An Arg-Lys insertion at the hemagglutinin cleavage site of an H5N2 avian influenza isolate

Transient RNA structures underlie highly pathogenic avian influenza virus genesis

Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease and high fatality in poultry1. They emerge exclusively from H5 and H7 low pathogenic avian influenza viruses (LPAIVs)2. Although insertion of a furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene was identified decades ago as the genetic basis for LPAIV-to-HPAIV transition3,4, the exact mechanisms underlying said insertion have remained unknown. Here we used an innovative combination of bioinformatic models to predict RNA structures forming around the influenza virus RNA polymerase during replication, and circular sequencing5 to reliably detect nucleotide insertions. We show that transient H5 hemagglutinin RNA structures predicted to trap the polymerase on purine-rich sequences drive nucleotide insertions characteristic of MBCSs, providing the first strong empirical evidence of RNA structure involvement in MBCS acquisition. Insertion frequencies at the H5 cleavage site were strongly affected by substitutions in flanking genomic regions altering predicted transient RNA structures. Introduction of H5-like cleavage site sequences and structures into an H6 hemagglutinin resulted in MBCS-yielding insertions never observed before in H6 viruses. Our results demonstrate that nucleotide insertions that underlie H5 HPAIV emergence result from a previously unknown RNA-structure-driven diversity-generating mechanism, which could be shared with other RNA viruses.

Hemagglutinin Subtype Specificity and Mechanisms of Highly Pathogenic Avian Influenza Virus Genesis

Highly Pathogenic Avian Influenza Viruses (HPAIVs) arise from low pathogenic precursors following spillover from wild waterfowl into poultry populations. The main virulence determinant of HPAIVs is the presence of a multi-basic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein. The MBCS allows for HA cleavage and, consequently, activation by ubiquitous proteases, which results in systemic dissemination in terrestrial poultry. Since 1959, 51 independent MBCS acquisition events have been documented, virtually all in HA from the H5 and H7 subtypes. In the present article, data from natural LPAIV to HPAIV conversions and experimental in vitro and in vivo studies were reviewed in order to compile recent advances in understanding HA cleavage efficiency, protease usage, and MBCS acquisition mechanisms. Finally, recent hypotheses that might explain the unique predisposition of the H5 and H7 HA sequences to obtain an MBCS in nature are discussed.

In Silico Analyses of the Role of Codon Usage at the Hemagglutinin Cleavage Site in Highly Pathogenic Avian Influenza Genesis

A vast diversity of 16 influenza hemagglutinin (HA) subtypes are found in birds. Interestingly, viruses from only two subtypes, H5 and H7, have so far evolved into highly pathogenic avian influenza viruses (HPAIVs) following insertions or substitutions at the HA cleavage site by the viral polymerase. The mechanisms underlying this striking subtype specificity are still unknown. Here, we compiled a comprehensive dataset of 20,488 avian influenza virus HA sequences to investigate differences in nucleotide and amino acid usage at the HA cleavage site between subtypes and how these might impact the genesis of HPAIVs by polymerase stuttering and realignment. We found that sequences of the H5 and H7 subtypes stand out by their high purine content at the HA cleavage site. In addition, fewer substitutions were necessary in H5 and H7 HAs than in HAs from other subtypes to acquire an insertion-prone HA cleavage site sequence, as defined based on in vitro and in vivo data from the literature. Codon usage was more favorable for HPAIV genesis in sequences of viruses isolated from species or geographical regions in which HPAIV genesis is more frequently observed in nature. The results of the present analyses suggest that the subtype restriction of HPAIV genesis to H5 and H7 influenza viruses might be due to the particular codon usage at the HA cleavage site in these subtypes.

Pathobiological Origins and Evolutionary History of Highly Pathogenic Avian Influenza Viruses

High-pathogenicity avian influenza (HPAI) viruses have arisen from low-pathogenicity avian influenza (LPAI) viruses via changes in the hemagglutinin proteolytic cleavage site, which include mutation of multiple nonbasic to basic amino acids, duplication of basic amino acids, or recombination with insertion of cellular or viral amino acids. Between 1959 and 2019, a total of 42 natural, independent H5 (n = 15) and H7 (n = 27) LPAI to HPAI virus conversion events have occurred in Europe (n = 16), North America (n = 9), Oceania (n = 7), Asia (n = 5), Africa (n = 4), and South America (n = 1). Thirty-eight of these HPAI outbreaks were limited in the number of poultry premises affected and were eradicated. However, poultry outbreaks caused by A/goose/Guangdong/1/1996 (H5Nx), Mexican H7N3, and Chinese H7N9 HPAI lineages have continued. Active surveillance and molecular detection and characterization efforts will provide the best opportunity for early detection and eradication from domestic birds.

Emergence of highly pathogenic H5N2 and H7N1 influenza A viruses from low pathogenic precursors by serial passage in ovo

Highly pathogenic (HPAI) strains emerge from their low pathogenic (LPAI) precursors and cause severe disease in poultry with enormous economic losses, and zoonotic potential. Understanding the mechanisms involved in HPAI emergence is thus an important goal for risk assessments. In this study ostrich-origin H5N2 and H7N1 LPAI progenitor viruses were serially passaged seventeen times in 14-day old embryonated chicken eggs and Ion Torrent ultra-deep sequencing was used to monitor the incremental changes in the consensus genome sequences. Both virus strains increased in virulence with successive passages, but the H7N1 virus attained a virulent phenotype sooner. Mutations V63M, E228V and D272G in the HA protein, Q357K in the nucleoprotein (NP) and H155P in the neuraminidase protein correlated with the increased pathogenicity of the H5N2 virus; whereas R584H and L589I substitutions in the polymerase B2 protein, A146T and Q220E in HA plus D231N in the matrix 1 protein correlated with increased pathogenicity of the H7N1 virus in embryos. Enzymatic cleavage of HA protein is the critical virulence determinant, and HA cleavage site motifs containing multibasic amino acids were detected at the sub-consensus level. The motifs PQERRR/GLF and PQRERR/GLF were first detected in passages 11 and 15 respectively of the H5N2 virus, and in the H7N1 virus the motifs PELPKGKK/GLF and PELPKRR/GLF were detected as early as passage 7. Most significantly, a 13 nucleotide insert of unknown origin was identified at passage 6 of the H5N2 virus, and at passage 17 a 42 nucleotide insert derived from the influenza NP gene was identified. This is the first report of non-homologous recombination at the HA cleavage site in an H5 subtype virus. This study provides insights into how HPAI viruses emerge from low pathogenic precursors and demonstrated the pathogenic potential of H5N2 and H7N1 strains that have not yet been implicated in HPAI outbreaks.

Protection of White Leghorn chickens by recombinant fowlpox vector vaccine with an updated H5 insert against Mexican H5N2 avian influenza viruses

Despite decades of vaccination, surveillance, and biosecurity measures, H5N2 low pathogenicity avian influenza (LPAI) virus infections continue in Mexico and neighboring countries. One explanation for tenacity of H5N2 LPAI in Mexico is the antigenic divergence of circulating field viruses compared to licensed vaccines due to antigenic drift. Our phylogenetic analysis indicates that the H5N2 LPAI viruses circulating in Mexico and neighboring countries since 1994 have undergone antigenic drift away from vaccine seed strains. Here we evaluated the efficacy of a new recombinant fowlpox virus vector containing an updated H5 insert (rFPV-H5/2016), more relevant to the current strains circulating in Mexico. We tested the vaccine efficacy against a closely related subcluster 4 Mexican H5N2 LPAI (2010 H5/LP) virus and the historic H5N2 HPAI (1995 H5/HP) virus in White Leghorn chickens. The rFPV-H5/2016 vaccine provided hemagglutinin inhibition (HI) titers pre-challenge against viral antigens from both challenge viruses in almost 100% of the immunized birds, with no differences in number of birds seroconverting or HI titers among all tested doses (1.5, 2.0, and 3.1 log₁₀ mean tissue culture infectious doses/bird). The vaccine conferred 100% clinical protection and a significant decrease in oral and cloacal virus shedding from 1995 H5/HP virus challenged birds when compared to the sham controls at all tested doses. Virus shedding titers from vaccinated 2010 H5/LP virus challenged birds significantly decreased compared to sham birds especially at earlier time points. Our results confirm the efficacy of the new rFPV-H5/2016 against antigenic drift of LPAI virus in Mexico and suggest that this vaccine would be a good candidate, likely as a primer in a prime-boost vaccination program.

Upregulating endogenous genes by an RNA-programmable artificial transactivator

To promote expression of endogenous genes ad libitum, we developed a novel, programmable transcription factor prototype. Kept together via an MS2 coat protein/RNA interface, it includes a fixed, polypeptidic transactivating domain and a variable RNA domain that recognizes the desired gene. Thanks to this device, we specifically upregulated five genes, in cell lines and primary cultures of murine pallial precursors. Gene upregulation was small, however sufficient to robustly inhibit neuronal differentiation. The transactivator interacted with target gene chromatin via its RNA cofactor. Its activity was restricted to cells in which the target gene is normally transcribed. Our device might be useful for specific applications. However for this purpose, it will require an improvement of its transactivation power as well as a better characterization of its target specificity and mechanism of action.

Human H7N9 avian influenza virus infection: a review and pandemic risk assessment

China is undergoing a recent outbreak of a novel H7N9 avian influenza virus (nH7N9) infection that has thus far involved 132 human patients, including 37 deaths. The nH7N9 virus is a reassortant virus originating from the H7N3, H7N9 and H9N2 avian influenza viruses. nH7N9 isolated from humans contains features related to adaptation to humans, including a Q226L mutation in the hemagglutinin cleavage site and E627K and D701N mutations in the PB2 protein. Live poultry markets provide an environment for the emergence, spread and maintenance of nH7N9 as well as for the selection of mutants that facilitate nH7N9 binding to and replication in the human upper respiratory tract. Innate immune suppression conferred by the internal genes of H9N2 may contribute to the virulence of nH7N9. The quail may serve as the intermediate host during the adaptation of avian influenza viruses from domestic waterfowl to gallinaceous poultry, such as chickens and related terrestrial-based species, due to the selection of viral mutants with a short neuraminidase stalk. Infections in chickens, common quails, red-legged partridges and turkeys may select for mutants with human receptor specificity. Infection in Ratitae species may lead to the selection of PB2-E627K and PB2-D701N mutants and the conversion of nH7N9 to a highly pathogenic avian influenza virus.

Comparison of serum treatments to remove nonspecific inhibitors from chicken sera for the hemagglutination inhibition test with inactivated H5N1 and H9N2 avian Influenza A virus subtypes

The hemagglutination inhibition (HI) assay is the standard diagnostic test for detection of antibodies to avian influenza viruses. It is well known that chicken serum does not require additional serum pretreatment to remove nonspecific inhibitors (NSIs). However, NSIs were recognized in certain Korean local breeds. In the present study, various treatments were compared to remove such NSIs. Heat treatment, red blood cell adsorption, and kaolin treatment did not remove NSIs effectively, and treatment with periodate only partly eliminated the NSIs. Receptor destroying enzyme (RDE) treatment appeared to effectively remove NSIs from chicken sera, regardless of breeds. It is proposed that RDE treatment should be included in the HI tests for serological diagnosis of avian Influenza A virus.

Avian influenza: public health and food safety concerns

Avian influenza (AI) is a disease or asymptomatic infection caused by Influenzavirus A. AI viruses are species specific and rarely cross the species barrier. However, subtypes H5, H7, and H9 have caused sporadic infections in humans, mostly as a result of direct contact with infected birds. H5N1 high pathogenicity avian influenza (HPAI) virus causes a rapid onset of severe viral pneumonia and is highly fatal (60% mortality). Outbreaks of AI could have a severe economic and social impact on the poultry industry, trade, and public health. Surveillance data revealed that H5N1 HPAI has been detected in imported frozen duck meat from Asia, and on the surface and in contaminated eggs. However, there is no direct evidence that AI viruses can be transmitted to humans via the consumption of contaminated poultry products. Implementing management practices that incorporate biosecurity principles, personal hygiene, and cleaning and disinfection protocols, as well as cooking and processing standards, are effective means of controlling the spread of the AI viruses.

Rapid PCR-based molecular pathotyping of H5 and H7 avian influenza viruses

While the majority of avian influenza virus (AIV) subtypes are classified as low-pathogenicity avian influenza viruses (LPAIV), the H5 and H7 subtypes have the ability to mutate to highly pathogenic avian influenza viruses (HPAIV) in poultry and therefore are the etiological agents of notifiable AIV (NAIV). It is of great importance to distinguish HPAIV from LPAIV variants during H5/H7 outbreaks and surveillance. To this end, a novel and fast strategy for the molecular pathotyping of H5/H7 AIVs is presented. The differentiation of the characteristic hemagglutinin (HA) protein cleavage sites (CSs) of HPAIVs and LPAIVs is achieved by a novel PCR method where the samples are interrogated for all existing CSs with a 484-plex primer mixture directly targeting the CS region. CSs characteristic for HP or LP H5/H7 viruses are distinguished in a seminested duplex real-time PCR format using plexor fluorogenic primers. Eighty-six laboratory isolates and 60 characterized NAIV-positive clinical specimens from poultry infected with H5/H7 both experimentally and in the field were successfully pathotyped in the validation. The method has the potential to substitute CS sequencing in the HA gene for the determination of the molecular pathotype, thereby providing a rapid means to acquire additional information concerning NAIV outbreaks, which may be critical to their management. The new assay may be extended to the LP/HP differentiation of previously unknown H5/H7 isolates. It may be considered for integration into surveillance and control programs in both domestic and wild bird populations.

H9 avian influenza reassortant with engineered polybasic cleavage site displays a highly pathogenic phenotype in chicken

In the field, highly pathogenic avian influenza viruses (HPAIV) originate from low-pathogenic strains of the haemagglutinin (HA) serotypes H5 and H7 that have acquired a polybasic HA cleavage site. This observation suggests the presence of a cryptic virulence potential of H5 and H7 low-pathogenic avian influenza viruses (LPAIV). Among all other LPAIV, the H9N2 strains are of particular relevance as they have become widespread across many countries in several avian species and have been transmitted to humans. To assess the potential of these strains to transform into an HPAIV, we introduced a polybasic cleavage site into the HA of a contemporary H9N2 isolate. Whereas the engineered polybasic HA cleavage site mutant remained a low-pathogenic strain like its parent virus, a reassortant expressing the modified H9 HA with engineered polybasic cleavage site and all the other genes from an H5N1 HPAIV became highly pathogenic in chicken with an intravenous pathogenicity index of 1.23. These results suggest that an HPAIV with a subtype other than H5 or H7 would only emerge under conditions where the HA gene could acquire a polybasic cleavage site and the other viral genes carry additional virulence determinants.

Characterization of recent H5 subtype avian influenza viruses from US poultry

In the US, the isolation of H5 subtype avian influenza (AI) viruses has been uncommon in commercial chickens and turkeys, although sporadic isolations have been made from the live bird markets or its supply chain since 1986. In 2002, two different outbreaks of H5 AI occurred in commercial chicken or turkey operations. The first occurred in Texas and was identified as a H5N3 subtype AI virus. The second outbreak was caused by a H5N2 virus isolated from a turkey farm in California. In this study we analyzed recent H5 subtype AI viruses from different avian species and different sources in the US. Most recent H5 subtype isolates shared a high sequence identity and phylogenetically assorted into a separate clade from the Pennsylvania/83 lineage isolates. However, no established lineage was found within this clade and the recent H5 subtype isolates seemed to be the result of separate introductions from the wild bird reservoir. The Texas H5N3 isolate shared the lowest homology with the other recent isolates in the haemagglutinin gene and had a unique haemagglutinin cleavage site sequence of REKR/G (other recent isolates have the typical avirulent motif, RETR/G). Furthermore, this isolate had a 28 amino acid deletion in the stalk region of the neuraminidase protein, a common characteristic of chicken adapted influenza viruses, and may indicate that this virus had actually been circulating in poultry for an extended period of time before it was isolated. In agreement with genetic evidence, the Texas H5N3 isolate replicated better than other H5 isolates in experimentally infected chickens. The outbreak in Texas with a more chicken-adapted H5N3 virus underscores the importance of ongoing surveillance and control efforts regarding the H5 subtype AI virus in the US.

Amino acids adjacent to the haemagglutinin cleavage site are relevant for virulence of avian influenza viruses of subtype H5

The prime virulence determinant of highly pathogenic avian influenza viruses (HPAIVs) is the polybasic haemagglutinin (HA) cleavage site. However, engineering of a polybasic cleavage site into an avian influenza virus of low pathogenicity does not result in transformation into an HPAIV, indicating the importance of other adaptations. Here, the influence of amino acids adjacent to the HA cleavage site on virulence was studied. Most HPAIVs of subtype H5 carry serine or threonine at position 346 (corresponding to position 323 according to H3 numbering), whereas almost all low-pathogenic H5 viruses have valine. Moreover, all H5 low-pathogenic strains carry threonine at position 351 (corresponding to position 328 according to H3 numbering), suggesting that acquisition of a polybasic cleavage site involves several steps. This study generated a virus mutant derived from HPAIV A/Swan/Germany/R65/06 H5N1 (R65) with a monobasic cleavage site, R65(mono)-S-ER, and the following additional mutants: R65(mono)-V-ER with serine changed to valine at position 346, and R65(mono)-S-ETR and R65(mono)-V-ETR with threonine inserted at position 351. Moreover, in the R65 HA, serine was replaced with valine at position 346 (R65-V). Infection of chickens with R65(mono)-S-ETR or R65(mono)-S-ER led to slight transient respiratory symptoms, whereas R65-infected animals died within 2 days. However, chickens infected with R65-V survived longer than R65-infected animals, indicating that serine 346 in R65 HA contributes to virulence. These data suggest that evolution of H5 HPAIVs from low-pathogenic precursors, besides acquisition of a polybasic cleavage site, involves adaptation of neighbouring regions.

First isolation of an H1N1 avian influenza virus from wild terrestrial non-migratory birds in Argentina

A type A avian influenza (AI) virus was isolated from dead or severely ill red-winged tinamous (Rhynchotus rufescens) found in a hunting ground in April 2008 in Argentina. The subtype of A/red-winged tinamou/Argentina/MP1/2008 was determined as H1N1 by sequence analysis. The cleavage site of the viral hemagglutinin corresponded to a low pathogenic influenza virus, although the clinical presentation and pathological studies suggest that the virus was pathogenic for red-winged tinamous. Phylogenetic analysis of the viral genome suggested that while the hemagglutinin and neuraminidase genes were related to AIV from North America, the internal genes were most closely related to other South American isolates. These findings support the postulated South American phylogenetic lineage for AIV PB2, PB1, PA, M and NS genes, and suggest that the evolutionary pathways of HA and NA genes involve exchanges between the Northern and Southern hemispheres.

Rapid pathotyping of recent H5N1 highly pathogenic avian influenza viruses and of H5 viruses with low pathogenicity by RT-PCR and restriction enzyme cleavage pattern (RECP)

Rapid and accurate diagnosis of avian influenza virus infections of poultry and humans comprises detection, subtyping, and, in case of subtypes H5 and H7, pathotyping of such viruses. Reliable methods for pathotyping of H5 avian influenza viruses (AIV) are based on determination of the intravenous pathogenicity index (IVPI) in specific pathogen free (SPF) chickens and on characterization of the hemagglutinin (HA) gene cleavage site by sequencing. The number of basic amino acids (arginine and lysine) at the cleavage site is an important indicator of pathogenicity. In this paper, a new rapid method for pathotyping of H5 subtype avian influenza viruses is described which is based on RT-PCR and restriction enzyme cleavage pattern (RECP) assay using the MboII restriction enzyme. Validation of the method using 28 H5 subtype reference isolates from different animal species revealed good performance characteristics regarding sensitivity and specificity, especially when targeting recent highly pathogenic AIV (HPAIV) of subtype H5N1 and Asian origin. In addition, RECP results were validated by testing 47 field samples from different sources and by sequencing of their RT-PCR products. This approach for H5 AIV pathotyping proved to be fast, reliable, and comparatively sensitive and is suitable especially for laboratories lacking sequencing or in vivo pathotyping facilities.

Assessing potential pathogenicity of avian influenza virus: current and experimental system

An avian influenza (AI) isolate can be classified as a high pathogenicity avian influenza (HPAI) virus based upon the results of the standard intravenous pathogenicity index test; molecular classification, which is derived by sequencing the hemagglutinin gene across the site coding for the cleavage site; or a combination. However, discordant results between the molecular classification and virulence for experimentally infected chickens have been observed with several H5 and H7 subtype AI viruses. Because the declaration of HPAI virus results in severe effects on trade for the entire country, the gap between the genetic and phenotypic markers is an important issue, and it requires us to reexamine what should be considered an HPAI virus by the Office International des Epizooties standards. To better understand and assess the true virulence of the virus, potential pathogenicity of H5 and H7 subtype AI virus isolates has been assessed by examining the plaquing efficiency of the virus in chicken embryo fibroblast cells, conducting 14-day-old embryo passage and selection system, and applying in vitro mutagenesis coupled with reverse genetics. The potential value of these complimentary methods in assessing potential pathogenicity of the AI virus is discussed.

Low pathogenicity H5N2 avian influenza outbreak in Japan during the 2005-2006

At the end of May 2005, a low-pathogenicity avian influenza (LPAI) virus of subtype H5N2 was isolated for the first time from chickens in Japan. Through active and epidemiological surveillance, 5.78 million chickens on 41 farms were found to be affected and 16 H5N2 viruses were isolated. Antigenic analysis revealed antigenic similarity of these isolates. Phylogenetic analysis showed that they originated from a common ancestor and clustered with the H5N2 strains prevalent in Central America that have been circulating since 1994. Experimental infection of chickens with the index isolate (A/chicken/Ibaraki/1/05) demonstrated that this virus replicated efficiently in the respiratory tract without clinical signs, and dust-borne and/or droplet-borne transmission was considered as a possible mode of transmission. These results suggested that the H5N2 LPAI viruses isolated in Japan were highly adapted to chickens.

Avian influenza virus: prospects for prevention and control by vaccination

Although vaccination does not always prevent infection of avian influenza (AI) virus, the clear benefit of vaccination is in its ability to prevent disease and to reduce the amount of virus in circulation. Thus, judicious use of vaccination can be an important component of an AI control program. However, the long-term use of vaccination without eradication may result in the selection of the antigenically divergent strains, which compromises the value of vaccination. In this review, the effectiveness of currently available and future AI vaccines is discussed with suggestions for the ideal use of vaccination even with antigenic drift of the virus.

H5N2 avian influenza outbreak in Texas in 2004: the first highly pathogenic strain in the United States in 20 years?

In early 2004, an H5N2 avian influenza virus (AIV) that met the molecular criteria for classification as a highly pathogenic AIV was isolated from chickens in the state of Texas in the United States. However, clinical manifestations in the affected flock were consistent with avian influenza caused by a low-pathogenicity AIV and the representative virus (A/chicken/Texas/298313/04 [TX/04]) was not virulent for experimentally inoculated chickens. The hemagglutinin (HA) gene of the TX/04 isolate was similar in sequence to A/chicken/Texas/167280-4/02 (TX/02), a low-pathogenicity AIV isolate recovered from chickens in Texas in 2002. However, the TX/04 isolate had one additional basic amino acid at the HA cleavage site, which could be attributed to a single point mutation. The TX/04 isolate was similar in sequence to TX/02 isolate in several internal genes (NP, M, and NS), but some genes (PA, PB1, and PB2) had sequence of a clearly different origin. The TX/04 isolate also had a stalk deletion in the NA gene, characteristic of a chicken-adapted AIV. By analyzing viruses constructed by in vitro mutagenesis followed by reverse genetics, we found that the pathogenicity of the TX/04 virus could be increased in vitro and in vivo by the insertion of an additional basic amino acid at the HA cleavage site and not by the loss of a glycosylation site near the cleavage site. Our study provides the genetic and biologic characteristics of the TX/04 isolate, which highlight the complexity of the polygenic nature of the virulence of influenza viruses.

Sero-prevalence of avian influenza among broiler-breeder flocks in Jordan

Thirty blood samples were collected randomly from each of the 38 breeder-broiler farms in Jordan. Serum samples were examined using indirect ELISA for specific antibodies to avian influenza virus. The overall true flock-level sero-prevalence of avian influenza was 71% (95% CI: 55,83). Positive flocks had 2-30 sero-positive chickens and half of flocks had >20 sero-positive birds. The number of sero-positive flocks varied in the studied localities with more sero-positives in farms located within the migratory route of migratory wild fowl. The examined broiler-breeder flocks had no clinical signs, or noticeable decrease in egg production; mortalities were within the normal range (0.1-1%). The number of positive sera/flock correlated with flock size. There were a no significant (Pearsons r=0.21, p=0.21) correlation between positive flocks and age. A non-pathogenic AI virus infects broiler-breeder farms in Jordan. Wild local and migrating birds might promote the further spread of this virus in Jordan and other countries.

Effect of vaccine use in the evolution of Mexican lineage H5N2 avian influenza virus

An outbreak of avian influenza (AI) caused by a low-pathogenic H5N2 type A influenza virus began in Mexico in 1993 and several highly pathogenic strains of the virus emerged in 1994-1995. The highly pathogenic virus has not been reported since 1996, but the low-pathogenic virus remains endemic in Mexico and has spread to two adjacent countries, Guatemala and El Salvador. Measures implemented to control the outbreak and eradicate the virus in Mexico have included a widespread vaccination program in effect since 1995. Because this is the first case of long-term use of AI vaccines in poultry, the Mexican lineage virus presented us with a unique opportunity to examine the evolution of type A influenza virus circulating in poultry populations where there was elevated herd immunity due to maternal and active immunity. We analyzed the coding sequence of the HA1 subunit and the NS gene of 52 Mexican lineage viruses that were isolated between 1993 and 2002. Phylogenetic analysis indicated the presence of multiple sublineages of Mexican lineage isolates at the time vaccine was introduced. Further, most of the viruses isolated after the introduction of vaccine belonged to sublineages separate from the vaccine's sublineage. Serologic analysis using hemagglutination inhibition and virus neutralization tests showed major antigenic differences among isolates belonging to the different sublineages. Vaccine protection studies further confirmed the in vitro serologic results indicating that commercial vaccine was not able to prevent virus shedding when chickens were challenged with antigenically different isolates. These findings indicate that multilineage antigenic drift, which has not been observed in AI virus, is occurring in the Mexican lineage AI viruses and the persistence of the virus in the field is likely aided by its large antigenic difference from the vaccine strain.

Pathogenicity of a Ratite-Origin Influenza A H5 Virus in Ostriches (Struthio camelus)

Ostriches were inoculated with a highly pathogenic avian influenza (HPAI) virus of ratite origin, A/emu/Texas/39924/93 (H5N2) done clB. The aim of this study was to evaluate the pathogenicity of this isolate for ostriches and to assess the ability of routine virologic and serologic tests to detect infection. Avian influenza virus (AIV) was isolated from tracheal swabs from 2 to 12 days postinfection and from cloacal swabs from 3 to 10 days postinfection. AIV was also isolated from a wide range of tissues. Birds seroconverted as early as 7 days postinfection. This study indicates that HPAI virus of ratite origin replicates extensively in infected ostriches without causing significant clinical disease or mortality.

Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay

The clinical presentation of infections caused by the heterogeneous group of the respiratory viruses can be very similar. Thus, the implementation of virological assays that rapidly identify the most important viruses involved is of great interest. A new multiplex reverse transcription nested-polymerase chain reaction (RT-PCR) assay that is able to detect and type different respiratory viruses simultaneously is described. Primer sets were targeted to conserved regions of nucleoprotein genes of the influenza viruses, fusion protein genes of respiratory syncytial viruses (RSV), and hexon protein genes of adenoviruses. Individual influenza A, B, and C viruses, RSV (A and B), and a generic detection of the 48 serotypes of adenoviruses were identified and differentiated by the size of the PCR products. An internal amplification control was included in the reaction mixture to exclude false-negative results due to sample inhibitors and/or extraction failure. Detection levels of 0.1 and 0.01 TCID50 of influenza A and B viruses and 1-10 molecules of cloned amplified products of influenza C virus, RSV A and B, and adenovirus serotype 1 were achieved. The specificity was checked using specimens containing other respiratory viruses and no amplified products were detected in any case. A panel of 290 respiratory specimens from the 1999-2000 and 2000-2001 seasons was used to validate the assay. Accurately amplifying RNA from influenza and RSV prototype strains and DNA from all adenovirus serotypes demonstrates the use of this method for both laboratory routine diagnosis and surveillance of all these viruses.

[Factors affecting the virulence and pathogenicity of avian and human viral strains (influenza virus type A)]

Most studies performed in avian viral strains seem to indicate that virulence is a polygenic phenomenon. However, hemagglutinin and neuraminidase and the genes codifying these substances (genes 4 and 6) play an essential role in viral pathogenesis. Avian strains can be classified as avirulent or virulent according to the ability of hemagglutinin to be activated by endoproteases of the respiratory tract only or by proteases from other tissues. This ability is based on the progressive development of mutations that lead to the substitution of the normal amino acids at the point of hemagglutinin hydrolysis by the other basic amino acids that determine the amplification of the spectrum of hydrolysis and activation. Neuraminidase participates in the acquisition of virulence through its capacity to bind to plasminogen and by increasing the concentration of activating proteases. Adaptation to the host, through recognition of the cell receptor, is another factor determining the virulence and interspecies transmission of avian strains. From an epidemiological point of view, viral strains should be subtyped and the activating capacity of hemagglutinin should be determined to identify their degree of virulence.

Avian influenza virus subtypes inside and outside the live bird markets, 1993-2000: a spatial and temporal relationship

Between 1993 and 2000, gallinaceous birds, waterfowl, and environmental specimens from the live bird markets (LBMs) of the northeastern United States and non-LBM premises were tested for the presence of avian influenza virus (AIV), pathogenic properties of AIV subtypes, especially of hemagglutinin (H) subtypes H5 and H7, and a possible association between LBM and non-LBM infections. Ten H subtypes of AIV were isolated from the LBM specimens: H1, H2, H3, H4, H5, H6, H7, H9, H10, and H11. During this period, the 10 subtypes also were isolated from birds in non-LBM premises. In the LBMs, subtypes H2, H3, H4, H6, H7, and H11 were present for 5-8 yr despite efforts to clean and disinfect the premises. The H5 or H7 subtypes present during the same year in both LBMs and non-LBMs within a state or in contiguous states were (subtype/year): H5N2/1993, 1999, and H7N2/1994-99. The AIV subtypes including the H5 and H7 that were evaluated for pathogenicity in chickens were low pathogenic. The deduced amino acid sequence at the H cleavage site of H5 and H7 subtypes was consistent with those of low pathogenic AIV. Although the H5N2 and H7N2 subtypes remained low pathogenic, they did undergo mutations and acquired an additional basic amino acid at the H cleavage site; however, the minimum number of basic amino acids in correct sequence (B-X-B-R, where B = basic amino acid, X = need not be basic amino acid, and R = arginine) required for high pathogenicity was lacking. A low pathogenic H5 or H7 subtype may become highly pathogenic by acquiring additional basic amino acids at the H cleavage site. The LBMs have been and will likely continue to be a source of AIV for commercial poultry.

Influenza Aviária: Uma Revisão dos Últimos Dez Anos

A influenza aviária é doença exótica no Brasil. O sistema de vigilância implementado pelo Programa Nacional de Sanidade Avícola (PNSA) mantém monitoração permanente das aves das principais espécies domésticas, tanto do material genético importado para a indústria avícola, por exemplo, da espécie das galinhas (Gallus gallus formadomestica), perus (Meleagris gallopavo formadomestica), codornas (Coturnix coturnix japonica), patos (Anas), primários (elite), bisavós e avós para postura ou corte, como aves de espécies de exploração mais recente, exóticas, por exemplo avestruzes (Struthio camelus) ou nativas, por exemplo emas (Rhea americana). Os plantéis de reprodutores em produção são também acompanhados por amostragens periódicas, conforme previsto no PNSA, além da monitoração das respostas aos programas de vacinação, por exemplo, contra bronquite infecciosa e doença infecciosa bursal. O PNSA estabelece as normas de atuação para o controle e erradicação da doença de Newcastle (ND) e Influenza Aviária (AI) (Projeto de Vigilância, 2001), a saber: I - Notificação de focos da doença (e confirmação laboratorial no LARA-Campinas); II - Assistência a focos; III - Medidas de desinfecção; IV - Sacrifício sanitário; V - Vazio sanitário; VI - Vacinação dos plantéis ou esquemas emergenciais; VII - Controle e fiscalização dos animais susceptíveis; VIII - Outras medidas sanitárias; A vigilância e atenção ao foco exige o diagnóstico laboratorial e diferencial de AI e ND, que segue as normas do PNSA, conforme o sumário abaixo: 1- Interdição e coleta de materiais para exame laboratorial oficial; 2- Registro das aves: espécie(s), categoria(s), número(s), manutenção de aves; utensílios e produtos no local; proibição de trânsito de e para a(s) propriedade(s) em um raio de 10 km; controle de todos os animais e materiais possíveis fontes de propagação; desinfecção de vias de entradas e saídas à(s) propriedade(s); inquérito epidemiológico. 3- Confirmação laboratorial: isolamento de agente letal hemaglutinante em ovos embrionados de galinhas SPF, não inibido (inibição da hemaglutinação) ou não neutralizado (soroneutralização) por soro específico para o vírus da doença de Newcastle; caracterização do agente como vírus da influenza aviária (AIV) por detecção de antígenos da nucleoproteína e/ou matriciais de AIV e de seu subtipo por ensaios específicos para a caracterização da hemaglutinina e neuraminidase (imunodifusão, imunoenzimáticos ou moleculares). 4- Abate e destruição imediata (cremação) de todas as aves, resíduos, carnes e ovos da(s) propriedade(s) atingida(s) e vizinhas (raio de 3 km); limpeza e desinfecção das instalações; vazio sanitário (mínimo 21 dias); 5- Permitir o transporte para o abate ou incubação dentro da zona de vigilância (raio de 10 km). 6- Proibir feiras, exposições, mercados na zona de vigilância (10 km). 7- Aplicar estas medidas por mínimo de 21 dias após a destruição das fontes de propagação e desinfecção das instalações, proibir a retirada de aves e produtos na zona de proteção (3 km) por 21 dias e 15 dias na zona de vigilância (10 km). A certificação de área livre segue as normas da OIE e PNSA, considerando AI exótica no Brasil (país livre), e exige: 1- AI de alta patogenicidade não diagnosticada pelo sistema de vigilância pelos últimos 3 anos; 2- Um período de 6 meses após o abate, destruição das aves e resíduos e desinfecção após surto; O sistema de criação da avicultura predominante no Brasil (galinhas e perus) emprega a mais atual tecnologia e conhecimento científico na produção, no qual os plantéis são gerenciados com biossegurança, avaliação permanente dos pontos críticos, sistema de qualidade total e programas de vacinações que garantem a prevenção de inúmeros problemas sanitários. A prevenção de influenza aviária é especialmente favorecida por essas características. O sistema e tipo de construção (galpões) para o alojamento dos plantéis dessas espécies dificultam também o desafio eventualmente imposto pelas aves de vida livre. A localização geográfica da avicultura nacional, localizada fora das rotas migratórias das aves-reservatório, pode também exercer papel importante na ausência de focos de influenza no Brasil. Além disso, o baixo índice de replicação dos AIV nas aves migratórias durante a estada na região subtropical também influi para a menor ocorrência. As espécies de aves domésticas de importância comercial mais sensíveis à infecção e potencialmente envolvidas no papel de fonte de infecção, conforme citadas na literatura internacional, perus e patos, são mantidas em galpões industriais com sistema de biossegurança e de distribuição geográfica bastante restrita, em contraste com as criações dos países com relatos permanentes de surtos, em que se associam as condições de desafio naturais geográficas ditadas pelas rotas migratórias, mais alta replicação na ave na estação (países temperados) e a criação em campo aberto.

Pandemic threat posed by avian influenza A viruses

Influenza pandemics, defined as global outbreaks of the disease due to viruses with new antigenic subtypes, have exacted high death tolls from human populations. The last two pandemics were caused by hybrid viruses, or reassortants, that harbored a combination of avian and human viral genes. Avian influenza viruses are therefore key contributors to the emergence of human influenza pandemics. In 1997, an H5N1 influenza virus was directly transmitted from birds in live poultry markets in Hong Kong to humans. Eighteen people were infected in this outbreak, six of whom died. This avian virus exhibited high virulence in both avian and mammalian species, causing systemic infection in both chickens and mice. Subsequently, another avian virus with the H9N2 subtype was directly transmitted from birds to humans in Hong Kong. Interestingly, the genes encoding the internal proteins of the H9N2 virus are genetically highly related to those of the H5N1 virus, suggesting a unique property of these gene products. The identification of avian viruses in humans underscores the potential of these and similar strains to produce devastating influenza outbreaks in major population centers. Although highly pathogenic avian influenza viruses had been identified before the 1997 outbreak in Hong Kong, their devastating effects had been confined to poultry. With the Hong Kong outbreak, it became clear that the virulence potential of these viruses extended to humans.

Structural features of the avian influenza virus hemagglutinin that influence virulence

Analysis of the structure of the avian influenza (AI) virus hemagglutinin (HA) gene and protein has yielded a wealth of information on the virulence mechanisms of influenza viruses. The AI hemagglutinin appears to be unique in its capacity to accept basic amino acids at its proteolytic cleavage site (PCS). The association of multiple basic (MB) amino acids, HA cleavage, tissue spread and virulence by AI strains first proposed in the late 1970s and early 1980s [Klenk, H.D., Rott, R., Orlich, M., 1977. J. Gen. Virol. 36, 151-161; Bosch, F.X., Garten, W., Klenk, H.D., Rott, R., 1981. Virology 113, 725-735] has held fast for two decades now. While other structural characteristics and other genes can certainly influence virulence, the presence of MB amino acids at the PCS has provided a hallmark structural feature which justifies continuing sequence analysis of emerging field isolates of AI strains. In addition to this structural feature, the distal tip of the HA is prone to appearance and disappearance of glycosylation sites, some of which have been associated with virulence. The recent outbreaks of highly pathogenic AI in Mexico, Australia, Pakistan, Hong Kong and in the ongoing outbreak of moderately pathogenic H7 avian influenza in the northeast US have all provided new and useful information regarding the role of HA RNA and protein structure in both virulence and host adaptation. We have previously noted that stable RNA secondary structure near the PCS is related to the acquisition of virulence and have proposed that the secondary structure may promote the insertion of basic amino acids. In this report we evaluate the phylogenetic relationships for three recent isolates of highly pathogenic avian influenza viruses and the possible virulence factors associated with their primary and secondary structure.

Role of hemagglutinin cleavage for the pathogenicity of influenza virus

Although human epidemics of influenza occur on nearly an annual basis and result in a significant number of "excess deaths," the viruses responsible are not generally considered highly pathogenic. On occasion, however, an outbreak occurs that demonstrates the potential lethality of influenza viruses. The human pandemic of 1918 spread worldwide and killed millions, and the limited human outbreak of highly pathogenic avian viruses in Hong Kong at the end of 1997 is a warning that this could happen again. In avian species such as chickens and turkeys, several outbreaks of highly pathogenic influenza viruses have been documented. Although the reason for the lethality of the human 1918 viruses remains unclear, the pathogenicity of the avian viruses, including those that caused the human 1997 outbreak, relates primarily to properties of the hemagglutinin glycoprotein (HA). Cleavage of the HA precursor molecule HA0 is required to activate virus infectivity, and the distribution of activating proteases in the host is one of the determinants of tropism and, as such, pathogenicity. The HAs of mammalian and nonpathogenic avian viruses are cleaved extracellularly, which limits their spread in hosts to tissues where the appropriate proteases are encountered. On the other hand, the HAs of pathogenic viruses are cleaved intracellularly by ubiquitously occurring proteases and therefore have the capacity to infect various cell types and cause systemic infections. The x-ray crystal structure of HA0 has been solved recently and shows that the cleavage site forms a loop that extends from the surface of the molecule, and it is the composition and structure of the cleavage loop region that dictate the range of proteases that can potentially activate infectivity. Here influenza virus pathogenicity is discussed, with an emphasis on the role of HA0 cleavage as a determining factor.

Virulence-associated sequence duplication at the hemagglutinin cleavage site of avian influenza viruses

Recent highly pathogenic (HP) field isolates of avian influenza (AI) virus from Mexico all possess an insertion of at least two basic amino acids (arg-lys) at the cleavage site of the hemagglutinin (HA) glycoprotein. One HP isolate has additional information which yields a 4 amino acid insert (arg-lys-arg-lys). We present here the nucleotide sequence of the HA gene of this unique isolate and compare it to recent H5N2 and other avian influenza isolates. The complete HA nucleotide sequence of the isolate and phylogenetic relationship suggest that it was derived in direct succession from a non-pathogenic strain isolated about 1 month earlier. The unique insertion sequence is a direct duplication of part of the purine-rich region preceding the arginine codon at the HA cleavage site. This evidence along with other data in this report provide compelling support for a proposed model explaining the mechanism of spontaneous, virulence-related insertions in type A influenza viruses.