Comparison of real-time reverse transcription-PCR and virus isolation for estimating prevalence of avian influenza virus in hunter-harvested wild birds at waterfowl wintering grounds along the Texas mid-Gulf Coast (2005-2006 through 2008-2009)

Avian influenza virus surveillance in hunter-harvested waterfowl, Texas coast, September 2009-January 2010

Wild waterfowl are considered the natural reservoir of type A influenza viruses, and the migratory nature of many waterfowl species presents a possible vehicle for global dissemination of these infectious agents. In order to fully understand the ecology of influenza viruses, multiyear surveillance efforts are critical, particularly in understudied areas, such as waterfowl wintering areas. Herein we report results obtained during the fifth year ofa 5-yr avian influenza virus (AIV) surveillance project conducted on waterfowl wintering grounds of the Texas Coast. During year 5, the 2009-2010 hunting season (September, November-January), 655 cloacal swabs were collected from hunter-harvested waterfowl and screened for AIV by real-time RT-PCR (rRT-PCR) followed by virus isolation on all positive samples. Molecular methods were used for subtyping all AIV isolates. Sixty-five (9.5%) samples were positive for AIV by rRT-PCR, and 24 (3.7%) AIVs were isolated. Eight different hemagglutinin (H3, 4, 5, 6, 8, 9, 10, and 11) and seven different neuraminidase (N1, 2, 3, 4, 6, 8, and 9) subtypes were identified. This was the first year H8 and H9 were isolated throughout the 5-yr survey. Our results support the fact that continued multiyear surveillance of natural reservoirs, particularly in understudied areas, is needed in order to better understand the ecology of AIVs in nature.

The effect of swab sample choice on the detection of avian influenza in apparently healthy wild ducks

Historically, avian influenza viruses have been isolated from cloacal swab specimens, but recent data suggest that the highly pathogenic avian influenza (HPAI) H5N1 virus can be better detected from respiratory tract specimens. To better understand how swab sample type affects the detection ability of low pathogenic avian influenza (LPAI) viruses we collected and tested four swab types: oropharyngeal swabs (OS), cloacal swabs (CS), the two swab types combined in the laboratory (LCS), and the two swab types combined in the field (FCS). A total of 1968 wild waterfowl were sampled by each of these four methods and tested for avian influenza virus using matrix gene reverse-transcription (RT)-PCR. The highest detection rate occurred with the FCS (4.3%) followed by the CS (4.0%). Although this difference did not achieve traditional statistical significance, Bayesian analysis indicated that FCS was superior to CS with an 82% probability. The detection rates for both the LCS (2.4%) and the OS (0.4%) were significantly different from the FCS. In addition, every swab type that was matrix RT-PCR positive was also tested for recovery of viable influenza virus. This protocol reduced the detection rate, but the ordering of swab types remained the same: 1.73% FCS, 1.42% CS, 0.81% LCS, and 0% OS. Our data suggest that the FCS performed at least as well as any other swab type for detecting LPAI viruses in the wild ducks tested. When considering recent studies showing that HPAI H5N1 can be better detected in the respiratory tract, the FCS is the most appropriate sample to collect for HPAI H5N1 surveillance while not compromising LPAI studies.

Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds

Current avian influenza (AI) virus surveillance programs involving wild birds rely on sample collection methods that require refrigeration or low temperature freezing to maintain sample integrity for virus isolation and/or reverse-transcriptase (RT) PCR. Maintaining the cold chain is critical for the success of these diagnostic assays but is not always possible under field conditions. The aim of this study was to test the utility of Finders Technology Associates (FTA) cards for reliable detection of AI virus from cloacal and oropharyngeal swabs of wild birds. The minimum detectable titer was determined, and the effect of room temperature storage was evaluated experimentally using multiple egg-propagated stock viruses (n = 6). Using real time RT-PCR, we compared results from paired cloacal swab and samples collected on FTA cards from both experimentally infected mallards (Anasplatyrhynchos) and hunter-harvested waterfowl sampled along the Texas Gulf Coast. Based on the laboratory trials, the average minimal detectable viral titer was determined to be 1 x 10(4.7) median embryo infectious dose (EID50)/ml (range: 1 x 10(4.3) to 1 x 10(5.4) EID50/ml), and viral RNA was consistently detectable on the FTA cards for a minimum of 20 days and up to 30 days for most subtypes at room temperature (23 C) storage. Real-time RT-PCR of samples collected using the FTA cards showed fair to good agreement in live birds when compared with both real-time RT-PCR and virus isolation of swabs. AI virus detection rates in samples from several wild bird species were higher when samples were collected using the FTA cards compared with cloacal swabs. These results suggest that FTA cards can be used as an alternative sample collection method when traditional surveillance methods are not possible, especially in avian populations that have historically received limited testing or situations in which field conditions limit the ability to properly store or ship swab samples.

Influenza a viruses from wild birds in Guatemala belong to the North American lineage

The role wild bird species play in the transmission and ecology of avian influenza virus (AIV) is well established; however, there are significant gaps in our understanding of the worldwide distribution of these viruses, specifically about the prevalence and/or significance of AIV in Central and South America. As part of an assessment of the ecology of AIV in Guatemala, we conducted active surveillance in wild birds on the Pacific and Atlantic coasts. Cloacal and tracheal swab samples taken from resident and migratory wild birds were collected from February 2007 to January 2010.1913 samples were collected and virus was detected by real time RT-PCR (rRT-PCR) in 28 swab samples from ducks (Anas discors). Virus isolation was attempted for these positive samples, and 15 isolates were obtained from the migratory duck species Blue-winged teal. The subtypes identified included H7N9, H11N2, H3N8, H5N3, H8N4, and H5N4. Phylogenetic analysis of the viral sequences revealed that AIV isolates are highly similar to viruses from the North American lineage suggesting that bird migration dictates the ecology of these viruses in the Guatemalan bird population.

Cross-seasonal patterns of avian influenza virus in breeding and wintering migratory birds: a flyway perspective

The spread of avian influenza viruses (AIV) in nature is intrinsically linked with the movements of wild birds. Wild birds are the reservoirs for the virus and their migration may facilitate the circulation of AIV between breeding and wintering areas. This cycle of dispersal has become widely accepted; however, there are few AIV studies that present cross-seasonal information. A flyway perspective is critical for understanding how wild birds contribute to the persistence of AIV over large spatial and temporal scales, with implications for how to focus surveillance efforts and identify risks to public health. This study characterized spatio-temporal infection patterns in 10,389 waterfowl at two important locations within the Pacific Flyway--breeding sites in Interior Alaska and wintering sites in California's Central Valley during 2007-2009. Among the dabbling ducks sampled, the northern shoveler (Anas clypeata) had the highest prevalence of AIV at both breeding (32.2%) and wintering (5.2%) locations. This is in contrast to surveillance studies conducted in other flyways that have identified the mallard (Anas platyrhynchos) and northern pintail (Anas acuta) as hosts with the highest prevalence. A higher diversity of AIV subtypes was apparent at wintering (n=42) compared with breeding sites (n=17), with evidence of mixed infections at both locations. Our study suggests that wintering sites may act as an important mixing bowl for transmission among waterfowl in a flyway, creating opportunities for the reassortment of the virus. Our findings shed light on how the dynamics of AIV infection of wild bird populations can vary between the two ends of a migratory flyway.

Multiyear surveillance for avian influenza virus in waterfowl from wintering grounds, Texas coast, USA

This surveillance can help in assessments of the prevalence of wild animal-to-human transmission.

We studied the prevalence of influenza A virus in wintering waterfowl from the Central Flyway on the Gulf Coast of Texas. Of 5,363 hunter-harvested migratory and resident waterfowl and wetland-associated game birds sampled during 3 consecutive hunting seasons (September–January 2006–07, 2007–08, and 2008–09), real-time reverse transcription–PCR detected influenza A matrix sequences in 8.5% of samples, H5 in 0.7%, and H7 in 0.6%. Virus isolation yielded 134 influenza A viruses, including N1–N9, H1–H7, H10, and H11 subtypes. Low-pathogenicity H7 subtype was isolated during January, September, and November 2007 and January 2008; low-pathogenicity H5 subtype was isolated during November and December 2007.

Shedding light on avian influenza H4N6 infection in mallards: modes of transmission and implications for surveillance

BACKGROUND

Wild mallards (Anas platyrhychos) are considered one of the primary reservoir species for avian influenza viruses (AIV). Because AIV circulating in wild birds pose an indirect threat to agriculture and human health, understanding the ecology of AIV and developing risk assessments and surveillance systems for prevention of disease is critical.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, mallards were experimentally infected with an H4N6 subtype of AIV by oral inoculation or contact with an H4N6 contaminated water source. Cloacal swabs, oropharyngeal swabs, fecal samples, and water samples were collected daily and tested by real-time RT-PCR (RRT-PCR) for estimation of viral shedding. Fecal samples had significantly higher virus concentrations than oropharyngeal or cloacal swabs and 6 month old ducks shed significantly more viral RNA than 3 month old ducks regardless of sample type. Use of a water source contaminated by AIV infected mallards, was sufficient to transmit virus to naïve mallards, which shed AIV at higher or similar levels as orally-inoculated ducks.

CONCLUSIONS

Bodies of water could serve as a transmission pathway for AIV in waterfowl. For AIV surveillance purposes, water samples and fecal samples appear to be excellent alternatives or additions to cloacal and oropharyngeal swabbing. Furthermore, duck age (even within hatch-year birds) may be important when interpreting viral shedding results from experimental infections or surveillance. Differential shedding among hatch-year mallards could affect prevalence estimates, modeling of AIV spread, and subsequent risk assessments.