, the amplifying host of Japanese encephalitis virus (JEV), decreased the risk for JEV transmission to humans in northern Australia, we collected mosquitoes for virus detection. Detection of JEV in mosquitoes after pig relocation indicates that pig relocation did not eliminate JEV risk.

Operational trials of remote mosquito trap systems for Japanese encephalitis virus surveillance in the Torres Strait, Australia.

Japanese encephalitis virus (JEV) appears nearly annually in the Torres Strait in far northern Queensland, Australia, and is a threat to invade the Australian mainland. Surveillance has involved the use of sentinel pigs that develop detectable viremias and antibody titers to JEV. However, pigs are amplifying hosts for JEV, and thus pose a health risk to the public and to pig handlers who bleed the pigs. A remote mosquito trap system would not have these risks. We report on trials using a remote mosquito trap system for the surveillance of JEV in the Torres Strait. The Mosquito Magnet (MM) Pro, MM Liberty Plus, and a novel updraft trap, the NAQS Mozzie Trap, were run at Badu and Moa islands in the Torres Strait and at Bamaga in the northern Cape York Peninsula from 2002-2005. TaqMan real-time polymerase chain reaction (PCR) was used to detect JEV nucleic acid in weekly mosquito collections. Sentinel pigs located at Badu were also bled and the serum processed by reverse transcriptase (RT)-PCR for JEV antigen and enzyme-linked immunosorbent assay (ELISA) for anti-JEV antibodies. JEV was detected in mosquito collections each year but not in each trap. No JEV was detected in trapped mosquitoes before detection in sentinel pigs. The mosquito trap system cost ca. AU$10,000 per site, about AU$5,000 less than a pig-based system. However, trap failures caused by mosquito-clogged motors, electrical faults, and blocked gas lines reduced the efficacy of some mosquito traps. Nonetheless, a remote mosquito trap system, employing stand alone traps and PCR for viral antigen detection, can be a safe, economical way to detect arbovirus activity in remote areas.

Development and evaluation of real-time polymerase chain reaction assays to identify mosquito (Diptera: Culicidae) bloodmeals originating from native Australian mammals.

Real-time TaqMan polymerase chain reaction (PCR) assays were developed for the identification of mosquito (Diptera: Culicidae) bloodmeals originating from three groups of native Australian mammals. Primers and probes were designed to amplify a partial fragment of the cytochrome b gene of the agile wallaby, Macropus agilis (Gould); brushtail possum, Trichosurus vulpecula (Kerr); and the consensus sequence of the four species of Australian flying fox: Pteropus alecto Temminck, Pteropus conspicillatus Gould, Pteropus poliocephalus Temminck, and Pteropus scapulatus Peters. When tested on DNA extracted from whole tissue, each assay was shown to be specific for the vertebrate host that it was designed to identify. To evaluate the TaqMan assays, 137 field-collected blood-fed mosquitoes were analyzed, from which 128 (93.4%) were identified using one of the assays. Compared with other PCR-based techniques for bloodmeal identification, the TaqMan assays are sensitive, specific, and provide a rapid result without the need for post-PCR manipulation and visualization of products.

Expectoration of Flaviviruses during sugar feeding by mosquitoes (Diptera: Culicidae).

Biological transmission of arboviruses to a vertebrate host occurs when virions are expelled along with saliva during blood feeding by a hematophagous arthropod. We undertook experiments to determine whether mosquitoes expectorate flaviviruses in their saliva while sugar feeding. Batches of Culex annulirostris Skuse and Culex gelidus Theobald (Diptera: Culicidae) were orally infected with Japanese encephalitis (family Flaviviridae, genus Flavivirus, JEV), Kunjin (family Flaviviridae, genus Flavivirus, KUNV; a subtype of West Nile virus), and Murray Valley encephalitis (family Flaviviridae, genus Flavivirus, MVEV) viruses. After a 7-d extrinsic incubation, these mosquitoes were offered sucrose meals via cotton pledgets, which were removed daily and processed for viral RNA by using real-time TaqMan reverse transcriptase-polymerase chain reaction (RT-PCR) assays. JEV, MVEV, and KUNV RNA was detected in all pledgets removed from batches of Cx. gelidus on days 7-14 postexposure. In contrast, detection rates were variable for Cx. annulirostris, with KUNV detected in 0.3 M sucrose pledgets on all days postexposure, and JEV and MVEV detected on 57 and 50% of days postexposure, respectively. Higher concentrations of sucrose in the pledget did not increase virus detection rates. When individual JEV-infected Cx. gelidus were exposed to the sucrose pledget, 73% of mosquitoes expectorated virus with titers that were detectable by TaqMan RT-PCR. These results clearly show that flaviviruses are expectorated by infected mosquitoes during the process of sugar feeding on artificial pledgets. Potential applications of the method for arboviral bioassays and field surveillance are discussed.

Infection and dissemination of dengue virus type 2 in Aedes aegypti, Aedes albopictus, and Aedes scutellaris from the Torres Strait, Australia.

To determine their relative roles in transmission of dengue virus (DENV) in the Torres Strait region of northern Australia, we examined infection and dissemination of a sympatric strain of dengue virus type 2 (DENV-2) in Aedes scutellaris, Ae. albopictus, and Ae. aegypti. In experiments using membrane feeders for virus exposure, infection rates were 83% and 43% for Ae. scutellaris and Ae. aegypti, respectively. Salivary gland infection rates for both species were 43%. In experiments using pledgets for virus exposure, infection rates for Ae. aegypti, Ae. scutellaris, and Ae. albopictus were 68%, 55%, and 37%, respectively. Aedes albopictus exhibited the greatest barriers to infection with only 7% tested developing a salivary gland infection, compared to 42% and 24% of Ae. aegypti and Ae. scutellaris, respectively. These results suggest that Ae. scutellaris may have been responsible for DENV transmission on Torres Strait islands, where Ae. aegypti does not occur. In contrast, Ae. albopictus may not be an important vector of DENV-2 from the Torres Strait.

Short report: the first isolation of Japanese encephalitis virus from mosquitoes collected from mainland Australia.

In response to an incursion of Japanese encephalitis virus (JEV) on Cape York Peninsula, Australia, in 2005, 23,144 Culex mosquitoes were processed for virus detection. A single isolate of JEV was obtained from a pool of Culex sitiens subgroup mosquitoes. This is the first reported mosquito isolate of JEV from the Australian mainland.

An assessment of the interval between booster doses of Japanese encephalitis vaccine in the Torres Strait.

OBJECTIVE: Japanese encephalitis (JE) emerged for the first time in the Torres Strait, north Australia, in 1995. The inactivated mouse-brain derived JE vaccine was offered to all residents of the outer Torres Strait Islands prior to the 1996 wet season. This study was undertaken to determine the appropriateness of the recommended three-year interval between booster doses of the vaccine. METHODS: JE neutralising antibody was measured in residents of Badu Island for whom 30-36 months had passed since either a previous booster or the completion of the primary immunisation series. RESULTS: Only 70 (32%) of 219 eligible individuals had protective antibodies; 50 (37%) of the adults were immune, compared with 20 (24%) of the children (odds ratio (OR) 1.93; 95% confidence interval (CI) 1.01-3.74). CONCLUSIONS: This low level of immunity suggests that there is little in the way of natural boosting from either JE or other closely related viruses. Given the apparent low level of risk of exposure to the JE virus in the Torres Strait, and the logistical complexities involved in delivering the booster doses, the current recommendation of a three-year interval is not inappropriate. IMPLICATIONS: It would be advantageous to have a JE vaccine that is not only safer but also more immunogenic, so that it might be possible to further increase the booster dose interval.

Sucrose density gradient centrifugation and cross-flow filtration methods for the production of arbovirus antigens inactivated by binary ethylenimine.

BACKGROUND: Sucrose density gradient centrifugation and cross-flow filtration methods have been developed and standardised for the safe and reproducible production of inactivated arbovirus antigens which are appropriate for use in diagnostic serological applications. METHODS: To optimise the maximum titre of growth during the propagation of arboviruses, the multiplicity of infection and choice of cell line were investigated using stocks of Ross River virus and Barmah Forest virus grown in both mosquito and mammalian cell lines. To standardise and improve the efficacy of the inactivation of arboviral suspensions, stocks of Ross River virus, Barmah Forest virus, Japanese encephalitis virus, Murray Valley encephalitis virus and Alfuy virus were chemically inactivated using binary ethylenimine at a final concentration of 3 mM. Aliquots were then taken at hourly intervals and crude inactivation rates were determined for each virus using a plaque assay. To ensure complete inactivation, the same aliquots were each passaged 3 times in Aedes albopictus C6/36 cells and the presence of viral growth was detected using an immunofluorescent assay. For larger quantities of viral suspensions, centrifugation on an isopycnic sucrose density gradient or cross-flow filtration was used to produce concentrated, pure antigens or partially concentrated, semi-purified antigens respectively. RESULTS: The results of the propagation experiments suggested that the maximum viral titres obtained for both Ross River virus and Barmah Forest virus were affected by the incubation period and choice of cell line, rather than the use of different multiplicity of infection values. Results of the binary ethylenimine inactivation trial suggested that standardised periods of 5 or 8 hours would be suitable to ensure effective and complete inactivation for a number of different arboviral antigens. CONCLUSION: Two methods used to prepare inactivated arbovirus antigens have been standardised to minimise production failure and expenditure and to provide reagents that conform to the highest quality and safety requirements of a diagnostic serology laboratory. The antigens are suitable for use in either enzyme linked immunosorbent assays or haemagglutination inhibition assays and the optimised protocols can be directly applied to produce antigens from new or emerging arboviral pathogens.

Detection of Australian bat lyssavirus using a fluorogenic probe.

BACKGROUND: Australian bat lyssavirus (ABLV) has been transmitted to humans following a scratch or bite from an infected bat in two cases. Following a scratch or bite to a person, the bat is usually submitted for testing and diagnosis is made using a direct fluorescent antibody test on a brain smear. A nested RT-PCR assay has also been utilised to confirm diagnosis. If positive for lyssavirus, post-exposure prophylaxis is administered. OBJECTIVES: The TaqMan assay was developed to improve the diagnosis of ABLV infection, following problems encountered with the generation of spurious PCR products in the nested RT-PCR and also to reduce the high risk of contamination inherent with nested PCRs. STUDY DESIGN: RNA was extracted from 161 bat brains and the samples were compared using a conventional RT-PCR and the TaqMan based assay. Samples from a patient with an ABLV infection collected antemortem and postmortem were also tested. RESULTS: The sensitivity of the new TaqMan based PCR assay compared favourably with the nested PCR previously in use in our laboratory. This assay was able to detect RNA in samples collected antemortem and postmortem for the diagnosis of a human case of ABLV. CONCLUSIONS: The major advantage of the TaqMan based assay was the speed of diagnosis with a result within minutes of completing the PCR (a result within 4 h of receiving the specimen). This test greatly reduces the chance of false positives through the elimination of second-round PCR and the requirement for agarose gels. The assay is sensitive and specific and should be invaluable for future antemortem and postmortem diagnosis of ABLV infection in humans.

Detection of Australasian Flavivirus encephalitic viruses using rapid fluorogenic TaqMan RT-PCR assays.

The development of single, sensitive, fluorogenic reverse transcriptase-polymerase chain reaction (TaqMan) assays were required for the rapid and specific detection of three encephalitic viruses found in the Australasian region, namely; Japanese encephalitis virus (JEV), Murray Valley encephalitis virus (MVEV), and Kunjin virus (KUNV). Primers and a fluorogenic probe were individually designed to be complementary to a nucleotide region encompassing the 3' terminus of the nonstructural (NS) 5 gene and a portion of the 3' untranslated region (NS5-3'UTR) of each of the viral genomes respectively. Synthetically produced primer and probe controls were developed to minimize the likelihood of contamination and generation of false positives. Viral RNA from singly infected mosquitoes could be detected in pools of 1000 mosquitoes and positive mosquito pools collected from the field have been identified using each assay, indicating a high level of sensitivity and suitability for use in mosquito surveillance programs. In addition, the JEV TaqMan assay has been used to detect successfully viral RNA in sentinel pig serum samples. These assays potentially offer superior and timely detection of encephalitic viruses from surveillance samples, which is essential for the rapid implementation of vector control measures and continued monitoring of virus activity in the Australasian region.

A quantitative PCR (TaqMan) assay for pathogenic Leptospira spp.

BACKGROUND: Leptospirosis is an emerging infectious disease. The differential diagnosis of leptospirosis is difficult due to the varied and often "flu like" symptoms which may result in a missed or delayed diagnosis. There are over 230 known serovars in the genus Leptospira. Confirmatory serological diagnosis of leptospirosis is usually made using the microscopic agglutination test (MAT) which relies on the use of live cultures as the source of antigen, often performed using a panel of antigens representative of local serovars. Other techniques, such as the enzyme linked immunosorbent assay (ELISA) and slide agglutination test (SAT), can detect different classes of antibody but may be subject to false positive reactions and require confirmation of these results by the MAT. METHODS: The polymerase chain reaction (PCR) has been used to detect a large number of microorganisms, including those of clinical significance. The sensitivity of PCR often precludes the need for isolation and culture, thus making it ideal for the rapid detection of organisms involved in acute infections. We employed real-time (quantitative) PCR using TaqMan chemistry to detect leptospires in clinical and environmental samples. RESULTS AND CONCLUSIONS: The PCR assay can be applied to either blood or urine samples and does not rely on the isolation and culture of the organism. Capability exists for automation and high throughput testing in a clinical laboratory. It is specific for Leptospira and may discriminate pathogenic and non-pathogenic species. The limit of detection is as low as two cells.

Field evaluation of a sentinel mosquito (Diptera: Culicidae) trap system to detect Japanese encephalitis in remote Australia.

Incursions of Japanese encephalitis (JE) virus into northern Queensland are currently monitored using sentinel pigs. However, the maintenance of these pigs is expensive, and because pigs are the major amplifying hosts of the virus, they may contribute to JE transmission. Therefore, we evaluated a mosquito-based detection system to potentially replace the sentinel pigs. Single, inactivated JE-infected Culex annulirostris Skuse and C. sitiens Wiedemann were placed into pools of uninfected mosquitoes that were housed in a MosquitoMagnet Pro (MM) trap set under wet season field conditions in Cairns, Queensland for 0, 7, or 14 d. JE viral RNA was detected (cycling threshold [CT] = 40) in 11/12, 10/14, and 2/5 pools containing 200, 1,000, and 5,000 mosquitoes, respectively, using a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR). The ability to detect virus was not affected by the length of time pools were maintained under field conditions, although the CT score tended to increase with field exposure time. Furthermore, JE viral RNA was detected in three pools of 1,000 mosquitoes collected from Badu Island using a MM trap. These results indicated that a mosquito trap system employing self-powered traps, such as the MosquitoMagnet, and a real-time PCR system, could be used to monitor for JE in remote areas.

Vector competence of Australian mosquitoes for chikungunya virus.

Chikungunya virus (CHIKV) is a globally emerging arbovirus responsible for unprecedented outbreaks in the western Indian Ocean, the Indian subcontinent and Italy. To assess the receptivity of Australia to CHIKV, we exposed 10 Australian mosquito species to a 2006 strain of CHIKV isolated from a viremic traveler from Mauritius. In susceptibility trials, the infectious dose required to infect 50% of the mosquitoes was 10(0.6) cell culture infectious dose (CCID)(50)/mosquito for Aedes procax, 10(1.7) CCID(50)/mosquito for Aedes albopictus, 10(2.1) CCID(50)/mosquito for Aedes vigilax, and 10(2.6) CCID(50)/mosquito for Aedes aegypti and Aedes notoscriptus. When exposed to blood meals containing between 10(3.5) and 10(4.1) CCID(50)/mosquito of CHIKV, infection rates in these five species, plus Coquillettidia linealis, were >or=81%. Subsequent transmission rates ranged between 20% for Ae. notoscriptus and 76% for Ae. vigilax. In contrast, Culex spp. were poor laboratory vectors, with infection and dissemination rates

Transmission of Japanese Encephalitis virus from the black flying fox, Pteropus alecto, to Culex annulirostris mosquitoes, despite the absence of detectable viremia.

To determine the potential role of flying foxes in transmission cycles of Japanese encephalitis virus (JEV) in Australia, we exposed Pteropus alecto (Megachiroptera: Pteropididae) to JEV via infected Culex annulirostris mosquitoes or inoculation. No flying foxes developed symptoms consistent with JEV infection. Anti-JEV IgG antibodies developed in 6/10 flying foxes exposed to infected Cx. annulirostris and in 5/5 inoculated flying foxes. Low-level viremia was detected by real-time reverse transcriptase polymerase chain reaction in 1/5 inoculated flying foxes and this animal was able to infect recipient mosquitoes. Although viremia was not detected in any of the 10 flying foxes that were exposed to JEV by mosquito bite, two animals infected recipient mosquitoes. Likewise, an inoculated flying fox without detectable viremia infected recipient mosquitoes. Although infection rates in recipient mosquitoes were low, the high population densities in roosting camps, coupled with migratory behavior indicate that flying foxes could play a role in the dispersal of JEV.