Distribution Of Avian Influenza Viruses Research Articles

Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia

Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections.The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.

Distribution of avian influenza viruses according to environmental surveillance during 2014\u20132018, China

BackgroundRecurrent infections of animal hosts with avian influenza viruses (AIVs) have posted a persistent threat. It is very important to understand the avian influenza virus distribution and characteristics in environment associated with poultry and wild bird. The aim of this study was to analyze the geographic and seasonal distributions of AIVs in the 31 provinces, municipalities and autonomous region (PMA) of China, compare the AIVs prevalence in different collecting sites and sampling types, analyze the diversity of AIVs subtypes in environment.MethodsA total of 742 005 environmental samples were collected from environmental samples related to poultry and wild birds in different locations in the mainland of China during 2014–2018. Viral RNA was extracted from the environmental samples. Real-time RT-PCR assays for influenza A, H5, H7 and H9 subtypes were performed on all the samples to identify subtypes of influenza virus. The nucleic acid of influenza A-positive samples were inoculated into embryonated chicken eggs for virus isolation. Whole-genome sequencing was then performed on Illumina platform. SPSS software was used to paired t test for the statistical analysis. ArcGIS was used for drawing map. Graphpad Prism was used to make graph.ResultsThe nucleic acid positivity rate of influenza A, H5, H7 and H9 subtypes displayed the different characteristics of geographic distribution. The nucleic acid positivity rates of influenza A were particularly high (25.96%–45.51%) in eleven provinces covered the Central, Eastern, Southern, Southwest and Northwest of China. The nucleic acid positivity rates of H5 were significantly high (11.42%–13.79%) in two provinces and one municipality covered the Southwest and Central of China. The nucleic acid positivity rates of H7 were up to 4% in five provinces covered the Eastern and Central of China. The nucleic acid positivity rates of H9 were higher (13.07%–2.07%) in eleven PMA covered the Southern, Eastern, Central, Southwest and Northwest of China. The nucleic acid positivity rate of influenza A, H5, H7 and H9 showed the same seasonality. The highest nucleic acid positivity rates of influenza A, H5, H7, H9 subtypes were detected in December and January and lowest from May to September. Significant higher nucleic acid positivity rate of influenza A, H5, H7 and H9 were detected in samples collected from live poultry markets (LPM) (30.42%, 5.59%, 4.26%, 17.78%) and poultry slaughterhouses (22.96%, 4.2%, 2.08%, 12.63%). Environmental samples that were collected from sewage and chopping boards had significantly higher nucleic acid positivity rates for influenza A (36.58% and 33.1%), H5 (10.22% and 7.29%), H7(4.24% and 5.69%)and H9(21.62% and 18.75%). Multiple subtypes of AIVs including nine hemagglutinin (HA) and seven neuraminidase (NA) subtypes were isolated form the environmental samples. The H5, H7, and H9 subtypes accounted for the majority of AIVs in environment.ConclusionsIn this study, we found the avian influenza viruses characteristics of geographic distribution, seasonality, location, samples types, proved that multiple subtypes of AIVs continuously coexisted in the environment associated with poultry and wild bird, highlighted the need for environmental surveillance in China.Graphic

Prevalence and Distribution of Avian Influenza Viruses in Domestic Ducks at the Waterfowl-Chicken Interface in Wetlands.

Ducks are a natural reservoir of influenza A viruses (IAVs) and can act as a reassortment vessel. Wetlands, such as Hakaluki and Tanguar haor in Bangladesh, have unique ecosystems including domestic duck (Anas platyrhynchos domesticus) rearing, especially household and free-range ducks. A cross-sectional study was, therefore, conducted to explore avian influenza status and its distribution and risk factors in the wetland areas. During the three consecutive winters of 2015–2017, specifically in December of these years, we collected a total of 947 samples including blood, oropharyngeal and cloacal swabs from domestic ducks (such as free-range ducks (n = 312 samples) and household ducks (n = 635 samples) in wetlands. We screened serum samples using a nucleoprotein competitive enzyme-linked immunosorbent assay (c-ELISA) to estimate seroprevalence of IAV antibodies and swab samples by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) to detect IA viral M gene. Eleven M gene positive samples were subjected to sequencing and phylogenetic analysis. Serological and viral prevalence rates of IAVs were 63.8% (95% CI: 60.6–66.8) and 10.7% (8.8–12.8), respectively. Serological and viral RNA prevalence rates were 51.8% (95% CI: 47.2–56.4) and 10.2% (7.6–13.3) in Hakaluki haor, 75.6% (71.5–79.4) and 11.1% (8.5–14.3) in Tanguar haor, 66.3% (62.5–69.9) and 11.2% (8.8–13.9) in household ducks and 58.7% (52.9–64.2) and 9.6% (6.5–13.4) in free-range ducks, respectively. The risk factors identified for higher odds of AI seropositive ducks were location (OR = 2.9, 95% CI: 2.2–3.8, p < 0.001; Tanguar haor vs. Hakaluki haor), duck-rearing system (OR = 1.4, 1.1–1.8, household vs. free-range), farmer’s education status (OR = 1.5, 1.2–2.0, p < 0.05 illiterate vs. literate) and contact type (OR = 3.0, 2.1–4.3, p < 0.001; contact with chicken vs. no contact with chicken). The risk factors identified for higher odds of AI viral RNA positive ducks were farmer’s education status (OR = 1.5, 1.0–2.3, p < 0.05 for illiterate vs literate), contact type (OR = 2.7, 1.7–4.2, p < 0.001; ducks having contact with chicken vs. ducks having contact with waterfowl). The phylogenetic analysis of 11 partial M gene sequences suggested that the M gene sequences detected in free-range duck were very similar to each other and were closely related to the M gene sequences of previously reported highly pathogenic avian influenza (HPAI) and low pathogenic avian influenza (LPAI) subtypes in waterfowl in Bangladesh and Southeast Asian countries. Results of the current study will help provide significant information for future surveillance programs and model IAV infection to predict the spread of the viruses among migratory waterfowl, free-range ducks and domestic poultry in Bangladesh.

Molecular Detection of Influenza A virus in Domestic Ducks and Geese in Basra Province, Southern Iraq

Avian influenza is one of the important viral diseases in poultry that can cause serious economic losses in many countries around the world, and occasionally infect human causing mild to severe illness. It is caused by avian influenza A viruseswhich have been isolated from avian species, particularly waterfowls that are considered the main reservoir for all influenza A virus subtypes. The aim of this study was to detect influenza virus from domestic ducks and geese in different geographical regions(Abu Al-Khasseb, Shatt Al-Arab, Zubair, and Al-Qurnah) of Basrah province, Southern Iraq. The study was conducted on 115 cloacal swabs collected from 60 ducks and 55 geese distributed in different regions of Basrah province. Samples were processed for RT-PCR to amplify matrix (M) gene that is conserved between all influenza A subtypes by using a set of universal primer. We demonstrated that influenza A viruses is prevalent in domestic waterfowls with a significantly higher percentage in ducks than geese; 42 samples (29 ducks and 13geese) were positive to viral M gene. In addition, the virus prevalence was significantly higher in the North of Basrah (Al-Qurnah region) than the other geographical regions. The overall findings of this study obtained a primary picture about the distribution of avian influenza viruses in our region, which is importantto prevent the spread of infection to poultry and eventually minimize the risk of acquiring infection to humans. According toour knowledge, this is the first study aimed to identify avian influenza viruses in waterfowls in Basrah province, Southern Iraq.

Historical prevalence and distribution of avian influenza virus A(H7N9) among wild birds.

We examined 48 published studies for which sample sizes could be ascertained to determine the historic prevalence of influenza A(H7N9) virus in wild bird populations and reviewed GenBank data to further establish its distribution. Low prevalence (0.0093%) in Asia suggests > 30,000 samples would be required to detect the H7N9 subtype in wild birds.

Influenza A Viruses in Wild Birds of the Pacific Flyway, 2005–2008

Avian influenza viruses (AIVs) pose a significant threat to public health, and viral subtypes circulating in natural avian reservoirs can contribute to the emergence of pathogenic influenza viruses in humans. We investigated the prevalence and distribution of AIVs in 8826 migratory and resident wild birds in North America along the Pacific flyway, which is a major north-south migration pathway that overlaps with four other flyways in Alaska providing opportunities for mixing of Eurasian and American origin influenza viruses. Overall, the prevalence of AIVs was low (1%) among the wide range of avian species tested, but we detected AIVs in 69 hunter-harvested waterfowl (Anseriformes) sampled at a national wildlife refuge in California from October 2007 to January 2008. A wide range of subtypes were detected in waterfowl with H6N1, H10N7, H7N3, and H3N5 being the most common. We suspect H6N1 was introduced or remerged in 2007 at this key wintering site for waterfowl along the Pacific Flyway. Over a 3-week period, 13 H6N1 AIVs were isolated from two northern pintails (Anas acuta), three northern shovelers (Anas clypeata), three ring-necked ducks (Aythya collaris), four American widgeon (Anas americana), and one gadwall (Anas strepera). We conclude that a diverse array of AIVs was present and that cross-species transmission was occurring among waterfowl in the central valley wetlands of California.

Influenza A viruses isolated from waterfowl in two wildlife management areas of Pennsylvania.

A survey was conducted at two wildlife management areas of Pennsylvania (USA) to evaluate an antigen capture enzyme-linked immunosorbent assay (AC-ELISA) for the detection of avian influenza viruses (AIV) in cloacal swabs from waterfowl and to determine the influenza A virus subtypes and the distribution of these viruses among waterfowl. We collected 330 cloacal swabs from hunter-killed waterfowl in the fall of 1990 and from cage-captured waterfowl in the summer of 1991. Thirty-one hemagglutinating agents were isolated by chicken embryo inoculation (CEI) of which 27 were influenza A viruses and four Newcastle disease viruses (NDV). The prevalence of AIV infection was 8.2%. Compared to CEI, AC-ELISA was only 15% sensitive and 61% specific. Based on the distribution of AIV by species of waterfowl, mallards (Anas platyrhynchos) and American wigeons (Anas americana) were at equal risk of AIV infection even though most of the AIV isolates came from mallards. Although significant crude effects of sampling site and season on AIV recovery could be established, juvenile age was identified as the primary risk factor of AIV recovery. Twelve AIV subtypes were identified by hemagglutination inhibition (HI) and neuraminidase inhibition (NI) tests. The most prevalent subytpes were H4N8 and H6N8. We concluded that AC-ELISA was not useful for the detection of AIV in cloacal swabs from waterfowl and that CEI, HI, and NI tests remain as the method of choice for AIV screening in waterfowl. Based on the results AIV infected preferentially the young which represent the high risk group in waterfowl populations.(ABSTRACT TRUNCATED AT 250 WORDS)