Phylogenetic analysis of H9N2 avian influenza viruses in Afghanistan (2016-2017)

In vitro antiviral activity of NanB bacterial sialidase against avian influenza H9N2 virus in MDCK cells

The avian influenza virus is an infectious agent that may cause global health problems in poultry and is potentially zoonotic. In the recent decades, bacterial-derived sialidases have been extensively studied for their ability to inhibit avian influenza virus infections. In this study, the antiviral activity of NanB sialidase from Pasteurella multocida was investigated through in vitro analysis using Madin-Darby canine kidney (MDCK) cells. NanB sialidase was purified from P. multocida to test its toxicity and its ability to hydrolyse its sialic acid receptors on MDCK cells. The H9N2 challenge virus was propagated in MDCK cells until cytopathic effects appeared. Antiviral activity of NanB sialidase was tested using MDCK cells, and then observed based on cell morphology, viral copy number, and expression of apoptosis-mediating genes. NanB sialidase effectively hydrolysed Neu5Acα(2,6)-Gal sialic acid at a dose of 129 mU/ml, while at 258 mU/ml, it caused toxicity to MDCK cells. Antiviral activity of sialidase was evident based on the significant decrease in viral copy number at all doses administered. The increase of p53 and caspase-3 expression was observed in infected cells without sialidase. Our study demonstrates the ability of NanB sialidase to inhibit H9N2 virus replication based on observations of sialic acid hydrolysis, reduction in viral copy number, and expression of apoptosis-related genes. The future application of sialidase may be considered as an antiviral strategy against avian influenza H9N2 virus infections. RESEARCH HIGHLIGHTSNanB sialidase effectively hydrolyses Neu5Acα(2,6)-Gal at a dose of 129 mU/ml.NanB sialidase from Pasteurella multocida can inhibit the entry of H9N2 virus into cells.NanB sialidase of Pasteurella multocida prevents infection-induced cell apoptosis.NanB sialidase reduces the H9N2 viral copy number in MDCK cells.

A perspective of the prevalent H9N2 virus with a special focus on molecular and pathological aspects in commercial broiler chicken in Punjab, Pakistan

Abstract Frequent outbreaks of avian influenza H9N2 virus in Pakistan revealed that this subtype has become endemic in the poultry industry and, besides economic losses, poses a threat to public health. The present study describes the molecular characterization and pathological alterations in naturally infected broiler chickens with the current H9N2 field strain and their phylogenomic dynamics. In this study, tissue samples (trachea, lung, kidney and intestine) from 100 commercial chicken flocks were collected from July 2018 to August 2019. Samples were subjected to molecular detection, phylogeny and subsequent pathological examination. The complete length of the HA gene was successfully amplified in five samples. Nucleotide sequencing revealed positive samples placed in a clade belonging to the B2 sub-lineage of the G1 genotype and categorized as LPAIV based on the amino acid sequence of the HA gene at the cleavage site (PAKSSR/G). Genetic analysis of the haemagglutinin (HA) gene revealed nt: 80.5%-99.5%; aa: 83.8%-98.9% homology to H9N2 strains reported previously from Pakistan, neighbouring countries, and (A/Quail/Hong Kong/G1/97). Gross lesions include a slight airsacculitis, mild hemorrhages, diffuse congestion and purulent exudate in tracheal mucosa, fibrinonecrotic cast in the trachea lumen and mild pulmonary congestion. Histopathological alterations include sloughing of epithelial cells and infiltration of inflammatory cells in the trachea, mononuclear cells (MNCs) infiltration, pulmonary congestion and exudate in the lumen of parabronchi, peritubular congestion in the kidneys with degeneration of tubular epithelial cells and degenerative changes in the intestinal villi epithelial cells and goblet cell hyperplasia. Immunohistochemistry analysis confirmed the presence of AIVH9N2 antigen in the trachea, lungs, kidney and intestine. Electron microscopy revealed ultrastructural changes in the trachea, including degenerated cilia, mitochondrial swelling and enlarged endoplasmic reticulum. Based on all essential analysis, the present study revealed the distribution of the H9N2 virus of G1 genotype in Punjab, Pakistan, with mild to moderate pathogenicity.

Phylogenetic Analysis of Hemagglutinin Gene and Evaluation of the Viral Shedding of H9N2 Avian Influenza Viruses Using Real-time RT-PCR in SPF Chickens

In recent years, the H9N2 influenzavirus has been circulating widely in poultry farms causing extensive damage. The hemagglutinin (HA) genes of the two virus isolates of H9N2 subtype in specific pathogen-free chickens were studied to determine the shedding rate in the host’s oropharyngeal and cloacal routes and their genetic relationship. The sequence analysis and phylogenetic study of the samples were performed by comparing each isolate with other H9N2 isolates in the gene bank. In the present study, the chickens were inoculated with low pathogenic avian influenza virus (LPAIV) (A/Chicken/Iran/ZMT-101/1998 [H9N2]) through the intranasal route. Oropharyngeal and cloacal swabs were collected from the chickens within 1-10 days after inoculation. The rate of viral shedding was measured within the previous 10 days by the real-time reverse transcriptase polymerase chain reaction molecular technique. No clinical symptoms were observed during the experiment in the chickens. The results obtained from this technique showed that the main route of shedding for LPAIV was oropharyngeal areas (p <0.05). Both isolates had a similar proteolytic R-S-S-R sequence at the cleavage site of the HA gene and contained glutamine (Q) amino acid at position 226 of the HA receptor-binding site, indicating that these isolates were nonpathogenic. Phylogenetic analysis demonstrated that both isolates belonged to the Eurasian clade. The comparison of these isolates with other isolates in the gene bank showed that they had the greatest similarity with the isolates in clade 1 and the least homology with the isolates in clade 4.

Avian Influenza (H9N2 Subtype) in Iranian Broiler Farms: A Cross-sectional Study

The present study aimed to determine the seroprevalence of H9N2 influenza in broiler farms at the time of slaughter in Iran. A total of 747 birds were sampled from 74 Farms in 13 provinces within 2013-2016. The obtained sera were investigated using the hemagglutination inhibition (HI) test. Out of 74 sampled farms and 747 birds, 57 farms (77%) and 445 (59.57%) birds were reported to be seropositive. In 2013, 10 farms and 110 birds were sampled out of which three farms (29.6%) and 29 birds (30%) were seropositive. In 2014, 24 farms and 220 birds were sampled out of which 22 farms (91.6%) and 220 birds (86.6%) were positive in six provinces. In 2015, 30 farms and 278 birds were sampled out of which 5 farms (16%) and134 birds (48.2%) were positive in four provinces. Finally, in 2016, 7 farms (70%) out of 10 sampled farms and 62 birds (59%) out of 105 sampled birds were positive for H9N2 in eight provinces. The mean titer of units in 2013 was statistically lower, as compared to that in 2014 (p <0.01). In addition, the proportion of positive serum units in 2013 was statistically lower, as compared to that in 2014 (p <0.001). In general, the prevalence of H9N2 was high indicating the continuous circulation of the virus in Iran. Given the importance and impact of this virus on the poultry industry, people’s livelihood, and public health, more epidemiological studies are needed to evaluate the effectiveness of the adopted measures and methods in controlling the H9N2 virus.

Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq

Background and Aim:

Infectious bronchitis (IB) has an influential economic impact on the poultry industry, causing huge losses each year due to the condemnation of infected chickens. Despite the use of many kinds of vaccines in Iraq, it is common to find IB problems in vaccinated chickens. Information about the strains that affect Iraqi chickens is very limited. Therefore, we aimed to detect the currently circulating strains of IB virus that cause frequent outbreaks in egg layers despite the use of vaccination against the virus.

Materials and Methods:

Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples).

Results:

The isolated strain was different from other strains, especially the strain isolated in the North of Iraq (Sulemania Strain) and shares 98% homology with an Israeli strain (Israel variant 2, IS 1494).

Conclusion:

Although more studies are needed to detect IB virus strains circulating in Iraq, this work lays the foundation for making a good strategy to control the disease and selecting vaccines that should be used in farms.

H9 Influenza Viruses: An Emerging Challenge

Influenza A viruses (IAVs) of the H9 subtype are enzootic in Asia, the Middle East, and parts of North and Central Africa, where they cause significant economic losses to the poultry industry. Of note, some strains of H9N2 viruses have been linked to zoonotic episodes of mild respiratory diseases. Because of the threat posed by H9N2 viruses to poultry and human health, these viruses are considered of pandemic concern by the World Health Organization (WHO). H9N2 IAVs continue to diversify into multiple antigenically and phylogenetically distinct lineages that can further promote the emergence of strains with pandemic potential. Somewhat neglected compared with the H5 and H7 subtypes, there are numerous indicators that H9N2 viruses could be involved directly or indirectly in the emergence of the next influenza pandemic. The goal of this work is to discuss the state of knowledge on H9N2 IAVs and to provide an update on the contemporary global situation.

A Global Perspective on H9N2 Avian Influenza Virus

H9N2 avian influenza viruses have become globally widespread in poultry over the last two decades and represent a genuine threat both to the global poultry industry but also humans through their high rates of zoonotic infection and pandemic potential. H9N2 viruses are generally hyperendemic in affected countries and have been found in poultry in many new regions in recent years. In this review, we examine the current global spread of H9N2 avian influenza viruses as well as their host range, tropism, transmission routes and the risk posed by these viruses to human health.

PB2 mutations arising during H9N2 influenza evolution in the Middle East confer enhanced replication and growth in mammals

Avian influenza virus H9N2 has been endemic in birds in the Middle East, in particular in Egypt with multiple cases of human infections since 1998. Despite concerns about the pandemic threat posed by H9N2, little is known about the biological properties of H9N2 in this epicentre of infection. Here, we investigated the evolutionary dynamics of H9N2 in the Middle East and identified phylogeny-associated PB2 mutations that acted cooperatively to increase H9N2 replication/transcription in human cells. The accumulation of PB2 mutations also correlated with an increase in H9N2 virus growth in the upper and lower airways of mice and in virulence. These mutations clustered on a solvent-exposed region in the PB2-627 domain in proximity to potential interfaces with host factors. These PB2 mutations have been found at high prevalence during evolution of H9N2 in the field, indicating that they have provided a selective advantage for viral adaptation to infect poultry. Therefore, continuous prevalence of H9N2 virus in the Middle East has generated a far more fit or optimized replication phenotype, leading to an expanded viral host range, including to mammals, which may pose public health risks beyond the current outbreaks.

The G1-like clade of H9N2 influenza viruses can undergo genetic reassortment with other influenza virus subtypes to produce novel zoonotic viruses, such as the Gs/GD lineage H5N1, H7N9, H10N8, and H5N8 viruses. Since 1998, the G1-like subclade of H9N2 influenza virus has been widely circulating in birds in Central Asia and the Middle East and a number of human cases have been reported. However, little is known about the biological properties of H9N2 viruses in this epicentre of infection. Our data showed that, during about two decades of evolution in nature, G1-like subclade strains evolved to produce strains with appreciably higher replication phenotypes in Central Asia and the Middle East, which led to their expanded host range, including to humans. Therefore, G1-like subclade strains in these areas may accumulate mutations to produce novel viruses and the large gene pool in these areas would enable reassortment with other influenza viruses. This study indicated the need for studies of H9N2 viruses in such areas to monitor their evolutionary dynamics and possible genetic changes.

Avian influenza overview October 2016-August 2017

The A(H5N8) highly pathogenic avian influenza (HPAI) epidemic occurred in 29 European countries in 2016/2017 and has been the largest ever recorded in the EU in terms of number of poultry outbreaks, geographical extent and number of dead wild birds. Multiple primary incursions temporally related with all major poultry sectors affected but secondary spread was most commonly associated with domestic waterfowl species. A massive effort of all the affected EU Member States (MSs) allowed a descriptive epidemiological overview of the cases in poultry, captive birds and wild birds, providing also information on measures applied at the individual MS level. Data on poultry population structure are required to facilitate data and risk factor analysis, hence to strengthen science-based advice to risk managers. It is suggested to promote common understanding and application of definitions related to control activities and their reporting across MSs. Despite a large number of human exposures to infected poultry occurred during the ongoing outbreaks, no transmission to humans has been identified. Monitoring the avian influenza (AI) situation in other continents indicated a potential risk of long-distance spread of HPAI virus (HPAIV) A(H5N6) from Asia to wintering grounds towards Western Europe, similarly to what happened with HPAIV A(H5N8) and HPAIV A(H5N1) in previous years. Furthermore, the HPAI situation in Africa with A(H5N8) and A(H5N1) is rapidly evolving. Strengthening collaborations at National, EU and Global levels would allow close monitoring of the AI situation, ultimately helping to increase preparedness. No human case was reported in the EU due to AIVs subtypes A(H5N1), A(H5N6), A(H7N9) and A(H9N2). Direct transmission of these viruses to humans has only been reported in areas, mainly in Asia and Egypt, with a substantial involvement of wild bird and/or poultry populations. It is suggested to improve the collection and reporting of exposure events of people to AI.