The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status

Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.

Avian Influenza Virus Subtype H9N2 Affects Intestinal Microbiota, Barrier Structure Injury, and Inflammatory Intestinal Disease in the Chicken Ileum

Avian influenza virus subtype H9N2 (H9N2 AIV) has caused significant losses to the poultry industry due to the high mortality associated with secondary infections attributable to E. coli. This study tries to address the underlying secondary mechanisms after H9N2 AIV infection. Initially, nine day-old specific pathogen-free chickens were assigned to control (uninfected) and H9N2-infected groups, respectively. Using Illumina sequencing, histological examination, and quantitative real-time PCR, it was found that H9N2 AIV caused intestinal microbiota disorder, injury, and inflammatory damage to the intestinal mucosa. Notably, the genera Escherichia, especially E. coli, significantly increased (p < 0.01) at five days post-infection (dpi), while Lactobacillus, Enterococcus, and other probiotic organisms were significantly reduced (p < 0.01). Simultaneously, the mRNA expression of tight junction proteins (ZO-1, claudin 3, and occludin), TFF2, and Muc2 were significantly reduced (p < 0.01), indicating the destruction of the intestinal epithelial cell tight junctions and the damage of mucin layer construction. Moreover, the mRNA expression of proinflammatory cytokines IFN-γ, IL-22, IFN-α, and IL-17A in intestinal epithelial cells were significantly upregulated, resulting in the inflammatory response and intestinal injury. Our findings may provide a theoretical basis for observed gastroenteritis-like symptoms such as diarrhea and secondary E. coli infection following H9N2 AIV infection.

Evaluation of the pooling of swabs for real-time PCR detection of low titre shedding of low pathogenicity avian influenza in turkeys

The purpose of this study was to determine whether pooling avian influenza (AI)-positive swabs with negative swabs has a detrimental effect on the sensitivity of AI real-time reverse transcription-polymerase chain reactions (rRT-PCRs). Cloacal and buccal swabs were sampled daily from 12 turkeys infected with A/goose/England/07(H2N2). For half the turkeys, each swab was mixed with four swabs from known AI-negative turkeys, and for the other half the swabs were tested individually. Bayesian modelling was used to (i) determine whether pooling the positive swabs compromised the cycle threshold (C(t)) value obtained from the rRT-PCRs, and (ii) estimate the likelihood of detection of an H2N2 infected turkey flock via rRT-PCR for pooled and individually tested swabs (cloacal and buccal) vs. the number of days post-infection of the flock. Results indicated that there was no significant effect of compromising AI rRT-PCR sensitivity by pooling a weak positive swab with negative swabs on the Ct values which were obtained. Pooled sampling was able to widen the detection window compared to individual sampling, for the same number of rRT-PCR tests. This indicates that pooled sampling would be an effective method of reducing the number of tests to be performed to determine flock status during an AI outbreak and for surveillance.

Qualitative detection of avian influenza A (H5N1) viruses: a comparative evaluation of four real-time nucleic acid amplification methods

The aim of this study was to determine the performance of real-time amplification based methods - NASBA, TaqMan, RT-FRET, and RT-PCR LUXtrade mark formats - for the detection of influenza A (H5N1) virus RNA. In an analysis of 54 samples obtained from a range of animal species in Thailand during the period 2003-2006, results showed that the NASBA (H5=98.2%, N1=96.3%), TaqMan (H5=98.2%, N1=96.3%) and FRET (H5=98.2%, N1=96.3%) had significantly higher rates of positive detection than LUX (H5=94.4%, N1=50.0%; P<0.001) for influenza A, H5 and N1 isolates. There were no false-positive results from any methods used in the negative-control group of samples. The limits of analytical detection were at least 10copies/reaction in real-time NASBA and LUX assays, while FRET and TaqMan assay appeared to be less sensitive at > or =100copies/reaction. The assays were relatively specific without cross-reactivity to a number of other influenza strains or viral pathogens. In conclusion, our study demonstrated that real-time NASBA, TaqMan and FRET assays can be used to detect influenza A (H5N1) from a wide range of hosts, and be specific for H5N1 samples obtained during different outbreaks (2003-2006). All assays provided the benefit of rapid influenza H5N1 identification for early diagnosis, in the range of hours, and they are well suited to high throughput analyses.

Analysis of the 1999–2000 highly pathogenic avian influenza (H7N1) epidemic in the main poultry-production area in northern Italy

We evaluated the effects of risk factors and control policies following the highly pathogenic avian influenza (HPAI) epidemic that struck northern Italy's poultry industry in the winter of 1999-2000. The epidemic was caused by a type-A influenza virus of the H7N1 subtype, that originated from a low-pathogenic AI virus which spread among poultry farms in northeastern Italy in 1999 and eventually became virulent by mutation. Most infected premises (IP) were located in the regions of Lombardy and Veneto (382 out of 413, 92.5%), and the eradication measures provided for in the European legislation were enforced. In Veneto, where flock density was highest, infection-control was also accomplished by means of depopulation of susceptible flocks through a ban on restocking and pre-emptive slaughter of flocks that were in the vicinities of or that had dangerous contacts with IPs. In Lombardy, such control measures were applied to a lesser extent. Infection incidence rate (IR) was 2.6 cases per 1000 flocks per day in Lombardy and 1.1 in Veneto. After the implementation of infection-control measures, the at-risk population, the percentage of flocks < or =1.5 km from IPs, and the HPAI-IR underwent a greater reduction in Veneto than in Lombardy. Although the proximity (< or =1.5 km) to IPs in the temporal risk window (TRW) was a major risk factor for HPAI at the individual flock level, its effect at the population level (population-attributable fraction) did not exceed 31.3%. Viral transmission therefore also occurred among relatively distant flocks. Turkey flocks were characterised by greater IR of HPAI compared with other bird species such as layer hens, broilers, gamebirds, and waterfowl, even when located at distances >1.5 km from IPs. In Lombardy, IR for species other than turkeys was also relatively high.

No new human infections with A/H5N1 in Turkey but national measures and international support continue

There have been no new human cases of A/H5N1 diagnosed in Turkey since mid-January, and only three patients were still receiving care in hospital at 27 January

Two fatal human infections with avian influenza H5, Turkey, January 2006

Two teenagers in Turkey have died from infections with influenza H5 virus subtype, the Turkish ministry of health has confirmed

Changes in influenza A (H5N1) epidemiology discussed at World Health Organization intercountry consultation in Manila

In May 2005 the World Health Organization (WHO) organised an intercountry consultation in Manila to discuss the implications of an apparent change in the epidemiology of Influenza A (H5N1) infection in Asia

Emergence of a potentially pathogenic H5N2 influenza virus in chickens

Highly pathogenic influenza A viruses periodically infect both humans and nonhuman animals, including chickens. To gain insight into the origin of influenza outbreaks in poultry, we investigated two H5N2 viruses, A/chicken/Pennsylvania/13609/93 (Ck/PA/93) and A/chicken/Florida/25717/93 (Ck/FLA/93), that had been isolated in live-bird markets in Pennsylvania and Florida during surveillance studies in 1993. Phylogenetic analysis of the HA genes of these isolates, as well as H5N2 viruses isolated from ruddy turnstone surfbirds in 1991 (A/ruddy turnstone/Delaware/244/91 [RT/DE/91]) and other known H5 strains, indicated that Ck/PA/93 and Ck/FLA/93 share a common ancestor with RT/DE/91 and did not originate from A/chicken/Pennsylvania/1370/83 (Ck/PA/1370/83), which devastated chicken populations in 1983-1984. Both isolates were nonpathogenic in chickens by experimental infection and their HA protein (HA0) could not be cleaved into HA1 and HA2 without trypsin. The sequences at the HA cleavage sites of Ck/PA/93 and Ck/FLA/93 (R-K-T-R) appear to be intermediate between those of virulent and avirulent viruses, raising the possibility that a single mutation could promote virulence in chickens. We therefore recommend eradication of such viruses as soon as they appear.

Deduced amino acid sequences of the haemagglutinin of H5N1 avian influenza virus isolates from an outbreak in turkeys in Norfolk, England

The deduced amino acid sequences of the haemagglutinins of avian influenza viruses, isolated from an outbreak in turkeys in Norfolk, England in 1991/92, were determined by PCR amplification and cycle sequencing. Both the highly pathogenic and avirulent isolates had the same cleavage site sequence with multiple-basic amino acids, which normally would be expected only for the former. Clones derived by plaque picking from the highly pathogenic isolate ranged from low to very high pathogenicity in vivo and these, and the original isolates, showed nucleotide and amino acid variation at one or more of five possible sites, none of which were at the cleavage site. None of these site variations correlated with pathogenicity, suggesting that the factor responsible for the suppression of the expected effects of the multiple-basic amino acid haemagglutinin cleavage site in the avirulent isolate may not have been part of the haemagglutinin amino acid sequence.

Antigen-capture enzyme immunoassay for detection of avian influenza virus in turkeys

A double-antibody sandwich ELISA (DAS-ELISA) was developed for detection of avian influenza virus (AIV) antigen. A monoclonal antibody to the viral nucleoprotein (NP) was used to coat the ELISA plates. A direct DAS-ELISA and an indirect DAS-ELISA were evaluated. In the direct DAS-ELISA, monoclonal antibody to the AIV NP conjugated with horseradish peroxidase was used. The direct DAS-ELISA was evaluated for its sensitivity to detect purified NP; this procedure detected as little as 0.1 ng. In the indirect DAS-ELISA, rabbit NP antibody and horseradish peroxidase-conjugated goat anti-rabbit immunoglobin were used as primary and secondary antibodies, respectively. The indirect DAS-ELISA was evaluated for its ability to detect the AIV antigen in tracheal and cloacal specimens from turkeys inoculated with AIV. Results of indirect DAS-ELISA were compared with those of conventional virus isolation. Percentage agreement between indirect DAS-ELISA and virus isolation in AIV-positive samples was found to be 76.1% and, in AIV-negative samples, it was found to be 82.1%. These results indicate that the DAS-ELISA might be a viable alternative to virus isolation because of its rapidity, compared with virus isolation.

Effect of temperature on the stability of avian influenza virus antigens under different storage conditions

The combined effect of time and temperature on the stability of two avian influenza virus (AIV) isolates concentrated with polyethylene glycol (PEG), stored at different temperatures, and used in the preparation of avian influenza vaccine was evaluated in turkeys at 24 hr and at 12, 24, 30, 36, and 42 months of storage. The differences detected between antibodies raised in turkeys by vaccines made from isolates under different storage conditions, times, and temperatures were not significant (P > 0.05), especially with vaccines prepared from one isolate. Virus recovery rates following challenge studies of vaccinated birds were similar. However, birds that were vaccinated twice had lower rates of virus recovery from the trachea, lungs, pancreas, and fecal samples following challenge infection. The results suggest that if stable isolates of AIV can be identified, such isolates can be rapidly concentrated with PEG and stored at -20 C or -196 C for at least 42 months without any loss of potency in the vaccine prepared from these isolates. This would reduce the costs associated with vaccine storage and subsequent expiration dates.

Comparative evaluation of tissue trophism characteristics in turkeys and mallard ducks after intravenous inoculation of type A influenza viruses

Ten avian type A influenza viruses consisting of seven waterfowl-origin, one pheasant-origin, and two turkey-origin viruses were evaluated for their pathogenicity potential after intravenous inoculation into domestic turkeys and mallard ducks (Anas platyrhynchos). The replicative abilities and tissue trophism properties of each virus isolate were examined in both species. The overall virus-isolation rate and histopathological lesion score were greater in the turkeys than in the ducks. The waterfowl-origin viruses caused more tissue damage in turkeys than in ducks but had a narrower tissue distribution range. The pheasant isolate was extremely pathogenic in turkeys but had limited distribution and little effect in ducks. The turkey isolates were more pathogenic in turkeys than in ducks. The pancreas was the most severely affected organ in turkeys, followed by kidney and liver. The spleen and bursa were the most commonly affected organs in ducks.

[Classical fowl plague and milder influenza infections in birds and mammals]

Wild waterfowl are currently considered the largest reservoir of the various haemagglutinin (H) and neuraminidase (N) subtypes of influenza virus. Until now thirteen different H-types and nine different N-types have been detected in these populations. In the first instance, virus transmission from fowl to other animal species and to man is not causing disease problems. However, small changes at the molecular level of a given HN-subtype recently caused a dramatic increase in virulence for chickens. Genes fragments coding for haemagglutinin or neuraminidase can be exchanged between viruses which propagate in the same individual. This phenomenon-'genetic reassortment'-is of major epidemiological significance when it occurs in pigs. New influenza epidemics in the human population consistently originate in areas where waterfowl, pigs and human beings live close together. At the moment, the virological and serological diagnosis of influenza A infections is based ELISAs for antigen and antibody detection. Both ELISAs employ a monoclonal antibody directed against a conserved antigenic determinant of the influenza A nucleoprotein. The use of these tests can simplify the diagnosis of and screening for influenza A infections, particularly in those species which harbour several H- and N-subtypes.

Nephrotropic properties demonstrated by A/chicken/Alabama/75 (H4N8) following intravenous challenge of chickens

Tissue tropism properties of A/chicken/Alabama/75 (H4N8) were examined after intravenous inoculation of 5-week-old specific-pathogen-free chickens. From 14 clinically normal chickens euthanatized on days 1-20 postinoculation, the frequencies of virus recovery were highest for cloacal swabs (86%), bursal swabs (64%), and kidney tissues (64%) and lowest for tracheal swabs (14%), thymus tissues (14%), bone-marrow swabs (7%), and brain tissues (0%). Evidence that the high frequency of virus recovery from kidney tissues was associated with virus replication in the kidney tissues was provided by high virus titers, ranging up to 10(9.5) mean embryo infectious dose per gram of kidney tissue, and by identification of intranuclear and intracytoplasmic type A influenza nucleoprotein in kidney cells using immunohistochemistry. Virus-recovery and virus titer results from three chickens that died on days 4 and 5 postinoculation paralleled the results from the clinically normal chickens. These findings indicate that A/chicken/Alabama/75 has nephrotropic properties similar to nephrotropic properties previously reported for waterfowl-origin type A influenza viruses and provide evidence that kidney lesions could be manifestations of systemic influenza infections in commercial laying chickens.

Evaluation of the kidney as a potential site of avian influenza virus persistence in chickens

One-day-old chickens were inoculated intravenously with one of three low-pathogenicity avian-origin influenza isolates. On day 5 postinoculation (PI), the frequency of influenza virus isolation from cloacal swabs following challenge with each isolate ranged from 83% to 100% for clinically normal euthanatized chickens. Influenza virus was also frequently isolated from kidneys of these chickens (47%) and from chickens that died (100%). Kidneys positive for virus isolation had lesions of nephrosis and/or acute nephritis, and influenza viral nucleoprotein was demonstrated in nuclei and cytoplasm of necrotic renal tubule epithelium. On sampling days 28 and 45/60 PI, influenza virus was neither isolated from nor immunohistochemically demonstrated in kidneys (0/125); however, the kidneys (47%) did have chronic histologic lesions that suggested previous influenza virus infection of the kidneys. Influenza virus was isolated from cloacal swabs of two of 44 chickens on day 28 PI, but all cloacal swabs were negative for virus recovery on sampling day 45/60 PI (0/81). These results indicate that replication of influenza virus in renal tubule epithelial cells did not result in persistence of type A influenza virus in this immunologically privileged site.

Re-evaluation of the pathogenicity of A/chicken/Alabama/75 (H4N8) influenza virus

Avian influenza (AI) virus A/chicken/Alabama/7395/75 (H4N8), a putatively non-pathogenic virus associated with a self-limiting outbreak of severe disease in commercial layers, was selectively passed in chickens or in cell cultures and then in chickens to determine whether virus with increased pathogenicity would emerge. When 20 derivatives of the parental virus were each inoculated intranasally and intratracheally in leghorn hens, mortality rates ranged from zero (0/24) to 25% (6/24); mortality was 4% (1/24) for hens inoculated with the parental virus. Many virus reisolates (51/144) from hens that died exhibited high pathogenicity, killing at least six of eight intravenously inoculated 4-week-old chickens. Most derivatives examined produced plaques in trypsin-free cell cultures more efficiently than the parental virus, but the highest plaquing efficiencies observed (10%) were lower than would be expected (100%) for highly pathogenic subtype H5 or H7 AI viruses. These results confirm that the Alabama H4N8 virus can acquire increased pathogenicity upon passage in chickens and suggest that it may have acted alone in producing the severe disease observed in laying chickens in Alabama.

Genetic relatedness of the nucleoprotein (NP) of recent swine, turkey, and human influenza A virus (H1N1) isolates

The sequences of nucleoprotein (NP) genes of recent human and turkey isolates of influenza A viruses, which serologically could be correlated to contemporary swine viruses, were determined. These sequences were closely related to the NPs of these swine viruses and they formed a separate branch on the phylogenetic tree. While the early swine virus from 1931 resembled the avian strains in consensus amino acids of the NP and in its ability to rescue NP ts mutants of fowl plague virus in chicken embryo cells, the later strains on that branch were different: at 15 positions they have their own amino acids and they rescued the NP ts mutants only poorly. Of the NPs of the human New Jersey/76 isolates analysed, one clustered with the recent H1N1 swine viruses of the U.S.A., the other one with contemporary human strains. Since the NP is one of the main determinants of species specificity it is concluded that, although the H1N1 swine isolates from the U.S.A. form their own branch in the phylogenetic tree, they can be transmitted to humans and turkeys, but they do not spread further in these populations and so far have not contributed to human pandemics. It is not very likely that they will do so in future, since its branch in the phylogenetic tree develops further away from the human and avian branch.

Biological properties of waterfowl-origin type A influenza viruses in chickens

The replicative abilities and tissue tropism properties of 13 non-pathogenic or low-pathogenic waterfowl-origin type A influenza isolates recovered in 1986 were examined in chickens. Following intravenous challenge, reisolation of challenge virus was attempted from swabs of the luminal surfaces of the cloaca, jejunum, ileum, bursa, trachea, and air sacs and from swabs of bone marrow and liver tissues. Virus-isolation attempts were also accomplished on brain, thymus, spleen, pancreas, gonad, kidney, blood, and lung tissues. The overall frequency of influenza virus recovery for each experiment ranged from 3.1% to 49.3%. For all experiments combined, 58.3% of the kidney tissues and 62.9% of the cloacal swab samples collected on days 1 to 10 postinoculation were positive for challenge virus recovery. Virus titers up to 10(8.7) mean embryo infective dose per gram of kidney tissue were demonstrated in clinically normal chickens. Distinct biological variations and nephrotropism appear to exist among the corporate properties of virus populations making up each of the 13 waterfowl-origin type A influenza isolates.

A quantitative measurement of the effect of avian influenza virus on the ability of turkeys to eliminate Pasteurella multocida from the respiratory tract

The effect of avian influenza virus (AIV) infection on the ability of turkeys to eliminate Pasteurella multocida from the respiratory tract was evaluated. Four-week-old turkeys were experimentally infected with an apathogenic AIV subtype (H5N2) by the oculonasal route and subsequently superinfected with P multocida (Urbach strain) by the intranasal route three days after infection with AIV. Quantitative clearance of P multocida from the trachea and lung was determined using a pour plate technique on samples collected at intervals after infection. Samples from turkeys which had been infected with AIV were found to yield more P multocida than those from turkeys which had not been infected with AIV. The numbers of P multocida increased in infected birds to a greater extent than in birds which had not been infected with the virus. The present study suggests that AIV infection may contribute to the increased numbers and a decreased clearance of P multocida in turkeys.

Isolation of H13N2 influenza A virus from turkeys and surface water

This is the first report of the isolation of H13N2 avian influenza virus (AIV) subtype from domestic turkeys. This subtype was also isolated from nearby surface water. The observation of large numbers of gulls in close association with turkeys on range before the virus isolations suggests that this virus subtype was transmitted from gulls to range turkeys. Turkey flocks infected by this virus subtype did not show any clinical signs of the disease, although seroconversion did occur. The H13N2 isolates were found to be non-pathogenic in chickens.

Emergence of highly pathogenic virus during selective chicken passage of the prototype mildly pathogenic chicken/Pennsylvania/83 (H5N2) influenza virus

The prototype mildly pathogenic A/chicken/Pennsylvania/21525/83 (H5N2) avian influenza virus, which was isolated more than 5 months before the emergence of highly pathogenic virus in the major 1983 Pennsylvania outbreak, was examined for the presence of minority subpopulations of highly pathogenic virus. Selective serial passage of the parental mildly pathogenic virus in leghorn hens did not lead to recovery of highly pathogenic virus. However, several highly pathogenic reisolates were recovered from hens inoculated with either of two mildly pathogenic virus clones selected for their ability to efficiently produce plaques in trypsin-free chicken embryo fibroblasts. Unlike the parental virus, these reisolates caused high mortality in chickens and produced postmortem lesions typical of highly pathogenic avian influenza. Electrophoretic mobilities of the hemagglutinin glycoproteins of the highly pathogenic derivatives resembled those of the prototype highly pathogenic A/chicken/Pennsylvania/1370/83 (H5N2) virus isolated in October 1983. These results suggest that unrecognized subpopulations of highly pathogenic virus may have infected Pennsylvania chickens for several months before emerging as the clinically manifest component of the virus population.

Assessing pathogenicity potential of waterfowl-origin type A influenza viruses in chickens

Intravenous pathogenicity index (IVPI) tests on 29 wild duck-origin type A influenza viruses, two turkey-origin type A influenza viruses, and one chicken-origin type A influenza virus resulted in indices ranging from 0.0 to 0.49. Most of the wild duck-origin viruses and the two turkey-origin viruses had indices of 0.0, indicating they are not pathogenic. Six of the duck-origin viruses had indices ranging from 0.25 to 0.49, and the IVPI for A/chicken/Alabama/75 (H4N8) was 0.49, indicating they had low pathogenic potential. An IVPI of 1.25 up to the maximum score of 3.0 is necessary for a type A influenza virus to be classified as highly pathogenic. Gross lesions observed in chickens dying following intravenous viral challenge included kidney swelling with more prominent lobular patterns, but visceral urate deposits were not present. The usefulness of the IVPI test in evaluating the pathogenicity potential of nonpathogenic and low-pathogenic strains of avian influenza virus may be limited.

The critical cut-off temperature of avian influenza viruses

We have measured the pathogenicity for 6-week-old chicks of infection by H7 avian influenza viruses. One virus, strain S3 from A/FPV/Rostock/34(H7N1) showed a temperature sensitive phenotype at 41.5 degrees C and reduced pathogenicity. By analysis of reassortants made between virus S3 and A/FPV/Dobson/27(H7N7), a fully pathogenic virus, two conclusions arise. (1) The critical cut-off temperature for avian influenza virus in 6-week-old chicks is 41.5 degrees. (2) RNA segment 1 of virus S3 is responsible for the lack of pathogenicity in reassortant viruses. Nucleotide sequencing of RNA segment 1 from S3 and its parent, A/FPV/Rostock/34 has revealed a single mutation at nucleotide 1561. This results in a substitution of isoleucine for leucine at amino acid position 512 in the cap-binding protein, PB2.

Lack of persistence of influenza virus genetic information in ducks

Clearance of infectious virus and RNA occurred concurrently after oral infection of ducks with influenza virus. There was no evidence from polymerase chain reaction (PCR) analysis of the hemagglutinin (HA) gene for persistence of viral genetic information. No detectable RNA was found in the spleen indicating processing of antigen near the site of replication.

Avian influenza viruses from migratory and resident ducks of coastal Louisiana

Cloacal and tracheal swabs were collected from 1389 hunter-killed ducks in Cameron Parish, Louisiana, during the 1986 and 1987 waterfowl seasons. Twenty-eight avian influenza viruses (AIVs) were isolated from 605 blue-winged teal (Anas discors), 75 mottled ducks (A. fulvigula), 375 gadwalls (A. stepera) and 334 green-winged teal (A. crecca). Prevalence estimates of AIV in ducks sampled during September, November, and December through January were 3.1%, 2.0%, and 0.4%, respectively. Differences in prevalence were detected by season (P = 0.044) and age class (P = 0.036). Two isolations from resident mottled ducks document transmission of AIV on these wintering areas. Much subtype diversity was present, with nine of 13 hemagglutinin (HA) and nine of nine neuraminidase (NA) subtypes recovered. Predominant HA and NA subtypes were typical of AIVs commonly associated with waterfowl. Results indicate that AIVs are transmitted in the wintering areas, and, although prevalence is low, these viruses continue to circulate within these duck populations during winter.

Replication of a waterfowl-origin influenza virus in the kidney and intestine of chickens

Intravenous inoculation of chickens with a waterfowl-origin type A influenza virus resulted in high titers of virus in kidney tissues and viral nucleoprotein in renal tubular epithelial cells and in intestinal mucosal epithelial cells. Virus titers in kidneys of four of eight clinically normal chickens sampled on days 3 and 5 postinoculation (PI), one dead chicken on day 3 PI, and one dead chicken on day 7 PI exceeded 10(6) mean embryo infectious dose per gram of tissue. Using immunofluorescent and immunoperoxidase staining, viral nucleoprotein was identified in the cytoplasm and nucleus of tubular epithelial cells in kidneys and in nucleus of mucosal epithelial cells lining villi in the lower small intestine. Based on the low intravenous pathogenicity index for this virus (0.3) along with the high virus titers in kidney tissues and localization of viral antigen in kidney important site for replication of avian influenza (AI) virus of low pathogenicity. Recovery of type A influenza viruses from cloacal swabs could result from viral replication in kidneys as well as in the lower intestine and/or the bursa of Fabricius.

Close relationship between mink influenza (H10N4) and concomitantly circulating avian influenza viruses

Strains of an influenza H10N4 virus have been isolated during an outbreak of a respiratory disease in mink on the south-east coast of Sweden. This was the first example of a disease in mammals caused by the H10 subtype. We compared the A/mink/Sweden/84 strain with two recent avian H10N4 isolates, one from fowl and another from a mallard, both isolated in Great Britain in 1985 as well as the prototype A/chicken/Germany/N/49 (H10N7). The comparison was carried out by genomic analysis of the strains by oligonucleotide fingerprinting and in bioassays on mink. The oligonucleotide fingerprint analysis revealed a high degree of genomic homology of around 98% between the viruses from mink, mallard and fowl. Only the recent avian isolates, that from the mallard and fowl could infect mink by contact, causing similar pathological and clinical signs and inducing seroconversion as did the mink virus. However, the susceptibility of mink to the fowl and mallard viruses by contact was less pronounced than that to the mink virus. Both the genomic homology and the similarities from the infectivity and pathogenicity studies between the mink virus and the recent avian isolates point to a direct invasion of the mink population by an avian H10N4 virus.

Kidney lesions associated with mortality in chickens inoculated with waterfowl influenza viruses

Seventy-six type A influenza viruses recovered from waterfowl in Wisconsin, California, South Dakota, Florida, Texas, Alabama, and Nebraska were tested for virulence in chickens. The challenge to chickens was intravenous inoculation of first-, second-, or third-egg-passage virus. Each of the virus strains was tested separately in three or four chickens. Eighteen of the 76 viruses caused the death of one or more chickens following inoculation. Postmortem lesions were similar in all dead birds. In decreasing order of frequency, gross lesions included: swollen kidneys evident as accentuated lobular patterns, urates in the pericardial sac, and urates on the surface of the liver. Microscopic lesions present in kidneys were consistent with visceral gout. Mortality was associated with inoculations having higher concentrations of infectious virus. These results indicate that the influenza A viruses circulating in duck populations may include strains potentially pathogenic for chickens.

Antimicrobial resistance of Escherichia coli isolated from chickens

Faecal Escherichia coli isolated from healthy farm chickens, from farm chickens with avian influenza, and from chickens with diarrhoea were more resistant to antimicrobial agents (94-100%) than those isolated from healthy domestic chickens (20%). Transfer of drug resistance was readily achieved from strains isolated from both healthy and sick farm chickens, and from diarrhoeic chickens; it was more difficult to demonstrate in strains from domestic chickens. Resistant E. coli showing serotypes suspected to be enteropathogenic for man, i.e 0126:K71(B16), 044:K74 (L) and 0119:K69(B14), were isolated from faecal samples of healthy and sick farm chickens, but not from healthy domestic birds.

Antigenic and phenotypic variants of a virulent avian influenza virus selected during replication in ducks

To evaluate the replication of a highly virulent avian influenza A virus in a potential reservoir host, mallard ducks (Anas platyrhynchos) were inoculated with the virulent strain A/Ty/Ont/7732/66 (H5N9). Viruses recovered from the ducks were analyzed by hemagglutination inhibition (HI) and enzyme-linked immunosorbent assay (ELISA) and found to possess antigenically altered viral hemagglutinins. Plaque formation on the Madin-Darby Canine Kidney (MDCK) cell line and on primary chicken embryo cells was investigated, and isolates recovered from the ducks differed from the wild type by being unable to form plaques on MDCK cells without trypsin. This phenotype did not appear to be due to inefficient cleavage of the hemagglutinin by host cell proteases since hemagglutinin immunoprecipitated from cell lysates was cleaved. Although the plaquing phenotype suggested attenuation of the isolates from the ducks, they were not significantly altered in their virulence for chickens shown by infectivity studies in vivo. These results indicate that replication of influenza A/Ty/Ont/7732/66 virus in ducks can produce antigenic and phenotypic variants which are still highly virulent for domestic poultry.

Neutralizing epitopes of the H5 hemagglutinin from a virulent avian influenza virus and their relationship to pathogenicity

To define and characterize the major neutralizing epitopes of the H5 hemagglutinin, a panel of monoclonal antibodies specific for the H5 hemagglutinin of the virulent avian influenza virus A/Turkey/Ontario/7732/66 (H5N9) was prepared. Antibodies which neutralized infectivity of the virus were used to select a panel of escape mutants. Reactivity patterns of the panel of monoclonal antibodies against the panel of mutants by both enzyme-linked immunosorbent assay serology and hemagglutination inhibition operationally defined five distinct epitopes on the H5 molecule. The mutants were analyzed in vivo for virulence in chickens, and the findings indicate that viruses with mutations in four of five epitopes were no less virulent than the wild type, producing a rapidly fatal disease, while all viruses with mutations in the fifth epitope (group 1 mutants) were attenuated. These group 1 mutants were unaltered in the cleavage properties of the hemagglutinin, suggesting that the mechanism of attenuation is unrelated to processing of the hemagglutinin. One of the group 1 mutants, 77B1v, was characterized for its ability to produce necrosis of the spleen and was found to produce none of the lesions in the spleen which are characteristic of the wild-type virus, although virus was present in this organ. The results suggest an altered tissue tropism, perhaps sparing a population of cells critical to an effective immune response.

Biologic potential of amantadine-resistant influenza A virus in an avian model

Amantadine has been accepted for both the treatment and prophylaxis of influenza A virus infections. Although amantadine-resistant mutants have been shown to be readily generated both in the laboratory and in children treated with rimantadine, little is known about their biologic properties, such as genetic stability, transmissibility, or pathogenicity, compared with the parental virus. This study examined these properties using an avian influenza virus, A/chicken/Pennsylvania/1370/83 (H5N2). Variants that were amantadine-resistant, virulent, and capable of competing with wild-type virus for transmission to susceptible hosts in the absence of the drug were selected. These amantadine-resistant variants were also genetically stable, showing no reversion to wild-type after six passages in birds over a period of greater than 20 d. Thus, these virus variants had no detectable biologic impairment. The mutations conferring drug resistance were in the M2 polypeptide and were identical to mutations previously described in human amantadine-resistant virus. These results suggest that resistant mutants may have the potential to threaten the effective use of amantadine and rimantadine for the control of epidemic influenza.

Mutations at the cleavage site of the hemagglutinin after the pathogenicity of influenza virus A/chick/Penn/83 (H5N2)

Six variants that form plaques in chick embryo cells in the absence of trypsin have been isolated from the apathogenic avian influenza virus A/chick/Pennsylvania/1/83 (H5N2). Unlike the wild-type, the plaque variants contain a hemagglutinin that is cleaved in chick embryo cells and MDCK cells. The variants differ also from the wild-type in their pathogenicity for chickens. Nucleotide sequence and oligosaccharide analysis of the hemagglutinin have revealed that, unlike natural isolates with increased pathogenicity (Y. Kawaoka et al., 1984, Virology 139, 303-316; Y. Kawaoka and R. G. Webster, 1985, Virology 146, 130-137), the variants obtained in vitro have retained an oligosaccharide at asparagine 11 that is believed to interfere with the cleavage site of the wild-type. However, all variants showed mutations in the hemagglutinin resulting in an increased number of basic groups at the cleavage site. These observations demonstrate that masking of the cleavage site by an oligosaccharide is overcome by an enhancement of the basic charge at the cleavage site.

Destruction of lymphocytes by a virulent avian influenza A virus

Infection of chickens by a virulent avian influenza A virus, A/turkey/Ont/7732/66 (H5N9), was associated with a severe lymphopenia. High titres of infectious virus were found in lymphoid tissues early in infection and were accompanied by severe damage to the lymphocyte populations as demonstrated by histopathological examination. Non-lymphoid cell populations in these tissues were unaffected, as were other organs examined. The viral nucleoprotein was localized by immunoperoxidase staining to lymphocytes in affected tissues early in infection.

Intracerebral pathogenicity for chickens of avian influenza viruses isolated from free-living waterfowl in Japan

The pathogenicity for chickens of 91 strains of avian influenza A virus isolated from such free-living waterfowl as whistling swan, pintail, tufted duck, mallard and black-tailed gull in Japan was tested. The majority of the virus strains infected and were pathogenic for the chickens. The virulence of these viruses seemed not to be as high as that of fowl plague virus. There were no significant differences in the intracerebral index score among the viruses belonging to the same subtype, irrespective of year of isolation or host.

Highly pathogenic virus recovered from chickens infected with mildly pathogenic 1986 isolates of H5N2 avian influenza virus

A combination of in vitro and in vivo selection procedures was used to examine the possibility that certain mildly pathogenic field isolates of avian influenza (AI) virus may contain minority subpopulations of highly pathogenic virus. Two mildly pathogenic H5N2 isolates, A/chicken/New Jersey/12508/86 (NJ12508) and A/chicken/Florida/27716/86 (FL27716), recovered from chickens epidemiologically associated with urban live-bird markets, were cloned in trypsin-free chicken embryo fibroblast cultures. Selected clones were inoculated intranasally and intratracheally (IN/IT) into specific-pathogen-free laying hens, and virus reisolated from the hens that died was serially passed in hens by IN/IT inoculation. Several highly pathogenic reisolates were recovered from hens infected with the cloned NJ12508 or FL27716 virus. A highly pathogenic NJ12508 reisolate killed 19 of 24 IN/IT-inoculated hens, and a FL27716 reisolate killed all 24 inoculated hens; signs and lesions were typical of fowl plague. In contrast, uncloned NJ12508 stock virus killed 1 of 24 hens and FL27716 stock virus killed 4 of 24 hens, and neither produced the complete spectrum of lesions associated with fowl plague. Recovery of highly pathogenic viruses from these isolates demonstrates the coexistence of pathogenically distinct subpopulations of virus. Competition for dominance among such subpopulations could explain the variable pathogenicity of some AI viruses.

Interference between influenza A viruses with a cleavable and a noncleavable hemagglutinin; pH-stability after mixed infection

The infectivity of influenza A viruses like fowl plague virus (FPV) with a cleaved hemagglutinin (HA) is highly sensitive to treatment at pH 5, while strains like PR 8 or virus N with a noncleaved HA survive under this condition. After double infection of chick embryo cells with FPV and PR 8 or virus N, the yield of virus with the HA gene of FPV is greatly reduced. However, it can now survive treatment at pH 5, and the surviving FPV particles form plaques only in the presence of trypsin, indicating that they were coated by the HA of PR 8 or virus N, depending on the coinfecting virus. The results are discussed with respect to the build-up and maintenance of a large reservoir of nonpathogenic influenza A viruses with noncleavable HA in water fowl.

Is the gene pool of influenza viruses in shorebirds and gulls different from that in wild ducks?

Evidence is presented for a second major gene pool of influenza A viruses in nature. Shorebirds and gulls harbor influenza viruses when sampled in the spring and fall. Approximately half of the viruses isolated have the potential to infect ducks but the remainder do not. The hemagglutinin subtypes that are prevalent in wild ducks were rare or absent in shorebirds and gulls.

Host range of avian influenza virus in free-living birds

Isolation of avian influenza virus (AIV) has been reported from 12 orders and 88 species of free-living birds. Most isolations are reported from species in the orders Anseriformes and Charadriiformes and it is recognized that species in Anseriformes represent important reservoirs of AIV. Morbidity and mortality among free-living birds attributable to AIV infection are rare, but differences in prevalence of AIV occur within and between avian species. Seasonal variation has been reported from free-living and sentinel ducks with peak AIV infection occurring in late summer and early fall. Prevalence of AIV is age-related, with highest isolation rates reported from juvenile birds. Differences in susceptibility to AIV infection among species have been demonstrated under experimental conditions. The dynamics and epidemiology of species-related variation in populations of free-living birds require further study.

Isolation of influenza A viruses from migratory waterfowls in San-in District, Western Japan in winters of 1980-1982

In the two winters of 1980-1982, we surveyed migratory waterfowl of some species staying in San-in District, Western Japan for influenza virus at a few stations. From November 1980 to April 1981, only two strains of influenza virus, H13N1 and H11N6 subtypes, were isolated from 465 fecal samples from pintails but none from 255 samples from whistling swans nor from 625 black-tailed gulls. From November 1981 to March 1982, 17 viruses were isolated from 1156 fecal samples. Fourteen viruses, 10 H7N3, 2 H1N6 and 2 H3N8, were isolated from 459 feces samples from whistling swans. Two viruses, H13N3 and H13N6 subtypes, were isolated from 425 fecal samples from black-tailed gulls. A strain belonging to H1N3 subtype was isolated from 30 feces samples from mallards but no virus was isolated from 242 samples from pintails.

Molecular analyses of the hemagglutinin genes of H5 influenza viruses: origin of a virulent turkey strain

Comparative sequence analysis of the hemagglutinin (HA) genes of a highly virulent H5N8 virus isolated from turkeys in Ireland in 1983 and a virus of the same subtype detected simultaneously in healthy ducks showed only four amino acid differences between these strains. Partial sequencing of six of the other genes and antigenic similarity of the neuraminidases established the overall genetic similarity of these two viruses. Comparison of the complete sequence of two H5 gene sequences and partial sequences of other virulent and avirulent H5 viruses provides evidence for at least two different lineages of H5 influenza virus in the world, one in Europe and the other in North America, with virulent and avirulent members in each group. In vivo studies in domestic ducks showed that all of the H5 viruses that are virulent in chickens and turkeys replicate in the internal organs of ducks but did not produce any disease signs. Additionally, both viruses isolated from turkeys and ducks in Ireland were detected in the blood. These studies provide the first conclusive evidence for the possibility that fully virulent influenza viruses in domestic poultry can arise directly from viruses in wild aquatic birds. Studies on the cleavability of the HA of virulent and avirulent H5 viruses showed that the principles established for H7 viruses (F. X. Bosch, M. Orlich, H. D. Klenk, and R. Rott, 1979, Virology 95, 197-207; F. X. Bosch, W. Garten, H. D. Klenk, and R. Rott, 1981, Virology 113, 725-735) also apply to the H5 subtype. These are (1) only the HAs of virulent influenza viruses were cleaved in tissue culture in the absence of trypsin and (2) virulent H5 influenza viruses contain a series of basic amino acids at the cleavage site of the HA, whereas avirulent strains contain only a single arginine with the exception of the avirulent Chicken/Pennsylvania virus. Thus, a series of basic amino acids at the cleavage site probably forms a recognition site for the enzyme(s) responsible for cleavage.