Surveillance, epidemiological, and virological detection of highly pathogenic H5N1 avian influenza viruses in duck and poultry from Bangladesh

Phylodynamics of high pathogenicity avian influenza virus in Bangladesh identifying domestic ducks as the amplifying host reservoir

High pathogenicity avian influenza (HPAI) virus H5N1 first emerged in Bangladesh in 2007. Despite the use of vaccines in chickens since 2012 to control HPAI, HPAI H5Nx viruses have continued to infect poultry, and wild birds, resulting in notable mass mortalities in house crows (Corvus splendens). The first HPAI H5Nx viruses in Bangladesh belonged to clade 2.2.2, followed by clade 2.3.4.2 and 2.3.2.1 viruses in 2011. After the implementation of chicken vaccination in 2012, these viruses were mostly replaced by clade 2.3.2.1a viruses and more recently clade 2.3.4.4b and h viruses. In this study, we reconstruct the phylogenetic history of HPAI H5Nx viruses in Bangladesh to evaluate the role of major host species in the maintenance and evolution of HPAI H5Nx virus in Bangladesh and reveal the role of heavily impacted crows in virus epidemiology. Epizootic waves caused by HPAI H5N1 and H5N6 viruses amongst house crows occurred annually in winter. Bayesian phylodynamic analysis of clade 2.3.2.1a revealed frequent bidirectional viral transitions between domestic ducks, chickens, and house crows that was markedly skewed towards ducks; domestic ducks might be the source, or reservoir, of HPAI H5Nx in Bangladesh, as the number of viral transitions from ducks to chickens and house crows was by far more numerous than the other transitions. Our results suggest viral circulation in domestic birds despite vaccination, with crow epizootics acting as a sentinel. The vaccination strategy needs to be updated to use more effective vaccinations, assess vaccine efficacy, and extension of vaccination to domestic ducks, the key reservoir.

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh

Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, the dynamics of transmission and evolutionary patterns of AIV and its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted in nine districts of Bangladesh between 2019 and 2021, to determine the prevalence of AIV and its subtypes H5 and H9, as well as to identify risk factors and the phylodynamics of H5N1 clades circulating in domestic duck farms. The oropharyngeal and cloacal swab samples were tested for the AIV Matrix gene (M-gene) followed by H5, H7, and H9 subtypes using rRT-PCR. The exploratory analysis was performed to estimate AIV and its subtype prevalence in different production systems, and multivariable logistic regression model was used to identify the risk factors that influence AIV infection in ducks. Bayesian phylogenetic analysis was conducted to generate a maximum clade credibility (MCC) tree and the maximum likelihood method to determine the phylogenetic relationships of the H5N1 viruses isolated from ducks. AIV was detected in 40% (95% CI: 33.0-48.1) of the duck farms. The prevalence of AIV was highest in nomadic ducks (39.8%; 95% CI: 32.9-47.1), followed by commercial ducks (24.6%; 95% CI: 14.5-37.3) and backyard ducks (14.4%; 95% CI: 10.5-19.2). The H5 prevalence was also highest in nomadic ducks (19.4%; 95% CI: 14.0-25.7). The multivariable logistic regression model revealed that ducks from nomadic farms (AOR: 2.4; 95% CI: 1.45-3.93), juvenile (AOR: 2.2; 95% CI: 1.37-3.61), and sick ducks (AOR: 11.59; 95% CI: 4.82-32.44) had a higher risk of AIV. Similarly, the likelihood of H5 detection was higher in sick ducks (AOR: 40.8; 95% CI: 16.3-115.3). Bayesian phylogenetic analysis revealed that H5N1 viruses in ducks belong to two distinct clades, 2.3.2.1a, and 2.3.4.4b. The clade 2.3.2.1a (reassorted) has been evolving silently since 2015 and forming at least nine subgroups based on >90% posterior probability. Notably, clade 2.3.4.4b was introduced in ducks in Bangladesh by the end of the year 2020, which was genetically similar to viruses detected in wild birds in Japan, China, and Africa, indicating migration-associated transmission of an emerging panzootic clade. We recommend continuing AIV surveillance in the duck production system and preventing the intermingling of domestic ducks with migratory waterfowl in wetlands.

Prevalence and risk factors for avian influenza virus (H5 and H9) contamination in peri-urban and rural live bird markets in Bangladesh

Avian influenza viruses (AIV) have been frequently detected in live bird markets (LBMs) around the world, primarily in urban areas, and have the ability to spillover to other species, including humans. Despite frequent detection of AIV in urban LBMs, the contamination of AIV on environmental surfaces in rural and peri-urban LBMs in Bangladesh is poorly documented. Therefore, we conducted this study to determine the prevalence of AIV subtypes within a subset of peri-urban and rural LBMs in Bangladesh and to further identify associated risk factors. Between 2017 and 2018, we collected faecal and offal samples from 200 stalls in 63 LBMs across four sub-districts. We tested the samples for the AIV matrix gene (M-gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We performed a descriptive analysis of market cleanliness and sanitation practices in order to further elucidate the relationship between LBM biosecurity and AIV subtypes by species, sample types, and landscape. Subsequently, we conducted a univariate analysis and a generalized linear mixed model (GLMM) to determine the risk factors associated with AIV contamination at individual stalls within LBMs. Our findings indicate that practices related to hygiene and the circulation of AIV significantly differed between rural and peri-urban live bird markets. 42.5% (95% CI: 35.56-49.67) of stalls were positive for AIV. A/H5, A/H9, and A HA/Untyped were detected in 10.5% (95% CI: 6.62-15.60), 9% (95% CI: 5.42-13.85), and 24.0% (95% CI: 18.26-30.53) of stalls respectively, with no detection of A/H7. Significantly higher levels of AIV were found in the Sonali chicken strain compared to the exotic broiler, and in offal samples compared to fecal samples. In the GLMM analysis, we identified several significant risk factors associated with AIV contamination in LBMs at the stall level. These include: landscape (AOR: 3.02; 95% CI: 1.18-7.72), the number of chicken breeds present (AOR: 2.4; 95% CI: 1.01-5.67), source of birds (AOR: 2.35; 95% CI: 1.0-5.53), separation of sick birds (AOR: 3.04; 95% CI: 1.34-6.92), disposal of waste/dead birds (AOR: 3.16; 95% CI: 1.41-7.05), cleaning agent (AOR: 5.99; 95% CI: 2.26-15.82), access of dogs (AOR: 2.52; 95% CI: 1.12-5.7), wild birds observed on site (AOR: 2.31; 95% CI: 1.01-5.3). The study further revealed a substantial prevalence of AIV with H5 and H9 subtypes in peri-urban and rural LBMs. The inadequate biosecurity measures at poultry stalls in Bangladesh increase the risk of AIV transmission from poultry to humans. To prevent the spread of AIV to humans and wild birds, we suggest implementing regular surveillance at live bird markets and enhancing biosecurity practices in peri-urban and rural areas in Bangladesh.

Myxovirus resistance (Mx) Gene Diversity in Avian Influenza Virus Infections

Avian influenza viruses (AIVs) pose threats to animal and human health. Outbreaks from the highly pathogenic avian influenza virus (HPAIV) in indigenous chickens in Bangladesh are infrequent. This could be attributed to the Myxovirus resistance (Mx) gene. To determine the impact of Mx gene diversity on AIV infections in chicken, we assessed the Mx genes, AIVs, and anti-AIV antibodies. DNA from blood cells, serum, and cloacal swab samples was isolated from non-vaccinated indigenous chickens and vaccinated commercial chickens. Possible relationships were assessed using the general linear model (GLM) procedure. Three genotypes of the Mx gene were detected (the resistant AA type, the sensitive GG type, and the heterozygous AG type). The AA genotype (0.48) was more prevalent than the GG (0.19) and the AG (0.33) genotypes. The AA genotype was more prevalent in indigenous than in commercial chickens. A total of 17 hemagglutinating viruses were isolated from the 512 swab samples. AIVs were detected in two samples (2/512; 0.39%) and subtyped as H1N1, whereas Newcastle disease virus (NDV) was detected in the remaining samples. The viral infections did not lead to apparent symptoms. Anti-AIV antibodies were detected in 44.92% of the samples with levels ranging from 27.37% to 67.65% in indigenous chickens and from 26% to 87.5% in commercial chickens. The anti-AIV antibody was detected in 40.16%, 65.98%, and 39.77% of chickens with resistant, sensitive, and heterozygous genotypes, respectively. The genotypes showed significant association (p < 0.001) with the anti-AIV antibodies. The low AIV isolation rates and high antibody prevalence rates could indicate seroconversion resulting from exposure to the virus as it circulates. Results indicate that the resistant genotype of the Mx gene might not offer anti-AIV protection for chickens.

Semi-Scavenging Poultry as Carriers of Avian Influenza Genes

Ducks are the natural reservoir of influenza A virus and the central host for the avian influenza virus (AIV) subtype H5N1, which is highly pathogenic. Semi-scavenging domestic ducks allow for the reemergence of new influenza subtypes which could be transmitted to humans. We collected 844 cloacal swabs from semi-scavenging ducks inhabiting seven migratory bird sanctuaries of Bangladesh for the molecular detection of avian influenza genes. We detected the matrix gene (M gene) using real-time RT-PCR (RT-qPCR). Subtyping of the AIV-positive samples was performed by RT-qPCR specific for H5, H7, and H9 genes. Out of 844 samples, 21 (2.488%) were positive for AIV. Subtyping of AIV positive samples (n = 21) revealed that nine samples (42.85%) were positive for the H9 subtype, five (23.80%) were positive for H5, and seven (33.33%) were negative for the three genes (H5, H7, and H9). We detected the same genes after propagating the virus in embryonated chicken eggs from positive samples. Semi-scavenging ducks could act as carriers of pathogenic AIV, including the less pathogenic H9 subtype. This can enhance the pathogenicity of the virus in ducks by reassortment. The large dataset presented in our study from seven areas should trigger further studies on AIV prevalence and ecology.

Prevalence and risk factors of Avian Influenza Viruses among household ducks in Chattogram, Bangladesh

Avian influenza viruses (AIV) increase commercial and backyard poultry mortality and morbidity, reduces egg production, and elevates public health risk. Household ducks propagate and transmit HPAI and LPAI viruses between domesticated and wild birds in Southeast Asian countries, including Bangladesh. This study was conducted to identify epidemiological factors associated with AIV infection among household ducks at Chattogram, Bangladesh. We randomly selected and collected blood and oropharyngeal swab samples from 281 households ducks. We evaluated the serum for AIV antibody using cELISA and tested for H5 and H9 subtypes using the HI test. We tested the swabs with real-time reverse transcriptase PCR (rRT-PCR) for M gene, and H5, H9 subtypes. In the duck populations, the household level AIV sero-prevalence was 57.7% (95% CI: 51.6-63.3) and RNA prevalence was 2.4% (95% CI: 1.0-5.0). H5 and H9 subtype sero-prevalence was 31.5% (95% CI: 22.2-42.0) and 23.9% (95% CI: 15.6-33.9). H5 and H9 subtype RNA prevalence were 0% (95% CI: 0.0-1.3) and 2.4% (95% CI: 1.0-5.0). We determined household-level OR (Odds Ratios) for the "combined (mixed materials-mud and concrete or metallic)" category was 2.2 (95% CI: 1.1-4.2) compared with "wooden/bamboo" category (p = 0.02); 2.8 (95% CI: 1.2-6.6) in households with duck plague vaccine coverage compared with no coverage (p = 0.01); and 2.4 (95% CI: 0.6-9.7) in households that threw dead birds in bushes and the roadside compared with households that buried or threw dead birds in garbage pits (p = 0.21). M gene phylogenetic analysis compared M gene sequences to previously reported Bangladeshi H9N2 isolates. The evidence presented here shows AIV circulation in the Chattogram, Bangladesh study areas. AIV reduction can be achieved through farmer education of proper farm management practices.

Farm-Level Risk Factors Associated With Avian Influenza A (H5) and A (H9) Flock-Level Seroprevalence on Commercial Broiler and Layer Chicken Farms in Bangladesh

A cross-sectional study was conducted to identify farm-level risk factors associated with avian influenza A H5 and H9 virus exposure on commercial chicken farms in Bangladesh. For broiler farms, both H5 and H9 seropositivity were associated with visits by workers from other commercial chicken farms [odds ratio (OR) for H5 = 15.1, 95% confidence interval (CI): 2.8-80.8; OR for H9 = 50.1, 95% CI: 4.5-552.7], H5 seropositivity was associated with access of backyard ducks (OR = 21.5, 95% CI: 2.3-201.1), and H9 seropositivity with a number of farm employees (OR = 9.4, 95% CI: 1.1-80.6). On layer farms, both H5 and H9 seropositivity were associated with presence of stray dogs (OR for H5 = 3.1, 95% CI: 1.1-9.1; OR for H9 = 4.0, 95% CI: 1.1-15.3), H5 seropositivity with hatcheries supplying chicks (OR = 0.0, 95% CI: 0.0-0.3), vehicles entering farms (OR = 5.8, 95% CI: 1.5-22.4), number of farm employees (OR = 5.8, 95% CI: 1.2-28.2), and burying of dead birds near farms (OR = 4.6, 95% CI: 1.2-17.3); H9 seropositivity with traders supplying feed (OR = 5.9, 95% CI: 1.0-33.9), visits conducted of other commercial poultry farms (OR = 4.7, 95% CI: 1.1-20.6), number of spent layers sold (OR = 24.0, 95% CI: 3.7-155.0), and frequency of replacing chicken droppings (OR = 28.3, 95% CI: 2.8-284.2). Policies addressing these risk factors will increase the effectiveness of prevention and control strategies reducing the risk of avian influenza on commercial chicken farms.

Efficacy of two vaccines against recent emergent antigenic variants of clade 2.3.2.1a highly pathogenic avian influenza viruses in Bangladesh

H5N1 highly pathogenic avian influenza viruses (HPAIVs) have caused outbreaks in poultry in Bangladesh since 2007. While clade 2.2.2 and 2.3.4.2 HPAIVs have not been detected since 2012, clade 2.3.2.1a viruses have caused continuous outbreaks since 2012 despite the use of vaccines. In this study, we evaluated the efficacy of two H5 vaccines licensed in Bangladesh, RE-6 inactivated vaccine, and a recombinant herpesvirus of turkeys vaccine with an H5 insert (rHVT-H5), for protection against recent field viruses in chickens. We selected three viruses for efficacy tests (A/chicken/Bangladesh/NRL-AI-3237/2017, A/crow/Bangladesh/NRL-AI-8471/2017 and A/chicken/Bangladesh/NRL-AI-8323/2017) from 36 H5 viruses isolated from Bangladesh between 2016 and 2018 by comparing the amino acid sequences at five antigenic sites (A-E) and analyzing hemagglutination inhibition (HI) titers with reference antisera. The RE-6 and rHVT-H5 vaccines both conferred 80-100% clinical protection (i.e. reduced morbidity and mortality) against the three challenge viruses with no significant differences in protection. In addition, both vaccines significantly decreased viral shedding from infected chickens as compared to challenge control chickens. Based on these metrics, the current licensed H5 vaccines protected chickens against the recent field viruses. However, the A/crow/Bangladesh/NRL-AI-8471/2017 virus exhibited antigenic divergence including: several unique amino acid changes in antigenic epitope sites A and B and was a serological outlier in cross HI tests as visualized on the antigenic map. The continuing emergence of such antigenic variants which could alter the dominant antigenicity of field viruses should be continuously monitored and vaccines should be updated if field efficacy declines.

Patterns of Avian Influenza A (H5) and A (H9) virus infection in backyard, commercial broiler and layer chicken farms in Bangladesh

In order to control Highly Pathogenic Avian Influenza (HPAI) H5N1 and Low Pathogenic Avian Influenza (LPAI) H9N2 virus spread in endemically infected countries, a detailed understanding of infection patterns is required. We conducted cross-sectional studies in Bangladesh in 2016 and 2017, on 144 backyard, 106 broiler and 113 layer chicken farms. Although all sampled birds were negative for H5 virus by RT-PCR, H5 antibodies were detected in unvaccinated birds on all three farming systems. Higher H5 antibody prevalence was observed in ducks raised on backyard farms, 14.2% (95% CI: 10.0%-19.8%), compared to in-contact backyard chickens, 4.2% (95% CI: 2.8%-6.1%). The H5 antibody prevalence was lower in broiler chickens, 1.5% (95% CI: 0.9%-2.5%), compared to layer chickens, 7.8% (95% CI: 6.1%-9.8%). H9 viruses were detected by RT-PCR in 0.5% (95% CI: 0.2%-1.3%) and 0.6% (95% CI: 0.3%-1.5%) of broilers and layers, respectively, and in 0.2% (95% CI: 0.0%-1.2%) of backyard chickens. Backyard chickens and ducks showed similar H9 antibody prevalence, 16.0% (95% CI: 13.2%-19.2%) and 15.7% (95% CI: 11.3%-21.4%), which was higher compared to layers, 5.8% (95% CI: 4.3%-7.6%), and broilers, 1.5% (95% CI: 0.9%-2.5%). Over the course of a production cycle, H5 and H9 antibody prevalence increased with the age of backyard and layer chickens. Usually, multiple ducks within a flock were H5 antibody positive, in contrast to backyard chickens, broilers and layers where only individual birds within flocks developed H5 antibodies. Our findings highlight low virus circulation in healthy chickens of all production systems in Bangladesh, which is in contrast to high virus circulation reported from live bird markets. Data generated in this project can be used to adopt risk-based surveillance approaches in different chicken production systems in Bangladesh and to inform mathematical models exploring HPAI infection dynamics in poultry from the source of production.

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 (free-range duck (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 (11) 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 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.

Serological Evidence of Avian Influenza in Captive Wild Birds in a Zoo and Two Safari Parks in Bangladesh

Avian influenza (AI) is endemic and frequently causes seasonal outbreaks in winter in Bangladesh due to high pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2. Among avian influenza A viruses (AIV), H5, H7, and H9 subtypes have the most zoonotic potential. Captive birds in zoos and safari parks are used for educational, recreational, breeding, and conservational purposes in Bangladesh. To screen for AIV in captive birds to assess potential public health threats, we conducted a cross-sectional study in two safari parks and one zoo in Bangladesh for four months, from November to December 2013 and from January to February 2014. We collected blood samples, oropharyngeal, and cloacal swabs from 228 birds. We tested serum samples for AIV antibodies using competitive enzyme-linked immunosorbent assay (c-ELISA) and AIV sero-subtype H5, H7, and H9 using hemagglutination inhibition (HI) test. Swab samples were tested for the presence of avian influenza viral RNA using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Across all the samples, AIV antibody prevalence was 9.7% (95% CI: 6.1-14.2, n = 228) and AIV HA subtype H5, H7 and H9 sero-prevalence was 0% (95% CI: 0-1.6, n = 228), 0% (95% CI: 0-1.6, n = 228) and 6.6% (95% CI: 3.72-10.6, n = 228), respectively. No AI viral RNA (M-gene) was detected in any swab sample (0%, 95% CI: 0-1.6, n = 228). Birds in the Safari park at Cox's Bazar had a higher prevalence in both AIV antibody prevalence (13.5%) and AIV H9 sero-prevalence (9.6%) than any of the other sites, although the difference was not statistically significant. Among eight species of birds, Emu (Dromaius novaehollandiae) had the highest sero-positivity for both AIV antibody prevalence (26.1%) and AIV H9 prevalence (17.4%) followed by Golden pheasant (Chrysolophus pictus) with AIV antibody prevalence of 18.2% and AIV H9 prevalence of 11.4%. Our results highlight the presence of AI antibodies indicating low pathogenic AIV mingling in captive birds in zoos and safari parks in Bangladesh. Continuous programmed surveillance is therefore recommended to help better understand the diversity of AIVs and provide a clear picture of AI in captive wild birds, enabling interventions to reduce the risk of AIV transmission to humans.

Genetic evolution and transmission dynamics of clade 2.3.2.1a highly pathogenic avian influenza A/H5N1 viruses in Bangladesh

Asian lineage A/H5N1 highly pathogenic avian influenza viruses (HPAIVs) have been responsible for continuous outbreaks in Bangladesh since 2007. Although clades 2.2.2 and 2.3.4.2 HPAIVs have disappeared since poultry vaccination was introduced in 2012, clade 2.3.2.1a viruses have continued to be detected in Bangladesh. In this study, we identified A/H9N2 (n = 15), A/H5N1 (n = 19), and A/H5N1-A/H9N2 (n = 18) mixed viruses from live bird markets, chicken farms, and wild house crows (Corvus splendens) in Bangladesh from 2016 to 2018. We analyzed the genetic sequences of the H5 HPAIVs, to better understand the evolutionary history of clade 2.3.2.1a viruses in Bangladesh. Although seven HA genetic subgroups (B1-B7) and six genotypes (G1, G1.1, G1.2, G2, G2.1, and G2.2) have been identified in Bangladesh, only subgroup B7 and genotypes G2, G2.1, and G2.2 were detected after 2016. The replacement of G1 genotype by G2 in Bangladesh was possibly due to vaccination and viral competition in duck populations. Initially, genetic diversity decreased after introduction of vaccination in 2012, but in 2015, genetic diversity increased and was associated with the emergence of genotype G2. Our phylodynamic analysis suggests that domestic Anseriformes, including ducks and geese, may have played a major role in persistence, spread, evolution, and genotype replacement of clade 2.3.2.1a HPAIVs in Bangladesh. Thus, improvements in biosecurity and monitoring of domestic Anseriformes are needed for more effective control of HPAI in Bangladesh.

Development of a dual monoclonal antibody sandwich enzyme-linked immunosorbent assay for the detection of swine influenza virus using rabbit monoclonal antibody by Ecobody technology

A dual monoclonal antibody sandwich enzyme-linked immunosorbent assay (mAb sandwich ELISA) has been developed using rabbit monoclonal antibodies generated by Ecobody technology, which includes the isolation of single B cells binding to a specific antigen, amplification of the heavy and light chains of these immunoglobulins, and expression of the fragment of antigen binding (Fab) by cell-free protein synthesis (CFPS). A rabbit was immunized with swine influenza virus (SIV) vaccine, from which single B cells binding to the antigen were isolated. Then, immunoglobulin mRNA was amplified from single cells by reverse transcription-polymerase chain reaction, followed by the attachment of a T7 promoter, appropriate tags, and a T7 terminator for the expression of the Fab portion by CFPS. By taking advantage of two different peptide tags fused to the same Fab, optimal combinations for coating Fab on assay plates and detecting Fab, both synthesized by CFPS, were investigated for mAb sandwich ELISA. Pairs of Fab detected 0.5 ng SIV in the assay. In summary, this result showed the applicability of Ecobody technology for a variety of immunodetection kits for high throughput analyses.

A Decade of Avian Influenza in Bangladesh: Where Are We Now?

Highly pathogenic avian influenza (HPAI) has been a public health threat in Bangladesh since the first reported outbreak in poultry in 2007. The country has undertaken numerous efforts to detect, track, and combat avian influenza viruses (AIVs). The predominant genotype of the H5N1 viruses is clade 2.3.2.1a. The persistent changing of clades of the circulating H5N1 strains suggests probable mutations that might have been occurring over time. Surveillance has provided evidence that the virus has persistently prevailed in all sectors and caused discontinuous infections. The presence of AIV in live bird markets has been detected persistently. Weak biosecurity in the poultry sector is linked with resource limitation, low risk perception, and short-term sporadic interventions. Controlling avian influenza necessitates a concerted multi-sector ‘One Health’ approach that includes the government and key stakeholders.

Optimising the detectability of H5N1 and H5N6 highly pathogenic avian influenza viruses in Vietnamese live-bird markets

Live bird markets (LBMs) are major targets for avian influenza virus (AIV) surveillance programmes. While sampling the LBM environment has become a widely used alternative to the labour-intensive sampling of live poultry, the design of surveillance programmes and the interpretation of their results are compromised by the lack of knowledge about the effectiveness of these sampling strategies. We used latent class models and a unique empirical dataset collated in Vietnamese LBMs to estimate the sensitivity and specificity of five different sample types for detecting AIVs subtypes H5N1 and H5N6: oropharyngeal duck samples, solid and liquid wastes, poultry drinking water and faeces. Results suggest that the sensitivity of environmental samples for detecting H5N1 viruses is equivalent to that of oropharyngeal duck samples; however, taking oropharyngeal duck samples was estimated to be more effective in detecting H5N6 viruses than taking any of the four environmental samples. This study also stressed that the specificity of the current surveillance strategy in LBMs was not optimal leading to some false positive LBMs. Using simulations, we identified 42 sampling strategies more parsimonious than the current strategy and expected to be highly sensitive for both viruses at the LBM level. All of these strategies involved the collection of both environmental and oropharyngeal duck samples.

The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh

In Bangladesh, the poultry industry is an economically and socially important sector, but it is persistently threatened by the effects of H5N1 highly pathogenic avian influenza. Thus, identifying the optimal control policy in response to an emerging disease outbreak is a key challenge for policy-makers. To inform this aim, a common approach is to carry out simulation studies comparing plausible strategies, while accounting for known capacity restrictions. In this study we perform simulations of a previously developed H5N1 influenza transmission model framework, fitted to two separate historical outbreaks, to assess specific control objectives related to the burden or duration of H5N1 outbreaks among poultry farms in the Dhaka division of Bangladesh. In particular, we explore the optimal implementation of ring culling, ring vaccination and active surveillance measures when presuming disease transmission predominately occurs from premises-to-premises, versus a setting requiring the inclusion of external factors. Additionally, we determine the sensitivity of the management actions under consideration to differing levels of capacity constraints and outbreaks with disparate transmission dynamics. While we find that reactive culling and vaccination policies should pay close attention to these factors to ensure intervention targeting is optimised, across multiple settings the top performing control action amongst those under consideration were targeted proactive surveillance schemes. Our findings may advise the type of control measure, plus its intensity, that could potentially be applied in the event of a developing outbreak of H5N1 amongst originally H5N1 virus-free commercially-reared poultry in the Dhaka division of Bangladesh.

Ongoing circulation of avian influenza H5N1 viruses in poultry pose a global public health risk and cause extensive damage to the livestock industry. One of several countries in South Asia gravely affected is Bangladesh, where the poultry industry is an economically and socially important sector. Identifying the optimal control response in anticipation of further outbreaks is therefore a key challenge for policy-makers. This study tested a series of culling, vaccination and active surveillance intervention actions, assessing specific control objectives related to the burden or duration of H5N1 outbreaks among commercial poultry farms in the Dhaka division. This assessment was achieved through performing computational simulations of a previously developed H5N1 influenza transmission mathematical model. The findings of this assessment indicate that the impact of reactive culling and vaccination control policies are dependent upon transmission characteristics, control objectives and availability of resources to enact the control action, whereas proactive surveillance schemes significantly outperform reactive surveillance procedures irrespective of these conditions.

Avian influenza surveillance in domestic waterfowl and environment of live bird markets in Bangladesh, 2007-2012

Avian influenza viruses, including highly pathogenic strains, pose severe economic, animal and public health concerns. We implemented live bird market surveillance in Bangladesh to identify the subtypes of avian influenza A viruses in domestic waterfowl and market environments. We collected waterfowl samples monthly from 4 rural sites from 2007 to 2012 and environmental samples from 4 rural and 16 urban sites from 2009 to 2012. Samples were tested through real-time RT-PCR, virus culture, and sequencing to detect and characterize avian influenza A viruses. Among 4,308 waterfowl tested, 191 (4.4%) were positive for avian influenza A virus, including 74 (1.9%) avian influenza A/H5 subtype. The majority (99%, n = 73) of the influenza A/H5-positive samples were from healthy appearing waterfowl. Multiple subtypes, including H1N1, H1N3, H3N2, H3N6, H3N8, H4N1, H4N2, H4N6, H5N1 (clades 2.2.2, 2.3.2.1a, 2.3.4.2), H5N2, H6N1, H7N9, H9N2, H11N2 and H11N3, H11N6 were detected in waterfowl and environmental samples. Environmental samples tested positive for influenza A viruses throughout the year. Avian influenza viruses, including H5N1 and H9N2 subtypes were also identified in backyard and small-scale raised poultry. Live bird markets could be high-risk sites for harboring the viruses and have the potential to infect naive birds and humans exposed to them.

A large-scale study of a poultry trading network in Bangladesh: implications for control and surveillance of avian influenza viruses

BACKGROUND

Since its first report in 2007, avian influenza (AI) has been endemic in Bangladesh. While live poultry marketing is widespread throughout the country and known to influence AI dissemination and persistence, trading patterns have not been described. The aim of this study is to assess poultry trading practices and features of the poultry trading networks which could promote AI spread, and their potential implications for disease control and surveillance. Data on poultry trading practices was collected from 849 poultry traders during a cross-sectional survey in 138 live bird markets (LBMs) across 17 different districts of Bangladesh. The quantity and origins of traded poultry were assessed for each poultry type in surveyed LBMs. The network of contacts between farms and LBMs resulting from commercial movements of live poultry was constructed to assess its connectivity and to identify the key premises influencing it.

RESULTS

Poultry trading practices varied according to the size of the LBMs and to the type of poultry traded. Industrial broiler chickens, the most commonly traded poultry, were generally sold in LBMs close to their production areas, whereas ducks and backyard chickens were moved over longer distances, and their transport involved several intermediates. The poultry trading network composed of 445 nodes (73.2% were LBMs) was highly connected and disassortative. However, the removal of only 5.6% of the nodes (25 LBMs with the highest betweenness scores), reduced the network's connectedness, and the maximum size of output and input domains by more than 50%.

CONCLUSIONS

Poultry types need to be discriminated in order to understand the way in which poultry trading networks are shaped, and the level of risk of disease spread that these networks may promote. Knowledge of the network structure could be used to target control and surveillance interventions to a small number of LBMs.

Insight into live bird markets of Bangladesh: an overview of the dynamics of transmission of H5N1 and H9N2 avian influenza viruses

Highly pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2 viruses have been recognized as threats to public health in Bangladesh since 2007. Although live bird markets (LBMs) have been implicated in the transmission, dissemination, and circulation of these viruses, an in-depth analysis of the dynamics of avian transmission of H5N1 and H9N2 viruses at the human-animal interface has been lacking. Here we present and evaluate epidemiological findings from active surveillance conducted among poultry in various production sectors in Bangladesh from 2008 to 2016. Overall, the prevalence of avian influenza viruses (AIVs) in collected samples was 24%. Our data show that AIVs are more prevalent in domestic birds within LBMs (30.4%) than in farms (9.6%). Quail, chickens and ducks showed a high prevalence of AIVs (>20%). The vast majority of AIVs detected (99.7%) have come from apparently healthy birds and poultry drinking water served as a reservoir of AIVs with a prevalence of 32.5% in collected samples. HPAI H5N1 was more frequently detected in ducks while H9N2 was more common in chickens and quail. LBMs, particularly wholesale markets, have become a potential reservoir for various types of AIVs, including HPAI H5N1 and LPAI H9N2. The persistence of AIVs in LBMs is of great concern to public health, and this study highlights the importance of regularly reviewing and implementing infection control procedures as a means of reducing the exposure of the general public to AIVs.Emerging Microbes & Infections (2017) 6, e12; doi:10.1038/emi.2016.142; published online 8 March 2017.

Protection of human influenza vaccines against a reassortant swine influenza virus of pandemic H1N1 origin using a pig model

Since the pandemic H1N1 emergence in 2009 (pdmH1N1), many reassortant pdmH1N1 viruses emerged and found circulating in the pig population worldwide. Currently, commercial human subunit vaccines are used commonly to prevent the influenza symptom based on the WHO recommendation. In case of current reassortant swine influenza viruses transmitting from pigs to humans, the efficacy of current human influenza vaccines is of interest. In this study, influenza A negative pigs were vaccinated with selected commercial human subunit vaccines and challenged with rH3N2. All sera were tested with both HI and SN assays using four representative viruses from the surveillance data in 2012 (enH1N1, pdmH1N1, rH1N2 and rH3N2). The results showed no significant differences in clinical signs and macroscopic and microscopic findings among groups. However, all pig sera from vaccinated groups had protective HI titers to the enH1N1, pdmH1N1 and rH1N2 at 21DPV onward and had protective SN titers only to pdmH1N1and rH1N2 at 21DPV onward. SN test results appeared more specific than those of HI tests. All tested sera had no cross-reactivity against the rH3N2. Both studied human subunit vaccines failed to protect and to stop viral shedding with no evidence of serological reaction against rH3N2. SIV surveillance is essential for monitoring a novel SIV emergence potentially for zoonosis.

Modelling H5N1 in Bangladesh across spatial scales: Model complexity and zoonotic transmission risk

Highly pathogenic avian influenza H5N1 remains a persistent public health threat, capable of causing infection in humans with a high mortality rate while simultaneously negatively impacting the livestock industry. A central question is to determine regions that are likely sources of newly emerging influenza strains with pandemic causing potential. A suitable candidate is Bangladesh, being one of the most densely populated countries in the world and having an intensifying farming system. It is therefore vital to establish the key factors, specific to Bangladesh, that enable both continued transmission within poultry and spillover across the human-animal interface. We apply a modelling framework to H5N1 epidemics in the Dhaka region of Bangladesh, occurring from 2007 onwards, that resulted in large outbreaks in the poultry sector and a limited number of confirmed human cases. This model consisted of separate poultry transmission and zoonotic transmission components. Utilising poultry farm spatial and population information a set of competing nested models of varying complexity were fitted to the observed case data, with parameter inference carried out using Bayesian methodology and goodness-of-fit verified by stochastic simulations. For the poultry transmission component, successfully identifying a model of minimal complexity, which enabled the accurate prediction of the size and spatial distribution of cases in H5N1 outbreaks, was found to be dependent on the administration level being analysed. A consistent outcome of non-optimal reporting of infected premises materialised in each poultry epidemic of interest, though across the outbreaks analysed there were substantial differences in the estimated transmission parameters. The zoonotic transmission component found the main contributor to spillover transmission of H5N1 in Bangladesh was found to differ from one poultry epidemic to another. We conclude by discussing possible explanations for these discrepancies in transmission behaviour between epidemics, such as changes in surveillance sensitivity and biosecurity practices.