Single and combination diagnostic test efficiency and cost analysis for detection and isolation of avian influenza virus from wild bird cloacal swabs

Avian Influenza Virus Isolation, Propagation, and Titration in Embryonated Chicken Eggs

Avian influenza virus and some mammalian influenza A viruses can be isolated, propagated, and titrated in embryonated chicken eggs (ECEs). Most sample types can be accommodated in ECE culture with appropriate processing. Isolation may also be accomplished in cell culture, and if a mammalian lineage influenza A is expected to be in an avian sample, for example swine influenza in turkey specimens, mammalian cell may be preferable. Culture in ECEs is highly sensitive but is not specific for influenza A, which may be an advantage because a sample may be screened for several agents at once. Once an agent is isolated in culture, the presence of influenza viruses can be confirmed by hemagglutination inhibition assay, antigen immunoassay, agar gel immunodiffusion assay, or RT-PCR. Finally, ECEs may be used to propagate and titrate an avian influenza virus.

Risk factors and spatial relative risk assessment for influenza A virus in poultry and swine in backyard production systems of central Chile

Backyard production systems (BPS) are a common form of poultry and swine production worldwide. The limited implementation of biosecurity standards in these operations makes BPS a potential source for the emergence of pathogens that have an impact on both animal and public health. Information regarding circulation of influenza A virus (IAV) in poultry and swine raised in BPS is scarce; particularly in South American countries. The objective of this study was to estimate prevalence and seroprevalence of IAV in BPS in central Chile, identify subtype diversity, evaluate risk factors and spatial relative risk for IAV. Samples were collected from 329 BPS from central Chile. Seroprevalence at BPS level was 34.7% (95% CI: 23.1%–46.2%), 19.7% (95% CI: 9.9%–30.6%) and 11.7% (95% CI: 7.2%–16.4%), whereas prevalence at BPS level was 4.2% (95% CI: 0.0%–8.8%), 8.2% (95% CI: 0.8%–14.0%) and 9.2% (95% CI: 4.8%–13.1%), for the Metropolitan, Valparaiso and LGB O’Higgins regions, respectively. Spatial analysis revealed that central‐western area of Metropolitan region and the southern province of Valparaiso region could be considered as high‐risk areas for IAV (spatial relative risk = 2.2, p < .05). Logistic regression models identified the practice of breeding both poultry and pigs at the BPS as a risk factor (95% CI 1.06–3.75). From 75 IAV ELISA‐positive sera, 20 chicken sera had haemagglutination inhibition titres ranging from 20 to 160, and of these, 11 had microneutralization titres ranging from 40 to 960 for one or more IAV subtypes. Identified subtypes were H1, H3, H4, H9, H10 and H12. Results from this study highlight the need for further IAV surveillance programmes in BPS in Chile. Early detection of IAV strains circulating in backyard animals, especially in regions with large human populations, could have an enormous impact on animal and public health.

Circulation of influenza in backyard productive systems in central Chile and evidence of spillover from wild birds

Backyard productive systems (BPS) are recognized as the most common form of animal production in the world. However, BPS frequently exhibit inherent biosecurity deficiencies, and could play a major role in the epidemiology of animal diseases and zoonoses. The aim of this study was to determine if influenza A viruses (IAV) were prevalent in backyard poultry and swine BPS in central Chile. Through active surveillance in Valparaiso and Metropolitan regions from 2012 - 2014, we found that influenza virus positivity by real-time RT-PCR (qRT-PCR) ranged from 0% during winter 2012-45.8% during fall 2014 at the farm level. We also obtained an H12 hemagglutinin (HA) sequence of wild bird origin from a domestic Muscovy duck (Cairina moschata), indicating spillover from wild birds into backyard poultry populations. Furthermore, a one-year sampling effort in 113 BPS in the Libertador Bernardo O'Higgins (LGB ÓHiggins) region showed that 12.6% of poultry and 2.4% of swine were positive for IAV by enzyme-linked immunosorbent assay (ELISA), indicative of previous exposure of farm animals to IAV. This study highlights the need for improved IAV surveillance in backyard populations given the close interaction between domestic animals, wild birds and people in these farms, particularly in an understudied region, like South America.

Avian influenza: virology, diagnosis and surveillance

Avian influenza virus (AIV) is the causative agent of a zoonotic disease that affects populations worldwide with often devastating economic and health consequences. Most AIV subtypes cause little or no disease in waterfowl, but outbreaks in poultry can be associated with high mortality. Although transmission of AIV to humans occurs rarely and is strain dependent, the virus has the ability to mutate or reassort into a form that triggers a life-threatening infection. The constant emergence of new influenza strains makes it particularly challenging to predict the behavior, spread, virulence or potential for human-to-human transmission. Because it is difficult to anticipate which viral strain or what location will initiate the next pandemic, it is difficult to prepare for that event. However, rigorous implementation of biosecurity, vaccination and education programs can minimize the threat of AIV. Global surveillance programs help record and identify newly evolving and potentially pandemic strains harbored by the reservoir host.

Avian influenza virus isolation, propagation, and titration in embryonated chicken eggs

Avian influenza virus and some mammalian influenza A viruses are usually isolated, propagated, and titrated in embryonated chicken eggs (ECE). Most any sample type can be accommodated for culture with appropriate processing. Isolation may also be accomplished in cell culture particularly if mammalian lineage isolates are suspected, for example, swine influenza in turkey specimens. Culture is highly sensitive, but is not specific for influenza A, which may be an advantage because a sample may be screened for several agents at once. Once an agent is isolated in culture, the presence of influenza viruses is confirmed with any of several assays. The methods for propagating virus isolates in ECE are described.

Avian influenza: mixed infections and missing viruses

A high prevalence and diversity of avian influenza (AI) viruses were detected in a population of wild mallards sampled during summer 2011 in California, providing an opportunity to compare results obtained before and after virus culture. We tested cloacal swab samples prior to culture by matrix real-time PCR, and by amplifying and sequencing a 640bp portion of the hemagglutinin (HA) gene. Each sample was also inoculated into embryonated chicken eggs, and full genome sequences were determined for cultured viruses. While low matrix Ct values were a good predictor of virus isolation from eggs, samples with high or undetectable Ct values also yielded isolates. Furthermore, a single passage in eggs altered the occurrence and detection of viral strains, and mixed infections (different HA subtypes) were detected less frequently after culture. There is no gold standard or perfect reference comparison for surveillance of unknown viruses, and true negatives are difficult to distinguish from false negatives. This study showed that sequencing samples prior to culture increases the detection of mixed infections and enhances the identification of viral strains and sequences that may have changed or even disappeared during culture.

Prevalence and characterization of influenza viruses in diverse species in Los Llanos, Colombia

While much is known about the prevalence of influenza viruses in North America and Eurasia, their prevalence in birds and mammals in South America is largely unknown. To fill this knowledge gap and provide a baseline for future ecology and epidemiology studies, we conducted 2 years of influenza surveillance in the eastern plains (Los Llanos) region of Colombia. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) identified influenza viruses in wild birds, domestic poultry, swine and horses. Prevalence ranged from 2.6% to 13.4% across species. Swine showed the highest prevalence and were infected primarily with 2009 pandemic H1N1 (pH1N1) viruses genetically related to those in humans. In addition, we isolated H5N2 viruses from two resident species of whistling ducks (genus Dendrocygna) that differed completely from previous South American isolates, instead genetically resembling North American wild bird viruses. Both strains caused low pathogenicity in chickens and mammals. The prevalence and subtype diversity of influenza viruses isolated from diverse species within a small area of Colombia highlights the need for enhanced surveillance throughout South America, including monitoring of the potential transmissibility of low-pathogenic H5N2 viruses from wild birds to domestic poultry and the emergence of reassortant viruses in domestic swine.

Evaluation of different embryonating bird eggs and cell cultures for isolation efficiency of avian Influenza A Virus and Avian paramyxovirus serotype 1 from real-time reverse transcription polymerase chain reaction–positive wild bird surveillance samples

Virus isolation rates for influenza A virus (FLUAV) and Avian paramyxovirus serotype 1 (APMV-1) from wild bird surveillance samples are lower than molecular detection rates for the specific viral genomes. The current study was conducted to examine the possibility of increased virus isolation rates from real-time reverse transcription polymerase chain reaction (real-time RT-PCR) using alternative virus isolation substrates such as embryonating duck eggs (EDEs), embryonating turkey eggs (ETEs), Madin–Darby canine kidney (MDCK) cell cultures, and African green monkey kidney (Vero) cell cultures. Rectal swabs of birds in the orders Anseriformes and Charadriiformes were tested by real-time RT-PCR for the presence of FLUAV and APMV-1 genomes, and virus isolation (VI) was attempted on all real-time RT-PCR–positive samples. Samples with threshold cycle (Ct) ≤37 had VI rates for FLUAV of 62.5%, 50%, 43.8%, 31.5%, and 31.5% in embryonating chicken eggs (ECEs), ETEs, EDEs, MDCK cells, and Vero cells, respectively. A higher isolation rate was seen with ECEs compared to either cell culture method, but similar isolation rates were identified between the different embryonating avian eggs. Virus isolation rates for APMV-1 on samples with real-time RT-PCR Ct ≤37 were 75%, 100%, 100%, 0%, and 37.5% in ECEs, ETEs, EDEs, MDCK cells, and Vero cells, respectively. Significantly higher VI rates were seen with ECEs as compared to either cell culture method for all real-time RT-PCR–positive samples. Because of the limited availability and high cost of ETEs and EDEs, the data support the continuing usage of ECEs for primary isolation of both FLUAV and APMV-1 from real-time RT-PCR–positive wild bird surveillance samples.

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.