Risk factors for avian influenza virus in backyard poultry flocks and environments in Zhejiang Province, China: a cross-sectional study

Field and laboratory investigation of highly pathogenic avian influenza H5N6 and H5N8 in Quang Ninh province, Vietnam, 2020 to 2021

BACKGROUND

Avian influenza (AI) is a contagious disease that causes illness and death in poultry and humans. High pathogenicity AI (HPAI) H5N6 outbreaks commonly occur in Quang Ninh province bordering China. In June 2021, the first HPAI H5N8 outbreak occurred at a Quang Ninh chicken farm.

OBJECTIVES

This study examined the risk factors associated with HPAI H5N6 and H5N8 outbreaks in Quang Ninh.

METHODS

A retrospective case-control study was conducted in Quang Ninh from Nov 2021 to Jan 2022. The cases were households with susceptible poultry with two or more clinical signs and tested positive by real-time reverse transcription polymerase chain reaction. The controls were households in the same village as the cases but did not show clinical symptoms of the disease. Logistic regression models were constructed to assess the risk factors associated with HPAI outbreaks at the household level.

RESULTS

There were 38 cases with H5N6 clade 2.3.4.4h viruses (n = 35) and H5N8 clade 2.3.4.4b viruses (n = 3). Compared to the 112 controls, raising poultry in uncovered or partially covered ponds (odds ratio [OR], 7.52; 95% confidence interval [CI], 1.44-39.27), poultry traders visiting the farm (OR, 8.66; 95% CI, 2.7-27.69), farms with 50-2,000 birds (OR, 3.00; 95% CI, 1.06-8-51), and farms with ≥ 2,000 birds (OR, 11.35; 95% CI, 3.07-41.94) were significantly associated with HPAI outbreaks.

CONCLUSIONS

Combining biosecurity measures, such as restricting visitor entry and vaccination in farms with more than 50 birds, can enhance the control and prevention of HPAI in Quang Ninh and its spread across borders.

Analysis of data from two influenza surveillance hospitals in Zhejiang province, China, for the period 2018-2022

PURPOSE

To assess the epidemiology of seasonal influenza in Huzhou City, Zhejiang Province, China, during 2018-2022 and provide insights for influenza prevention.

METHODS

Following the National Influenza Surveillance Program, we conducted pathogen surveillance by randomly sampling throat swabs from cases with influenza-like illness (ILI) at two sentinel hospitals.

RESULTS

From 2018 to 2022, a total of 3,813,471 cases were treated at two hospitals in Huzhou, China. Among them, there were 112,385 cases of Influenza-Like Illness (ILI), accounting for 2.95% of the total number of cases. A total of 11,686 ILI throat swab samples were tested for influenza viruses, with 1,602 cases testing positive for influenza virus nucleic acid, resulting in a positivity rate of 13.71%. Among the positive strains, there were 677 strains of A(H3N2) virus, 301 strains of A(H1N1) virus, 570 strains of B/Victoria virus, and 54 strains of B/Yamagata virus. The ILI percentage (ILI%) and influenza nucleic acid positivity rate showed winter-spring peaks in the years 2018, 2019, 2021, and 2022, with the peaks concentrated in January and February. Additionally, a small peak was observed in August 2022 during the summer season. No peak was observed during the winter-spring season of 2020. The highest proportion of ILI cases was observed in children aged 0-4 years, followed by school-age children aged 5-14 years. There was a positive correlation between ILI% and influenza virus nucleic acid positivity rate (r = 0.60, p < 0.05).

CONCLUSIONS

The influenza outbreak in Huzhou from 2020 to 2022 was to some extent influenced by the COVID-19 pandemic and public health measures. After the conclusion of the COVID-19 pandemic, the influenza outbreak in Huzhou may become more severe. Therefore, it is crucial to promptly assess the influenza outbreak trends based on the ILI% and the positivity rate of influenza virus nucleic acid tests.

Risk Prediction of Three Different Subtypes of Highly Pathogenic Avian Influenza Outbreaks in Poultry Farms: Based on Spatial Characteristics of Infected Premises in South Korea

From 2003 to 2017, highly pathogenic avian influenza (HPAI) epidemics, particularly H5N1, H5N8, and H5N6 infections in poultry farms, increased in South Korea. More recently, these subtypes of HPAI virus resurged and spread nationwide, heavily impacting the entire poultry production and supply system. Most outbreaks in poultry holdings were concentrated in the southwestern part of the country, accounting for 58.3% of the total occurrences. This geographically persistent occurrence demanded the investigation of spatial risk factors related to the HPAI outbreak and the prediction of the risk of emerging HPAI outbreaks. Therefore, we investigated 12 spatial variables for the three subtypes of HPAI virus-infected premises [(IPs), 88 H5N1, 339 H5N8, and 335 H5N6 IPs]. Then, two prediction models using statistical and machine learning algorithm approaches were built from a case-control study on HPAI H5N8 epidemic, the most prolonged outbreak, in 339 IPs and 626 non-IPs. Finally, we predicted the risk of HPAI H5N1 and H5N6 occurrence at poultry farms using a Bayesian logistic regression and machine learning algorithm model [extreme gradient boosting (XGBoost) model] built on the case-control study. Several spatial variables showed similar distribution between two subtypes of IPs, although there were distinct heterogeneous distributions of spatial variables among the three IP subtypes. The case-control study indicated that the density of domestic duck farms and the minimum distance to live bird markets were leading risk factors for HPAI outbreaks. The two prediction models showed high predictive performance for H5N1 and H5N6 occurrences [an area under the curve (AUC) of receiver operating characteristic of Bayesian model > 0.82 and XGBoost model > 0.97]. This finding emphasizes that spatial characteristics of the poultry farm play a vital role in the occurrence and forecast of HPAI outbreaks. Therefore, this finding is expected to contributing to developing prevention and control strategies.

Hierarchical Clustering on Principal Components Analysis to Detect Clusters of Highly Pathogenic Avian Influenza Subtype H5N6 Epidemic across South Korean Poultry Farms

Several outbreaks of highly pathogenic avian influenza (HPAI) in poultry have already been documented across the world, causing major economic losses. Research on diverse perspectives for future HPAI outbreaks’ prevention is desperately needed. It is critical to determine high-risk areas for HPAI outbreaks in order to develop high-level biosecurity in all such areas. The aim of this study is to identify high-risk areas as hotspots for high rates of birds’ infection and mortality and culling. We used “hierarchical clustering on principal components” (HCPC) to classify infected poultry farms in South Korea based on the point prevalence rate, infections, and deaths in susceptible birds. The linear combination of the original predictors was determined using “principal component analysis (PCA)”. Based on PCA, we applied the hierarchical clustering algorithm, which divided the data into four clusters based on the dissimilarity matrix. These four groups of poultry farms were identified on the basis of five variables. According to the findings based on the HCPC method, poultry farms in “cluster 4” had significantly higher average bird infections with high mortality when compared to other clusters. Similarly, the poultry farms in “cluster 2” had robust average bird culling in place to limit bird infectivity and mortality due to a high number of susceptible birds. The poultry farms belonging to “cluster 3” had a significantly higher average point prevalence rate of HPAI H5N6 cases than the rest of the clusters. Based on this study, it is recommended that poultry farms with a high number of infections and mortality in susceptible birds should implement proper biosecurity management to control HPAI infections while avoiding the culling of a large number of birds.

The impact of the epidemic experience on the recovery of production of pig farmers after the outbreak-Evidence from the impact of African swine fever (ASF) in Chinese pig farming

The African swine fever (ASF) has triggered considerable shocks to the pig farming industry, which has become a significant animal disease epidemic. The study explores the effect of epidemic experience on post-outbreak production recovery from resilience and risk perception based on 340 micro-survey data from Sichuan, Henan, and Shandong provinces. Epidemic experience has been shown to impact the degree of post-outbreak production recovery positively, and farmers who have endured epidemics are more likely to recover their production after outbreaks. The mechanistic study indicates that past epidemics in African swine fever shocks can effectively improve farmers' cognitive resilience and management capability, enhance recovery, and reduce risk perception in the aftermath of production recovery. In order to alleviate the endogenous problems caused by selection bias, missing variables, and two-way causality. This paper uses factor analysis to comprehensively measure production recovery capacity and production risk perception, and uses propensity score matching(PSM), instrumental variable method and replacement measurement methods to conduct robustness tests, and find the conclusions are still robust. The empirical analysis shows that the experience of the epidemic will promote the recovery of farmers after the outbreak; the experience of the epidemic will significantly impact the recovery of production after the outbreak for both free-range and professional farmers.

Impact of inland waters on highly pathogenic avian influenza outbreaks in neighboring poultry farms in South Korea

Background

Since 2003, the H5 highly pathogenic avian influenza (HPAI) subtype has caused massive economic losses in the poultry industry in South Korea. The role of inland water bodies in avian influenza (AI) outbreaks has not been investigated. Identifying water bodies that facilitate risk pathways leading to the incursion of the HPAI virus (HPAIV) into poultry farms is essential for implementing specific precautionary measures to prevent viral transmission.

Objectives

This matched case-control study (1:4) examined whether inland waters were associated with a higher risk of AI outbreaks in the neighboring poultry farms.

Methods

Rivers, irrigation canals, lakes, and ponds were considered inland water bodies. The cases and controls were chosen based on the matching criteria. The nearest possible farms located within a radius of 3 km of the case farms were chosen as the control farms. The poultry farms were selected randomly, and two HPAI epidemics (H5N8 [2014–2016] and H5N6 [2016–2017]) were studied. Conditional logistic regression analysis was applied.

Results

Statistical analysis revealed that inland waters near poultry farms were significant risk factors for AI outbreaks. The study speculated that freely wandering wild waterfowl and small animals contaminate areas surrounding poultry farms.

Conclusions

Pet birds and animals raised alongside poultry birds on farm premises may wander easily to nearby waters, potentially increasing the risk of AI infection in poultry farms. Mechanical transmission of the AI virus occurs when poultry farm workers or visitors come into contact with infected water bodies or their surroundings. To prevent AI outbreaks in the future, poultry farms should adopt strict precautions to avoid contact with nearby water bodies and their surroundings.

Genetic analysis and biological characteristics of novel clade 2.3.4.4 reassortment H5N6 avian influenza viruses from poultry in eastern China in 2016

OBJECTIVES

The continuous evolution of highly pathogenic H5N6 avian influenza viruses (AIVs) causes outbreaks in wildfowl and poultry, and occasional human infections. The aim of this study was to better understand the genetic relationships between these H5N6 AIVs from eastern China and other AIVs.

METHODS

In 2016, 1623 cloacal swabs were sampled from poultry in 18 LPMs in eastern China, and subsequently characterized systematically using gene sequencing, phylogenetic studies, and antigenic analysis. In addition, their pathogenicity in mammals was studied in BALB/c mice, which were inoculated with viruses, with survival rate and body weight recorded daily for 14 days.

RESULTS

In total, 56 H5N6 AIVs were isolated in eastern China and five representative isolates were selected for further study. In our study, the H5N6 AIVs clustered into clade 2.3.4.4, Group C, and their six internal segments were derived from H6N6 and H9N2 viruses, or both, suggesting extensive reassortant among H5N6 AIVs with other subtypes. These H5N6 viruses could replicate in the lungs without prior adaptation, and exhibited slight-to-moderate virulence in mice.

CONCLUSIONS

The continuous circulation of these novel H5N6 viruses suggests the importance of persistent surveillance of H5N6 AIVs in poultry.

Serosurvey of Avian Influenza Viruses (H5, H7, and H9) and Associated Risk Factors in Backyard Poultry Flocks of Lahore District, Pakistan

Rural poultry constitutes 56% of the total poultry population in Pakistan; however, epidemiological information about avian influenza viruses (AIVs) in backyard poultry flocks is lacking. A cross-sectional survey of villages of Lahore district was conducted from July 2009 to August 2009 using two-stage cluster sampling and probability proportional to size (PPS) sampling to estimate seroprevalence and its associated risk factors. A random selection of 35 clusters from 308 villages of Lahore were considered, and from each cluster, six chickens aged >2 months were selected. A total of 210 serum samples were collected and examined by the hemagglutination inhibition (HI) test for specific antibodies against AIV subtypes H5, H7, and H9. Overall weighted seroprevalence for AIVs was 65.2% (95% CI: 55.6–74.8%), and for subtype H5, H7 & H9 was 6.9% (95% CI: 10.8–23.0%), 0% (95% CI: 0–1.7%), and 62.0% (95% CI: 52.2–71.8%) respectively. However, none of the samples were positive for H7. The average flock size was 17.3 birds, and the main purpose of keeping poultry was for eggs/meat (70.6%, 95% CI: 59.7–81.4). A majority of them were reared in a semi-caged system (83%, 95% CI: 74.5–91.3). Backyard birds were received from different sources, that is, purchased from the market or received as a gift from friends or any NGO, and were 5.7 times more likely to become avian influenza (AI) seropositive than those that were not exposed to these sources (CI 95%: 2.0–716.0). Backyard birds which were received from different sources, that is, purchased from the market or received from friends or any NGO, were 5.7 times more likely to become AI seropositive compared to those that were not (CI 95%: 2.5–18.7). To reduce the risk of AIV in Pakistan, continuous surveillance of backyard poultry would be needed.

A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.

A Review of Pathogen Transmission at the Backyard Chicken-Wild Bird Interface

Habitat conversion and the expansion of domesticated, invasive species into native habitats are increasingly recognized as drivers of pathogen emergence at the agricultural-wildlife interface. Poultry agriculture is one of the largest subsets of this interface, and pathogen spillover events between backyard chickens and wild birds are becoming more commonly reported. Native wild bird species are under numerous anthropogenic pressures, but the risks of pathogen spillover from domestic chickens have been historically underappreciated as a threat to wild birds. Now that the backyard chicken industry is one of the fastest growing industries in the world, it is imperative that the principles of biosecurity, specifically bioexclusion and biocontainment, are legislated and implemented. We reviewed the literature on spillover events of pathogens historically associated with poultry into wild birds. We also reviewed the reasons for biosecurity failures in backyard flocks that lead to those spillover events and provide recommendations for current and future backyard flock owners.

Avian influenza at animal-human interface: One-health challenge in live poultry retail stalls of Chakwal, Pakistan

Background

Live poultry retail stalls (LPRSs) are believed to be the source of human infection with avian influenza viruses (AIVs); however, little is known about epidemiology of these viruses in LPRSs of Pakistan.

Objectives

The current study was conducted to estimate the virological and serological prevalence of AIVs in humans and poultry and associated risk factors among seropositive butchers.

Methods

A field survey of LPRSs of Chakwal District was conducted between December 2015 and March 2016. In total, 322 samples (sera = 161 and throat swab = 161) from butchers and 130 pooled oropharyngeal swabs and 100 sera from birds were collected. Baseline sera (n = 100) from general population were also tested. Data were collected by structured questionnaires. Sera were tested by hemagglutination inhibition (HI) test further confirmed by micro‐neutralization test (MN). Swabs were processed by real‐time RT‐PCR. Logistic regression analyses were conducted to identify risk factors.

Results

In butchers, 15.5% sera were positive for antibodies against H9 virus using a cutoff of ≥40 in HI titer; 6% sera from general population were positive for H9. Seroprevalence in poultry was 89%, and only 2.30% swabs were positive for H9. Presence of another LPRS nearby and the number of cages in the stall were risk factors (OR > 1) for H9 seroprevalence in butchers.

Conclusions

This study provides evidence of co‐circulation of H9 virus in poultry and exposure of butchers in the LPRSs, which poses a continued threat to public health. We suggest regular surveillance of AIVs in occupationally exposed butchers and birds in LPRSs.

Host Innate Immune Response of Geese Infected with Clade 2.3.4.4 H5N6 Highly Pathogenic Avian Influenza Viruses

Since 2014, highly pathogenic avian influenza (HPAI) H5N6 viruses have circulated in waterfowls and caused human infections in China, posing significant threats to the poultry industry and the public health. However, the genetics, pathogenicity and innate immune response of H5N6 HPAIVs in geese remain largely unknown. In this study, we analyzed the genetic characteristic of the two H5N6 viruses (GS38 and DK09) isolated from apparently healthy domestic goose and duck in live poultry markets (LPMs) of Southern China in 2016. Phylogenetic analysis showed that the HA genes of the two H5N6 viruses belonged to clade 2.3.4.4 and were clustered into the MIX-like group. The MIX-like group viruses have circulated in regions such as China, Japan, Korea, and Vietnam. The NA genes of the two H5N6 viruses were classified into the Eurasian sublineage. The internal genes including PB2, PB1, PA, NP, M, and NS of the two H5N6 viruses derived from the MIX-like. Therefore, our results suggested that the two H5N6 viruses were reassortants of the H5N1 and H6N6 viruses and likely derived from the same ancestor. Additionally, we evaluated the pathogenicity and transmission of the two H5N6 viruses in domestic geese. Results showed that both the two viruses caused serious clinical symptoms in all inoculated geese and led to high mortality in these birds. Both the two viruses were transmitted efficiently to contact geese and caused lethal infection in these birds. Furthermore, we found that mRNA of pattern recognition receptors (PRRs), interferons (IFNs), and stimulated genes (ISGs) exhibited different levels of activation in the lungs and spleens of the two H5N6 viruses-inoculated geese though did not protect these birds from H5N6 HPAIVs infection. Our results suggested that the clade 2.3.4.4 waterfowl-origin H5N6 HPAIVs isolated from LPMs of Southern China could cause high mortality in geese and innate immune-related genes were involved in the geese innate immune response to H5N6 HPAIVs infection. Therefore, we should pay more attention to the evolution, pathogenic variations of these viruses and enhance virological surveillance of clade 2.3.4.4 H5N6 HPAIVs in waterfowls in China.

A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China

BACKGROUND

Avian influenza A (H5N6) virus poses a great threat to the human health since it is capable to cross the species barrier and infect humans. Although human infections are believed to largely originate from poultry contaminations, the transmissibility is unclear and only limited information was available on poultry environment contaminations, especially in Fujian Province.

METHODS

A total of 4901 environmental samples were collected and tested for Avian Influenza Virus (AIV) from six cities in Fujian Province through the Fujian Influenza Surveillance System from 2013 to 2017. Two patient-related samples were taken from Fujian's first confirmed H5N6 human case and his backyard chicken feces in 2017. Chi-square test or Fisher's exact probability test was used to compare the AIV and the viral subtype positive rates among samples from different Surveillance cities, surveillance sites, sample types, and seasons. Phylogenetic tree analysis and molecular analysis were conducted to track the viral transmission route of the human infection and to map out the evolutions of H5N6 in Fujian.

RESULTS

The overall positive rate of the H5 subtype AIVs was 4.24% (208/4903). There were distinctive differences (p < 0.05) in the positive rates in samples from different cities, sample sites, sample types and seasons. The viruses from the patient and his backyard chicken feces shared high homologies (99.9-100%) in all the eight gene segments. Phylogenetic trees also showed that these two H5N6 viruses were closely related to each other, and were classified into the same genetic clade 2.3.4.4 with another six H5N6 isolates from the environmental samples. The patient's H5N6 virus carried genes from H6N6, H5N8 and H5N6 viruses originated from different areas. The R294K or N294S substitution was not detected in the neuraminidase (NA). The S31 N substitution in the matrix2 (M2) gene was detected but only in one strain from the environmental samples.

CONCLUSIONS

The H5 subtype of AIVs has started circulating in the poultry environments in Fujian Province. The patient's viral strain originated from the chicken feces in his backyard. Genetic reassortment in H5N6 viruses in Fujian Province was indicated. The H5N6 viruses currently circulating in Fujian Province were still commonly sensitive to Oseltamivir and Zanamivir, but the resistance against Amantadine has emerged.

Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens

Vietnamese poultry are host to co‐circulating subtypes of avian influenza viruses, including H5N1 and H9N2, which pose a great risk to poultry productivity and to human health. AIVs circulate throughout the poultry trade network in Vietnam, with live bird markets being an integral component to this network. Traders at LBMs exhibit a variety of trading practices, which may influence the transmission of AIVs. We identified trading practices that impacted on AIV prevalence in chickens marketed in northern Vietnamese LBMs. We generated sequencing data for 31 H9N2 and two H5N6 viruses. Viruses isolated in the same LBM or from chickens sourced from the same province were genetically closer than viruses isolated in different LBMs or from chickens sourced in different provinces. The position of a vendor in the trading network impacted on their odds of having AIV‐infected chickens. Being a retailer and purchasing chickens from middlemen was associated with increased odds of infection, whereas odds decreased if vendors purchased chickens directly from large farms. Odds of infection were also higher for vendors having a greater volume of ducks unsold per day. These results indicate how the spread of AIVs is influenced by the structure of the live poultry trading network.

Comparison of Avian Influenza Virus Contamination in the Environment Before and After Massive Poultry H5/H7 Vaccination in Zhejiang Province, China

Background

Information regarding comparison of the environmental prevalence of avian influenza virus (AIVs), before and after massive poultry vaccinations, is limited. Our study aimed to detect differences in the prevalence of AIVs type A and subtypes H5, H7, and H9 before and after the September 2017 massive poultry vaccination, across different sampling places and types.

Methods

We collected 55 130 environmental samples from 11 cities in Zhejiang Province (China) between March 2013 and December 2018. Multivariate logistic regression analyses were conducted to determine the prevalence of AIV type A and subtypes H5, H7, and H9 across different sampling places and types, before and after massive poultry vaccination.

Results

After the vaccination, contamination risk of AIV type A (adjusted odds ratio [aOR] = 1.08; 95% confidence interval [CI], 1.03–1.14) and subtype H9 (aOR = 1.58; 95% CI, 1.48–1.68) increased, and that of subtype H7 (aOR = 0.12; 95% CI, 0.10–0.14) decreased. Statistically significant decreased risk for H7 subtype contamination and increased risk for H9 subtype contamination were observed in backyard poultry flocks, live poultry markets, and slaughtering/processing plants. Swabs from poultry cages and slaughtering tables showed a statistically significant increased risk for H5 subtype contamination. The prevalence of H7 subtype decreased statistically significantly, whereas that of H9 subtype increased across the 5 sample types (poultry cages swabs, slaughtering table swabs, poultry feces, poultry drinking water, and poultry sewage).

Conclusions

Despite the sharp decrease in H7 subtype prevalence, reduction measures for AIV circulation are still imperative, given the high type A prevalence and the increase in H9 subtype contamination across different sampling places and types.