The role of live poultry movement and live bird market biosecurity in the epidemiology of influenza A (H7N9): A cross-sectional observational study in four eastern China provinces

Amplification of avian influenza virus circulation along poultry marketing chains in Bangladesh: A controlled field experiment

The prevalence of avian influenza viruses is commonly found to increase dramatically as birds are transported from farms to live bird markets. Viral transmission dynamics along marketing chains are, however, poorly understood. To address this gap, we implemented a controlled field experiment altering chicken supply to a live bird market in Chattogram, Bangladesh. Broilers and backyard chickens traded along altered (intervention) and conventional (control) marketing chains were tested for avian influenza viruses at different time points. Upon arrival at the live bird market, the odds of detecting avian influenza viruses did not differ between control and intervention groups. However, 12 h later, intervention group odds were lower, particularly for broilers, indicating that viral shedding in live bird markets resulted partly from infections occurring during transport and trade. Curtailing avian influenza virus prevalence in live bird markets requires mitigating risk in marketing chain nodes preceding chickens' delivery at live bird markets.

Zoonotic infections by avian influenza virus: changing global epidemiology, investigation, and control

Avian influenza virus continues to pose zoonotic, epizootic, and pandemic threats worldwide, as exemplified by the 2020-23 epizootics of re-emerging H5 genotype avian influenza viruses among birds and mammals and the fatal jump to humans of emerging A(H3N8) in early 2023. Future influenza pandemic threats are driven by extensive mutations and reassortments of avian influenza viruses rooted in frequent interspecies transmission and genetic mixing and underscore the urgent need for more effective actions. We examine the changing global epidemiology of human infections caused by avian influenza viruses over the past decade, including dramatic increases in both the number of reported infections in humans and the spectrum of avian influenza virus subtypes that have jumped to humans. We also discuss the use of advanced surveillance, diagnostic technologies, and state-of-the-art analysis methods for tracking emerging avian influenza viruses. We outline an avian influenza virus-specific application of the One Health approach, integrating enhanced surveillance, tightened biosecurity, targeted vaccination, timely precautions, and timely clinical management, and fostering global collaboration to control the threats of avian influenza viruses.

Effect of avian influenza scare on transmission of zoonotic avian influenza: A case study of influenza A (H7N9)

Avian influenza scare is a human psychological factor that asserts both positive and negative effects on the transmission of zoonotic avian influenza. In order to study the dichotomous effect of avian influenza scare on disease transmission, taking H7N9 avian influenza as a typical case, a two-patch epidemic model is proposed. The global dynamics and the threshold criteria are established by LaSalle invariant principle and the theory of asymptotic autonomous system. To mitigate the negative effects and curb illegal poultry trade, a game-theoretic model is adopted to explore the optimal policy of culling subsidies to reasonably compensate stakeholders for their economic losses resulting from the scare. The optimal policy of culling subsidy is found to heavily depend on the penalty of illegal poultry trade, the stakeholders' income, the intensity of control measures, and the prevalence level of the disease. The negative effect of avian influenza scare on disease transmission is considerably more significant than the positive effect. In order to avoid a widespread outbreak of zoonotic avian influenza across the region, a comprehensive national global control strategy is essential and effective, even in the presence of the negative effect of the avian influenza scare.

Mixed selling of different poultry species facilitates emergence of public-health-threating avian influenza viruses

Live poultry markets (LPMs) are regarded as hubs for avian influenza virus (AIV) transmission in poultry and are a major risk factor in human AIV infections. We performed an AIV surveillance study at a wholesale LPM, where different poultry species were sold in separate stalls, and nine retail LPMs, which received poultry from the wholesale LPM but where different poultry species were sold in one stall, in Guangdong province from 2017 to 2019. A higher AIV isolation rate was observed at the retail LPMs than the wholesale LPM. H9N2 was the dominant AIV subtype and was mainly present in chickens and quails. The genetic diversity of H9N2 viruses was greater at the retail LPMs, where a complex system of two-way transmission between different poultry species had formed. The isolated H9N2 viruses could be classed into four genotypes: G57 and the three novel genotypes, NG164, NG165, and NG166. The H9N2 AIVs isolated from chickens and quails at the wholesale LPM only belonged to the G57 and NG164 genotypes, respectively. However, the G57, NG164, and NG165 genotypes were identified in both chickens and quails at the retail LPMs. We found that the replication and transmission of the NG165 genotype were more adaptive to both poultry and mammalian models than those of its precursor genotype, NG164. Our findings revealed that mixed poultry selling at retail LPMs has increased the genetic diversity of AIVs, which might facilitate the emergence of novel viruses that threaten public health.

Evaluation of Pre-Pandemic Trivalent COBRA HA Vaccine in Mice Pre-Immune to Historical H1N1 and H3N2 Influenza Viruses

Initial exposure to influenza virus(es) during early childhood produces protective antibodies that may be recalled following future exposure to subsequent viral infections or vaccinations. Most influenza vaccine research studies use immunologically naïve animal models to assess vaccine effectiveness. However, most people have an extensive influenza immune history, with memory cells produced by viruses or vaccines representing multiple influenza viruses. In this study, we explored the effect influenza seasonal virus-induced immunity has on pre-pandemic influenza virus vaccination. The mice that were pre-immune to historical H1N1 and H3N2 seasonal influenza viruses were vaccinated with adjuvanted pre-pandemic (H2, H5, and H7) HA-based computationally optimized broadly reactive antigen (COBRA) vaccines, and were fully protected from lethal challenge, whereas the mock-vaccinated mice, with or without pre-immunity, were not protected from morbidity or mortality. Detectable antibody titers were present in the pre-immune mice vaccinated with a single dose of vaccine, but not in the immunologically naïve mice. The mice vaccinated twice with the trivalent COBRA HA vaccine had similar antibody titers regardless of their pre-immune status. Overall, seasonal pre-immunity did not interfere with the immune responses elicited by pre-pandemic COBRA HA vaccines or the protection against pre-pandemic viruses.

A dataset of a proxy variable for the poultry trade flows in China

Understanding the intercity poultry trading network is crucial for assessing the risk of avian influenza prevalence. Unfortunately, the poultry trading network in China has rarely been described. Here, with a modified radiation model, we obtain values for a proxy variable for poultry trade flows among 318 prefecture-level cities in China in 2015 utilizing the product capacity and demand quantity of poultry of the cities. The results are validated by comparing the proxy variable values with the trade volumes investigated in the literature, and it is found that the modified radiation model can accurately predict the main poultry trade flows among cities. This is the first dataset on China's poultry trade pattern, and it can be used to analyze the production and consumption structure of poultry in prefecture-level cities within China. The dataset can be a tool for avian influenza epidemic risk assessment as well as a basis to develop prevention and control measures during an epidemic.

Research and Innovation Opportunities to Improve Epidemiological Knowledge and Control of Environmentally Driven Zoonoses

While zoonotic diseases are defined by transmission processes between animals and humans, for many of these diseases the presence of a contaminated environmental source is the cause of transmission. Most zoonoses depend on complex environmentally driven interactions between humans and animals, which occur along an occupational and recreational environmental continuum, including farming and animal marketing systems, environmental management systems, and community leisure environments. Environmentally driven zoonoses (EDZs) are particularly challenging to diagnose and control as their reservoirs are in the natural environment and thus often escape conventional surveillance systems that rely on host monitoring. Changes in the environment as a result of climate change [1], human population density [2], and intensification of agriculture [3] have been linked to increasing transmission events for this group of infections. As such, there is a recognised need to be able to detect the presence of EDZs in the environment as a means to better anticipate transmission events and improve source attribution investigations. Finally, the recognition that a One Health approach is needed to combat these infections is signalling to governments the need to develop policy that optimises trade-offs across human, animal, and environmental health sectors. In this review, we discuss and critically appraise the main challenges relating to the epidemiology, diagnosis, and control of environmental zoonotic disease. Using a set of exemplar diseases, including avian influenza and antimicrobial resistant pathogens, we explore the epidemiological contexts (risk factors) within which these infections not only impact human health but also contribute to animal health and environmental impacts. We then critically appraise the surveillance challenges of monitoring these infections in the environment and examine the policy trade-offs for a more integrated approach to mitigating their impacts.

Spatio-temporal spread and evolution of influenza A (H7N9) viruses

The influenza A (H7N9) virus has been seriously concerned for its potential to cause an influenza pandemic. To understand the spread and evolution process of the virus, a spatial and temporal Bayesian evolutionary analysis was conducted on 2,052 H7N9 viruses isolated during 2013 and 2018. It revealed that the H7N9 virus was probably emerged in a border area of Anhui Province in August 2012, approximately 6 months earlier than the first human case reported. Two major epicenters had been developed in the Yangtze River Delta and Peral River Delta regions by the end of 2013, and from where the viruses have also spread to other regions at an average speed of 6.57 km/d. At least 24 genotypes showing have been developed and each of them showed a distinct spatio-temporal distribution pattern. Furthermore, A random forest algorithm-based model has been developed to predict the occurrence risk of H7N9 virus. The model has a high overall forecasting precision (> 97%) and the monthly H7N9 occurrence risk for each county of China was predicted. These findings provide new insights for a comprehensive understanding of the origin, evolution, and occurrence risk of H7N9 virus. Moreover, our study also lays a theoretical basis for conducting risk-based surveillance and prevention of the disease.

Isolation, Identification, and Molecular Characterization of Newcastle Disease Virus from Field Outbreaks in Chickens in Afghanistan

Newcastle disease viruses (NDVs) in Afghanistan were isolated from three chicken farms and identified using a hemagglutination test and reverse transcription-polymerase chain reaction assay. Three isolates from each farm were sequenced to characterize the part of their fusion protein gene around the cleavage site. The characteristics of the fusion protein genes of the three isolates shown by phylogenic analysis indicated that the isolates were velogenic, belonged to the class II subgenotype VII 1.1, and were closely related to an identified Chinese NDV isolate. To our knowledge, this is the first time that NDV isolates from Afghanistan have been partially sequenced.

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.

Emerging threat and vaccination strategies of H9N2 viruses in poultry in Indonesia: A review

Avian influenza virus subtype H9N2 was first documented in Indonesia in 2017. It has become prevalent in chickens in many provinces of Indonesia as a result of reassortment in live bird markets. Low pathogenic avian influenza subtype H9N2 virus-infected poultry provides a new direction for influenza virus. According to the latest research, the Indonesian H9N2 viruses may have developed through antigenic drift into new genotype, posing a significant hazard to poultry and public health. The latest proof of interspecies transmission proposes that, the next human pandemic variant will be avian influenza virus subtype H9N2. Manipulation and elimination of H9N2 viruses in Indonesia, constant surveillance of viral mutation, and vaccines updates are required to achieve effectiveness. The current review examines should be investigates/assesses/report on the development and evolution of newly identified H9N2 viruses in Indonesia and their vaccination strategy.

Emerging threats and vaccination strategies of H9N2 viruses in poultry in Indonesia: A review

Avian influenza virus subtype H9N2 was first documented in Indonesia in 2017. It has become prevalent in chickens in many provinces of Indonesia as a result of reassortment in live bird markets. Low pathogenic avian influenza subtype H9N2 virus-infected poultry provides a new direction for the influenza virus. According to the latest research, the Indonesian H9N2 viruses may have developed through antigenic drift into a new genotype, posing a significant hazard to poultry and public health. The latest proof of interspecies transmission proposes that the next human pandemic variant will be the avian influenza virus subtype H9N2. Manipulation and elimination of H9N2 viruses in Indonesia, constant surveillance of viral mutation, and vaccine updates are required to achieve effectiveness. The current review examines should be investigates/assesses/report on the development and evolution of newly identified H9N2 viruses in Indonesia and their vaccination strategy.

Exploring the determinants of influenza A/H7N9 control intervention efficacy in China: disentangling the effect of the "1110" policy and poultry vaccination

: The influenza A virus of the H7N9 subtype (FLUAV H7N9) emerged in Eastern China provinces in 2013 causing illness in both poultry and humans. Most reported FLUAV H7N9 human cases were related to those associated with the live poultry market chain. From 2013 to 2017, there were five epidemic waves of human infections, and from the end of 2016, the number of human cases increased sharply. To control FLUAV H7N9 in the market chain, the so-called "1110" policy at live poultry markets and a national vaccination programme were implemented. The relative efficacy of these two measures on the number of poultry and human infections has not been quantified and compared. To explore their efficacy, a cross-sectional study was conducted in six provinces of China, and the vaccination and surveillance data of H7N9 were analysed. Our survey data showed that poultry vendors were not widely aware of and did not accept the "1110" policy. For subjective and objective factors, some measures of the "1110" policy were not implemented in live bird markets (LBMs). However, the national vaccination programme achieved good immune effects and sharply decreased poultry FLUAV H7N9 infections. The detection rates of FLUAV H7N9 in LBMs and farms gradually decreased since the vaccination programme was implemented. Our analysis also indicated that human infections were closely related to poultry virus carriage rates; therefore, controlling FLUAV H7N9 circulation in poultry was an effective measure to control FLUAV H7N9 infections in humans. Although LBMs play a significant role in human infections, the management measures may not be implemented efficiently; hence, we need to conduct more investigations before developing related policies. This article is protected by copyright. All rights reserved.

Distinct but connected avian influenza virus activities in wetlands and live poultry markets in Bangladesh, 2018-2019

From April 2018 to October 2019, we continued active surveillance for influenza viruses in Bangladeshi live poultry markets (LPMs) and in Tanguar Haor, a wetland region of Bangladesh where domestic ducks have frequent contact with migratory birds. The predominant virus subtypes circulating in the LPMs were low pathogenic avian influenza (LPAI) H9N2 and clade 2.3.2.1a highly pathogenic avian influenza (HPAI) H5N1 viruses of the H5N1-R1 genotype, like those found in previous years. Viruses of the H5N1-R2 genotype, which were previously reported as co-circulating with H5N1-R1 genotype viruses in LPM, were not detected. In addition to H9N2 viruses, which were primarily found in chicken and quail, H2N2, H3N8 and H11N3 LPAI viruses were detected in LPMs, exclusively in ducks. Viruses in domestic ducks and/or wild birds in Tanguar Haor were more diverse, with H1N1, H4N6, H7N1, H7N3, H7N4, H7N6, H8N4, H10N3, H10N4 and H11N3 detected. Phylogenetic analyses of these LPAI viruses suggested that some were new to Bangladesh (H2N2, H7N6, H8N4, H10N3 and H10N4), likely introduced by migratory birds of the Central Asian flyway. Our results show a complex dynamic of viral evolution and diversity in Bangladesh based on factors such as host populations and geography. The LPM environment was characterised by maintenance of viruses with demonstrated zoonotic potential and H5N1 genotype turnover. The wetland environment was characterised by greater viral gene pool diversity but a lower overall influenza virus detection rate. The genetic similarity of H11N3 viruses in both environments demonstrates that LPM and wetlands are connected despite their having distinct influenza ecologies.

Spatiotemporal Associations and Molecular Evolution of Highly Pathogenic Avian Influenza A H7N9 Virus in China from 2017 to 2021

Highly pathogenic (HP) H7N9 avian influenza virus (AIV) emerged in China in 2016. HP H7N9 AIV caused at least 33 human infections and has been circulating in poultry farms continuously since wave 5. The genetic divergence, geographic patterns, and hemagglutinin adaptive and parallel molecular evolution of HP H7N9 AIV in China since 2017 are still unclear. Here, 10 new strains of HP H7N9 AIVs from October 2019 to April 2021 were sequenced. We found that HP H7N9 was primarily circulating in Northern China, particularly in the provinces surrounding the Bohai Sea (Liaoning, Hebei, and Shandong) since wave 6. Of note, HP H7N9 AIV phylogenies exhibit a geographical structure compatible with high levels of local transmission after unidirectional rapid geographical expansion towards the north of China in 2017. In addition, we showed that two major subclades were continually expanding with the viral population size undergoing a sharp increase after 2018 with an obvious seasonal tendency. Notably, the hemagglutinin gene showed signs of parallel evolution and positive selection. Our research sheds light on the current epidemiology, evolution, and diversity of HP H7N9 AIV that can help prevent and control the spreading of HP H7N9 AIV.

Analysis of the movement of live broilers in Guangxi, China and implications for avian influenza control

Most Chinese provinces have a daily-updated database of live animal movements; however, the data are not efficiently utilized to support interventions to control H7N9 and other avian influenzas. Based on official records, this study assessed the spatio-temporal patterns of live broilers moved out of and within Guangxi in 2017. The yearly and monthly networks were analyzed for inter- and intra-provincial movements, respectively. Approximately 200,000 movements occurred in 2017, involving the transport of 200 million live broilers from Guangxi. Although Guangxi exported to 24 out of 32 provinces of China, 95% of inter-provincial movements occurred with three bordering provinces. Within Guangxi, counties were highly connected through the live broiler movements, creating conditions for rapid virus spreading throughout the province. Interestingly, a peak in movements during the Chinese Lunar New Year celebrations, late January in 2017, was not observed in this study, likely due to H7N9-related control measures constraining live bird trading. Both intra- and inter-provincial movements in March 2017 were significantly higher than in other months of that year, suggesting that dramatic price changes may influence the movement's network and reshape the risk pathways. However, despite these variations, the same small proportion of counties (less than 20%) exporting/importing more than 90% of inter- and intra-provincial movements remains the same throughout the year. Interventions, particularly surveillance and improving biosecurity, targeted to those counties are thus likely to be more effective for avian influenza risk mitigation than implemented indiscriminately. Additionally, simulations further demonstrated that targeting counties according to their degree or betweenness in the movement network would be the most efficient way to limit disease transmission via broiler movements. The study findings provide evidence to support the design of risk-based control interventions for H7N9 and all other avian influenza viruses in broiler value chains in Guangxi.

Risk Areas for Influenza A(H5) Environmental Contamination in Live Bird Markets, Dhaka, Bangladesh

We evaluated the presence of influenza A(H5) virus environmental contamination in live bird markets (LBMs) in Dhaka, Bangladesh. By using Bernoulli generalized linear models and multinomial logistic regression models, we quantified LBM-level factors associated with market work zone–specific influenza A(H5) virus contamination patterns. Results showed higher environmental contamination in LBMs that have wholesale and retail operations compared with retail-only markets (relative risk 0.69, 95% 0.51–0.93; p = 0.012) and in March compared with January (relative risk 2.07, 95% CI 1.44–2.96; p<0.001). Influenza A(H5) environmental contamination remains a public health problem in most LBMs in Dhaka, which underscores the need to implement enhanced biosecurity interventions in LBMs in Bangladesh.

Live and Wet Markets: Food Access versus the Risk of Disease Emergence

Emerging zoonotic diseases exert a significant burden on human health and have considerable socioeconomic impact worldwide. In Asia, live animals as well as animal products are commonly sold in informal markets. The interaction of humans, live domestic animals for sale, food products, and wild and scavenging animals, creates a risk for emerging infectious diseases. Such markets have been in the spotlight as sources of zoonotic viruses, for example, avian influenza viruses and coronaviruses, Here, we bring data together on the global impact of live and wet markets on the emergence of zoonotic diseases. We discuss how benefits can be maximized and risks minimized and conclude that current regulations should be implemented or revised, to mitigate the risk of new diseases emerging in the future.

Different intervention strategies toward live poultry markets against avian influenza A (H7N9) virus: Model-based assessment

BACKGROUND

Different interventions targeting live poultry markets (LPMs) are applied in China for controlling avian influenza A (H7N9), including LPM closure and "1110" policy (i.e., daily cleaning, weekly disinfection, monthly rest day, zero poultry stock overnight). However, the interventions' effectiveness has not been comprehensively assessed.

METHODS

Based on the available data (including reported cases, domestic poultry volume, and climate) collected in Guangdong Province between October 2013 and June 2017, we developed a new compartmental model that enabled us to infer H7N9 transmission dynamics. The model incorporated the intrinsic interplay among humans and poultry as well as the impacts of absolute humidity and LPM intervention, in which intervention strategies were parameterized and estimated by Markov chain Monte Carlo method.

RESULTS

There were 258 confirmed human H7N9 cases in Guangdong during the study period. If without interventions, the number would reach 646 (95%CI, 575-718) cases. Temporal, seasonal and permanent closures of LPMs can substantially reduce transmission risk, which might respectively reduce human infections by 67.2% (95%CI, 64.3%-70.1%), 75.6% (95%CI, 73.8%-77.5%), 86.6% (95%CI, 85.7-87.6%) in total four epidemic seasons, and 81.9% (95%CI, 78.7%-85.2%), 91.5% (95%CI, 89.9%-93.1%), 99.0% (95%CI, 98.7%-99.3%) in the last two epidemic seasons. Moreover, implementing the "1110" policy from 2014 to 2017 would reduce the cases by 34.1% (95%CI, 20.1%-48.0%), suggesting its limited role in preventing H7N9 transmission.

CONCLUSIONS

Our study quantified the effects of different interventions and execution time toward LPMs for controlling H7N9 transmission. The results highlighted the importance of closing LPMs during epidemic period, and supported permanent closure as a long-term plan.

Association of Biosecurity and Hygiene Practices with Environmental Contamination with Influenza A Viruses in Live Bird Markets, Bangladesh

In Bangladesh, live bird market environments are frequently contaminated with avian influenza viruses. Shop-level biosecurity practices might increase risk for environmental contamination. We sought to determine which shop-level biosecurity practices were associated with environmental contamination. We surveyed 800 poultry shops to describe biosecurity practices and collect environmental samples. Samples from 205 (26%) shops were positive for influenza A viral RNA, 108 (14%) for H9, and 60 (8%) for H5. Shops that slaughtered poultry, kept poultry overnight, remained open without rest days, had uneven muddy floors, held poultry on the floor, and housed sick and healthy poultry together were more frequently positive for influenza A viruses. Reported monthly cleaning seemed protective, but disinfection practices were not otherwise associated with influenza A virus detection. Slaughtering, keeping poultry overnight, weekly rest days, infrastructure, and disinfection practices could be targets for interventions to reduce environmental contamination.

Global formal live poultry and hatching egg trade network (2004-2016): description and association with poultry disease reporting and presence

As international trade constitutes one of the main spread pathways of diseases, a better understanding of the trade behaviors of countries will help identify strengths and areas for improvement in the approach of national authorities to controlling poultry diseases globally. Using data reported to the United Nations Comtrade and the World Organisation for Animal Health (OIE) between 2004 and 2016 by 193 countries, we used a network analysis on trade data of poultry hatching eggs, live poultry of less than 185 g and live poultry of 185 g or more to determine that: 1) quantities traded between countries are substantial, and tend to increase (average increase of 800,000 poultry heads and 21,000 tons of hatching eggs each year equivalent to an increase by 2-fold in 17 yr); 2) the stability of the networks was low (a quarter to half of trade relationships maintained between 2 consecutive years) and the subnetworks favorable to the spread of diseases were in general consistent with regional clustering, trade exchanges being equally at intracontinental and intercontinental levels; 3) countries with highest number of partners were located in the same world regions for the 3 poultry networks - Americas and Europe for export (up to 107 partners) and Africa, Asia and Europe for import (up to 36 partners); 4) for live poultry, biggest exporting countries shared more poultry disease surveillance data, and reported more disease presence than others, which did not stop them from trading. Biggest importers reported less poultry disease surveillance data and reported more disease presence than others; and 5) the main structural and trend characteristics of the international trade networks were in general similar for the 3 networks. The information derived from this work underlines the importance of applying the preventive measures advocated by the OIE and will support countries to reduce the risk of introduction of pathogens causing poultry diseases.

Distribution of avian influenza viruses according to environmental surveillance during 2014-2018, China

Background

Recurrent 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.

Methods

A 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.

Results

The 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.

Conclusions

In 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 Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-021-00850-3.

Value chain analysis of yellow broiler industry in Guangxi, China to inform H7N9 influenza control strategies

Yellow broilers are the primary source of poultry consumption in China and the predominant trade of live poultry. However, knowledge of the value chain is limited, which is vital evidence for the effective control of H7N9 and other zoonotic avian influenzas. The aim of the study was to map the yellow broiler value chain in Guangxi Zhuang Autonomous Region, China and investigate its governance structure and practices relevant to the risk of H7N9 transmission. A value chain analysis was conducted in five areas of Guangxi from May to August 2018. To map the value chain, three focus group discussions (FGDs) were conducted and stakeholders, products and premises involved and their interactions were identified. Then, 55 key informant interviews (KIIs) collected qualitative data on stakeholders' profile, practices and interactions with other stakeholders and rules/norms that exist along the value chain. On-site observations were also carried out at different types of premises along the value chain to complement and validate findings of KIIs and FGDs. Participants were also asked to provide proportional estimates of each component in the value chain where possible. The qualitative data from FGDs, KIIs and on-site observations were analysed to create stakeholder profiles and a diagram of product flows and stakeholders' interactions. Thematic analysis was used to identify the governance structure of the value chains and practices relevant to the risk of H7N9 transmission. The stakeholders and premises involved in Guangxi yellow broiler production, wholesale and retail were described, as well as their interactions. Contract farming is extensively adopted in Guangxi; consequently yellow broiler grower companies are the dominant stakeholders. The trading platform was identified as a key premise linking farms and live bird markets. The thematic analysis highlighted poor biosecurity practices in different premises along the value chain, which was supported by on-site observations. The operation of trading platforms reported in this study presents a disease risk but is not considered in the current H7N9 control programs. The study suggested that biosecurity management gaps need to be addressed through government-industry partnerships that require engagement with private stakeholders in the planning and implementation of H7N9 control strategies incentivising participation of grower companies, wholesalers and retailers.

Exploring utility of genomic epidemiology to trace origins of highly pathogenic influenza A/H7N9 in Guangdong

The first highly pathogenic (HP) influenza A/H7N9 was reported in Guangdong in January 2017. To investigate the emergence and spread of HP A/H7N9 in Guangdong province, we sequenced 297 viruses (58 HP A/H7N9, 19 low pathogenic (LP) A/H7N9, and 220 A/H9N2) during 2016–2017. Our analysis showed that during the fifth wave, three A/H7N9 lineages were co-circulating in Guangdong: the local LP Pearl River Delta (PRD) lineage (13%), the newly imported LP Yangtze River Delta (YRD) lineage (23%), and the HP YRD lineage (64%). Previously circulating YRD-lineage LP during the third wave evolved to the YRD-lineage HP A/H7N9 in Guangdong. All YRD-lineage LP detected during the fifth wave most likely originated from newly imported viruses into Guangdong. Genotype comparison of HP A/H7N9 suggests limited outward spread of HP A/H7N9 to other provinces. The distribution of HP A/H7N9 cleavage site variants on live poultry markets differed from that found in humans, suggesting a V1-type cleavage site may facilitate human infections.

Antimicrobial Resistance and Virulence of Methicillin-Resistant Staphylococcus aureus from Human, Chicken and Environmental Samples within Live Bird Markets in Three Nigerian Cities

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a major threat to public health. This study investigated the occurrence of MRSA in humans, chickens, chicken meat and environmental samples within poultry farms and live bird markets in southwestern Nigeria. Methods: MRSA were isolated using selective culture and tested for antimicrobial susceptibility by broth microdilution. Selected isolates were characterized by whole genome sequencing (WGS). From WGS data, spa, dru, multilocus sequence typing (MLST) and SCCmec types, but also virulence and antimicrobial resistance genes, were identified. Results: Fifty-six MRSA isolates were detected in 734 samples. They showed resistance to β-lactams (100%), tetracycline (60.7%), ciprofloxacin (33.9%), erythromycin (28.6%), gentamicin (32.1%), and trimethoprim/sulfamethoxazole (10.7%). All 30 isolates investigated by WGS carried mecA, dfrG, and tet(38) genes. Other resistance genes detected were blaZ (83.3%), fosB (73.3%), tet(K) (60.0%), aacA-aphD (36.6%), aphA3 (33.3%), msr(A) (30.0%), mph(C) (30.0%), dfrS1 (3.3%), and sat4 (3.3%). Seven spa types (t091, t314, t657, t1476, t2331, t4690 and t12236), four known (dt9aw, dt10ao, dt10cj, and dt11a) and two novel (dt10dr and dt11dw) dru types, as well as five sequence types (ST8, ST121, ST152, ST772 and ST789) were found among the MRSA isolates. All ST121 isolates carried an SCCmec type IV cassette and were not dru-typeable. ST152 and ST121 were found only in specific sample categories within defined locations, while ST8 and ST772 were distributed across most sample categories and locations. Three SCCmec types, IVa, V and Vc, were identified. All MRSA isolates possessed virulence genes including aur, clpP, coa, fnbA, esaA, hly, hla, ica, isdA, srtB, sspA, and vWbp, among others. The toxic shock syndrome toxin gene (tst) was not detected in any isolate, whereas the Pantone-Valentine leukocidin genes lukF-PV/lukS-PV were present in all ST121, all ST772, and all but one ST152 isolates. Conclusion: The results of this study (i) showed that chicken meat is contaminated by MRSA and (ii) suggested that live bird markets may serve as focal points for the dissemination of MRSA within the community.

Geographical variation in the risk of H7N9 human infections in China: implications for risk-based surveillance

The influenza A (H7N9) subtype remains a public health problem in China affecting individuals in contact with live poultry, particularly at live bird markets. Despite enhanced surveillance and biosecurity at LBMs H7N9 viruses are now more widespread in China. This study aims to quantify the temporal relationship between poultry surveillance results and the onset of human H7N9 infections during 2013-2017 and to estimate risk factors associated with geographical risk of H7N9 human infections in counties in Southeast China. Our results suggest that poultry surveillance data can potentially be used as early warning indicators for human H7N9 notifications. Furthermore, we found that human H7N9 incidence at county-level was significantly associated with the presence of wholesale LBMs, the density of retail LBMs, the presence of poultry virological positives, poultry movements from high-risk areas, as well as chicken population density and human population density. The results of this study can influence the current AI H7N9 control program by supporting the integration of poultry surveillance data with human H7N9 notifications as an early warning of the timing and areas at risk for human infection. The findings also highlight areas in China where monitoring of poultry movement and poultry infections could be prioritized.

Live poultry market closure and avian influenza A (H7N9) infection in cities of China, 2013-2017: an ecological study

Background

Previous studies have proven that the closure of live poultry markets (LPMs) was an effective intervention to reduce human risk of avian influenza A (H7N9) infection, but evidence is limited on the impact of scale and duration of LPMs closure on the transmission of H7N9.

Method

Five cities (i.e., Shanghai, Suzhou, Shenzhen, Guangzhou and Hangzhou) with the largest number of H7N9 cases in mainland China from 2013 to 2017 were selected in this study. Data on laboratory-confirmed H7N9 human cases in those five cities were obtained from the Chinese National Influenza Centre. The detailed information of LPMs closure (i.e., area and duration) was obtained from the Ministry of Agriculture. We used a generalized linear model with a Poisson link to estimate the effect of LPMs closure, reported as relative risk reduction (RRR). We used classification and regression trees (CARTs) model to select and quantify the dominant factor of H7N9 infection.

Results

All five cities implemented the LPMs closure, and the risk of H7N9 infection decreased significantly after LPMs closure with RRR ranging from 0.80 to 0.93. Respectively, a long-term LPMs closure for 10–13 weeks elicited a sustained and highly significant risk reduction of H7N9 infection (RRR = 0.98). Short-time LPMs closure with 2 weeks in every epidemic did not reduce the risk of H7N9 infection (p > 0.05). Partially closed LPMs in some suburbs contributed only 35% for reduction rate (RRR = 0.35). Shenzhen implemented partial closure for first 3 epidemics (p > 0.05) and all closure in the latest 2 epidemic waves (RRR = 0.64).

Conclusion

Our findings suggest that LPMs all closure in whole city can be a highly effective measure comparing with partial closure (i.e. only urban closure, suburb and rural remain open). Extend the duration of closure and consider permanently closing the LPMs will help improve the control effect. The effect of LPMs closure seems greater than that of meteorology on H7N9 transmission.

Knowledge and remaining gaps on the role of animal and human movements in the poultry production and trade networks in the global spread of avian influenza viruses - A scoping review

Poultry production has significantly increased worldwide, along with the number of avian influenza (AI) outbreaks and the potential threat for human pandemic emergence. The role of wild bird movements in this global spread has been extensively studied while the role of animal, human and fomite movement within commercial poultry production and trade networks remains poorly understood. The aim of this work is to better understand these roles in relation to the different routes of AI spread. A scoping literature review was conducted according to the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) using a search algorithm combining twelve domains linked to AI spread and animal/human movements within poultry production and trade networks. Only 28 out of 3,978 articles retrieved dealt especially with the role of animal, human and fomite movements in AI spread within the international trade network (4 articles), the national trade network (8 articles) and the production network (16 articles). While the role of animal movements in AI spread within national trade networks has been largely identified, human and fomite movements have been considered more at risk for AI spread within national production networks. However, the role of these movements has never been demonstrated with field data, and production networks have only been partially studied and never at international level. The complexity of poultry production networks and the limited access to production and trade data are important barriers to this knowledge. There is a need to study the role of animal and human movements within poultry production and trade networks in the global spread of AI in partnership with both public and private actors to fill this gap.

Control of avian influenza in China: Strategies and lessons

In recent decades, multiple subtypes (i.e. H9N2, H5N1 and H7N9) of avian influenza virus (AIV) have become widespread in China, which has caused enormous economic losses and posed considerable threats to public health. In this review, with the aim to provide insights into and guidelines for the control of AIV spread in China and globally in the future, we analysed the reasons why AIV has persisted in China based on socio-economic features, including poultry biosecurity, live bird markets, live bird transportation, wild birds, poultry waterfowl, poultry density, poultry population and infected birds. We also described the present status of the AIV subtypes H9, H5 and H7 in China to elucidate the effectiveness of the strategies currently employed in China (i.e. culling, mass vaccination and biosecurity improvement) to control the disease based on a literature review and our unpublished surveillance data collected over a 12-year period from 2007 to 2018. We then summarized the lessons to be learned from the control experience in China, including whether culling of infected birds is of limited value for disease control and whether improved biosecurity is a better option than culling and vaccination for the long-term control of AIV, and when the vaccine strain should be updated.

Interventions in Live Poultry Markets for the Control of Avian Influenza: A Systematic Review and Meta-analysis

BACKGROUND

This review aimed to provide constructive suggestions for the control and management of avian influenza through quantitative and qualitative evaluation of the impact of different live poultry market (LPM) interventions.

METHODS

Both English and Chinese language databases were searched for articles that were published on or before 9 November 2018. After extraction and assessment of the included literature, Stata14.0 was applied to perform a meta-analysis to explore the impacts of LPM interventions.

RESULTS

A total of 19 studies were identified. In total, 224 human, 3550 poultry, and 13 773 environment samples were collected before the intervention; 181 people, 4519 poultry, and 9562 environments were sampled after LPM interventions. Avian influenza virus (AIV) detection rates in the LPM environment (odds ratio [OR], 0.393; 95% confidence interval [CI], 0.262-0.589) and the incidence of AIV infection (OR, 0.045; 95% CI, 0.025-0.079) were significantly lower after LPM interventions, while interventions were not significantly effective in reducing AIV detection in poultry samples (OR, 0.803; 95% CI, 0.403-1.597).

CONCLUSIONS

LPM interventions can reduce AIV human infections and the detection rate of AIV in market environments.

Pig trade networks through live pig markets in Guangdong Province, China

This study used social network analysis to investigate the indirect contact network between counties through the movement of live pigs through four wholesale live pig markets in Guangdong Province, China. All 14,118 trade records for January and June 2016 were collected from the markets and the patterns of pig trade in these markets analysed. Maps were developed to show the movement pathways. Evaluating the network between source counties was the primary objective of this study. A 1‐mode network was developed. Characteristics of the trading network were explored, and the degree, betweenness and closeness were calculated for each source county. Models were developed to compare the impacts of different disease control strategies on the potential magnitude of an epidemic spreading through this network. The results show that pigs from 151 counties were delivered to the four wholesale live pig markets in January and/or June 2016. More batches (truckloads of pigs sourced from one or more piggeries) were traded in these markets in January (8,001) than in June 2016 (6,117). The pigs were predominantly sourced from counties inside Guangdong Province (90%), along with counties in Hunan, Guangxi, Jiangxi, Fujian and Henan provinces. The major source counties (46 in total) contributed 94% of the total batches during the two‐month study period. Pigs were sourced from piggeries located 10 to 1,417 km from the markets. The distribution of the nodes' degrees in both January and June indicates a free‐scale network property, and the network in January had a higher clustering coefficient (0.54 vs. 0.39) and a shorter average pathway length (1.91 vs. 2.06) than that in June. The most connected counties of the network were in the central, northern and western regions of Guangdong Province. Compared with randomly removing counties from the network, eliminating counties with higher betweenness, degree or closeness resulted in a greater reduction of the magnitude of a potential epidemic. The findings of this study can be used to inform targeted control interventions for disease spread through this live pig market trade network in south China.

Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market

There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine-origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re-introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans.

Characterization of H7N9 avian influenza viruses isolated from duck meat products

Avian influenza H7N9 viruses have caused five epidemic waves of human infections since the first human cases were reported in 2013. In 2016, the initial low pathogenic avian influenza (LPAI) H7N9 viruses became highly pathogenic, acquiring multi-basic amino acids at the haemagglutinin cleavage site. These highly pathogenic avian influenza (HPAI) H7N9 viruses have been detected in poultry and humans in China, causing concerns of a serious threat to global public health. In Japan, both HPAI and LPAI H7N9 viruses were isolated from duck meat products carried illegally and relinquished voluntarily at the border by passengers on flights from China to Japan between 2016 and 2017. Some of the LPAI and HPAI H7N9 viruses detected at the border in Japan were characterized previously in chickens and ducks; however, their pathogenicity and replicative ability in mammals remain unknown. In this study, we assessed the biological features of two HPAI H7N9 virus isolates [A/duck/Japan/AQ-HE29-22/2017 (HE29-22) and A/duck/Japan/AQ-HE29-52/2017 (HE29-52); both of these viruses were isolated from duck meat at the border)] and an LPAI H7N9 virus isolate [A/duck/Japan/AQ-HE28-3/2016 (HE28-3)] in mice and ferrets. In mice, HE29-52 was more pathogenic than HE29-22 and HE28-3. In ferrets, the two HPAI virus isolates replicated more efficiently in the lower respiratory tract of the animals than did the LPAI virus isolate. Our results indicate that HPAI H7N9 viruses with the potential to cause severe diseases in mammals have been illegally introduced to Japan.

Global patterns of avian influenza A (H7): virus evolution and zoonotic threats

Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.

Reassortments among Avian Influenza A(H5N1) Viruses Circulating in Indonesia, 2015-2016

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses have been circulating since 2003 in Indonesia, with major impacts on poultry health, severe economic losses, and 168 fatal laboratory-confirmed human cases. We performed phylogenetic analysis on 39 full-genome H5N1 virus samples collected during outbreaks among poultry in 2015-2016 in West Java and compared them with recently published sequences from Indonesia. Phylogenetic analysis revealed that the hemagglutinin gene of all samples belonged to 2 genetic groups in clade 2.3.2.1c. We also observed these groups for the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 genes. Matrix, nonstructural protein, and polymerase basic 2 genes of some HPAI were most closely related to clade 2.1.3 instead of clade 2.3.2.1c, and a polymerase basic 2 gene was most closely related to Eurasian low pathogenicity avian influenza. Our results detected a total of 13 reassortment types among HPAI in Indonesia, mostly in backyard chickens in Indramayu.

Risk factors for H5 avian influenza virus prevalence on urban live bird markets in Jakarta, Indonesia-Evaluation of long-term environmental surveillance data

In the re-emergence of Highly Pathogenic Avian Influenza (HPAI), live bird markets have been identified to play a critical role. In this repeated cross-sectional study, we combined surveillance data collected monthly on Jakarta's live bird markets over a five-year period, with risk factors related to the structure and management of live bird markets, the trading and slaughtering of birds at these markets, and environmental and demographic conditions in the areas where the markets were located. Over the study period 36.7% (95% CI: 35.1, 38.3) of samples (N = 1315) tested HPAI H5 virus positive. Using General Estimation Equation approaches to account for repeated observations over time, we explored the association between HPAI H5 virus prevalence and potential risk factors. Markets where only live birds and carcasses were sold, but no slaughtering was conducted at or at the vicinity of the markets, had a significantly reduced chance of being positive for H5 virus (OR = 0.2, 95% CI 0.1-0.5). Also, markets, that used display tables for poultry carcasses made from wood, had reduced odds of being H5 virus positive (OR = 0.7, 95% CI 0.5-1.0), while having at least one duck sample included in the pool of samples collected at the market increased the chance of being H5 virus positive (OR = 5.7, 95% CI 3.6-9.2). Markets where parent stock was traded, were more at risk of being H5 virus positive compared to markets where broilers were traded. Finally, the human population density in the district, the average distance between markets and origins of poultry sold at markets and the total rainfall per month were all positively associated with higher H5 virus prevalence. In summary, our results highlight that a combination of factors related to trading and marketing processes and environmental pressures need to be considered to reduce H5 virus infection risk for customers at urban live bird markets. In particular, the relocation of slaughter areas to well-managed separate locations should be considered.

Knowledge, attitudes, and practices associated with avian influenza along the live chicken market chains in Eastern China: A cross-sectional survey in Shanghai, Anhui, and Jiangsu

The avian influenza (AI) virus of the H7N9 subtype emerged in China in 2013. Live bird markets (LBMs) selling live meat chickens were indicated to present a high-risk of the virus dissemination. This study aimed to quantify the level of knowledge, attitudes, and practices (KAP) on AI and to measure the associated risk factors among different actors along the live chicken market chain within H7N9-affected Eastern provinces in China. A cross-sectional survey was conducted in these provinces from June to July 2014. Structured questionnaires about KAP on AI were delivered to chicken farmers, chicken vendors, and consumers in LBMs. Multivariable generalized least squares regression models were developed to identify predictors of KAP scores among different actors. Our results indicate that KAP scores of chicken farmers were generally higher than those of chicken vendors. Chicken farmers who worked for more than 15 years had significantly lower total KAP scores than those who worked for less than 6 years. Chicken farmers who worked more than 15 hrs in a day had significantly lower attitude scores than those who worked less than 6 hrs. For chicken vendors, females and individuals > 35 years old had significantly lower knowledge scores compared to the reference categories. Practice scores were significantly higher in female vendors and those vendors who also conducted slaughter compared to males and vendors who did not conduct slaughter. Consumers who bought chicken at least once every month had better risk awareness compared to those who bought chicken at least once every week. In addition, female consumers had significantly better practice scores than male consumers. In conclusion, risk-based health promotion interventions should be developed and implemented by animal health agencies (targeting farmers and vendors) and public health agencies (targeting frequent and male consumers) to prevent transmission of H7N9 along the market chain in China.

Status and influencing factors of farmers' private investment in the prevention and control of sheep brucellosis in China: A cross-sectional study

Background

Brucellosis is one of the most common zoonoses worldwide, causing direct losses to the livestock industry and threatening human health. Little is known about the status and factors affecting farmers’ private investment in the prevention and control of sheep brucellosis in China.

Methodology/Principal findings

From April to October 2017, a cross-sectional, house-based study was conducted in 7 Chinese provinces. A total of 1037 households included in the study were analyzed. The average amount of private investment in the prevention and control of brucellosis was $0.73±0.54 per sheep. Multivariable analysis showed that factors facilitating private investment included older age of householder (OR = 1.07, 95%CI: 1.03–1.11), herd size >100 (OR = 2.49, 95%CI: 1.38–4.51), a higher percentage of income from sheep farming comparing to the total household income (OR = 1.14, 95%CI: 1.11–1.16), higher score of brucellosis knowledge (OR = 3.85, 95%CI: 1.40–10.51), actively learning related knowledge (OR = 2.98, 95%CI: 1.55–5.74), actively participating in related training courses (OR = 3.07, 95%CI: 1.52–6.18), care about other people’s attitudes (OR = 1.75, 95%CI: 1.35–2.28), concern about the health of neighbors’ livestock (OR = 1.75, 95%CI: 1.23–2.51). The analysis found a discouraging factor for private investment, supporting culling policy (OR = 0.67, 95%CI: 0.49–0.91).

Conclusions/Significance

In addition to providing interventions related to farmers’ knowledge, attitudes and practices, guidance must be offered to help farmers understanding the importance of private investment in the prevention and control of brucellosis.

Brucellosis is one of the most common zoonoses worldwide. The disease is endemic in China and the prevention and control of brucellosis mainly depends on government investment. From the perspective of economic theory, private investment can help supplement public investment. Thus, it is important to describe the status of farmers’ private investment in brucellosis prevention and control in epidemic areas and to explore the factors influencing this investment.

Influenza A(H7N9) virus emerged and resulted in human infections in Chongqing, southwestern China since 2017

OBJECTIVES

Influenza A(H7N9) virus has emerged and resulted in human infections in Chongqing, southwestern China since 2017. This study aimed to describe the epidemiological characteristics of the first epidemic in this region.

METHODS

The epidemiological data of patients were collected. Live poultry markets (LPMs), commercial poultry farms (CPFs) and backyard poultry farms (BPFs) were monitored, and poultry sources were registered. Samples derived from the patients, their close contacts, and the environments were tested for influenza A(H7N9) virus by real-time reverse transcriptase polymerase chain reaction. Genetic sequencing and phylogenetic analysis were also conducted.

RESULTS

Since the confirmation of the first patient infected with influenza A(H7N9) virus on March 5, 2017, nine patients had been identified within four months in Chongqing. Their mean age was 45 years, 77.8% were male, 66.7% were urban residents and 55.6% were of poultry related occupation. All patients became infected after exposure to live chickens. The median time interval from initial detection of influenza A(H7N9) virus in Chongqing to the patients' onset was 75 days. Since initial detection in February 2017, influenza A(H7N9) virus was detected in 21 (53.8%) counties within four months. The proportion of positive samples was 2.94% (337/11,451) from February 2017 to May 2018, and was higher (χ²=75.78, P<0.001) in LPMs (3.66%, 329/8979) than that in CPFs (0.41%, 5/1229) and BPFs (0.24%, 3/1243). The proportion of positive samples (34.4%, 22/64) at the premises to which the patients were exposed was significantly higher than that (5.7%, 257/4474) in premises with no patients. Phylogenetic analysis indicated that the viruses isolated in Chongqing belonged to the Yangtze River Delta lineage and resembled those circulated in Jiangsu and Anhui provinces between late 2016 and early 2017.

CONCLUSION

Influenza A(H7N9) virus was newly introduced into Chongqing most likely between late 2016 and early 2017, which swept across half of Chongqing territory and resulted in human infections within months. The most impacted premises and population were LPMs and poultry related workers respectively in the epidemic.

Spatiotemporal Distributions and Dynamics of Human Infections with the A H7N9 Avian Influenza Virus

In 2013 in mainland China, a novel avian influenza virus H7N9 began to infect humans and had aroused severe fatality in the infected humans, followed by the annual outbreaks. By methods of GIS and kriging interpolation, we get the geographical distributions. We obtain the longitudinal characteristics of these outbreaks based on statistics and diagrams. After these spatiotemporal distributions, an eco-epidemiological model is established and analyzed. In this model, the general incidence functions, the factor of fully killed infected poultry, and the virus in environment are taken into account. Theoretical analysis shows that the endemic will be formed to a large extent once the H7N9 avian influenza virus exists in poultry. On the basis of dynamics, we explore the possible disease control measures by numerical simulations. Simulations indicate that measures of vaccination in poultry and stopping live poultry transactions are the primary choices for disease control in humans, and strengthened inhibition effects and environmental disinfections can effectively control the outbreak.

Repeated detection of H7N9 avian influenza viruses in raw poultry meat illegally brought to Japan by international flight passengers

H7N9 highly and low pathogenic avian influenza viruses (HPAIV and LPAIV, respectively) have been isolated from duck meat products that were brought illegally into Japan by flight passengers in their hand luggage. These H7N9 virus isolates were phylogenetically closely related to those prevailing in China. Antigenic analysis revealed that the hemagglutinin of the H7N9 HPAIV isolate was slightly different from those of the H7N9 LPAIV and older H7 strains. These meat products contaminated with AIVs repeatedly brought into Japan lead to increased risks of poultry and public health. Continuous border disease control based on the detection and culling of infected poultry and meat products is, thus, essential for the prevention of introduction and spread of AIVs.

Changing Geographic Patterns and Risk Factors for Avian Influenza A(H7N9) Infections in Humans, China

The fifth epidemic wave of avian influenza A(H7N9) virus in China during 2016–2017 demonstrated a geographic range expansion and caused more human cases than any previous wave. The factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry, and wetland variables on all epidemic waves. Poultry predictor variables became much more important in the last 2 epidemic waves than they were previously, supporting the assumption of much wider H7N9 transmission in the chicken reservoir. We show that the future range expansion of H7N9 to northern China may increase the risk of H7N9 epidemic peaks coinciding in time and space with those of seasonal influenza, leading to a higher risk of reassortments than before, although the risk is still low so far.

Westward Spread of Highly Pathogenic Avian Influenza A(H7N9) Virus among Humans, China

We report infection of humans with highly pathogenic avian influenza A(H7N9) virus in Shaanxi, China, in May 2017. We obtained complete genomes for samples from 5 patients and from live poultry markets or farms in 4 cities. Results indicate that H7N9 is spreading westward from southern and eastern China.

Estimating disease burden of a potential A(H7N9) pandemic influenza outbreak in the United States

BACKGROUND

Since spring 2013, periodic emergence of avian influenza A(H7N9) virus in China has heightened the concern for a possible pandemic outbreak among humans, though it is believed that the virus is not yet human-to-human transmittable. Till June 2017, A(H7N9) has resulted in 1533 laboratory-confirmed cases of human infections causing 592 deaths. The aim of this paper is to present disease burden estimates (measured by infection attack rates (IAR) and number of deaths) in the event of a possible pandemic outbreak caused by human-to-human transmission capability acquired by A(H7N9) virus. Even though such a pandemic will likely spread worldwide, our focus in this paper is to estimate the impact on the United States alone.

METHOD

The method first uses a data clustering technique to divide 50 states in the U.S. into a small number of clusters. Thereafter, for a few selected states in each cluster, the method employs an agent-based (AB) model to simulate human A(H7N9) influenza pandemic outbreaks. The model uses demographic and epidemiological data. A few selected non-pharmaceutical intervention (NPI) measures are applied to mitigate the outbreaks. Disease burden for the U.S. is estimated by combining results from the clusters applying a method used in stratified sampling.

RESULTS

Two possible pandemic scenarios with R 0 = 1.5 and 1.8 are examined. Infection attack rates with 95% C.I. (Confidence Interval) for R 0 = 1.5 and 1.8 are estimated to be 18.78% (17.3-20.27) and 25.05% (23.11-26.99), respectively. The corresponding number of deaths (95% C.I.), per 100,000, are 7252.3 (6598.45-7907.33) and 9670.99 (8953.66-10,389.95).

CONCLUSIONS

The results reflect a possible worst-case scenario where the outbreak extends over all states of the U.S. and antivirals and vaccines are not administered. Our disease burden estimations are also likely to be somewhat high due to the fact that only dense urban regions covering approximately 3% of the geographic area and 81% of the population are used for simulating sample outbreaks. Outcomes from these simulations are extrapolated over the remaining 19% of the population spread sparsely over 97% of the area. Furthermore, the full extent of possible NPIs, if deployed, could also have lowered the disease burden estimates.

Prevalence of and risk factors for cystic echinococcosis among herding families in five provinces in western China: a cross-sectional study

Echinococcosis is a severe zoonosis that endangers the health of herdsmen in China’s western provinces. This study aimed to examine the prevalence of this disease and identify potential factors associated with human echinococcosis among herding families.

A cross-sectional study was conducted in five provinces in western China from May 1, 2016 to November 30, 2016, and 1500 herding families participated in the study. A total of 1211 completed questionnaires were analyzed. The prevalence of Cystic echinococcosis (CE) among surveyed herding families was 1.55%. The results of multivariate analysis revealed that the sheep immunization (OR=0.35, 95%CI 0.21-0.58), being concerned about family members echinococcosis (OR=0.49, 95%CI 0.28-0.84) were protective factors, while allowing dogs to roam free (OR=3.17, 95%CI 1.89-5.31), feeding dogs with viscera (OR=3.04, 95%CI 1.83, 5.03), slaughter at home (OR=3.53, 95%CI 2.04-6.12), drinking non-boiled water (OR=2.15, 95%CI 1.28-3.63), eating raw vegetables (OR=1.87, 95%CI 1.13-3.10), not washing hands before meals (OR=3.08, 95%CI 1.68-5.65), and often seeing stray dogs (OR=2.60 95%CI 1.38-4.91) and wild animals (OR=1.92, 95%CI 1.17-3.14) near habitations were more associated with increased risk of infection.

Immunizing sheep, appropriately managing domestic and stray dogs, and improving living environments and behavioral factors may help to reduce the risk of human echinococcosis in western China.

Epidemiology, Evolution, and Pathogenesis of H7N9 Influenza Viruses in Five Epidemic Waves since 2013 in China

H7N9 influenza viruses were first isolated in 2013 and continue to cause human infections. H7N9 infections represent an ongoing public health threat that has resulted in 1344 cases with 511 deaths as of April 9, 2017. This highlights the continued threat posed by the current poultry trade and live poultry market system in China. Until now, there have been five H7N9 influenza epidemic waves in China; however, the steep increase in the number of humans infected with H7N9 viruses observed in the fifth wave, beginning in October 2016, the spread into western provinces, and the emergence of highly pathogenic (HP) H7N9 influenza outbreaks in chickens and infection in humans have caused domestic and international concern. In this review, we summarize and compare the different waves of H7N9 regarding their epidemiology, pathogenesis, evolution, and characteristic features, and speculate on factors behind the recent increase in the number of human cases and sudden outbreaks in chickens. The continuous evolution of the virus poses a long-term threat to public health and the poultry industry, and thus it is imperative to strengthen prevention and control strategies.

H7N9 avian influenza A virus in China: a short report on its circulation, drug resistant mutants and novel antiviral drugs

INTRODUCTION

The first human H7N9 avian influenza virus case was reported in Shanghai in 2013. Shortly thereafter, this virus spread to other regions in China. Molecular analysis indicated that the H7N9 virus is a reassortant virus containing internal genes from the H9N2 virus and previously described mammalian adaption markers, which could allow the virus to adapt efficiently to a mammalian host. Fortunately, there is no evidence of sustained person-to-person spread. Most of the human H7N9 cases have a history of exposure to live poultry markets (LPMs). The circulating H7N9 were low pathogenic viruses, however highly pathogenic H7N9 viruses were recently identified in human cases. Areas covered: In the present article, the circulation of H7N9 in LPMs of China, the five waves of H7N9 infection in humans, recently identified drug resistant mutants and potential antiviral drugs against H7N9 are discussed; this may provide further understanding of the evolution and pandemic potential of the H7N9 influenza viruses. Expert commentary: All the data reveal that the major source of H7N9 viruses are LPMs and the H7N9 virus is still circulating widely in China. It is concerning that the recent emergence of highly pathogenic H7N9 viruses may result in highly transmissible viruses in mammalian species.

Modeling the live-pig trade network in Georgia: Implications for disease prevention and control

Live pig trade patterns, drivers and characteristics, particularly in backyard predominant systems, remain largely unexplored despite their important contribution to the spread of infectious diseases in the swine industry. A better understanding of the pig trade dynamics can inform the implementation of risk-based and more cost-effective prevention and control programs for swine diseases. In this study, a semi-structured questionnaire elaborated by FAO and implemented to 487 farmers was used to collect data regarding basic characteristics about pig demographics and live-pig trade among villages in the country of Georgia, where very scarce information is available. Social network analysis and exponential random graph models were used to better understand the structure, contact patterns and main drivers for pig trade in the country. Results indicate relatively infrequent (a total of 599 shipments in one year) and geographically localized (median Euclidean distance between shipments = 6.08 km; IQR = 0-13.88 km) pig movements in the studied regions. The main factors contributing to live-pig trade movements among villages were being from the same region (i.e., local trade), usage of a middleman or a live animal market to trade live pigs by at least one farmer in the village, and having a large number of pig farmers in the village. The identified villages' characteristics and structural network properties could be used to inform the design of more cost-effective surveillance systems in a country which pig industry was recently devastated by African swine fever epidemics and where backyard production systems are predominant.

Assessment of hygienic conditions of live bird markets on avian influenza in Chittagong metro, Bangladesh

Live Bird Markets (LBMs) in Asian countries are considered as hubs for the spread and maintenance of different infectious diseases. In Bangladesh, LBMs are the major source of live and dressed poultry to consumers and until now only a few studies have been conducted targeting infectious agent status such as avian influenza virus (AIV) prevalence of LBMs in Bangladesh. Therefore, a cross sectional study was conducted using all 40 LBMs within the Chittagong Metropolitan Area (CMA) of Bangladesh targeting demographic information and hygienic status of LBMs in concurrence with AIV prevalence and its subtype distribution, as well as the associated risk factors for AIV. Pooled environmental swab samples were collected from 2 to 9 different sites per stall, with epidemiological data being obtained from a total of 290 stalls across 40 LBMs. The samples were evaluated by Real Time Reverse Transcriptase Polymerase Chain Reaction. The prevalence of AIV was 40% (95% CI: 20-60%; N=40) at a LBM level followed by 20.3% (CI: 10-30%, N=290) at a stall level. Specifically, the prevalence of H5, H7 and H9 subtypes at stall level were 2.8% (95% CI: 1-5%), 0% (CI: 0-1.3%) and 3.1% (CI: 1-6%), respectively. Generalized Estimating Equation model identified that the type of species sold (OR=2.5: Chicken and non-duck species versus Duck with other species), bird holding areas (OR=1.9: Cage versus Floor) and Hygienic score (OR=3.1: Score 3 or more versus score less than 3) as potential risk factors for the detection of AIV at stall level. These results suggest that housing chickens and ducks together in the stalls, birds kept on floors, and lack of adequate hygienic measures of the stall were the crucial factors for spreading AIV. This research outcome could be used to develop a proof-based program concerning environmental sanitation along with development of an effective surveillance system to reduce the AIV transmission through LBMs in Bangladesh.