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H7N3 in Saskatchewan Canada[/B]
Recombinomics Commentary
September 27, 2007
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Although the current outbreak is almost certainly linked to wild birds, the influenza surveillance program in Canada failed to detect high or low path H7 in wild birds this year or last year.
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I will be attending the conference tomorrow.
If anyone has relevant questions, points or comments that they would like to have addressed, please let me know.
J.
Are there other effective ways to test large bird populations?This underscores the problems with the lack of scale in wild bird testing, making it a less useful resource
Could the water from lakes be tested, i.e., if lakes known to accomodate large migratory populations were tested every ?2? weeks, could they expect to find sufficient evidence of AI?
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Little is known about the ecology and evolution of avian influenza in the natural environment, despite how these affect the potential for transmission. Most work has focused on characterizing viruses isolated from hosts such as waterfowl, and there have also been several instances of isolation and detection from abiotic sources such as water and ice. We used RT-PCR to amplify and characterize the influenza virus sequences present in sediments of ponds that are used heavily by waterfowl. The detection rate of influenza virus was high (>50 %). Characterization of the viruses present by sequencing part of the haemagglutinin (HA) gene showed that there is a diverse collection of viruses in these sediments. We sequenced 117 partial HA gene clones from 11 samples and detected four different HA subtypes (H3, H8, H11 and H12), with approximately 65 % of clone sequences being unique. This culture-independent approach was also able to detect a virus subtype that was not found by sampling of birds in the same geographical region in the same year. Viruses were detected readily in the winter when the ponds were frozen, indicating that these sediments could be a year-to-year reservoir of viruses to infect birds using the ponds, although we have not shown that these viruses are viable. We demonstrate that this approach is a feasible and valuable way to assess the prevalence and diversity of viruses present in the environment, and can be a valuable complement to more difficult viral culturing in attempting to understand the ecology of influenza viruses.
5. Environmental sampling of water and bird feces: Waterfowl infected with or carrying avian influenza viruses release these viruses through the intestinal tract and the virus can be detected in both feces and water in which the birds swim. This provides a means of virus spread to new avian hosts and potentially to poultry or other livestock. Analysis of both water and fecal material from waterfowl habitat can provide evidence of avian influenza viruses circulating in wild bird populations. In 2006, USDA and others plan to collect 50,000 environmental samples from high-risk waterfowl habitats throughout the lower 48 states, Hawaii, as well as from other areas such as Guam and the U.S. Territories and Freely Associated States of the Pacific.
What is evident from this study is the virus was circulating in the barn sampled and in the surrounding environment. The estimated viral load yielded a value of 292 viral doses/m3 of barn air. The quantitative, spatial and temporal nature of the dispersion however remains undefined. It would be speculative to say more about the possibility of airborne dispersion without conducting a better-designed study to define viral presence in and around contiguously infected barns. Geomorphic mapping detailing viral plumes and their dynamics based on a meteorological continuum would be especially useful.
At farms B and C there were dead infected animals. The slit samplers should have captured particles from the exhaust fans. However, the slit samplers were all placed approximately 75-100m on opposite sides of the barn along the line of the forecast winds for the area. As the winds were variable it was not practical to shift the sampling array once set up. Because of the shifting winds it is possible that viral aerosols might not have reached the sampling sites. In addition, the sampling rate of the slit samplers was 30 lpm (as compared to the high volume XMX sampler which collected 800 lpm) which may have been insufficient to capture adequate material above a detectable limit. This speculation was partially confirmed by tracer smoke (electric smoke generator and smoke grenades provided to CFIA by the RCMP) that was used to determine the volume and direction of airflow from the barn exhaust fans. (figure 3). In both locations the exhaust fans were directed into the wind, resulting in smoke being forced back towards the barns and up over the roof. This meant that the exhausted air particles were well above ground level and would not be low enough to be sampled by the slit samplers positioned nearby (figure 4).
The negative results from the slit samplers may have resulted from a number of factors. As shown in table 1, there were no live viruses sampled from farm A. At this farm, the animals were not yet dying from infection and CFIA swab samples from these birds were positive only for PCR tests. Thus it is conceivable that no viable airborne infectious particles were produced at the time the slit samples were taken.
This suggested that the virus was hardy enough to withstand the physical impact imposed by this high volume sampling system.
Samples 3-6, which also were positive on the original PCR were not believed to be true positives, but rather resulted from the ?flushing? of residual material remaining in the sampler from samples one and two. This was supported by the rapid decrease in the concentration as determined by the semi-quantitative PCR, with samples 3 and 4 being two logs lower and with samples 5 and 6 being negative with the less sensitive PCR. The sampler was decontaminated after sample 7.
Although slit sampling technology has been successfully used for the collection of SARS virus indoors, it was not effective in collecting Avian influenza virus outdoors, as shown in this situation. The concentration of any circulating virus 75-100m from the barns was probably too low to be collected by the relatively low flow rate (30 lpm) of the slit samplers. In addition, the concept of using a fixed sampling position based on the forecast prevailing winds was not optimal as the local micrometeorology (interaction of wind with buildings and trees around the sampling area) resulted in shifting winds and dispersal of air from the barns (figure 3) at least 5-10m above ground level and far above the samplers.
The positive sample 10 was notable in that it was not collected at an infected premise but as part of a random collection of samples in different parts of Abbotsford. It was collected in an open field approximately 800 m away from farm B. We felt this was a true positive since samples 8-9 and 11-16 were all negative showing that there was no possibility of any cross contamination between samples. Although positive by the original PCR it was shown to be negative by culture and by the less sensitive semi-quantitative PCR. This indicates that the concentration was very low. Since the sample
was collected during daylight hours it was unlikely to find live virus in the sample. Any viable virus would probably have been inactivated by sunlight.
I really would like to see testing on airborne particles done again with proper equipment.